Datasets:

InMedData

/

Cardio_v2

like 0

Identification of two mutations for ataxia telangiectasia among the Druze community.

Ataxia telangiectasia (AT) is a rare autosomal recessive disease characterized by progressive cerebellar ataxia, immunodeficiency, susceptibility to lymphoreticular malignancies and cancer predisposition, hypersensitivity to ionic radiation and chromosomal instability. In this study, we report a founder effect of AT with two different mutations: 1339 C > T and 6672 del GG together with 6677 del TACG, found in four Israeli Druze clans originating from three different Druze centers in the Middle East (Lebanon, Syria and Jordan). The 1339 C > T mutation, which results in a stop codon at position 447 of the ATM protein, was observed in two unrelated clans originating from Lebanon and Jordan. The 6672 del GG/6677 del TACG mutation was observed in two unrelated clans originating from Syria and Lebanon. In the present study, simple and fast detection assays were developed for both mutations. The ability to identify AT carriers routinely provides a unique opportunity for prenatal diagnosis, genetic counseling as well as marriage guidance in the Druze community.

Enhanced insulin secretion and cholesterol metabolism in congenic strains of the spontaneously diabetic (Type 2) Goto Kakizaki rat are controlled by independent genetic loci in rat chromosome 8.

<AbstractText Label="AIMS/HYPOTHESIS" NlmCategory="OBJECTIVE">Genetic investigations in the spontaneously diabetic (Type 2) Goto Kakizaki (GK) rat have identified quantitative trait loci (QTL) for diabetes-related phenotypes. The aims of this study were to refine the chromosomal mapping of a QTL ( Nidd/gk5) identified in chromosome 8 of the GK rat and to define a pathophysiological profile of GK gene variants underlying the QTL effects in congenics.</AbstractText>Genetic linkage analysis was carried out with chromosome 8 markers genotyped in a GKxBN F2 intercross previously used to map diabetes QTL. Two congenic strains were designed to contain GK haplotypes in the region of Nidd/gk5 transferred onto a Brown Norway (BN) genetic background, and a broad spectrum of diabetes phenotypes were characterised in the animals.</AbstractText>Results from QTL mapping suggest that variations in glucose-stimulated insulin secretion in vivo, and in body weight are controlled by different chromosome 8 loci (LOD3.53; p=0.0004 and LOD4.19; p=0.00007, respectively). Extensive physiological screening in male and female congenics at 12 and 24 weeks revealed the existence of GK variants at the locus Nidd/gk5, independently responsible for significantly enhanced insulin secretion and increased levels of plasma triglycerides, phospholipids and HDL, LDL and total cholesterol. Sequence polymorphisms detected between the BN and GK strains in genes encoding ApoAI, AIV, CIII and Lipc do not account for these effects.</AbstractText><AbstractText Label="CONCLUSIONS/INTERPRETATION" NlmCategory="CONCLUSIONS">We refined the localisation of the QTL Nidd/gk5 and its pathophysiological characteristics in congenic strains derived for the locus. These congenic strains provide novel models for testing the contribution of a subset of GK alleles on diabetes phenotypes and for identifying diabetes susceptibility genes.</AbstractText>

Evaluation of the role of the SQSTM1 gene in sporadic Belgian patients with Paget's disease.

A positional cloning effort in French Canadian families with Paget's disease of bone (PDB) resulted in the identification of a mutation in the sequestosome1 (SQSTM1) gene in a subset of both familial and sporadic PDB cases. This was confirmed in samples of mainly United Kingdom (UK) origin. In this study, we performed both mutation analysis and association studies in order to evaluate the role of this gene in a collection of isolated Belgian PDB patients. A mutation in the SQSTM1 gene was found in only 6 of 111 patients (5.4%). In all cases it involves the P392L mutation, previously shown to be common in both familial and sporadic cases. To perform association studies, we selected 8 single nucleotide polymorphisms (SNPs) and looked for linkage disequilibrium (LD) between these. Haplotype analysis indicated that typing of 3 Tag SNPs (IVS1 + 633A/C, IVS5 - 23A/G, and 976A/G) enables us to identify the most common haplotypes. Association studies for the 3 selected SNPs, based on 105 PDB cases without a SQSTM1 mutation and 159 control individuals, did not support a possible influence of natural variants in the SQSTM1 gene either on the pathogenesis of PDB or on the disease severity. In conclusion, our study confirms that the P392L mutation is a recurrent mutation causing PDB in different populations. We were not able to show an association between SQSTM1 polymorphisms and PDB in our population but this clearly needs to be extended to other populations. The presented identification of haplotype Tag SNPs will be of major help for such studies.

MICA intron 1 sequences of conserved extended HLA haplotypes: implications for sequencing-based typing.

The human major histocompatibility complex (MHC) class I chain-related gene A (MICA) has a high degree of genetic diversity. Several methods have been used in MICA typing. Recent studies reported different results for the same reference cell lines typed by different methods. By searching the GenBank, we found an indel polymorphism in MICA intron 1 corresponding to the area where one of the sequencing-based typing primers used by others is located. We investigated this polymorphism in 43 reference samples by primer cycle sequencing. This approach revealed three haplotype-specific patterns of polymorphisms in intron 1. This study provided evidence that one of the primers commonly used in MICA typing may fail to amplify both alleles in certain heterozygous combinations. Our data showed a correlation between the three patterns in MICA intron 1 and exon 5 short tandem repeat (STR) alleles. Being neutral ones, the intron 1 and STR polymorphisms appeared to mark the ancestral lineages better than the coding region polymorphisms.

Engineering RENTA, a DNA prime-MVA boost HIV vaccine tailored for Eastern and Central Africa.

For the development of human immunodeficiency virus type 1 (HIV-1) vaccines, traditional approaches inducing virus-neutralizing antibodies have so far failed. Thus the effort is now focused on elicitation of cellular immunity. We are currently testing in clinical trials in the United Kingdom and East Africa a T-cell vaccine consisting of HIV-1 clade A Gag-derived immunogen HIVA delivered in a prime-boost regimen by a DNA plasmid and modified vaccinia virus Ankara (MVA). Here, we describe engineering and preclinical development of a second immunogen RENTA, which will be used in combination with the present vaccine in a four-component DNA/HIVA-RENTA prime-MVA/HIVA-RENTA boost formulation. RENTA is a fusion protein derived from consensus HIV clade A sequences of Tat, reverse transcriptase, Nef and gp41. We inactivated the natural biological activities of the HIV components and confirmed immunogenicities of the pTHr.RENTA and MVA.RENTA vaccines in mice. Furthermore, we demonstrated in mice and rhesus monkeys broadening of HIVA-elicited T-cell responses by a parallel induction of HIVA- and RENTA-specific responses recognizing multiple HIV epitopes.

Mapping complex disease loci in whole-genome association studies.

Identification of the genetic polymorphisms that contribute to susceptibility for common diseases such as type 2 diabetes and schizophrenia will aid in the development of diagnostics and therapeutics. Previous studies have focused on the technique of genetic linkage, but new technologies and experimental resources make whole-genome association studies more feasible. Association studies of this type have good prospects for dissecting the genetics of common disease, but they currently face a number of challenges, including problems with multiple testing and study design, definition of intermediate phenotypes and interaction between polymorphisms.

Genetically defined mouse models that mimic natural aspects of human prostate cancer development.

This review is focused on mouse models for prostate cancer that have been designed on the basis of genetic alterations that are frequently found in human prostate cancer. It begins with an analysis of the similarities and differences in the gross and microscopic anatomy of the mouse and human prostate glands, and extends to the pathologies induced in the genetically manipulated mouse prostate in comparison with the sporadic development of the disease in humans. Major achievements have been made in modeling human prostate cancer in mice in recent years. There are models which display slow, temporal development of increasingly severe preneoplastic lesions, which are remarkably restricted to the prostate gland, a property similar to the aging-related progression of these lesions in humans. Other models rapidly progress to local invasive adenocarcinoma, and, in some of them metastasis is manifested subsequently with defined kinetics. Global assessment of molecular changes in the prostate of the genetically manipulated mice is increasingly underscoring the validity of the models through identification of 'signature' genes which are associated with the organ-confined primary or distant metastases of human prostate cancer. Taken together, various 'natural' models depicting stages of the disease, ranging from the early preneoplastic lesions to metastatic prostate cancer, now provide new tools both for exploring the molecular mechanism underlying prostate cancer and for development or testing of new targeted therapies.

Outpatient clinic for genetic counseling and gene testing of retinoblastoma.

We report on the genetic counseling and gene testing of patients with retinoblastoma who visited the National Cancer Center Hospital, Tokyo, from April 1997 through September 2003. During this period, 73 probands visited the clinic, and gene testing was performed in 51 individuals. Germline mutations of the RBI gene were detected in 20 individuals (39%); the frequencies were 82% (9/11) in bilateral/familial retinoblastoma, 50% (2/4) in unilateral/familial retinoblastoma, 50% (8/16) in bilateral/nonfamilial retinoblastoma, and 5% (1/20) in unilateral/nonfamilial retinoblastoma. Gene testing is indicated in the medical practice of hereditary retinoblastoma for familial risk assessment, while prior counseling is important for an understanding of the risks and benefits of gene testing. With improvements in patient prognosis, counseling for adult survivors is increasing in importance. Assessment of genetic risk to the offspring and prevention of secondary cancer are the primary issues of concern. Presymptomatic diagnosis of infants is effective for the proper assessment of the genetic risk and for making follow-up schedules for the detection of the tumor at an early stage.

Isolation, characterization and beneficial effects of rice associated plant growth promoting bacteria from Zanzibar soils.

This study was undertaken to isolate and characterize plant growth promoting bacteria (PGPB) occurring in four soils of Zanzibar, Tanzania as well as to evaluate their potential use as biofertilizers for rice. A total of 12 PGPB strains were isolated from rice and studied for growth characteristics, carbon/nitrogen source utilization patterns using QTS-24 kits, phosphate solubilization, indole acetic acid (IAA) production, antibiotic resistance patterns and growth at different pH, temperature and salt concentrations. All the isolates were motile and gram negative except Z3-4. Acetylene reduction activity was detected in all isolates ranging from 5.9-76.4 nmole C2H2 reduced/h x mg protein while 9 isolates produced IAA ranged from 20-90.8 mg/l. Most of the isolates showed resistance against different environmental stresses like 10-40 degrees C temperature, 0.2-1 M salt concentration and 4-8.5 pH range. Only one isolate Z2-7 formed clear zones on Pikovskaia's medium showing its ability to solubilize phosphates. Z3-2 was used to develop fluorescent antibodies to check the cross reactivity of the isolates. Inoculation of these bacterial isolates resulted in higher plant biomass, root area, and total N and P contents on Tanzanian rice variety BKN PRAT3036B under controlled conditions. Bacillus sp. Z3-4 and Azospirillum sp. Z3-1 are effective strains and, after further testing under field conditions, can be used for inoculum production of rice in Tanzania. The plant growth promoting effects of these PGPRs suggest that these can be exploited to improve crop productivity of rice in Tanzania.

Juvenile neuronal ceroid lipofuscinosis (Batten disease) CLN3 mutation (Chrom 16p11.2) with different phenotypes in a sibling pair and low intensity in vivo autofluorescence.

The neuronal ceroid lipofuscinoses (Batten disease) are a heterogeneous group of autosomal recessively inherited disorders causing progressive neurological failure, mental deterioration, seizures and visual loss secondary to retinal dystrophy. The juvenile type is of special interest to the ophthalmologist as visual loss is the earliest symptom of the disorder.</AbstractText>We present two siblings with severe retinal dystrophy due to juvenile Batten disease. Sibling A (age 10) presented with visual loss, photophobia and night blindness, starting at age 4. His vision was perception of light by the age of 10.5 years. Fundus examination revealed severe pigmentary retinopathy. Sibling B (age 7) presented with night vision difficulties. Fundus examination revealed a bull's eye maculopathy with minimal peripheral atrophic changes. In vivo autofluorescence level was found to be very low. Electroretinography (ERG) showed generalized retinal dysfunction involving both cone and rod systems, with an electronegative maximal response. In both siblings vacuolated lymphocytes were found on a peripheral blood film and on molecular genetic testing both were homozygous for the commonly reported 1.02-kb deletion of the CLN3 gene.</AbstractText>Although there is no effective treatment, the early diagnosis allowed accurate genetic and social counseling.</AbstractText>Juvenile Batten disease should be considered in children with a retinal dystrophy, especially where there is a bull's eye maculopathy and an abnormal full field ERG. The novel finding of very low in vivo autofluorescence is consistent with histopathological studies and may be secondary to photoreceptor cell loss.</AbstractText>

Haplotype analysis of BRCA1 gene reveals a new gene rearrangement: characterization of a 19.9 KBP deletion.

Germ-line mutations in the BRCA1 gene cause hereditary predisposition to breast and ovarian cancer. BRCA1 and BRCA2 mutations account for about 40% of high-risk families. Mutation-screening methods generally focus on genomic DNA and are usually PCR based; they enable the detection of sequence alterations such as point mutations and small deletions and insertions. However, they do not allow the detection of partial or entire exon(s) loss, because the presence of the homologous allele results in a positive PCR signal, giving rise to a false-negative result. Identification of unusual haplotypes in patient samples by an expectation maximization algorithm has recently been suggested as a method for identifying hemizygous regions caused by large intragenic deletions. Using a similar approach, we identified a novel BRCA1 genomic rearrangement in a breast/ovarian cancer family negative at the first mutation screening; we detected a deletion encompassing exons 14-19, probably due to replication slippage between Alu sequences.

Correlations between fitness and heterozygosity at allozyme and microsatellite loci in the Atlantic salmon, Salmo salar L.

The relationship between heterozygosity at genetic markers (six allozyme and eight microsatellite loci), and fluctuating asymmetry (FA), length and weight was investigated in two samples of Atlantic salmon (Salmo salar L.) with different timings of first active feeding (early (EA) and late (LA) salmon). This trait had previously been related to fitness. EA fish show smaller values of FA, are longer, heavier and are more heterozygous at allozyme loci than are conspecific LA fish. Also within both samples, heterozygosity at allozyme loci was inversely related to FA and was positively related to weight and length. However, no significant differences in microsatellite diversity (heterozygosity and mean d2 measurements) were observed between samples (EA vs LA). Furthermore, no association was observed between the variability at microsatellite loci and FA, weight or length within each sample. These results suggest that allozyme loci, in themselves, influence fitness components, rather than associations arising from associative overdominance.

SCE analysis in G2 lymphocyte prematurely condensed chromosomes after exposure to atrazine: the non-dose-dependent increase in homologous recombinational events does not support its genotoxic mode of action.

Several studies have been carried out to evaluate the mutagenic and carcinogenic potential of atrazine, the most prevalent of triazine herbicides classified as a "possible human carcinogen". The majority of these studies have been negative but positive responses have been also reported including mammary tumors in female Sprague-Dawley rats. Sister chromatid exchanges (SCEs) caused by the presence of DNA lesions at the moment of DNA replication have been extensively used for genotoxicity testing, but for non-cytotoxic exposures to atrazine controversial results have been reported. Even though exposures to higher concentrations of atrazine could provide clear evidence for its genotoxicity, conventional SCE analysis at metaphase cells cannot be used because affected cells are delayed in G2-phase and do not proceed to mitosis. As a result, the genotoxic potential of atrazine may have been underestimated. Since clear evidence has been recently reported relating SCEs to homologous recombinational events, we are testing here the hypothesis that high concentrations of atrazine will cause a dose-dependent increase in homologous recombinational events as quantified by the frequency of SCEs analyzed in G2-phase. Towards this goal, a new cytogenetic approach is applied for the analysis of SCEs directly in G2-phase prematurely condensed chromosomes (PCCs). The methodology enables the visualization of SCEs in G2-blocked cells and is based on drug-induced PCCs in cultured lymphocytes. The results obtained for high concentrations of atrazine do not demonstrate a dose-dependent increase in homologous recombinational events. They do not support, therefore, a genotoxic mode of action. However, they suggest that an important part in the variation of SCE frequency reported by different laboratories when conventional SCE analysis is applied after exposure to a certain concentration of atrazine, is due to differences in cell cycle kinetics of cultured lymphocytes, rather than to a true biological variation in the cytogenetic end point used.

Heritable translocations induced by dermal exposure of male mice to acrylamide.

Acrylamide (AA) is an important industrial chemical used mainly in the production of polymers. It can be absorbed through the skin. AA was shown to be a germ cell clastogen that entails a genetic risk for exposed workers. The genetic risk calculation was based on mouse heritable translocation test data obtained after acute intraperitoneal (ip) exposure (Adler et al., 1994). To obtain a correction factor between ip and dermal exposure, dominant lethal and heritable translocation tests were carried out with dermal exposure of male mice to AA. In the dominant lethal test, male (102/El x C3H/El)F1 mice were exposed by dermal application to the shaved backs of 50 mg/kg AA per day on five consecutive days or to five daily ip injections of 50 mg/kg AA. One day after the end of exposure, the males were mated to untreated females of the same hybrid stock for four days and females were changed every four days for a total of five matings. Dominant lethal effects were found during matings 1-3. For ip exposure, these values were 81.7, 85.7 and 45.4%, respectively; for dermal exposure the corresponding values were 22.1, 30.6 and 16.5%, respectively. In the heritable translocation assay, male C3H/El mice were treated with five dermal exposures of 50 mg/kg AA and mated 1.5-8.5 days after the end of exposure to untreated female 102/El mice. Pregnant females were allowed to come to term and all offspring were raised to maturity. Translocation carriers among the F1 progeny were selected by a sequential fertility testing and cytogenetic analysis including G-band karyotyping and M-FISH. A total of 475 offspring were screened and 41 translocation carriers were identified. The observed translocation frequency after dermal exposure was 8.6% as compared to 21.9% after similar ip exposure (Adler, 1990). The calculated ratio of ip vs. dermal exposure of 0.39 can be applied to obtain a more realistic calculation of genetic risk for dermally exposed workers.

A nonsense mutation in the glucosaminyl (N-acetyl) transferase 2 gene (GCNT2): association with autosomal recessive congenital cataracts.

To identify the genetic defect associated with autosomal recessive congenital cataract in four Arab families from Israel.</AbstractText>Genotyping was performed using microsatellite markers spaced at approximately 10 cM intervals. Two-point lod scores were calculated using MLINK of the LINKAGE program package. Mutation analysis of the glucosaminyl (N-acetyl) transferase 2 gene (GCNT2) gene was performed by direct sequencing of PCR-amplified exons.</AbstractText>The cataract locus was mapped to a 13.0-cM interval between D6S470 and D6S289 on Chr. 6p24. A maximum two-point lod score of 8.75 at theta = 0.019 was obtained with marker D6S470. Sequencing exons of the GCNT2 gene, mutations of which have been associated with cataracts and the i blood group phenotype, revealed in these families a homozygous G--&gt;A substitution in base 58 of exon-2, resulting in the formation of premature stop codons W328X, W326X, and W328X, of the GCNT2A, -B, and -C isoforms, respectively. Subsequent blood typing of affected family members confirmed the possession of the rare adult i blood group phenotype.</AbstractText>A nonsense mutation in the GCNT2 gene isoforms is associated with autosomal recessive congenital cataract in four distantly related Arab families from Israel. These findings provide further insight into the dual role of the I-branching GCNT2 gene in the lens and in reticulocytes.</AbstractText>

How reliable is the allopurinol load in detecting carriers for ornithine transcarbamylase deficiency?

The allopurinol test aims to distinguish carriers and noncarriers for ornithine transcarbamylase (OTC) deficiency. We have evaluated the reliability of the test in at-risk females of known genotype. Results based on urine orotidine and/or orotic acid measurement were compared in terms of sensitivity and specificity. Retrospectively, we analysed the results of allopurinol tests in 42 women (22 confirmed heterozygotes and 20 noncarriers) from 23 pedigrees at risk of being carriers for OTC deficiency. Using a cut-off of 2 standard deviations above the mean of controls, the highest sensitivity (91%) was given by orotidine alone or in combination with orotic acid, but specificity was only 70% and 65%, respectively. We conclude that the value of the allopurinol test for detecting OTC carriers in at-risk females is limited. This needs to be recognized when counselling families. The test still has a role as a safe, quick, noninvasive screen of individuals at risk, but test results in possible carriers should be interpreted with caution. In the absence of other supportive evidence, confirmation by mutation analysis is required.

Lung tumorigenicity in A/J and rasH2 transgenic mice following mainstream tobacco smoke inhalation.

Hypothesizing that their respective genetic backgrounds would confer an increased sensitivity to lung tumorigenesis, the plausibility of selected rodent models for the inhalation testing of mainstream tobacco smoke (MTS) was evaluated. Strain A/J and rasH2 transgenic (Tg) mice were exposed to MTS from Kentucky 1R4F research cigarettes using either a whole-body or nose-only exposure regimen. The whole-body regimen consisted of a 20-week exposure period [0.200 mg wet total particulate matter/liter (WTPM/l), 6 h/day, 5 days/week]; nose-only dosing proceeded for 28 weeks [0.040, 0.125, or 0.400 mg WTPM/l, 3 h/day, 5 days/week]. Both regimens included a 16-week recovery period. Gross and microscopic examinations of the lungs were used to evaluate tumor formation, with experimental results supporting the following conclusions: 1. Evaluation of MTS-induced tumorigenicity based on gross evaluation versus microscopic confirmation provides strikingly disparate results, indicating that serial sectioning is necessary for a definitive assessment of lung tumors. 2. While the dosing regimens employed do not allow for a definitive comparison, whole-body exposure appeared to be more effective for inducing statistical changes in tumor multiplicity and incidence compared to nose-only exposure. 3. Exposure-related stress, evidenced as reductions in both body weight gain and background tumor formation, represents a potential confounder during inhalation testing of MTS tumorigenicity, with additional investigation warranted to validate the specificity of exposure-related responses. 4. Comparative findings between A/J and rasH2 Tg mice suggest that the former may be overly sensitive to exposure-related stress, potentially influencing tumorigenic responses.

Predictors of participation in psychosocial telephone counseling following genetic testing for BRCA1 and BRCA2 mutations.

Although adjunctive educational and psychosocial programs are now being developed for BRCA1 and BRCA2 (BRCA1/2) mutation carriers, limited information is available about whether mutation carriers will want to receive such programs or about the characteristics of individuals who participate. The goals of the present study were to describe rates of completing a psychosocial telephone counseling (PTC) intervention that was offered to female BRCA1/2 mutation carriers and to identify sociodemographic and psychological factors associated with decisions to complete the intervention. Subjects were 66 BRCA1/2 mutation carriers who were randomized to receive a PTC intervention following receipt of genetic test results. Sociodemographic and psychological factors were evaluated before notification of assignment to the PTC intervention. Completion of the intervention was determined from study records. Overall, 75.8% of subjects completed the PTC intervention. Compared to unaffected subjects, those affected with breast and/or ovarian cancer were 76% less likely to complete the intervention [odds ratio (OR) = 0.24, 95% confidence interval (CI) = 0.06, 0.98, P = 0.05]. In addition, subjects with higher levels of cancer-specific distress [OR = 4.74, 95% CI = 1.02, 22.03, P = 0.05] and those with greater perceptions of social support [OR = 5.81, 95% CI = 1.29, 26.16, P = 0.02] were also most likely to complete the intervention. The results of this study suggest that while most BRCA1/2 mutation carriers are likely to complete an adjunctive psycho-educational program, personal history of cancer, cancer-specific distress, and perceptions of social support are likely to influence participation.

High-throughput association testing on DNA pools to identify genetic variants that confer susceptibility to acute myeloid leukemia.

We have evaluated the use of allele-specific PCR (AS PCR) on DNA pools as a tool for screening inherited genetic variants that may be associated with risk of adult acute myeloid leukemia (AML). Two DNA pools were constructed, one of 444 AML cases, and another of 823 matched controls. The pools were validated using individual genotyping data for GSTP1 and LTalpha variants. Allele frequencies for variants in GSTP1 and LTalpha were estimated using quantitative AS PCR, and when compared to individual genotyping data, a high degree of concordance was seen. AS primer pairs were designed for nine candidate genetic variants in DNA repair and cell cycle/apoptotic regulatory genes, including Cyclin D1 [codon 870 splice site variant (A&gt;G)]; BRCA1, P871L; ERCC2, K751Q; FAS -1377 (G&gt;A); hMLH1 -93 (G&gt;A) and V219I; p21, S31R; and the XRCC1 R194W and R399Q variants. For six of these assays, there was at least 95% concordance between AS PCR genotyping and an alternative approach carried out on individual samples. Furthermore, these six AS PCR assays all accurately estimated allele frequencies in the pools that had been calculated using individual genotyping data. A significant disease association was seen with AML for the -1377 variant in FAS (odds ratio 1.76, 95% confidence interval 1.26-2.44). These data suggest that quantitative AS PCR can be used as an efficient screening technique for disease associations of genetic variants in DNA pools made from case-control studies.

Factors predicting prostate specific antigen testing among first-degree relatives of prostate cancer patients.

First-degree relatives (FDRs) of prostate cancer patients are known to be at increased risk for the disease, yet relatively little is known about their screening behaviors. The current lack of consensus about the value of prostate cancer screening underscores the importance of examining why some men at increased risk participate in screening and others do not. In this study, variables from Protection Motivation Theory were used to identify predictors of prostate specific antigen (PSA) testing in this at-risk population. Toward this end, scales assessing perceived vulnerability, perceived severity, response efficacy, and self-efficacy for prostate cancer screening were administered to 82 unaffected male FDRs aged 40 and older. When recontacted approximately 14 months later, 50% of FDRs were found to have undergone PSA testing in the interim. Older age, prior prostate cancer screening, and a greater sense of personal efficacy about being able to undergo prostate cancer screening were found to be significant (P &lt; 0.05) predictors of subsequently undergoing PSA testing. These findings provide partial support for the predictive validity of Protection Motivation Theory variables and suggest the importance of considering efficacy beliefs in attempting to understand decision-making about PSA testing in at-risk individuals.

Fertility intentions following testing for a BRCA1 gene mutation.

To test whether fertility intentions differed among persons who tested positive, tested negative, or did not know their genetic status for a mutation of the BRCA1 gene.</AbstractText>Participants were members of a large Utah-based kindred with an identified mutation at the BRCA1 locus. Participants received genetic counseling prior to testing and were interviewed at baseline before testing and at three points after receiving test results from a genetic counselor. The sample included men and women who completed all interviews, were between ages 18 and 45, and were fertile, resulting in a sample of 101 respondents. The primary dependent variable measured whether a subject indicated that they were moderately or very sure at all three post-testing interviews that they intended to have additional children. Effects of BRCA1 mutation status on fertility intentions were estimated using multivariate logistic regressions where we controlled for gender, age, marital status, and baseline fertility intentions.</AbstractText>Female carriers were less likely to want additional children in relation to female noncarriers (odds ratio 0.12, 95% confidence interval 0.01-1.23; P = 0.074). No differences were found among men. There was a significant difference in the effect of mutation status on fertility intentions between males and females (Gender x Carrier status interaction; P = 0.009). Persons who did not know their mutation status were less likely to want more children than noncarriers (odds ratio 0.09, 95% confidence interval 0.01-0.75; P = 0.027).</AbstractText>Predictive genetic testing for late-onset cancer susceptibility affects family planning decision-making. Persons contemplating predictive testing should be informed about possible effects such testing may have on their plans for future fertility.</AbstractText>

Linkage disequilibrium between HLA class II region and autoimmune hepatitis in pediatric patients.

<AbstractText Label="BACKGROUND/AIMS" NlmCategory="OBJECTIVE">Susceptibility HLA class II alleles associated with autoimmune hepatitis (AIH) were only described in case-control studies.</AbstractText>The transmission/disequilibrium test was used in 50 simplex families with AIH, to determine if affected offspring received the disease-associated allele more frequently than its alternate. HLA-DRB1 and DQB1 allele genotyping and autoimmune regulator (AIRE) polymorphisms located in exons 6, 8 and 10 were investigated by PCR-based methods.</AbstractText>HLA-DRB1*03 allele was significantly transmitted from heterozygous parent to affected offspring (81.5%) with type 1 AIH compared to random expected frequency (50.0%; P=0.004) or to unaffected offspring (42.8%; P=0.03). HLA-DRB1*1301 allele showed an excess transmission to affected children (100%) than expected frequency (P&lt;0.0001) or unaffected offspring (P=0.001). The transmission of DQB1*201 or DQB1*0603 alleles showed significant deviation in patients compared to random frequencies: (84.8%; P&lt;0.0001 for DQB1*0201 or 100%; P&lt;0.0001 for DQB1*0603). HLA-DQB1*0201 showed a strong association with type 2 AIH in children (100.0%, P=0.0005).</AbstractText>HLA-DRB1 gene is the major genetic determinant in HLA class II region for children with type 1 AIH. Type 2 AIH is associated with the HLA-DQB1gene. Finally, AIRE gene abnormality does not contribute to the development of isolated AIH.</AbstractText>

The contribution of farm animals to human health.

Farm animals and their products have a longstanding and successful history of providing significant contributions to human nutrition, clothing, facilitation of labour, research, development and medicine and have thus been essential in improving life expectancy and human health. With the advent of transgenic technologies the potential of farm animals for improving human health is growing and many areas remain to be explored. Recent breakthroughs in reproductive technologies, such as somatic cloning and in vitro embryo production, and their merger with molecular genetic tools, will further advance progress in this field. Here, we have summarized the contribution of farm animals to human health, covering the production of antimicrobial peptides, dietary supplements or functional foods, animals used as disease models and the contribution of animals to solving urgent environmental problems and challenges in medicine such as the shortage of human cells, tissues and organs and therapeutic proteins. Some of these areas have already reached the level of preclinical testing or commercial application, others will be further advanced only when the genomes of the animals concerned have been sequenced and annotated. Provided the necessary precautions are being taken, the transmission of pathogens from animals to humans can be avoided to provide adequate security. Overall, the promising perspectives of farm animals and their products warrant further research and development in this field.

NOD2/CARD15: relevance in clinical practice.

So far, the relevance of NOD2/CARD15 genotyping for clinical practice is modest. The current data almost unanimously show that NOD2/CARD15 mutations in Crohn's disease are associated with small-bowel involvement. More studies are needed to determine whether NOD2/CARD15 mutations are also associated with a fibrostenotic behaviour of the disease. If CARD15 variants would predict a more aggressive disease course, then a more aggressive treatment is justified in these patients after NOD2/CARD15 genetic testing. It is not clear whether NOD2/CARD15 genotyping is helpful in differentiating indeterminate colitis patients. Although CARD15 variants do not predict response to the TNF alpha monoclonal antibodies, the role of the gene in response to other drugs is not known. Finally, screening unaffected relatives of CD patients is not recommended until preventive strategies are available.

Genetic influence on variability in human acute experimental pain sensitivity associated with gender, ethnicity and psychological temperament.

While a variety of cultural, psychological and physiological factors contribute to variability in both clinical and experimental contexts, the role of genetic factors in human pain sensitivity is increasingly recognized as an important element. This study was performed to evaluate genetic influences on variability in human pain sensitivity associated with gender, ethnicity and temperament. Pain sensitivity in response to experimental painful thermal and cold stimuli was measured with visual analogue scale ratings and temperament dimensions of personality were evaluated. Loci in the vanilloid receptor subtype 1 gene (TRPV1), delta opioid receptor subtype 1 gene (OPRD1) and catechol O-methyltransferase gene (COMT) were genotyped using 5' nuclease assays. A total of 500 normal participants (306 females and 194 males) were evaluated. The sample composition was 62.0% European American, 17.4% African American, 9.0% Asian American, and 8.6% Hispanic, and 3.0% individuals with mixed racial parentage. Female European Americans with the TRPV1 Val(585) Val allele and males with low harm avoidance showed longer cold withdrawal times based on the classification and regression tree (CART) analysis. CART identified gender, an OPRD1 polymorphism and temperament dimensions of personality as the primary determinants of heat pain sensitivity at 49 degrees C. Our observations demonstrate that gender, ethnicity and temperament contribute to individual variation in thermal and cold pain sensitivity by interactions with TRPV1 and OPRD1 single nucleotide polymorphisms.

Diagnosis and management of medullary thyroid carcinoma.

Successful treatment of MTC depends heavily on early diagnosis and treatment. Often, this is not possible for sporadic MTC; however, genetic testing for hereditary MTC makes this possible if genetic carriers have surgery before C cells undergo malignant transformation. All patients who have MTC should be tested for RET mutations, including putative sporadic cases. The leukocytes of suspected carriers and sporadic MTC cases should be tested for MEN2-associated germ-line mutations by polymerase chain reaction amplification of the appropriate RET gene exons, including 10, 11,13, 14, 15, and 16 (see Table I). When a RET mutation is found, all first-degree relatives must be screened to determine which individuals carry the gene. If these exons are negative, the other 15 should be sequenced because a small risk of hereditary MTC remains if no germ-line mutation is found. The probability that a first-degree relative will inherit an autosomal dominant gene for MTC from an individual who has sporadic MTC in whom no germ-line mutation is found is 0.18% . Patients who have MEN2B or RET codon 883 or 918 mutation should have a total thyroidectomy within the first 6 months of life, preferably within the first month of life. Patients who have 634 mutations, which account for approximately 70% of all MTC mutations, should undergo thyroidectomy by age 5 years. The recommendations for the timing of prophylactic thyroidectomy are not consistent for the less common mutations (see Table 2). There is a balance between performing prophylactic thyroidectomy earlier than at the youngest age at with MTC has been reported to occur for a specific RET mutation (see Fig. 3 and Table 2) and the complications of thyroidectomy, including permanent hypoparathyroidism and laryngeal nerve damage. Preoperative measurement of plasma free metanephrine and neck ultrasonography always should be done if the diagnosis of MTC is known preoperatively. Initial treatment of MTC is total thyroidectomy, regardless of its genetic type or putative sporadic nature, because surgery offers the only chance for a cure. Treatment with 1311 has no place in the management of MTC. Plasma CT measurements provide an accurate estimate of tumor burden and are especially useful in identifying patients who have residual tumor. Pentagastrin- or calcium-stimulated plasma CT testing is useful in identifying CCH or early MTC in carriers of RET mutations that are associated with late onset MTC. Pheochromocytoma may occur before or after MTC and is an important cause of mortality, even in young patients. HPT is an important aspect of MEN2A and requires surgery according to current guidelines for the management of primary HPT. Early thyroidectomy and appropriate management of pheochromocytoma clearly have modified the course of this disease, but more research is necessary in kindreds who have rare MTC mutations. Moreover, new treatments for widespread MTC are necessary because current chemotherapy agents offer little benefit. New drugs that lock the action of tyrosine kinase offer some hope.

Development of a highly efficient system for assessing recombinant gene expression in plant cell suspensions via Agrobacterium tumefaciens transformation.

A transient gene-expression system was developed and used to characterize promoter strength, to verify suitability of bacterial gene modifications for expression in plant cells, and to express active antibody molecules. The system is based on suspension tobacco cells transformed by Agrobacterium in a transient way. Conditions such as pre-culture of tobacco cells and the co-cultivation period were identified as determinants to achieve high expression levels. Under established conditions the activity strength of CaMV (cauliflower mosaic virus) 35 S and ToMoTV (tomato mottle taino virus) AL1 promoters were compared. A modified cry gene sequence from Bacillus thuringiensis was expressed and detected by Western-blot analysis. A monoclonal antibody against anti-(hepatitis B virus surface antigen) was produced in such quantities as to allow testing of biological activity and preliminary characterization.

Sperm DNA damage and its clinical relevance in assessing reproductive outcome.

The routine examination of semen, which assesses sperm concentration, percentage motility and morphology, does not identify subtle defects in sperm chromatin architecture. The focus on the genomic integrity of the male gamete has intensified recently due to the growing concern that genetic diseases may be transmitted via assisted reproductive techniques (ART). Accordingly, the intent of this review is to describe the details of the information pertaining to mitochondrial/nuclear sperm DNA damage with an emphasis on its clinical significance and its relationship with male infertility. Assessment of sperm DNA damage appears to be a potential tool for evaluating semen samples prior to their use in ART. Testing DNA integrity may help select spermatozoa with intact DNA or with the least amount of DNA damage for use in assisted conception. In turn, this may alleviate the financial, social and emotional problems associated with failed ART attempts.

[Mental retardation].

This paper describes recent advances in the neurobiology of mental retardation, emphasizing new diagnostic resources provided by cytogenetics, molecular testing, and neuroimaging.</AbstractText>MEDLINE (January 2000 through October 2003), using the following key words: mental retardation, developmental disability, child, and adolescent. Search of the Pediatrics and New England Journal of Medicine websites using the key word mental retardation. The Online Mendelian Inheritance in Man (OMIM) database was searched for information on clinical genetics.</AbstractText>In October 2003, the number of genetic syndromes associated with mental retardation reached 1,149. Considering the genetic or environmental and congenital or acquired causes of mental retardation, current diagnostic investigation is able to detect the etiology in 50 to 70% of cases.</AbstractText>Diagnostic evaluation should follow a stepwise approach in order to make rational use of the expensive tools of cytogenetics, molecular biology, and neuroimaging.</AbstractText>

Methylation assay by nucleotide incorporation: a quantitative assay for regional CpG methylation density.

Although the aberrant methylation in CpG islands is of great interest as a causative role in human malignancies, it has been very difficult to accurately determine methylation density. Here we report a novel microplate-based quantitative methylation assay, designated MANIC, for a region containing a number of CpG sites based on incorporation of hapten-labeled dCTP at cytosine sites where the methylated cytosines have not been converted to uracil by the bisulfite treatment. Validation using control DNAs revealed that the method was sensitive enough to detect &lt; 1.25% methylated DNA and that calibration curve was linear. With this approach, we determined relative methylation density of O6-methylguanine-DNA methyltransferase gene promoter containing 12 CpG sites among the 12 colorectal cancers and corresponding normal mucosal tissues. Consequently, MANIC showed a high concordance with results by a quantitative method, bisulfite PCR single-stranded conformational polymorphism (BiPS). MANIC is a technique that avoids cumbersome procedures such as electrophoresis or the use of radiolabeling and is applicable to any sequence regardless of the total number of CpG sites or heterogeneity in methylation status.

Natural settings trials--improving the introduction of clinical genetic tests.

Approaches to genetic testing differ in the research setting and the clinical setting. More data are needed to develop approaches that will best facilitate the use of new genetic tests in the clinical setting, especially settings where genetic testing has not been widely used, such as in primary care. Furthermore, data are needed to establish the clinical utility of new genetic tests in the general practice setting. Natural setting trials are proposed as a strategy to develop this information. While natural setting trials are clinical research studies and will expose participants to some degree of risk, the risks are different, and arguably less than the risks those same individuals would otherwise face if the test went directly into clinical practice. Ultimately, clinical practice and safety of new genetic tests can be improved by adding the evaluation provided by natural setting trials.

Evidence for ecology's role in speciation.

A principal challenge in testing the role of natural selection in speciation is to connect the build-up of reproductive isolation between populations to divergence of ecologically important traits. Demonstrations of 'parallel speciation', or assortative mating by selective environment, link ecology and isolation, but the phenotypic traits mediating isolation have not been confirmed. Here we show that the parallel build-up of mating incompatibilities between stickleback populations can be largely accounted for by assortative mating based on one trait, body size, which evolves predictably according to environment. In addition to documenting the influence of body size on reproductive isolation for stickleback populations spread across the Northern Hemisphere, we have confirmed its importance through a new experimental manipulation. Together, these results suggest that speciation may arise largely as a by-product of ecological differences and divergent selection on a small number of phenotypic traits.

Genetic and phenotype changes following in vitro interactions between Helicobacter pylori strains.

The purpose of the present paper was to determine whether in vitro interaction between different Helicobacter pylori strains leads to changes in antibiotic susceptibility, cagA, vacAM2 and DNA fingerprint patterns.</AbstractText>Three H. pylori strains with known antibiotic susceptibility, cagA, vacAM2 status and polymerase chain reaction-random amplified polymorphic DNA (PCR-RAPD) fingerprint analysis were suspended in phosphate buffered saline (PBS pH 7.0), and the suspensions were mixed in equal proportion prior to culture on chocolate agar plates. Subcultures were performed five times every 3 days. As a control, each of the three strains was also subcultured separately. Antibiotic susceptibility testing, PCR for cagA, vacAM2 and PCR-RAPD analysis were done.</AbstractText>Surviving strain of the two H. pylori strains in each combination demonstrated change in resistance to both antibiotics but no change in sensitivity. CagA status of the surviving strain varied as compared to the vacAM2 status, which did not change. The PCR-RAPD fingerprint showed unique band pattern.</AbstractText>DNA transformation follows in vitro interaction. Helicobacter pylori strain with antibiotic resistance is likely to dominate in such in vitro interactions between various strains.</AbstractText>

[Oculopharyngeal muscular dystrophy: study of patients from seven Spanish families with different GCG expansions in PABP2 gene].

Autosomal dominant oculopharyngeal muscular dystrophy (OPMD), with late onset due to ptosis and/or dysphagia, is caused by short (GCG)8-13 triplet-repeat expansions in the polyadenylation binding protein 2 (PABP2) gene, which is localized in chromosome 14q11. The severity of the dominant OPMD as well as the number of expansions that cause the disease are variable. (GCG)9 is mentioned as the most frequent and the genotype/phenotype has still not been well-determined.</AbstractText>To describe the type of expansions (GCG)n found in Spanish families with OPMD, establishing if there is variability of them and the possible geno-phenotypical correlations.</AbstractText>Clinicopathological and molecular studies have been performed in 15 consecutive patients, belonging to seven Spanish families with OPMD. The muscular biopsy study under electronmicroscopy shows intranuclear inclusions (INIs) in all the examined patients (one patient per family). The genetic findings confirm the cause of the disease in all the affected members and in one clinically asymptomatic member of one recently examined family: three families (six, one and one studied members, respectively) present the (GCG)9 expansion, two families (one studied member each one) present the (GCG)10 expansion and two families (one and four studied members respectively) present the (GCG)11 expansion. In these 15 patients with a short GCG expansion causing OPMD, clinical tests for OPMD and a follow-up study of their clinical course have been carefully assessed: in patients with the (GCG)9 expansion major abnormalities appeared in extrinsic ocular mobility and more precocious presentation of limb girld (lumbopelvic preferentially) weakness leading to a great disability before the seventh decade of life under the seventies in some patients and sometimes leading to death. In patients with (GCG)10 and (GCG)11 expansions, eye movements are always preserved and the limb girld muscles weakness did not appear before the seventh decade. No correlation seems to exist between age of onset of the ptosis or dysphagia and the different (GCG)n expansions and the surgical treatment of ptosis, performed in eight patients, showed good results independently of the (GCG)n mutation.</AbstractText>Although further clinical and genetic studies are necessary to establish a strict genotype/phenotype correlation in OPMD, we concluded that the (GCG)9 expansion involve more severe phenotypes than those related to the (GCG)10 or (GCG)11 expansions. Therefore, genetic testing could benefit prognosis in asymptomatic individuals.</AbstractText>

In silico mapping of quantitative trait loci in maize.

Quantitative trait loci (QTL) are most often detected through designed mapping experiments. An alternative approach is in silico mapping, whereby genes are detected using existing phenotypic and genomic databases. We explored the usefulness of in silico mapping via a mixed-model approach in maize (Zea mays L.). Specifically, our objective was to determine if the procedure gave results that were repeatable across populations. Multilocation data were obtained from the 1995-2002 hybrid testing program of Limagrain Genetics in Europe. Nine heterotic patterns comprised 22,774 single crosses. These single crosses were made from 1,266 inbreds that had data for 96 simple sequence repeat (SSR) markers. By a mixed-model approach, we estimated the general combining ability effects associated with marker alleles in each heterotic pattern. The numbers of marker loci with significant effects--37 for plant height, 24 for smut [Ustilago maydis (DC.) Cda.] resistance, and 44 for grain moisture--were consistent with previous results from designed mapping experiments. Each trait had many loci with small effects and few loci with large effects. For smut resistance, a marker in bin 8.05 on chromosome 8 had a significant effect in seven (out of a maximum of 18) instances. For this major QTL, the maximum effect of an allele substitution ranged from 5.4% to 41.9%, with an average of 22.0%. We conclude that in silico mapping via a mixed-model approach can detect associations that are repeatable across different populations. We speculate that in silico mapping will be more useful for gene discovery than for selection in plant breeding programs.

The allelic variant of LAR gene promoter -127 bp T--&gt;A is associated with reduced risk of obesity and other features related to insulin resistance.

Insulin resistance, which is pathogenic for type 2 diabetes (T2D), is under the control of largely unknown genetic determinants. LAR, a protein-tyrosine phosphatase which inhibits insulin signalling, is overexpressed in animal and human models of insulin resistance. We studied the entire sequence of the LAR gene by SSCP analysis and automatic DNA sequencing, with the aim of verifying whether its sequence variants might be associated with insulin resistance. In the 276 bp sequence upstream of the transcriptional start site (i.e. a region we have identified as having basal promoter activity) a -127 bp T--&gt;A SNP (5% frequency) was associated with lower body mass index (BMI) ( P=0.03), waist circumference ( P=0.01), blood pressure ( P=0.01) and urinary albumin/creatinine ratio ( P=0.04) in 589 non-diabetic unrelated individuals from the Gargano region (central east coast of Italy). To quantify the risk for a high body weight conferred by the -127 T--&gt;A SNP, the whole cohort was divided into tertiles according to the individual BMI. The risk of belonging to the heavier tertile, as compared to the leaner one, was reduced by approximately 60%. In a population from East Sicily ( n=307), T/A genotype carriers ( n=13) showed lower triglyceride levels ( P=0.04) and higher insulin sensitivity as indicated by lower plasma glucose ( P=0.03) and serum insulin ( P=0.006) during oral glucose tolerance testing (OGTT). Promoter activity, studied by cDNA transfection experiments, was similar for the A and T alleles. In conclusion, a genetic variant of the LAR gene promoter is consistently associated with features of insulin resistance in two different Caucasian populations. Although the biological relevance of this variant has yet to be determined, this finding underlines the potential importance of the LAR gene in dysregulation of insulin sensitivity and related disorders.

Cancer genetics services: a systematic review of the economic evidence and issues.

This paper systematically reviews the published economic research upon cancer genetics services for families at risk of having familial breast, ovarian or colorectal cancer. A structured search was made of 15 electronic databases. The search identified 1030 papers, of which 31 fulfilled the inclusion criteria, two were cost-benefit studies, five were cost consequences, four were cost-effectiveness studies, one was a cost analysis, two were cost-minimisation studies, one was a cost-utility study, 10 modelled life years and six were reviews. Modelling studies indicate that surveillance, prophylactic and chemoprevention techniques extend survival for carriers of identified mutations. Genetic testing has been estimated to cost 70-2400 USD [48-1591 UK pounds] and genetic counselling 129-800 USD [89-551 UK pounds]. The technology of genetic testing has been found to be cost effective. Cost effectiveness was particularly influenced by targeting genetic services for patients with a strong family history of cancer rather than screening the entire population. Future economic evaluation must go beyond merely assessing health outcomes and mutation identification, and account for the impact of genetic services upon the individual, the family and society, establish the value of services to these groups and determine the most effective ways of delivering genetic services.

[Diagnosis and management of asymptomatic MEN 2 gene carriers].

RET genetic testing affords valid clinical strategies in the diagnosis and management of MEN 2. For at risk family members, the test provides accurate diagnosis of gene carriers and best chance of cure of medullary thyroid carcinoma by prophylactic total thyroidectomy. The test results, however, may have medical, psychological, ethical, and social effects on the individuals as well as their families, it is important for an individual to know the potential consequences and to give an informed consent before having the genetic test. Health care providers should make efforts to be aware of these potential effects and to support a tested individual throughout the entire screening process.

Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes.

We present a novel approach to disease-gene mapping via cladistic analysis of single-nucleotide polymorphism (SNP) haplotypes obtained from large-scale, population-based association studies, applicable to whole-genome screens, candidate-gene studies, or fine-scale mapping. Clades of haplotypes are tested for association with disease, exploiting the expected similarity of chromosomes with recent shared ancestry in the region flanking the disease gene. The method is developed in a logistic-regression framework and can easily incorporate covariates such as environmental risk factors or additional unlinked loci to allow for population structure. To evaluate the power of this approach to detect disease-marker association, we have developed a simulation algorithm to generate high-density SNP data with short-range linkage disequilibrium based on empirical patterns of haplotype diversity. The results of the simulation study highlight substantial gains in power over single-locus tests for a wide range of disease models, despite overcorrection for multiple testing.

Genomic approaches to antibacterial discovery.

This chapter describes two key strategies for the discovery of new antibacterial agents and illustrates the critical role played by genomics in each. The first approach is genomic target-based screening. Comparative genomics and bioinformatics are used to identify novel, selective antibacterial targets of the appropriate antibacterial spectrum. Genetic technologies integral for the success of this approach, such as essentiality testing, are also described. An unprecedented number of novel targets have been discovered via this approach, and a plethora of examples are discussed. This section concludes with the case history of a target successfully progressed from identification by genomics, to high-throughput screening, and onto proof of concept in curing experimental infections. The second approach is based on screening for compounds with antibacterial activity and then employing a broad variety of newer technologies to identify the molecular target of the antibacterial agent. The advantage of this approach is that compounds already possess antibacterial activity, which is a property often challenging to engineer into molecules obtained from enzyme-based screening approaches. The recent development of novel biochemical and genomic technologies that facilitate identification and characterization of the mode of action of these agents has made this approach as attractive as the genomic target-based screening strategy.

A population-based study of morbidity and mortality in mannose-binding lectin deficiency.

Reduced levels of wild-type mannose-binding lectin (MBL) may increase susceptibility for infection, other common diseases, and death. We investigated associations between MBL deficiency and risk of infection, other common diseases, and death during 24, 24, and 8 yr of follow-up, respectively. We genotyped 9,245 individuals from the adult Danish population for three MBL deficiency alleles, B, C, and D, as opposed to the normal noncarrier A allele. Hospitalization incidence per 10,000 person. yr was 644 in noncarriers compared with 631 in heterozygotes (log-rank: P = 0.39) and 658 in deficiency homozygotes (P = 0.53). Death incidence per 10,000 person. yr was 235 in noncarriers compared with 244 in heterozygotes (P = 0.44) and 274 in deficiency homozygotes (P = 0.12). After stratification by specific cause of hospitalization or death, only hospitalization from cardiovascular disorders was increased in deficiency homozygotes versus noncarriers (P = 0.02). When retested in two case control studies, this association could not be confirmed. Incidence of hospitalization or death from infections or other serious common disorders did not differ between deficiency homozygotes and noncarriers. In conclusion, in this large study in an ethnically homogeneous Caucasian population, there was no evidence for significant differences in infectious disease or mortality in MBL-deficient individuals versus controls. Our results suggest that MBL deficiency is not a major risk factor for morbidity or death in the adult Caucasian population.

Unexplained hypereosinophilia and the need for cytogenetic and molecular genetic analyses.

Idiopathic hypereosinophilic syndrome (HES) is a diagnosis made after the exclusion of other causes of eosinophilia. However, differentiation of idiopathic HES from eosinophilic leukemia is sometimes difficult. In some cases, these diagnoses can be differentiated by cytogenetic or molecular findings, as illustrated in the patients described herein.</AbstractText>We describe 3 patients with HES and associated pruritus; 1 patient also had recurrent lesions of eosinophilic cellulitis. All 3 patients were initially diagnosed as having idiopathic HES, but after evaluation and demonstration of molecular abnormalities, they were classified as having eosinophilic leukemia.</AbstractText>Patients with a diagnosis of idiopathic HES should be evaluated for cytogenetic or molecular genetic abnormalities. These abnormalities can establish a diagnosis of chronic eosinophilic leukemia and may provide clues for emerging therapies.</AbstractText>

Context-specific memory and apolipoprotein E (ApoE) epsilon 4: cognitive evidence from the NIMH prospective study of risk for Alzheimer's disease.

The aim of the study was to determine whether the epsilon 4 allele of the apolipoprotein E (ApoE) gene was associated primarily with context-specific memory among individuals at genetic risk for developing Alzheimer's disease. The effect of ApoE status on comprehensive neuropsychological results was examined in 176 healthy adults during baseline cognitive testing in the NIMH Prospective Study of Biomarkers for Older Controls at Risk for Alzheimer's Disease (NIMH Prospective BIOCARD Study). The presence of the epsilon 4 allele was associated with significantly lower total scores on the Logical Memory II subtest of the Wechsler Memory Scale-Revised and percent of information retained after delay. Further analysis indicated the prose recall and retention effect was partially explained by a small subgroup of epsilon 4 homozygotes, suggesting a gradually progressive process that may be presaged with specific cognitive measures. The current results may represent an epsilon 4-associated breakdown between gist-related information and context-bound veridical recall. This relative disconnection may be understood in light of putative epsilon 4-related preclinical accumulation of Alzheimer pathology (tangles and plaques) in the entorhinal cortex (EC) and among frontal networks, as well as the possibility of less-efficient compensatory strategies.

Impact of candidate sire number and sire relatedness on DNA polymorphism-based measures of exclusion probability and probability of unambiguous parentage.

Genetic paternity testing can provide sire identity data for offspring when females have been exposed to multiple males. However, correct paternity assignment can be influenced by factors determined in the laboratory and by size and genetic composition of breeding groups. In the present study, DNA samples from 26 commingled beef bulls and their calves from the Nebraska Reference Herd-1 (NRH1), along with previously reported Illinois Reference/Resource Families data, were used to estimate the impact of sire number and sire relatedness on microsatellite-based paternity testing. Assay performance was measured by exclusion probabilities and probabilities of unambiguous parentage (PUP) were derived. Proportion of calves with unambiguous parentage (PCUP) was also calculated to provide a readily understandable whole-herd measure of unambiguous paternity assignment. For NRH1, theoretical and observed PCUP values were in close agreement (85.3 and 85.8%, respectively) indicating good predictive value. While the qualitative effects on PUP values of altering sire number and sire relatedness were generally predictable, we demonstrate that the impacts of these variables, and their interaction effects, can be large, are non-linear, and are quantitatively distinct for different combinations of sire number and degree of sire relatedness. In view of the potentially complex dynamics and practical consequences of these relationships in both research and animal production settings, we suggest that a priori estimation of the quantitative impact of a given set of interacting breeding group-specific and assay-specific parameters on PUP may be indicated, particularly when candidate sire pools are large, sire relatedness may be high, and/or loci numbers or heterozygosity values may be limiting.

Verification of selective DNA pooling methodology through identification and estimation of the DGAT1 effect.

The discovery of markers linked to genes that are responsible for traits of interest to the dairy industry might prove useful because they could aid in selection and breeding decisions. We have developed a selective DNA pooling methodology to allow us to efficiently screen the bovine genome in order to find genes responsible for production traits. Using markers on chromosome 14 as a test case, we identified a gene (DGAT1) previously known to affect three traits (fat yield, protein yield and total milk yield). Furthermore, we predicted similar effects to those previously shown for DGAT1 in a New Zealand Holstein-Friesian herd. Additionally, we showed a low error rate (1.6%) for the pooling procedure. Hence we are confident that we can apply this procedure to an entire genome scan in the search for quantitative trait loci (QTL).

Equine laminitis: increased transcription of matrix metalloproteinase-2 (MMP-2) occurs during the developmental phase.

The dysadhesion and destruction of lamellar basement membrane of laminitis may be due to increased lamellar metalloproteinase activity. Characterising lamellar metalloproteinase-2 (MMP-2) and locating it in lamellar tissues may help determine if laminitis pathology is associated with increased MMP-2 transcription.</AbstractText>To clone and sequence the cDNA encoding lamellar MMP-2, develop antibody and in situ hybridisation probes to locate lamellar MMP-2 and quantitate MMP-2 transcription in normal and laminitis tissue.</AbstractText>Total RNA was isolated, fragmented by RT-PCR, cloned into vector and sequenced. Rabbit anti-equine MMP-2 and labelled MMP-2 riboprobe were developed to analyse and quantitate MMP-2 expression.</AbstractText>Western immunoblotting with anti-MMP-2 detected 72 kDa MMP-2 in hoof tissue homogenates and cross-reacted with human MMP-2. Immunohistochemistry and in situ hybridisation detected MMP-2 in the cytoplasm of basal and parabasal cells in close proximity to the lamellar basement membrane. Northern analysis and quantitative real-time PCR showed MMP-2 expression significantly (P &lt; 0.01) elevated in laminitis affected tissues.</AbstractText>The lamellar pathology of laminitis is associated with increased transcription of MMP-2.</AbstractText>Real-time PCR analysis of lamellar MMP-2 accurately monitors laminitis development at the molecular level and can be used diagnostically and for testing preventive strategies. Controlling increased MMP-2 transcription may ameliorate or prevent laminitis in high risk clinical situations. Our findings represent a warning to clinicians that the basement membrane lesion of laminitis is insidious and well under way before clinical signs are apparent.</AbstractText>

Denaturing high-performance liquid chromatography (DHPLC) as a reliable high-throughput prescreening method for aberrant promoter methylation in cancer.

Aberrant promoter hypermethylation of CpG dinucleotides is a frequent and significant mechanism of tumor suppressor gene (TSG) silencing in cancer. As increasing numbers of downregulated putative TSGs are emerging from large-scale expression profiling studies, high-throughput techniques are needed to screen for hypermethylation. DHPLC has been established as a reliable, highly sensitive technique for mutation analysis. In this study, the use of DHPLC as a prescreening method for the identification of CpG methylation was developed by analyzing DNA samples with different, well-characterized methylation patterns of the CDKN2A/p16 promoter. Bisulfite treatment of genomic DNA was followed by PCR-amplification of unmethylated as well as methylated CDKN2A/p16 promoter sequences. PCR products were denatured and renatured, permitting the formation of heteroduplex DNA detectable by DHPLC. Methylation of all CpG-sites results in a single peak (homoduplex) with a shift in retention time, whereas partial methylation can be recognized by additional signals representing diverse heteroduplex structures. After method development, 35 DNA samples from primary bladder and breast carcinomas were analyzed in a blinded fashion, revealing complete or partial methylation of the p16 promoter in eight cases and a heterozygous mutation in one case. In conclusion, DHPLC is a highly sensitive and convenient method for methylation screening.

Branchio-oto-renal syndrome: the mutation spectrum in EYA1 and its phenotypic consequences.<Pagination><StartPage>582</StartPage><EndPage>589</EndPage><MedlinePgn>582-9</MedlinePgn></Pagination><Abstract><AbstractText>EYA1 mutations cause branchio-oto-renal (BOR) syndrome. These mutations include single nucleotide transitions and transversions, small duplications and deletions, and complex genomic rearrangements. The last cannot be detected by coding sequence analysis of EYA1. We sought to refine the clinical diagnosis of BOR syndrome by analyzing phenotypic data from families segregating EYA1 disease-causing mutations. Based on genotype-phenotype analyses, we propose new criteria for the clinical diagnosis of BOR syndrome. We found that in approximately 40% of persons meeting our criteria, EYA1 mutations were identified. Of these mutations, 80% were coding sequence variants identified by SSCP, and 20% were complex genomic rearrangements identified by a semiquantitative PCR-based screen. We conclude that genetic testing of EYA1 should include analysis of the coding sequence and a screen for complex rearrangements.</AbstractText><CopyrightInformation>Copyright 2004 Wiley-Liss, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chang</LastName><ForeName>Eugene H</ForeName><Initials>EH</Initials><AffiliationInfo><Affiliation>Molecular Otolaryngology Research Labs, University of Iowa, Iowa City, Iowa 52242, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Menezes</LastName><ForeName>Maithilee</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Meyer</LastName><ForeName>Nicole C</ForeName><Initials>NC</Initials></Author><Author ValidYN="Y"><LastName>Cucci</LastName><ForeName>Robert A</ForeName><Initials>RA</Initials></Author><Author ValidYN="Y"><LastName>Vervoort</LastName><ForeName>Virginie S</ForeName><Initials>VS</Initials></Author><Author ValidYN="Y"><LastName>Schwartz</LastName><ForeName>Charles E</ForeName><Initials>CE</Initials></Author><Author ValidYN="Y"><LastName>Smith</LastName><ForeName>Richard J H</ForeName><Initials>RJ</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>OMIM</DataBankName><AccessionNumberList><AccessionNumber>113650</AccessionNumber><AccessionNumber>601653</AccessionNumber><AccessionNumber>602588</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Hum Mutat</MedlineTA><NlmUniqueID>9215429</NlmUniqueID><ISSNLinking>1059-7794</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D047908">Intracellular Signaling Peptides and Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009687">Nuclear Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015534">Trans-Activators</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.3.48</RegistryNumber><NameOfSubstance UI="C104381">EYA1 protein, human</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.3.48</RegistryNumber><NameOfSubstance UI="D017027">Protein Tyrosine Phosphatases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019280" MajorTopicYN="N">Branchio-Oto-Renal Syndrome</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="Y">diagnosis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004252" MajorTopicYN="N">DNA Mutational Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005820" MajorTopicYN="N">Genetic Testing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D047908" MajorTopicYN="N">Intracellular Signaling Peptides and Proteins</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008297" MajorTopicYN="N">Male</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="Y">Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009687" MajorTopicYN="N">Nuclear Proteins</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018807" MajorTopicYN="N">Polymorphism, Single-Stranded Conformational</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017027" MajorTopicYN="N">Protein Tyrosine Phosphatases</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015534" MajorTopicYN="N">Trans-Activators</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2004</Year><Month>5</Month><Day>18</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2004</Year><Month>9</Month><Day>25</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2004</Year><Month>5</Month><Day>18</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15146463</ArticleId><ArticleId IdType="doi">10.1002/humu.20048</ArticleId></ArticleIdList></PubmedData></PubmedArticle><PubmedArticle><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15146214</PMID><DateCompleted><Year>2004</Year><Month>06</Month><Day>16</Day></DateCompleted><DateRevised><Year>2016</Year><Month>11</Month><Day>24</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1521-4621</ISSN><JournalIssue CitedMedium="Print"><Issue>67</Issue><PubDate><Year>2004</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Toxicity report series</Title><ISOAbbreviation>Toxic Rep Ser</ISOAbbreviation></Journal>NTP technical report on the toxicity studies of 2- and 4-Methylimidazole (CAS No. 693-98-1 and 822-36-6) administered in feed to F344/N rats and B6C3F1 mice.

EYA1 mutations cause branchio-oto-renal (BOR) syndrome. These mutations include single nucleotide transitions and transversions, small duplications and deletions, and complex genomic rearrangements. The last cannot be detected by coding sequence analysis of EYA1. We sought to refine the clinical diagnosis of BOR syndrome by analyzing phenotypic data from families segregating EYA1 disease-causing mutations. Based on genotype-phenotype analyses, we propose new criteria for the clinical diagnosis of BOR syndrome. We found that in approximately 40% of persons meeting our criteria, EYA1 mutations were identified. Of these mutations, 80% were coding sequence variants identified by SSCP, and 20% were complex genomic rearrangements identified by a semiquantitative PCR-based screen. We conclude that genetic testing of EYA1 should include analysis of the coding sequence and a screen for complex rearrangements.<CopyrightInformation>Copyright 2004 Wiley-Liss, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chang</LastName><ForeName>Eugene H</ForeName><Initials>EH</Initials><AffiliationInfo><Affiliation>Molecular Otolaryngology Research Labs, University of Iowa, Iowa City, Iowa 52242, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Menezes</LastName><ForeName>Maithilee</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Meyer</LastName><ForeName>Nicole C</ForeName><Initials>NC</Initials></Author><Author ValidYN="Y"><LastName>Cucci</LastName><ForeName>Robert A</ForeName><Initials>RA</Initials></Author><Author ValidYN="Y"><LastName>Vervoort</LastName><ForeName>Virginie S</ForeName><Initials>VS</Initials></Author><Author ValidYN="Y"><LastName>Schwartz</LastName><ForeName>Charles E</ForeName><Initials>CE</Initials></Author><Author ValidYN="Y"><LastName>Smith</LastName><ForeName>Richard J H</ForeName><Initials>RJ</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>OMIM</DataBankName><AccessionNumberList><AccessionNumber>113650</AccessionNumber><AccessionNumber>601653</AccessionNumber><AccessionNumber>602588</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Hum Mutat</MedlineTA><NlmUniqueID>9215429</NlmUniqueID><ISSNLinking>1059-7794</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D047908">Intracellular Signaling Peptides and Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009687">Nuclear Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015534">Trans-Activators</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.3.48</RegistryNumber><NameOfSubstance UI="C104381">EYA1 protein, human</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.3.48</RegistryNumber><NameOfSubstance UI="D017027">Protein Tyrosine Phosphatases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019280" MajorTopicYN="N">Branchio-Oto-Renal Syndrome</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="Y">diagnosis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004252" MajorTopicYN="N">DNA Mutational Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005820" MajorTopicYN="N">Genetic Testing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D047908" MajorTopicYN="N">Intracellular Signaling Peptides and Proteins</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008297" MajorTopicYN="N">Male</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="Y">Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009687" MajorTopicYN="N">Nuclear Proteins</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018807" MajorTopicYN="N">Polymorphism, Single-Stranded Conformational</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017027" MajorTopicYN="N">Protein Tyrosine Phosphatases</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015534" MajorTopicYN="N">Trans-Activators</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2004</Year><Month>5</Month><Day>18</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2004</Year><Month>9</Month><Day>25</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2004</Year><Month>5</Month><Day>18</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15146463</ArticleId><ArticleId IdType="doi">10.1002/humu.20048</ArticleId></ArticleIdList></PubmedData></PubmedArticle><PubmedArticle><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15146214</PMID><DateCompleted><Year>2004</Year><Month>06</Month><Day>16</Day></DateCompleted><DateRevised><Year>2016</Year><Month>11</Month><Day>24</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1521-4621</ISSN><JournalIssue CitedMedium="Print"><Issue>67</Issue><PubDate><Year>2004</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Toxicity report series</Title><ISOAbbreviation>Toxic Rep Ser</ISOAbbreviation></Journal><ArticleTitle>NTP technical report on the toxicity studies of 2- and 4-Methylimidazole (CAS No. 693-98-1 and 822-36-6) administered in feed to F344/N rats and B6C3F1 mice.</ArticleTitle><Pagination><StartPage>1</StartPage><EndPage>G12</EndPage><MedlinePgn>1-G12</MedlinePgn></Pagination><Abstract>[Structure-see text] 2-Methylimidazole and 4-methylimidazole are intermediate/starting materials or components in the manufacture of pharmaceuticals, photographic and photothermographic chemicals, dyes and pigments, agricultural chemicals, and rubber; these chemicals have been identified as undesirable by-products in several foods and have been detected in mainstream and sidestream tobacco smoke. The National Cancer Institute nominated 2- and 4-methylimidazole as candidates for toxicity and carcinogenicity studies. Toxicity studies were carried out in male and female F344/N rats and B6C3F1 mice. Animals were exposed to 2- or 4-methylimidazole in feed for 15 days or 14 weeks; clinical pathology studies were conducted in the 14-week studies on days 8, 29, and 86 and at week 14. Genetic toxicity studies were conducted in Salmonella typhimurium, rat and mouse bone marrow, and mouse peripheral blood. Groups of five male and five female rats and mice were fed diets containing 0, 1,200, 3,300, or 10,000 ppm 2-methylimidazole (equivalent to average daily doses of approximately 115, 290, or 770 mg 2-methylimidazole/ kg body weight to rats; 220, 640, or 2,100 mg/kg to male mice; 300, 800, or 2,400 to female mice) for 15 days. Groups of five male and five female rats and mice were fed diets containing 0, 300, 800, or 2,500 ppm 4-methylimidazole (equivalent to average daily doses of approximately 30, 80, or 220 mg/kg for rats and 65, 170, or 500 mg/kg for mice) for 15 days. In the 15-day 2-methylimidazole studies, all animals survived to the end of the studies. The mean body weights of 10,000 ppm male rats and female mice were significantly less than those of the controls. Feed consumption by 10,000 ppm male and female rats was reduced. Enlarged thyroid glands were observed in 3,300 and 10,000 ppm male and female rats. The incidences of diffuse hyperplasia of follicular cells of the thyroid gland in 3,300 and 10,000 ppm male and female rats and pars distalis hypertrophy of the pituitary gland in 3,300 and 10,000 ppm males and 10,000 ppm females were increased compared to the controls. In all exposed groups of male and female mice, the incidences and severities of follicular cell hypertrophy of the thyroid gland and the severities of hematopoietic cell proliferation of the spleen generally increased with increasing exposure concentration. In the 4-methylimidazole studies, all animals survived to the end of the studies, and there were no significant differences in mean body weights, clinical findings, organ weights, or gross or microscopic lesions between exposed and control groups. Groups of 10 male and 10 female rats and mice were fed diets containing 0, 625, 1,250, 2,500, 5,000, or 10,000 ppm 2- or 4-methylimidazole (equivalent to average daily doses of approximately 40, 80, 160, 300, or 560 mg/kg 2- or 4-methylimidazole to rats; and 100, 165, 360, 780, or 1,740 mg/kg 2-methylimidazole or 100, 240, 440, 915, or 1,840 mg/kg 4-methylimidazole to male mice; and 90, 190, 400, 800, or 1,860 mg/kg 2-methylimidazole or 110, 240, 540, 1,130, or 3,180 mg/kg 4-methylimidazole to females) for 14 weeks. All animals survived to the end of the 14-week 2-methylimidazole studies. Compared to the controls, the mean body weights were significantly decreased in groups of male rats and mice exposed to 2,500 ppm or greater and in 5,000 and 10,000 ppm female rats and mice. In rats, 2-methylimidazole induced a transient erythrocytosis in females and a minimal, exposure concentration-related, microcytic, normochromic, nonresponsive anemia. 2-Methylimidazole increased thyroid-stimulating hormone concentrations and decreased thyroxine and triiodothyronine concentrations of male and female rats in an exposure concentration-related manner. 2-Methylimidazole induced a mild to moderate, exposure concentration-related, macrocytic, hyperchromic, responsive anemia in mice. Triiodothyronine concentrations were increased in exposed male and female mice, and thyroxine concentrations were decreased in exposed females. Relative to the control groups, clinical chemistry evaluations on day 29 and at week 14 identified decreases in alanine aminotransferase concentrations and total protein and albumin concentrations of rats. In the 2-methylimidazole studies, absolute spleen weights were significantly increased in all exposed groups of male rats. The heart and liver weights were increased in all exposed groups of male mice, as were the spleen weights of female mice exposed to 2,500 ppm or greater. Spermatid heads per testis and mean spermatid count were significantly decreased in 10,000 ppm male rats. The estrous cycle of 10,000 ppm female rats was significantly increased. Gross pathology observations included enlarged thyroid glands, small uteri, and mottled spleen in 5,000 and 10,000 ppm mice. The incidences of diffuse follicular cell hyperplasia of the thyroid gland were significantly increased in male rats exposed to 1,250 ppm or greater and female rats exposed to 2,500 ppm or greater. The incidence of testicular degeneration was significantly increased in 10,000 ppm male rats, and two males in the 10,000 ppm group had follicular cell adenoma of the thyroid gland. In mice, there were generally significant increases in the incidences of follicular cell hypertrophy of the thyroid gland, hematopoietic cell proliferation of the spleen, and hemosiderin pigmentation of the renal tubule in males exposed to 1,250 ppm or greater and females exposed to 2,500 ppm or greater. In the 14-week 4-methylimidazole studies, one 10,000 ppm male mouse was found dead during week 4, and seven 10,000 ppm female mice were found dead during weeks 1 and 2. Mean body weights were significantly less than those of the controls for male rats exposed to 2,500 ppm or greater, 5,000 and 10,000 ppm female rats, male mice exposed to 1,250 ppm or greater, and all exposed groups of female mice. Reduced feed consumption was observed in 5,000 and 10,000 ppm male and female rats. Clinical findings included nasal/eye discharge, ruffled fur, thinness, ataxia, and abnormal breathing in rats, and ruffled fur and dull coats in female mice. On days 29 and 82, functional observations in 5,000 and 10,000 ppm rats included labored or increased respiration, mild tremors, walking on tiptoes, hunched posture, piloerection, crouching over, impaired coordination of movement, ataxia, and pupillary constriction. 4-Methylimidazole induced a transient erythrocytosis and a minimal, exposure concentration-related, microcytic, normochromic, nonresponsive anemia in male and female rats. Clinical chemistry evaluations generally showed a cholestatic effect in exposed male and female rats. At week 14, there was a significant decrease in total protein and albumin concentrations of female rats exposed to 5,000 or 10,000 ppm. In mice, 4-methylimidazole induced a macrocytic, hyperchromic, responsive anemia and, particularly in males, increases in triiododthyronine concentrations and transient decreases in thyroxine concentrations. In the 4-methylimidazole studies, the liver weights of male rats exposed to 2,500 ppm or greater were significantly increased; spleen weights of female rats exposed to 2,500 ppm or greater were decreased. The absolute liver weight was decreased in 10,000 ppm male mice, and relative weights were significantly increased in all exposed groups of mice. In female mice, there was a significant decrease in the absolute weights and increase in the relative weights of the heart, right kidney, and liver in groups exposed to 2,500 ppm or greater. The epididymal spermatozoal concentration was significantly increased in 5,000 ppm male rats. Gross pathology observations included pale livers in male rats exposed to 2,500 ppm or greater and small testes and uteri in 10,000 ppm male and female rats. Microscopic analysis identified significantly increased incidences of cytoplasmic hepatocyte vacuolization of the liver of male rats exposed to 2,500 ppm or greater and 10,000 ppm female rats, hypospermia of the epididymis in 10,000 ppm male rats, atrophy and inflammation of the prostate gland in 10,000 ppm male rats, and degeneration of the testes in 5,000 and 10,000 ppm male rats. 2-Methylimidazole and 4-methylimidazole were negative in the S. typhimurium mutation assay when tested in strains TA97, TA98, TA100, and TA1535, with and without S9 activation enzymes. Testing of 2-methylimidazole in vivo for induction of chromosomal damage, as measured by micronucleated erythrocyte frequency, produced mixed results. When administered by intraperitoneal injection three times at 24-hour intervals, 2-methylimidazole produced negative results in bone marrow micronucleus tests in rats and mice. However, in the 14-week study of 2-methylimidazole, a significant exposure-related increase in the frequency of micronucleated normochromatic erythrocytes was noted in peripheral blood of male and female mice. In vivo, 4-methylimidazole produced uniformly negative results in three-injection bone marrow micronucleus tests in rats and mice and in 14-week peripheral blood micronucleus tests in male and female mice.

Risk and protective effects of the APOE gene towards Alzheimer's disease in the Kungsholmen project: variation by age and sex.

The risk effect of APOE epsilon 4 allele for Alzheimer's disease is acknowledged, whereas the putative protective effect of epsilon 2 allele remains in debate.</AbstractText>To investigate whether those inconsistent findings may be attributable to differences in age and sex composition of the study populations.</AbstractText>A community dementia free cohort (n = 985) aged &gt; or =75 years was followed up to detect Alzheimer's disease cases (DSM-III-R criteria). Data were analysed using Cox models with adjustment for major potential confounders.</AbstractText>Over a median 5.6 year follow up, Alzheimer's disease was diagnosed in 206 subjects. Compared with APOE epsilon 3/epsilon 3 genotype, the relative risk (RR) of Alzheimer's disease was 1.4 (95% confidence interval (CI), 1.0 to 2.0; p = 0.03) for heterozygous epsilon 4 allele and 3.1 (95% CI, 1.6 to 5.9) for homozygous epsilon 4 allele. The association between epsilon 4 allele and Alzheimer's disease risk was stronger in men than in women (RR related to the interaction term epsilon 4 allele by sex, 0.4; 95% CI, 0.2 to 0.9). The epsilon 4 allele accounted for one third of Alzheimer's disease cases among men, but only one tenth among women. The epsilon 2 allele was related to a reduced Alzheimer's disease risk mainly in people aged &lt;85 years (RR, 0.4; 95% CI, 0.2 to 0.8). The RR of Alzheimer's disease related to the interaction term of epsilon 2 allele by age was 2.4 (95% CI, 1.0 to 6.0; p = 0.06).</AbstractText>The APOE genotype specific effects on Alzheimer's disease vary by age and sex, in which the epsilon 4 allele has a stronger risk effect in men, and the epsilon 2 allele confers a protective effect only in younger-old people.</AbstractText>

A mixture model for estimating the local false discovery rate in DNA microarray analysis.

Statistical methods based on controlling the false discovery rate (FDR) or positive false discovery rate (pFDR) are now well established in identifying differentially expressed genes in DNA microarray. Several authors have recently raised the important issue that FDR or pFDR may give misleading inference when specific genes are of interest because they average the genes under consideration with genes that show stronger evidence for differential expression. The paper proposes a flexible and robust mixture model for estimating the local FDR which quantifies how plausible each specific gene expresses differentially.</AbstractText>We develop a special mixture model tailored to multiple testing by requiring the P-value distribution for the differentially expressed genes to be stochastically smaller than the P-value distribution for the non-differentially expressed genes. A smoothing mechanism is built in. The proposed model gives robust estimation of local FDR for any reasonable underlying P-value distributions. It also provides a single framework for estimating the proportion of differentially expressed genes, pFDR, negative predictive values, sensitivity and specificity. A cervical cancer study shows that the local FDR gives more specific and relevant quantification of the evidence for differential expression that can be substantially different from pFDR.</AbstractText>An R function implementing the proposed model is available at http://www.geocities.com/jg_liao/software</AbstractText>

Gene-expression profiling of the early stages of MOG-induced EAE proves EAE-resistance as an active process.

Experimental autoimmune encephalomyelitis (EAE) induced by myelin oligodendrocyte glycoprotein (MOG) is a well-established animal model of multiple sclerosis (MS) in rodents. It reflects the wide spectrum of disease pathology and serves as a valuable tool for studying the pathogenesis and for testing new therapies of MS. In order to identify genes responsible for resistance to and modulation of the disease, we compared the mRNA expression profile of more than 12,000 genes by DNA microarray technique in lymph nodes of the highly EAE-susceptible mouse strain C57Bl/6 (B6) and the resistant strain C57Bl/10.S (B10). The disease onset in B6 mice was day 15. We identified 84 genes that were up-regulated more than two-fold in B10 mice compared to vehicle-treated controls, whereas only two genes were up-regulated in B6 mice after 7 and 15 days post-immunization (p.i.), respectively. We were able to match five up-regulated genes in B10 mice to known quantitative trait loci (QTLs), which control for EAE susceptibility. Only 17, respectively 5, genes were down-regulated at both time points in B10 and B6 mice. Tests for immunoreactivity to MOG (T cell proliferation and interferon-gamma (IFN-gamma) secretion) revealed no stronger immune response in B6 compared to B10 mice supporting the hypothesis of an immunosuppressive effect as a target to prevent EAE in the B10 mice. We conclude that resistance to EAE (and possibly to MS) is an active process mediated by multiple genes up-regulated in peripheral lymphatic organs of resistant animals. Thus, monitoring of the expression of these new candidate genes may serve as a tool for the disease progression and the pharmaceutical treatment.

Accommodating risk: responses to BRCA1/2 genetic testing of women who have had cancer.

The relationship between risk awareness and anxiety has been the subject of extensive theoretical debate and empirical research. Previous studies of women with a family history of hereditary breast and ovarian cancer suggest that both healthy at-risk women and former cancer patients report increased anxiety upon learning about their increased risks of developing these diseases. Indeed, anxiety about genetic risks has been reported as influencing decisions about DNA-testing and risk-reducing surgery on healthy breasts and ovaries. This qualitative study of women who had been treated for breast/ovarian cancer investigated their perceptions of, and reactions to, their genetic risks of developing further cancers following genetic testing (BRCA1/2 mutation searching). In-depth interviews were undertaken with 30 women (10 mutation carriers, 8 awaiting a result and 12 who received an inconclusive test result). Whilst the majority of women in all three groups adopted a fatalistic approach with regard to their future health and did not regard their genetic risks as a threat to self, a few reported heightened anxiety on learning they were at increased risk of developing a second primary cancer. The data suggest that affected women understand their genetic risks of cancer within the context of their previous disease experiences. It is observed that women's responses to their genetic risk are influenced by the degree to which they have accommodated their risk status in their biography following their diagnosis and treatment of cancer.

Labelfree fully electronic nucleic acid detection system based on a field-effect transistor device.

The labelfree detection of nucleic acid sequences is one of the modern attempts to develop quick, cheap and miniaturised hand-held devices for the future genetic testing in biotechnology and medical diagnostics. We present an approach to detect the hybridisation of DNA sequences using electrolyte-oxide-semiconductor field-effect transistors (EOSFETs) with micrometer dimensions. These semiconductor devices are sensitive to electrical charge variations that occur at the surface/electrolyte interface, i.e. upon hybridisation of oligonucleotides with complementary single-stranded (ss) oligonucleotides, which are immobilised on the oxide surface of the transistor gate. This method allows direct, time-resolved and in situ detection of specific nucleic acid binding events without any labelling. We focus on the detection mechanism of our sensors by using oppositely charged polyelectrolytes (PAH and PSS) subsequently attached to the transistor structures. Our results indicate that the sensor output is charge sensitive and distance dependent from the gate surface, which pinpoints the need for very defined surface chemistry at the device surface. The hybridisation of natural 19 base-pair sequences has been successfully detected with the sensors. In combination with nano-transistors a PCR free detection system might be feasible in future.

A Drosophila temperature-sensitive seizure mutant in phosphoglycerate kinase disrupts ATP generation and alters synaptic function.

A novel paralytic mutant, nubian, was identified in a behavioral screen for conditional temperature-sensitive seizure mutants in Drosophila melanogaster. nubian mutants display reduced lifespan, abnormal motor behavior, altered synaptic structure, and defective neurotransmitter release. The nubian mutant disrupts phosphoglycerate kinase (PGK), an enzyme required for ATP generation in the terminal stage of the glycolytic pathway. Consistent with altered ATP generation in nubian animals, brain extracts show a threefold reduction in resting ATP levels compared with controls. Microarray analysis of nubian mutants reveals altered transcription of genes implicated in glucose and lipid metabolism. Disruption of ATP generation in nubian animals is accompanied by temperature-dependent defects in neuronal activity, with initial seizure activity, followed by an activity-dependent loss of synaptic transmission. nubian mutants also display structural defects at the synapse, with larger varicosity size but normal varicosity number, indicating that these synaptic parameters are regulated independently. Both exocytotic (NSF) and endocytotic (dynamin) ATPase/GTPase activity are required for normal synaptic transmission. Biochemical and physiological analyses indicate that synaptic defects in nubian animals are secondary to defective endocytosis, suggesting that endocytotic pathways may be generally more sensitive to altered ATP levels than those used for exocytosis. Alterations in ATP metabolism likely disrupt similar pathways in humans, because PGK deficiency is associated with mental retardation, seizures, and exercise intolerance. Given the behavioral similarities between disruptions of PGK function in Drosophila and humans, the analysis of nubian animals may reveal conserved neuronal responses associated with altered ATP generation within the brain.

A cytogeneticist's perspective on genomic microarrays.

The identification of cytogenetic imbalance is an important component of clinical genetics. About 1 in 154 newborns has a chromosome abnormality. Conventional cytogenetic analysis has enabled the identification of microscopic alterations of the chromosomes. The development of fluorescence in situ hybridization (FISH) and other molecular methodologies has made possible the identification of submicroscopic aberrations. An additional development was comparative genomic hybridization (CGH), a method that directly compares two genomes for DNA copy differences. As first developed, the substrate for CGH analysis is normal metaphase chromosomes. Recently, CGH has been applied to microarrays (array CGH) constructed from large insert clones to identify chromosome imbalance. Array CGH has many advantages over conventional cytogenetic and molecular cytogenetic techniques. Array CGH can be comprehensive (genome-wide), high resolution, amenable to automation, rapid, and sensitive. We anticipate that array CGH will be employed in the clinical cytogenetics laboratory in the near future and will lead to the identification of the chromosomal basis of new syndromes and existing genetic conditions.

Prevalence of alleles associated with HIV resistance in Russia.

Genetic polymorphisms of CCR5, CCR2, and SDF1 genes have been associated with resistance during human immunodeficiency virus type 1 (HIV-1) infection and disease progression. In the present report, we studied the frequency and co-occurrence of CCR5Delta32, CCR5-59029A/G, CCR2-64I, and SDF1-3'A allelic variants among HIV-1-seronegative individuals (n = 171) in Moscow. Observed allelic frequencies were 0.0906 [95% confidence interval (CI), 0.06-0.1212] for CCR5Delta32, 0.4072 (95% CI, 0.3542-0.4602) for CCR5-59029G, 0.1061 (95% CI, 0.0728-0.1394) for CCR2-64I, and 0.2218 (95% CI 0.1715-0.2721) for SDF1-3'A. A significant linkage disequilibrium (p = 0.0034) between CCR2-64I and SDF1-3'A alleles was observed.

Comparison of the validity of preimplantation genetic diagnosis for embryo chromosomal anomalies by fluorescence in situ hybridization on one or two blastomeres.

Is it necessary to analyze two blastomeres in preimplantation genetic diagnosis (PGD) by fluorescence in situ hybridization (FISH) or is one blastomere enough, as suggested by some teams? We analyzed the sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV), false positives (FP), false negatives (FN), and the efficiency (Eff) of FISH performed on one (Group I) or two (Group II) blastomeres. Ninety embryos were analyzed (day 3), 19 blastocysts were replaced (day 5), 64 embryos were reanalyzed (day 5), (Group I = 23; Group II = 41). No differences were observed between the two groups for all of the parameters considered, but one false negative was observed in Group I. Furthermore, two embryos from Group II, which had a discordant diagnosis at PGD (one blastomere being normal and one abnormal), were read as abnormal after reanalysis. The accidental biopsy of the normal blastomere could have lead to the selection of these 2 embryos for transfer, causing a misdiagnosis rate of 4.8%. We conclude that embryo reanalysis is a useful tool to test the reliability of PGD in each laboratory: that PGD on two blastomeres is safer because the practice of PGD on one blastomere can result in a false-negative misdiagnosis.

Reverse hybridization vs. DNA sequencing in the molecular diagnosis of Familial Mediterranean fever.

Familial Mediterranean fever (FMF) is an autosomal recessive inflammatory disorder predominantly affecting people living in or originating from areas around the Mediterranean Sea. It is caused by a number of mutations within the MEFV gene, which differently affect the severity of the disease phenotype. Because patients usually present with rather nonspecific clinical symptoms, MEFV genotyping can confirm and refine FMF diagnosis and improve treatment of affected individuals. We have performed a method comparison study on 100 Lebanese FMF patients to evaluate the potential of a rapid reverse-hybridization teststrip-based assay (FMF StripAssay) to serve as a first-line screening test for our population. When results obtained by reverse-hybridization and DNA sequencing of exons 2, 3, 5, and 10 were compared, the FMF StripAssay identified 144/149 mutations, and correctly typed all 12 different MEFV mutations covered. We conclude that reverse-hybridization provides a very rapid, accurate and easy-to-perform screening method, and, in combination with more comprehensive diagnostic methods, represents an efficient strategy for FMF genotyping.

Mutation carrier testing in Lesch-Nyhan syndrome families: HPRT mutant frequency and mutation analysis with peripheral blood T lymphocytes.

Mutations in the X chromosome hypoxanthine-guanine phosphoribosyl transferase (HPRT) gene are responsible for Lesch-Nyhan syndrome and related diseases in humans. Because the gene is on the X chromosome, males are affected and females in the families are at risk of being carriers of the mutation. Because there are so many different mutations that can cause the disease (218 different mutations in 271 families), genetic testing for carrier status of females requires detailed molecular analysis of the familial mutation. This analysis can be complicated by the unavailability of an affected male for study. In addition, when the mutation is a deletion (34 reported instances), molecular analysis in females is difficult because of the two X chromosomes. We have applied a peripheral blood T lymphocyte cloning assay that uses resistance to the purine analogue 6-thioguanine (TG) to measure the frequency of cells in females expressing a mutant HPRT allele to determine mutation carrier status in 123 females in 61 families. In families in which the HPRT mutation was determined and could be easily analyzed in samples from females, we found a mean (+/- SD) mutant frequency of 9.7 (+/- 8.7) x 10(-6) in noncarrier females and 2.9 (+/- 3.0) x 10(-2) in carrier females. The frequency in carrier females is less than the 0.5 expected for nonrandom X inactivation because of in vivo selection against HPRT mutation-expressing T lymphocytes or stem cells during prenatal development. The use of this cloning assay allows determination of the carrier status of females even when the HPRT mutation is not yet known or is difficult to determine in DNA samples from females. This approach provides a rapid assay that yields information on carrier status within 10 days of sample receipt.

Diagnostic test for Y chromosome microdeletion screening in male infertility.

Despite the current lack of understanding the mechanism of deleterious effects of Y chromosome microdeletions and their prognostic influence on male subfertility, the Y chromosome microdeletion test is widely used in the diagnostic evaluation of male subfertility. However, currently used diagnostic schemes have not been sufficiently evaluated for their diagnostic performance. The purpose of this study was to analyze a large database of published Y chromosome microdeletions to develop the optimal screening strategy for male subfertility. Therefore, we created a database from genetic and clinical data published in 52 peer-reviewed studies reporting on 512 cases with Y chromosome microdeletions. We developed a computerized procedure with the goal of minimizing the number of genetic markers included in the diagnostic set while maximizing the detection rate in patients with microdeletions. We estimate that 85.6% of all published Y chromosome microdeletions can be covered by a set of six genetic markers (sY84, sY127, sY152, RBMY1, sY147, sY254-DAZ). Inclusion of additional markers brings relatively little to the sensitivity of the test and is potentially related to the population origin.

Racial and ethnic variations in knowledge and attitudes about genetic testing.

This study was designed to shed light on whether differences in utilization of genetic testing by African-Americans, Latinos, and non-Hispanic Whites are due primarily to different preferences, or whether they instead reflect other values and beliefs or differential access. It explores the values, attitudes, and beliefs of African-Americans, Latinos, and non-Hispanic Whites with respect to genetic testing by means of a telephone survey of representative samples of these three groups. The study finds clear evidence that Latinos and African-Americans are, if anything, more likely to express preferences for both prenatal and adult genetic testing than White respondents. At the same time, they hold other beliefs and attitudes that may conflict with, and override, these preferences in specific situations. African-Americans and Latinos are also less knowledgeable about genetic testing than non-Hispanic Whites, and they are less likely to have the financial resources or insurance coverage that would facilitate access to testing.

Non-uptake of predictive genetic testing for BRCA1/2 among relatives of known carriers: attributes, cancer worry, and barriers to testing in a multicenter clinical cohort.

BRCA1/2 test decliners/deferrers have received almost no attention in the literature and this is the first study of this population in the United Kingdom. The aim of this multicenter study is to examine the attributes of a group of individuals offered predictive genetic testing for breast/ovarian cancer predisposition who did not wish to proceed with testing at the time of entry into this study. This forms part of a larger study involving 9 U.K. centers investigating the psychosocial impact of predictive genetic testing for BRCA1/2. Cancer worry and reasons for declining or deferring BRCA1/2 predictive genetic testing were evaluated by questionnaire following genetic counseling. A total of 34 individuals declined the offer of predictive genetic testing. Compared to the national cohort of test acceptors, test decliners are significantly younger. Female test decliners have lower levels of cancer worry than female test acceptors. Barriers to testing include apprehension about the result, traveling to the genetics clinic, and taking time away from work/family. Women are more likely than men to worry about receiving less screening if found not to be a carrier. The findings do not indicate that healthy BRCA1/2 test decliners are a more vulnerable group in terms of cancer worry. However, barriers to testing need to be discussed in genetic counseling.

Diagnostic genetic testing for hereditary breast and ovarian cancer in cancer patients: women's looking back on the pre-test period and a psychological evaluation.

The aim of this retrospective, exploratory study was to gain insight into how cancer patients who had a diagnostic genetic test for hereditary breast and/or ovarian cancer looked back on the pre-test period and to gain insight into the psychological impact of the genetic test result. Data were collected by semistructured interviews and self-report questionnaires in 19 BRCA1 or BRCA2 mutation carriers, 7 noncarriers, and 36 patients with an inconclusive genetic test result. Cancer patients had a genetic test mainly for other persons, especially relatives in the descendant line. Mutation carriers felt more in control, but they also reported negative effects of genetic testing such as negative emotional impact and being concerned about their children. Non-carriers were relieved. The group of women where no BRCA1 or BRCA2 mutation was found in the family was heterogeneous. Some misinterpreted the genetic test result as revealing the absence of a genetic predisposition. Others were relieved but also still aware of an increased risk, whereas a last group experienced continuing uncertainty and felt less in control. Self-report questionnaires did not reveal differences in general and cancer-specific distress as a function of the genetic test result. Furthermore, no differences among the three groups were found regarding perceived seriousness of breast and ovarian cancer and perceived control of breast cancer. Perceived control of ovarian cancer was highest in the inconclusive group.

Impact of genetic testing for breast-ovarian cancer susceptibility.

Previously, we have reported a clinical trial in which any woman in a defined geographic region who had a qualifying family history and who was referred by her physician or who was identified through a regional cancer registry was offered free genetic counseling, BRCA testing, and recommendations based on test results. Each family was represented by one affected and one unaffected person. Of the 87 families actually tested, 13 were found to have deleterious mutations. To assess the impact of the counseling and testing process, we contacted the tested individuals 1 month and 1 year after receiving the test result and those with an abnormal test result after 4 years. Index subjects, we found, differed significantly from relatives. Before coming for counseling, index subjects perceived both their general health and emotional health as worse than did their relatives. After counseling and testing, index subjects continue to worry more about breast cancer than do relatives. Affected subjects, we found, differed significantly from unaffected subjects. Before counseling, affected subjects knew more about breast cancer, perceived their general health as poorer, and reported greater adherence to recommended breast cancer surveillance than did unaffected subjects. After counseling and testing, affected subjects were less satisfied than unaffected subjects with having been tested. This study indicates that the group most prone to distress by cancer risk genetic counseling and testing is not the recruited relatives, nor even those affected with cancer, but rather the index patients themselves. The index patients, i.e., the ones who want the risk information most, appear to undergo the most stress in obtaining it.

Genetic equilibrium despite habitat fragmentation in an Afrotropical bird.

We examined the effects of habitat fragmentation of the white-starred robin Pogonocichla stellata metapopulation in the Taita Hills archipelago, a hotspot for biodiversity which was fragmented approximately 40 years ago. Using seven microsatellite markers, we analysed the robin's genetic structure and tested for equilibrium between migration and drift (testing the probability of decreased dispersal) as well as between mutation and drift (test for recent reduction in effective population size, i.e. bottlenecks). This metapopulation was found to retain relatively high levels of genetic variability (H(E) between 0.63 and 0.71) and to be in migration-drift equilibrium, suggesting that increased isolation between fragments did not have much effect on the dispersal between them. Furthermore, this equilibrium test greatly enhanced the interpretation of parameters (e.g. F(ST)) assumed to have reached an equilibrium value. In contrast to previous findings on the related and sympatric Taita thrush Turdus helleri (which is critically endangered), there were no indications for recent bottlenecks in any of the robin subpopulations. This difference can be attributed to the higher dispersal capacity of the robin compared with the thrush (deduced from both the genetic and capture-recapture data). Our results stress the importance of sustained dispersal for species conservation.

Past and current gene flow in the selfing, wind-dispersed species Mycelis muralis in western Europe.

The distribution of genetic diversity in Mycelis muralis, or wall lettuce, was investigated at a European scale using 12 microsatellite markers to infer historical and contemporary forces from genetic patterns. Mycelis muralis has the potential for long-distance seed dispersal by wind, is mainly self-pollinated, and has patchily distributed populations, some of which may show metapopulation dynamics. A total of 359 individuals were sampled from 17 populations located in three regions, designated southern Europe (Spain and France), the Netherlands, and Sweden. At this within-region scale, contemporary evolutionary forces (selfing and metapopulation dynamics) are responsible for high differentiation between populations (0.34 &lt; F(ST) &lt; 0.60) but, contrary to expectation, levels of within-population diversity, estimated by Nei's unbiased expected heterozygosity (H(E)) (0.24 &lt; H(E) &lt; 0.68) or analyses of molecular variance (50% of the variation found within-populations), were not low. We suggest that the latter results, which are unusual in selfing species, arise from efficient seed dispersal that counteracts population turnover and thus maintains genetic diversity within populations. At the European scale, northern regions showed lower allelic richness (A = 2.38) than populations from southern Europe (A = 3.34). In light of postglacial colonization hypotheses, these results suggest that rare alleles may have been lost during recolonization northwards. Our results further suggest that mutation has contributed to genetic differentiation between southern and northern Europe, and that Sweden may have been colonized by dispersers originating from at least two different refugia.

Tumour necrosis factor receptor superfamily member 6 gene mutation detection by denaturing high-performance liquid chromatography.

Denaturing high-performance liquid chromatography (DHPLC) was evaluated as a tool for diagnostic screening of polymorphisms in the tumour necrosis factor receptor superfamily member 6 (TNFRSF6) also known as CD95, Apo-1 or Fas gene. Exons 1-9 of the TNFRSF6 gene were amplified from genomic DNA of 38 individuals, of which three were known to carry mutations in the TNFRSF6 gene. The TNFRSF6 gene amplicons were analysed for heterozygosity by DHPLC. Samples that displayed heterozygous variation by DHPLC were further analysed by sequencing. Comparison of DHPLC analysis with sequencing results showed an overall 100% concordance for samples in which heterozygosity was detected by DHPLC. Importantly, DHPLC was in all cases able to demonstrate the presence or absence of mutations in exon 9 encoding the death domain of the TNFRSF6 gene, which have been implied as the most frequent genetic cause of autoimmune lymphoproliferative syndrome. Comparison of DHPLC analysis with sequencing results showed an overall 100% concordance for samples in which heterozygosity was detected by DHPLC. In conclusion, DHPLC is a suitable method for the detection of genetic variation in the TNFRSF6 gene.

The dark phase improves genetic discrimination for some high throughput mouse behavioral phenotyping.

Dark-phase testing has previously been shown by others to improve the outcome of some 'classical' behavior test situations. However, the importance of such ethological correctness and the effect of the light/dark cycle on high throughput behavioral testing situations such as 'mutant vs. wild type' and 'screening', are less or unknown, respectively. These testing situations differ from the 'classical' in that they are designed primarily to discriminate between genetically different mice rather than provide a detailed assessment of ability or psychosocial state. Here we test the hypotheses that dark-phase testing affects the outcome of high throughput behavioral tests and that dark-phase testing improves discrimination between genetically distinct mice (C57BL/6J, 129S1/SvImJ and B6129F1) using high throughput behavioral tests. Our results demonstrate that, although all successful tests showed some effect of phase, only the SHIRPA primary screen, open-field test and motor learning on the rotarod showed improved strain discrimination in the dark phase. Surprisingly, the social interaction test did not show a clear benefit to either phase, and interestingly, the tail-flick test discriminated strains better in the light phase. However, since the preponderance of our data shows that dark-phase testing improves, or does not affect, strain discrimination, we conclude that for these strains and tests, dark-phase testing provided superior outcomes. If discrimination is not achieved in the dark phase, then light phase-testing would be undertaken.

'I don't feel like a diabetic any more': the impact of stopping insulin in patients with maturity onset diabetes of the young following genetic testing.

Hepatocyte nuclear factor-1alpha (HNF-1alpha) maturity onset diabetes of the young (MODY) is the commonest cause of monogenic diabetes but is frequently misdiagnosed as type 1 diabetes. The availability of genetic testing in MODY has improved diagnosis. Sulphonylurea sensitivity in HNF-1alpha patients means that those on insulin from diagnosis can transfer to sulphonylureas and may improve glycaemic control. To gain insight into the implications for patients of stopping insulin, in-depth interviews were conducted with eight HNF-1alpha patients transferred to sulphonylureas after a median of 20 years on insulin. Thematic content analysis highlighted four key themes: Fear, anxiety and excitement regarding stopping insulin, particularly among those who had been on insulin for many years or had never omitted insulin in the past. Improved lifestyle and self image accompanied by feelings of relief and 'increased normality'. Reflections on their time on insulin, including feelings of annoyance, particularly when the need for insulin treatment had been questioned at diagnosis. Difficulty 'letting go' of insulin treatment--some patients found it hard to believe that they no longer required injections as this conflicted with messages previously received from healthcare professionals. Transferring from insulin to sulphonylureas had a positive impact on lifestyle but support was needed for patients to adjust, many having grown up with the belief they would be on insulin for life.

[Hemochromatosis: the most common of rare diseases].

Familial (hereditary) haemochromatosis (HH) is an iron storage disorder characterized by an increased intestinal absorption of iron and its accumulation in numerous tissues. The disease generates an iron overload with tissue damages also seen in haematologic disturbances (with dyserythropoiesis and haemolysis) and hepatic disorders. Besides typical mutations linked to HH (C282 Y and H63D, HFE locus), three other mutations have been identified and more have to be defined. A complete genetic testing is important to assess the risk of morbidity. Indeed, the clinical picture of HH is dependent upon the specific mutations as well as the individual context (sex, environment, associated hepatic and/or haematologic disorders). Porphyria cutanea tarda (PCT) has for long been found significantly associated with HH. It is now considered that hepatic iron overload related to the combination of heterogeneous genetic traits and environmental factors, including alcoholism and viral hepatitis, precipitates the expression of PCT through the inhibition of uroporphyrinogen decarboxylase (Uro.D).

Not all maps are equal: GIS and spatial analysis in epidemiology.

Recently, Geographical Information System (GIS) has emerged as an innovative and important component of many projects in public health and epidemiology. One of the most useful functions of GIS in epidemiology continues to be its utility in basic mapping. GIS may also involve more sophisticated spatial analysis of disease occurrence and contributing environmental factors. Depending on the quantity and quality of data and the methodology used in analysis, a given map may be either useful or misleading. Although visual analyses (mapped evidence) strengthened by exploratory analyses are mostly sufficient for epidemiologists, the formal testing of certain hypotheses or the estimation of relationships between measures of disease incidence and, for example, environmental covariates require quantitative modelling of disease distribution. It is a promising prospect that spatial statistics and GIS technology have slowly started to merge. However, whether GIS will be useful in the model-based approach and the prediction in, for example, epidemiology remains to be seen. The desired future development of GIS requires a switch of emphasis from data and information to knowledge.

Two independent RB1-inactivating mutations in peripheral blood DNA of a hereditary retinoblastoma patient.

We report the presence of a hemizygous inactivating germ-line RB1 mutation (a recurrent g.78250C--&gt;T transition, resulting in a stop codon in exon 17) in peripheral blood DNA from a patient with hereditary bilateral retinoblastoma. Hemizygosity was established by sequencing that showed no traces of the wild-type C nucleotide and by quantitative real-time PCR, which showed loss of one copy of exon 17. Genotyping of the RB1 locus with several polymorphic markers delineated a maximal deletion region between g.76875 and g.99426, including exons 15-17 and a large piece (21 kb) of intron 17. The heterozygosity for the mutation found in skin fibroblasts proves that the intragenic RB1 deletion probably took place in the definitive hematopoietic lineage of the patient. The presence of a null Rb-/- genotype in the hematopoietic cell lineage suggests that the white blood cells of the proband could be useful in the investigation of the role of complementary RBI family proteins in the control of the cell cycle.

Estimating the survival benefits gained from providing national cancer genetic services to women with a family history of breast cancer.

The aim of this paper is to compare a service offering genetic testing and presymptomatic surveillance to women at increased risk of developing breast cancer with its predecessor of no service at all in terms of survival and quality-adjusted survival (QALYs) by means of a Markov cohort chain simulation model. Genetic assessment and presymptomatic care provided between 0.07-1.61 mean additional life years and 0.05-1.67 mean QALYs over no services. Prophylactic surgery and surveillance extended mean life expectancy by 0.41-1.61 and 0.32-0.99 years, respectively over no services for high-risk women. Model outcomes were sensitive to all the parameters varied in the sensitivity analysis. Providing cancer genetic services increase survival and as long as services do not induce adverse psychological effects they also provide more QALYs. The greatest survival and QALY benefits were found for women with identified mutations. As more cancer genes are identified, the survival and cost-effectiveness of genetic services will improve. Although mastectomy provided most additional life years, when quality of life was accounted for oophorectomy was the optimal strategy. Delayed entry into coordinated genetic services was found to diminish the average survival and QALY gains for a woman utilising these services.

BRCA1/2 predictive testing: a study of uptake in two centres.

Differences in reported uptake of genetic testing for mutations in BRCA1 and BRCA2 can largely be accounted for by different methodologies and by studying research vs nonresearch families. In our joint study of 75 nonresearch families from two UK centres in which at least 3 years had elapsed since the initial proband had been informed of the availability of testing, only 45 and 34% of eligible individuals from Manchester and London, respectively, had come forward for counselling. Final uptake rates using a non-proactive approach were 53 and 29% for women and 11-12% for men, but the figure among those attending clinic was 73 and 62%, respectively. Unlike previous studies, we did not find that uptake had stabilised after a year with 25% of those being tested more than 2 years after the family was informed, and several delaying a considerable time between genetics appointments. We believe that the particularly low uptake even of counselling in men may need to be addressed by improving family communication or providing information sheets for family members to disseminate.

Use of human-derived liver cell lines for the detection of environmental and dietary genotoxicants; current state of knowledge.

This article gives an overview of the results of genotoxicity tests, which have been conducted within the last 5 years with the human liver cell line HepG2. It is an update of an earlier review from 1998 (by Knasm&#xfc;ller et al.). In addition, a number of publications are discussed which are relevant for the use of human derived liver cell lines in genetic toxicology. They concern the establishment of new endpoints, the development of new cell lines and possible pitfalls and problems. HepG2 cells have been used to test a wide variety of compounds over the last years. The most interesting observations are that the cells are highly sensitive toward polycyclic aromatic hydrocarbons and that genotoxic effects are seen with a number of carcinogenic mycotoxins, that give negative results in other in vitro assays. Carcinogenic metals such as As and Cd caused positive results as well, whereas only marginal or negative results were seen with nitrosamines. The low sensitivity toward these latter carcinogens is probably due to a lack of cytochrome P4502E1 which catalyses their activation. Also, a number of structurally different synthetic pesticides as well as bioactive plant constituents ("natural pesticides") have been tested and with some of them genotoxic effects were found. In most experiments, the formation of micronuclei was used as an endpoint; however also the single cell gel electrophoresis assay is increasingly used. Several transfectant lines of HepG2 have been constructed which express increased levels of phase I enzymes (such as CYP1A1, CYP1A2, CYP2E1 etc.); furthermore, cell lines became available which express human glutathione-S-transferases. These new clones might be particularly useful for the investigation of specific classes of genotoxicants and also for mechanistic studies. Apart from HepG2 cells, a number of other human derived liver cell lines have been isolated, but so far no data from genotoxicity experiments are available, except for Hep3B cells, which were compared with HepG2 and found to be less sensitive in general. Studies with HepG2 clones of a different origin indicate that the cells differ in regard to their sensitivity toward genotoxicants; also medium effects and the cultivation time might affect the outcome of genotoxicity studies. Overall, the results support the assumption that HepG2 cells are a suitable tool for genotoxicity testing.

DNA-based carrier screening in the Ashkenazi Jewish population.

Several relatively rare genetic diseases are found at greater frequencies in Ashkenazi Jewish populations. Most of these conditions are untreatable and shorten life expectancy. Genetic screening using molecular detection of a few common mutations for each of these diseases facilitates their prevention by identification of carrier couples. Conversely, couples with negative results are reassured by reduced carrier risks. Using a standardized format, a brief overview for each of the nine genetic diseases is presented. Known mutations, a short clinical summary, clinical and laboratory diagnostic methods and information on supportive treatments is provided for each. Finally, a brief discussion of available DNA testing technologies and a review of platforms for expanded testing options for Ashkenazi Jewish diseases under development are presented.

Candidate genetic polymorphisms for asthma in Chinese schoolchildren from Hong Kong.

Polymorphisms in several genes have been associated with asthma, atopy and bronchial hyperresponsiveness in white and Japanese populations. In this study we tested for associations of 11 polymorphisms with wheeze and asthma in 10-year-old Chinese schoolchildren.</AbstractText>The subjects were 107 children who had wheeze in the last 12 months and 118 without wheeze in the last 12 months. They were randomly selected from 3110 children who took part in Phase II of the International Study of Asthma and Allergies in Childhood. These schoolchildren underwent questionnaire, spirometry and methacholine challenge testing.</AbstractText>The A allele of the tumor necrosis factor-alpha (TNFA) G-308A polymorphism was significantly associated with wheeze in the last 12 months (odds ratio [OR] 2.1, P = 0.04) and current asthma (OR 2.6, P = 0.006). When stratified by gender, these associations were only seen in the female study participants. In girls, the OR for the TNFA-308A allele and wheeze in the last 12 months was 3.6 (P = 0.01) and for current asthma it was 6.0 (P = 0.0006).</AbstractText>The A allele of the TNFA G-308A polymorphism was a risk factor for asthma-related phenotypes in girls but not boys.</AbstractText>

Survey of embryonic stem cell line source strains in the water maze reveals superior reversal learning of 129S6/SvEvTac mice.

The availability of pluripotent embryonic stem (ES) cells for gene targeting has resulted in laboratory mice becoming important animal models of human neurological disease. Inbred strains of mice differ in many behavioural phenotypes, such that the same gene mutation can appear to have different phenotypic effects when introduced onto different genetic backgrounds. Prior knowledge of the behavioural phenotypes of the inbred strains used for gene targeting would, therefore, allow the selection of the most appropriate genetic background for the hypothesis to be tested. With this in mind, we tested eight strains of mice (129S1/SvImJ, 129S2/SvPasIcoCrlBR, 129S6/SvEvTac, B6129SF1/J, C57BL/6J, C57BL/6N, LP/J and SM/J), including the sources of five ES cell lines commonly used for gene targeting, in the spatial (submerged platform) version of the Morris water maze, the most widely used paradigm to evaluate the cognitive abilities of genetically modified mice. The three 129 substrain sources of ES cell lines demonstrated spatial learning in the water maze that was superior to that of C57BL/6J, the inbred strain most commonly used for the maintenance and phenotypic testing of mutations. In addition, 129S6/SvEvTac was unique amongst the eight strains tested in having a particular capacity for reversal learning, when the submerged platform was relocated to the opposite quadrant. We conclude that some substrains of 129 could provide suitable genetic backgrounds for testing gene mutations that might be expected to impair cognitive function, thus negating the need to backcross to C57BL/6J, thereby avoiding the so-called "flanking gene problem".

Fragile X mental retardation syndrome: from pathogenesis to diagnostic issues.

The Fragile X (FRAXA) syndrome is the most common cause of familial (monogenic) mental retardation and is widespread in human populations. This syndrome is characterised by an unusual mode of transmission for an X-linked disease. In affected families, one frequently finds clinically normal transmitting males, whose daughters - also clinically normal - have a high risk of having affected children. The risk of developing the disease (penetrance) thus appears to increase in successive generations of the same family through maternal transmission. As shown by molecular cloning of the fragile X locus, Fragile X mutations are unstable expansions of a CGG trinucleotide repeat, located in the first exon (non-protein-coding) of the FMR1 gene (for Fragile X Mental Retardation). Two main types of mutation are observed in affected families. A full mutation is found in patients with mental retardation and corresponds to large expansions of the repeat. Premutations are moderate expansions and are found in normal transmitting males and in the majority of clinically normal carrier females. About 15% of patients show a mosaic pattern consisting of both full mutations and premutations. Although analysis of the CGG expansion has led to the establishment of reliable tests for diagnosis and genetic counseling of Fragile X syndrome, care must be exercised to use these tools to answer the concerns of the families and avoid doing harm. In our opinion, testing in children should be restricted to those who show a developmental delay, cognitive deficits and/or abnormal behavior evocative of the syndrome. A carrier diagnosis in a girl who is clinically normal should probably only be performed at an age where she can understand the consequences for family planning and the options of prenatal diagnosis. When testing children with borderline cognitive deficits, a positive diagnosis should be used to improve educational strategies for the children - and not to stigmatise them.

Genetic testing in endocrinology: lessons learned from experience with multiple endocrine neoplasia type 2 (MEN2).

Multiple endocrine neoplasia type 2 (MEN2) is a syndrome characterized by medullary thyroid carcinoma (MTC), unilateral or bilateral pheochromocytoma and hyperparathyroidism. Familial MTC (FMTC) is a subvariant of MEN2 in which affected individuals develop MTC without other manifestations of MEN2. The identification of RET proto-oncogene mutations in MEN2 and FMTC have provided a precise method for identifying gene carriers. This review provides a concise discussion of the use of genetic testing in the management of hereditary MTC, discussing the appropriate use of this new technology with an emphasis on early intervention to prevent death or serious morbidity from this disease.

Integration of genetics into medical practice.

It has been a century since the first human genetic disorders were recognized, but only recently have there been any prospects that the genetic approach would become integral to medical practice. Throughout most of the 20th century, medical genetics has focused on rare monogenic and chromosomal disorders. There were major successes, including chromosomal analysis, prenatal diagnosis and newborn screening for inborn errors of metabolism, but the impact was confined to a relatively narrow corner of medicine. The situation has changed, however, with advances in genetics and especially with the sequencing of the human genome. The tools are now at hand to begin to understand the genetic basis of common as well as rare disorders. It is expected that this will lead to major advances in both diagnosis and treatment, so that physicians in all areas of medicine will be using the tools of genetics in their daily practice.

Four-color multiplex 5' nuclease assay for the simultaneous detection of the factor V Leiden and the prothrombin G20210A mutations.

We developed a real-time multiplex four-color assay for the simultaneous detection of the factor V Leiden (FVL) and prothrombin (PT) G20210A mutations in one closed tube using a single thermocycling protocol. The assay combines the power of multiplex PCR with the specificity provided by allele-specific oligonucleotide (ASO) hybridization using the 5' nuclease assay format. Human genomic DNA is prepared from whole blood with standard procedures. A 97-bp DNA sequence of the coagulation factor V gene is co-amplified with a 111-bp DNA sequence of the coagulation factor II (PT) gene using four PCR primers. In addition, the reactions included four differentially labeled ASO probes for the specific detection of the different FVL/PT G20210A genotypes. To evaluate the assay's performance characteristics, we performed a comparison of two methods. We analyzed DNA samples from 52 individuals with known FVL/PT G20210A genotypes that were previously genotyped with an assay that combined PCR with the use of restriction fragment length polymorphisms. We found a 100% concordance between the results generated by both methodologies. We conclude that the four-color multiplex assay is specific and reproducible for the detection of the FVL/PT G20210A mutations, and it can be easily adapted for the detection of other SNPs.

[Genetics of hypophosphatasia].

Hypophosphatasia is a rare inherited disorder characterized by defective bone and teeth mineralization and deficiency of serum and bone alkaline phosphatase activity. The symptoms are highly variable in their clinical expression, which ranges from stillbirth without mineralized bone to early loss of teeth without bone symptoms. Currently, there is no treatment for the disease. Recent developments in molecular biology allow to better understand the genetics of the disease, especially its transmission that may be recessive or dominant, to improve genetic counseling and molecular diagnosis, and offer new perspectives of treatment.

Primary aldosteronism--careful investigation is essential and rewarding.

Once considered rare, primary aldosteronism (PAL) is now regarded as the commonest potentially curable and specifically treatable form of hypertension. At Greenslopes Hospital Hypertension Unit (GHHU), the decision in 1991 to screen all (and not just hypokalemic or resistant) hypertensives by aldosterone/renin ratio (ARR) testing led to a 10-fold increase in detection rate of PAL and four-fold increase in removal rate of aldosterone-producing adenomas (APAs). The GHHU/Princess Alexandra Hospital Hypertension Unit PAL series stands at 977 patients and 250 APAs removed with hypertension cured in 50-60% (remainder improved). Reliable detection requires that interfering medications are withdrawn (or their effects considered) before ARR measurement, and reliable methods (such as fludrocortisone suppression testing) to confirm PAL. Adrenal venous sampling is the only dependable way to differentiate APA from bilateral adrenal hyperplasia. Genetic testing has facilitated detection of glucocorticoid-remediable, familial PAL. Identification of mutations causing the more common familial variety described by GHHU in 1991 should further aid in detection of PAL.

Communicating risk in prenatal genetic testing.

Prenatal testing for Down syndrome and neural tube defects has become routine, and testing for other genetic conditions is becoming commonplace. Counseling about these tests involves a discussion of risk information, so pregnant women and their partners can use the information effectively when they make choices about testing. Discussing risk can be challenging, as many individuals, particularly those of lower literacy, have a poor understanding of the numerical concept of risk. Furthermore, whether risk is comprehended accurately or not, it is interpreted by patients in light of their existing knowledge and past experiences. Strategies available to optimize understanding of risk include communication of risk figures as frequencies rather than as probabilities or percentages and explicit discussion of a woman's preconceptions about her risk and about the condition being tested for.

Genetic testing for breast and ovarian cancer susceptibility: a family experience.

The purpose of this article is to provide an overview of current knowledge concerning genetic testing for breast and ovarian cancer susceptibility. This overview includes 1) a brief history of genetic testing for breast and ovarian cancer susceptibility, 2) a review of factors that midwives and other health care providers need to consider before offering this type of testing to their clients, 3) management options for clients at high risk for hereditary breast and ovarian cancers, and 4) a discussion of preliminary findings from an ongoing study concerning the family experience of genetic testing, which illustrates some of the ethical issues that emerge for individuals and families during the family experience of genetic testing for breast and ovarian cancer susceptibility.

Bayesian class discovery in microarray datasets.

A novel approach to class discovery in gene expression datasets is presented. In the context of clinical diagnosis, the central goal of class discovery algorithms is to simultaneously find putative (sub-)types of diseases and to identify informative subsets of genes with disease-type specific expression profile. Contrary to many other approaches in the literature, the method presented implements a wrapper strategy for feature selection, in the sense that the features are directly selected by optimizing the discriminative power of the used partitioning algorithm. The usual combinatorial problems associated with wrapper approaches are overcome by a Bayesian inference mechanism. On the technical side, we present an efficient optimization algorithm with guaranteed local convergence property. The only free parameter of the optimization method is selected by a resampling-based stability analysis. Experiments with Leukemia and Lymphoma datasets demonstrate that our method is able to correctly infer partitions and corresponding subsets of genes which both are relevant in a biological sense. Moreover, the frequently observed problem of ambiguities caused by different but equally high-scoring partitions is successfully overcome by the model selection method proposed.

Thalassemia screening among Royal Thai Army medical cadets.

Thalassemia, common in Thailand, varies from mild to severe anemia, resulting in work inefficiency, particularly during exertion. Therefore, it is important for military cadets to be screened. The objective of this study was to screen for thalassemia and hemoglobinopathies among Royal Thai Army medical cadets. We tested 358 third-year Royal Thai Army medical cadets for complete blood count, red blood cell indices, hemoglobin (Hb) typing, inclusion bodies, and Hb A2, and Hb E. DNA analysis confirmed alpha-thalassemia, trait detection. The Hb E trait was the most frequent, respectively, in men and women, at 12.61% and 12%, followed by the a-thalassemia1 trait, at 3.3% and 4% and the beta-trait, at 1.5% and 0%. Two cases of homozygous Hb E were found only in men. Interestingly, a mild form of 1-thalassemia/Hb E was found in one male RTA medical cadet. These findings suggest that consistent thalassemia screening should be considered.

Colorectal cancer chemoprevention--an overview of the science.

The development and dissemination of sophisticated detection technologies have recently exposed the high prevalence of preinvasive colorectal neoplasia in the adult U.S. population. Although cancer screening and surveillance provide opportunities for risk stratification, they achieve risk reduction only when coupled with effective interventions. This review surveys the lead compounds for colorectal cancer prevention and the measures by which they may be prioritized for clinical testing. Clinical trials remain the rate-limiting step in agent development, and novel trial designs are needed to hasten agent identification and testing for cancer prevention. Innovative research models include the nesting of prevention end points within cancer treatment trials and within trials testing promising preventive compounds intended for nononcologic indications.

Linkage analysis of a complex disease through use of admixed populations.

Linkage disequilibrium arising from the recent admixture of genetically distinct populations can be potentially useful in mapping genes for complex diseases. McKeigue has proposed a method that conditions on parental admixture to detect linkage. We show that this method tests for linkage only under specific assumptions, such as equal admixture in the parental generation and admixture that occurs in a single generation. In practice, these assumptions are unlikely to hold for natural populations, resulting in an inflation of the type I error rate when testing for linkage by this method. In this article, we generalize McKeigue's approach of testing for linkage to allow two different admixture models: (1) intermixture admixture and (2) continuous gene flow. We calculate the sample size required for a genomewide search by this method under different disease models: multiplicative, additive, recessive, and dominant. Our results show that the sample size required to obtain 90% power to detect a putative mutant allele at a genomewide significance level of 5% can usually be achieved in practice if informative markers are available at a density of 2 cM.

[Complex craniofacial synostoses].

Complex craniofacial synostosis is a group of rare genetic disorders characterized by premature closure of the sutures in the craniofacial skeleton and which to varying degrees affects the extremities.</AbstractText>On the basis of relevant literature, we present a review of syndromal craniofacial synostosis.</AbstractText>Phenotypically, the complex craniofacial syndromes have many similarities. Synostosis of the sutures of the cranial vault can result in a variety of skull deformations, depending on the sutures involved, the sequence of premature closure, and the time of closure. Synostosis of the sutures in the skull base and facial skeleton leads to shallow orbits, exophthalmus, hypertelorism, midface retrusion, and prognathia.</AbstractText>Precise diagnosis of complex craniofacial syndromes may be difficult solely on the basis of a clinical examination. However, several of the most common syndromes are caused by mutations in genes that code for fibroblast growth-factor receptors. Children with a suspected complex craniofacial syndrome should be referred to genetic testing.</AbstractText>

Health economics and genetic service development: a familial cancer genetic example.

Advances in genetics are allowing a greater number of clinical genetics services to be offered to individuals with family histories of particular diseases. It is important that such services are not allowed to proliferate before they have been properly evaluated in terms of both their clinical and cost-effectiveness. A randomised controlled study of a new clinical genetics service in Wales for women with a family history of breast cancer has been undertaken. The health service costs from initial consultation and counselling through to mutation testing within families were assessed, along with patient travel costs. The extra cost of specialist genetics assessment (intervention) was pound 16.36 higher per woman than assessment by a breast surgeon at a District General Hospital (control). A further cost of pound 46.42 per initially presenting woman was also generated as a result of further counselling within the families of 48, and testing within the families of 36 of the 412 original presenting women. An explanation is given here of the costing methodology as an illustration of what is involved in such an exercise.

BRCA1 testing with definitive results: a prospective study of psychological distress in a large clinic-based sample.

To examine the short-term psychological impact of receiving definite results concerning BRCA1 mutation status in a clinical setting.</AbstractText>A test was offered for consecutive sample of 395 women from 53 families with demonstrated BRCA1 mutations. The sample included 50 women with a personal history of cancer, and 345 women without. Of the 287 women who chose to be tested and participated in the study, 79% of those with cancer 33% of those without cancer had a demonstrated BRCA1 mutation. Psychological distress was measured with the hospital anxiety and depression scale (HADS), the general health questionnaire (GHQ-28), the impact of event scale (IES) and Beck's hopelessness scale (BHS) at the time the patients were offered testing and six weeks after receiving the test result.</AbstractText>No significant changes were found in psychological distress from baseline to follow-up in any groups. Women with cancer were significantly more distressed than those without both at baseline and at six weeks, while women without cancer had levels of psychological distress comparable to or lower than normative data as measured by HADS.</AbstractText>Our sample had a low level of psychological distress at baseline. Receiving a definite positive or negative result on the BRCA1 test had minimal effects on short-term psychological distress. These findings indicate that establishing a special psychological service in relation to predictive BRCA1 testing could be superfluous.</AbstractText>

BRCA1 testing in breast and/or ovarian cancer families from northeastern France identifies two common mutations with a founder effect.

The purpose of this study was to determine whether two mutations detected frequently in a population of breast and/or ovarian cancer families originating from the northeastern part of France could be due to a founder effect.</AbstractText>83 index cases of families ascertained to have a familial breast and/or ovarian cancer history, were screened for mutations in all coding exons of the BRCA1 gene, using combined DGGE and direct sequencing. For haplotype analysis, six polymorphic markers were used for allelotyping of mutation carriers and non carriers from nine families with 3600del11 mutation and four families with G1710X mutation.</AbstractText>Of 83 index cases, 27 (32%) had 14 different BRCA1 mutations, one of which (G1710X), had not been reported in other populations. Two mutations were particularly common: 3600del11 in exon 11 accounted for 37% and the nonsense mutation G1710X in exon 18 for 15% of all mutations. We identified a common haplotype for each mutation suggesting a common founder for each recurrent mutation. No specific phenotype could be assigned to any of the common mutations.</AbstractText>These data demonstrate geographical clustering and suggest a founder effect for particular BRCA1 mutations, which identification will facilitate carrier detection in French families with breast cancer and breast and/or ovarian cancer.</AbstractText>

The 1100delAT BRCA1 and the 8765delAG BRCA2 mutations: occurrence in high-risk non-Ashkenazi Jews and haplotype comparison of Jewish and non-Jewish carriers.

Few mutations have been described in BRCA1 and BRCA2 in high-risk non-Ashkenazi Jews. In a Libyan family the 1100delAT BRCA1 mutation was detected and the 8765delAG BRCA2 mutation was previously described in two Jewish-Yemenite-families. In this study, the rate of these mutations in high-risk Jews of North African and Yemenite origin was assessed, and the BRCA1 -linked haplotype of Jewish and non-Jewish 1100delAT mutation carriers were compared. Genotyping included 64 high-risk Yemenite women (tested only for the BRCA 2 mutation) and 147 high-risk North African women, tested for both mutations. PCR amplification was followed by either restriction enzyme digestion or DGGE or dHPLC analyses and direct sequencing. For haplotyping, 5 BRCA1 -linked markers were used. Neither the 1100delAT BRCA1 nor the 8765delAG BRCA2 mutations were detected in any non-Ashkenazi individual. The haplotype of the non-Jewish 1100delAG mutation carrier differed from that of the Jewish-Libyan mutation carriers. We conclude that both1100delAT BRCA1 and 8765delAG BRCA2 mutations occur rarely in high-risk non-Ashkenazi Jews, and while the latter seems to be a founder mutation in some populations, the former occurs on a different background in ethnically diverse families.

Screening for mutations in the GJB3 gene in Brazilian patients with nonsyndromic deafness.

Deafness is a complex disorder that is affected by a high number of genes and environmental factors. Recently, enormous progress has been made in nonsyndromic deafness research, with the identification of 90 loci and 33 nuclear and 2 mitochondrial genes involved (http://dnalab-www.uia.ac.be/dnalab/hhh/). Mutations in the GJB3 gene, encoding the gap junction protein connexin 31 (Cx31), have been pathogenically linked to erythrokeratodermia variabilis and nonsyndromic autosomal recessive or dominant hereditary hearing impairment. To determine the contribution of the GJB3 gene to sporadic deafness, we analysed the GJB3 gene in 67 families with nonsyndromic hearing impairment. A single coding exon of the GJB3 gene was amplified from genomic DNA and then sequenced. Here we report on three amino acid changes: Y177D (c.529T &gt; G), 49delK (c.1227C &gt; T), and R32W (c.144-146delGAA). The latter substitution has been previously described, but its involvement in hearing impairment remains uncertain. We hypothesize that mutations in the GJB3 gene are an infrequent cause of nonsyndromic deafness.

ART in recurrent miscarriage: preimplantation genetic diagnosis/screening or surrogacy?

Recently, assisted reproductive techniques have been used to prevent further miscarriages in women with recurrent miscarriage. One approach uses either screening or diagnosis of embryonic chromosomes prior to embryo replacement [preimplantation genetic screening (PGS)/preimplantation genetic diagnosis (PGD)]. The second approach involves surrogacy. However, PGS/PGD assumes that the embryo is chromosomally abnormal, and that the mother should receive a chromosomally normal embryo. Surrogacy assumes that the embryo is normal and that the maternal environment needs to be substituted. This article examines the place of both techniques in different types of recurrent miscarriage, and tries to give guidelines as to which technique is preferable depending on the likelihood of an embryonic chromosome aberration. In repeated fetal aneuploidy or in the older patient, PGS or PGD are preferable. However, with high numbers of miscarriages, or in autoimmune pregnancy loss, surrogacy is preferable. In the light of recent work, it is uncertain which treatment mode is indicated in balanced parental chromosome aberrations. In conclusion, both techniques have a place, but probably only in those patients with a poor prognosis in whom assisted reproductive techniques will be shown to improve the subsequent live birth rate above the spontaneous rate.

Are you my mother? Bayesian phylogenetic inference of recombination among putative parental strains.

Reconstructing evolutionary relationships using Bayesian inference has become increasingly popular due to the ability of Bayesian inference to handle complex models of evolution. In this review we concentrate on inference of recombination events between strains of viruses when these events are sporadic, ie rare relative to point mutations. Bayesian inference is especially attractive in the detection of recombination events because it allows for simultaneous inferences about the presence, number and location of crossover points and the identification of parental sequences. Current frequentist recombination identification falls into a sequential testing trap. The most likely parental sequences and crossover points are identified using the data and then the certainty of recombination is assessed conditional on this identification. After briefly outlining basic phylogenetic models, Bayesian inference and Markov chain Monte Carlo (MCMC) computation, we summarise three different approaches to recombination detection and discuss current challenges in applying Bayesian phylogenetic inference of recombination.

Clinically validated benchmarking of normalisation techniques for two-colour oligonucleotide spotted microarray slides.

Acquisition of microarray data is prone to systematic errors. A correction, called normalisation, must be applied to the data before further analysis is performed. With many normalisation techniques published and in use, the best way of executing this correction remains an open question. In this study, a variety of single-slide normalisation techniques, and different parameter settings for these techniques, were compared over many replicated microarray experiments. Different normalisation techniques were assessed through the distribution of the standard deviation of replicates from one biological sample across different slides. It is shown that local normalisation outperformed global normalisation, and intensity-based 'LOWESS' outperformed trimmed mean and median normalisation techniques. Overall, the top performing normalisation technique was a print-tip-based LOWESS with zero robust iterations. Lastly, we validated this evaluation methodology by examining the ability to predict oestrogen receptor-positive and -negative breast cancer samples with data that had been normalised using different techniques.

Increased NPC1 mRNA in skin fibroblasts from Niemann-Pick disease type C patients.

Niemann-Pick disease type C (NP-C) is an autosomal recessive lipid-storage disease that is characterized by progressive neurodegeneration and hepatosplenomegaly. Since identification of the NPC1 gene in 1997, a total of 120 disease-causing mutations have been reported. In this study, two novel mutations were identified, namely c.2508[-2509]A del (837Fs-838X) in exon 16 and T3194G (V1065G) in exon 21. To explore the impact of NPC1 mutations on transcription of this gene, we analyzed NPC1 mRNA levels in skin fibroblasts derived from NP-C patients. Fibroblasts from patients with missense mutations showed increased levels of NPC1 mRNA while fibroblasts from patients with a specific frameshift mutation showed mRNA levels similar to those of normal control subjects. These results suggest that NPC1 transcription levels are altered in cells with mutations in the NPC1 gene.