mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences
BackgroundFor the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. However, recent research has shown that using mtDNA phylogeny and referring to known mtDNA haplotypes can be useful for checking the quality of sequence data.ResultsWe developed a Web-based bioinformatics resource "mtDNAmanager" that offers a convenient interface supporting the management and quality analysis of mtDNA sequence data. The mtDNAmanager performs computations on mtDNA control-region sequences to estimate the most-probable mtDNA haplogroups and retrieves similar sequences from a selected database. By the phased designation of the most-probable haplogroups (both expected and estimated haplogroups), mtDNAmanager enables users to systematically detect errors whilst allowing for confirmation of the presence of clear key diagnostic mutations and accompanying mutations. The query tools of mtDNAmanager also facilitate database screening with two options of "match" and "include the queried nucleotide polymorphism". In addition, mtDNAmanager provides Web interfaces for users to manage and analyse their own data in batch mode.ConclusionThe mtDNAmanager will provide systematic routines for mtDNA sequence data management and analysis via easily accessible Web interfaces, and thus should be very useful for population, medical and forensic studies that employ mtDNA analysis. mtDNAmanager can be accessed at http://mtmanager.yonsei.ac.kr.

title: Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father–son pairs
abstract: We analyzed 369 Korean father/son haplotype transfers in 355 families at 22 Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS388, DYS437, DYS438, DYS439, DYS446, DYS447, DYS448, DYS449, DYS456, DYS458, DYS464, DYS635, and GATA H4.1). A total of 350 haplotypes were observed with an overall haplotype diversity of 0.9999. Among these, 345 were unique and five were found twice. Furthermore, 36 mutations were identified, giving locus-specific mutation rate estimates between 0.0 and 19.0 × 10−3 per generation and an average mutation rate estimate of 3.9 × 10−3 (95% CI 2.7–5.4 × 10−3). The compilation of Y-STR mutation events for the present study and previous studies demonstrates that DYS449, DYS458, DYS635, DYS456 and DYS439 are the most prone to mutations and that their overall average mutation rate estimate is 2.36 × 10–3 (95% CI 2.03–2.73 × 10–33).

title: DNA typing for the identification of old skeletal remains from Korean War victims.
abstract: The identification of missing casualties of the Korean War (1950-1953) has been performed using mitochondrial DNA (mtDNA) profiles, but recent advances in DNA extraction techniques and approaches using smaller amplicons have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Therefore, 21 skeletal remains of Korean War victims and 24 samples from biological relatives of the supposed victims were selected based on circumstantial evidence and/or mtDNA-matching results and were analyzed to confirm the alleged relationship. Cumulative likelihood ratios were obtained from autosomal short tandem repeat, Y-chromosomal STR, and mtDNA-genotyping results, and mainly confirmed the alleged relationship with values over 10⁵. The present analysis emphasizes the value of mini- and Y-STR systems as well as an efficient DNA extraction method in DNA testing for the identification of old skeletal remains.

title: A one step multiplex PCR assay for rapid screening of East Asian mtDNA haplogroups on forensic samples.
abstract: The mitochondrial DNA (mtDNA) haplogroup typing has become an essential tool to study human evolutionary history and to infer the matrilineal bio-geographic ancestry. In forensic field, the screening of mtDNA haplogroups by genotyping of mtDNA single nucleotide polymorphisms (SNPs) can help guarantee the quality of mtDNA sequence data as well as can reduce the need to sequence samples that do not match. Here, a multiplex mutagenically separated (MS) polymerase chain reaction (PCR) system was developed for simultaneous rapid detection of 14 coding region SNPs and one deletion motif representing common mtDNA haplogroups of East Asia. The multiplex MS PCR system we developed has the advantage of being a one step procedure that requires only a single PCR amplification with allele-specific primers and allowing straightforward designation of haplogroups along the branches of the phylogenetic tree. Therefore, it would be a simple, rapid, and reliable detection method useful for large-scale screening of mtDNA variations to determine East Asian mtDNA haplogroups.

title: Differential distribution of human mitochondrial DNA in somatic tissues and hairs.
abstract: To investigate mitochondrial DNA (mtDNA) distribution within tissues during life, we observed length heteroplasmy in a polycytosine tract of the mitochondrial HV2 region by size-based separation of PCR products, using a mutagenic primer which was designed to avoid stutter production. Blood, brain, heart, liver, skeletal muscle and hair shaft samples were collected during autopsies of 25 individuals. Here, we demonstrate differences in the level of mtDNA length heteroplasmy both within and between individuals and tissues. We also show that mtDNA is distributed randomly in varying proportions in various somatic tissues during growth, resulting in an imbalance in the composition of mtDNA pools among tissues. This mtDNA distribution appears not to be strictly random, and can be explained by the random somatic segregation of nucleoids. On the other hand, significant qualitative/quantitative mtDNA peak pattern variations in hair shafts are thought to be a result of the different developmental origins of hairs. Each hair shaft may have a restricted or clonal set of mtDNA molecules derived from a discrete group of stem cells.

title: Genetic Characterization and Assessment of Authenticity of Ancient Korean Skeletal Remains
abstract: To study the maternal lineage history of Korea, we extracted DNA from the skeletal remains of 35 museum samples (some dating back to the Paleolithic Age) excavated from 11 local burial sites scattered throughout southern Korea. Mitochondrial DNA (mtDNA) control region sequences (HV1, HV2, and HV3) were successfully determined for 11 samples with no sharing of the control region polymorphisms with individuals involved in the laboratory analyses. Each of the 11 mtDNAs was assigned to the appropriate East Asian mtDNA haplogroup according to the haplogroup-specific control region mutation motif and diagnostic coding region single nucleotide polymorphism. The successful mtDNA haplogroup determination for each ancient Korean mtDNA and the confirmation of the absence of abnormal mutations based on the haplogroup-directed database comparisons indicates that there is no mosaic structure from cross-contamination or sample mix-up or other errors in our mtDNA sequences. The presence of haplogroups B, D, and G in the prehistoric age is consistent with the hypothesis that the early Korean population has a common origin in the northern regions of the Altai Mountains and Lake Baikal of southeastern Siberia. In addition, the modern Korean population, which possesses lineages from both southern and northern haplogroups, suggests additional gene flow from southern Asian haplogroups in recent times, but many more ancient samples need to be analyzed to directly tell whether there was regional continuity or replacement of early lineages by other lineages in ancient Korea.

title: Surgical anatomy of the sphenopalatine artery in lateral nasal wall.
abstract: We investigated the surgical anatomy of the sphenopalatine artery. First, the location of the sphenopalatine foramen on the lateral nasal wall and the pattern of the main branches of the sphenopalatine artery from the sphenopalatine artery were studied. Second, the course of the posterior lateral nasal artery with respect to the posterior wall of the maxillary sinus, the perpendicular plate of the palatine bone, and the pattern of distribution of its branches on the fontanelle was determined. Third, the distribution pattern on the inferior turbinate was analyzed.



Fifty midsagittal sections of randomly selected Korean adult cadaver heads with intact sphenoid sinus and surrounding structures were used in the study.



The mucosa on the sphenopalatine foramen and its surrounding mucosa were removed with a microscissors, a fine forceps, and a pick to expose the sphenopalatine artery under an operating microscope (original magnification x6).



The feeding vessels of the superior turbinate were from the septal artery in 36 cases (72%). The feeding vessels to the middle turbinate branch originated from the proximal portion of the posterior lateral nasal artery just after exiting the sphenopalatine foramen in 44 cases (88%). Some portion of the posterior lateral nasal artery ran anterior to the posterior wall of the maxillary sinus in 38%. The major feeding arteries to the fontanelle were from the inferior turbinate branch in 25 cases (50%). In most cases, the inferior turbinate branch was the end artery of the posterior lateral nasal artery (98%).



The study provides detailed information concerning the sphenopalatine artery, which we hope will help explain the arterial bleeding that may occur during ethmoidectomy, middle meatal antrostomy, conchotomy, and endoscopic ligation of the sphenopalatine artery.

title: Comparing upper gastrointestinal X-ray and endoscopy for gastric cancer diagnosis in Korea.
abstract: To compare the cost and accuracy of upper gastrointestinal (GI) X-ray and upper endoscopy for diagnosis of gastric cancer using data from the 2002-2004 Korean National Cancer Screening Program (NCSP).



The study population included 1,503,646 participants in the 2002-2004 stomach cancer screening program who underwent upper GI X-ray or endoscopy. The accuracy of screening was defined as the probability of detecting gastric cancer. We calculated the probability by merging data from the NCSP and the Korea Central Cancer Registry. We estimated the direct costs of the medical examination and the tests for upper GI X-ray, upper endoscopy, and biopsy.



The probability of detecting gastric cancer via upper endoscopy was 2.9-fold higher than via upper GI X-ray. The unit costs of screening using upper GI X-ray and upper endoscopy were $32.67 and $34.89, respectively. In 2008, the estimated cost of identifying one case of gastric cancer was $53,094.64 using upper GI X-ray and $16,900.43 using upper endoscopy. The cost to detect one case of gastric cancer was the same for upper GI X-ray and upper endoscopy at a cost ratio of 1:3.7.



Upper endoscopy is slightly more costly to perform, but the cost to detect one case of gastric cancer is lower.

title: FOXO3a turns the tumor necrosis factor receptor signaling towards apoptosis through reciprocal regulation of c-Jun N-terminal kinase and NF-kappaB.
abstract: We evaluated the full range effects of FOXO3a in endothelial cells (ECs) by microarray analysis and investigated the role of FOXO3a regulating TNF receptor signaling pathway.



Human umbilical vein endothelial cells (HUVECs) were transfected with adenoviral vectors expressing constitutively active FOXO3a (Ad-TM-FOXO3a). Ad-TM-FOXO3a transfection caused remarkable apoptosis, which were accompanied with upregulation of genes related with TNF receptor signaling, such as TNF-alpha, TANK (TRAF-associated NF-kappaB activator), and TTRAP (TRAF and TNF receptor-associated protein). Furthermore, kappaB-Ras1 (IkappaB-interacting Ras-like protein-1) which is known to block IkappaB degradation was found increased, and intranuclear translocation of NF-kappaB was inhibited. GADD45beta and XIAP, negative regulators of c-Jun N-terminal kinase (JNK), were suppressed and JNK activity was increased. Attenuation of TNF signaling pathway either by blocking antibody for TNF receptor or by blocking JNK with DMAP (6-dimethylaminopurine) or Ad-TAM67 (dominant negative c-Jun) cotransfection, significantly reduced FOXO3a-induced apoptosis. Finally, treatment of vasculature with heat shock, an activator of endogenous FOXO3a, resulted in EC apoptosis, which was completely rescued by Ad-TAM67.



FOXO3a promotes apoptosis of ECs, through activation of JNK and suppression of NF-kappaB. These data identify a novel role of FOXO3a to turn TNF receptor signaling to a proapoptotic JNK-dependent pathway.

title: New CT response criteria in non-small cell lung cancer: proposal and application in EGFR tyrosine kinase inhibitor therapy.
abstract: We aimed to devise new CT response criteria (new response criteria, NRC) in patients with non-small cell lung cancer (NSCLC) and to evaluate the efficacy of the criteria for stratifying patient responses and predicting patient survival compared to that of the traditional size-based criteria RECIST version 1.1. Our institutional review board approved this study with a waiver of informed consent. We enrolled 80 NSCLC patients as an experimental arm and treated them with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR TKIs). Two blinded, independent radiologists assessed CT images for tumor response using the NRC, which were also validated in a separate arm (75 NSCLC patients). Tumor responses evaluated by RECIST 1.1 and the new criteria were compared from each other and correlated with patient survival. For statistical analyses, Kaplan-Meier method and kappa statistics were used. In the experimental arm (n=80), interobserver agreements for the assessment of patient response were excellent for both RECIST and NRC. Sixteen RECIST nonresponding patients achieved a designation of partial response according to NRC. In the validation arm (n=75), patients of optimal response (partial response) with the new criteria had median overall survival of 18.4 months compared with 8.5 months in patients with poor response (P=.04). However, RECIST failed to show survival difference between the two response groups. In NSCLC patients treated with EGFR-TKIs, new CT criteria reflecting additional morphological characteristics of target lesions are reproducible and have statistically significant association with overall survival.

title: Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression
abstract: Quantifying the dynamics of intrahost HIV-1 sequence evolution is one means of uncovering information about the interaction between HIV-1 and the host immune system. In the chronic phase of infection, common dynamics of sequence divergence and diversity have been reported. We developed an HIV-1 sequence evolution model that simulated the effects of mutation and fitness of sequence variants. The amount of evolution was described by the distance from the founder strain, and fitness was described by the number of offspring a parent sequence produces. Analysis of the model suggested that the previously observed saturation of divergence and decrease of diversity in later stages of infection can be explained by a decrease in the proportion of offspring that are mutants as the distance from the founder strain increases rather than due to an increase of viral fitness. The prediction of the model was examined by performing phylogenetic analysis to estimate the change in the rate of evolution during infection. In agreement with our modeling, in 13 out of 15 patients (followed for 3–12 years) we found that the rate of intrahost HIV-1 evolution was not constant but rather slowed down at a rate correlated with the rate of CD4+ T-cell decline. The correlation between the dynamics of the evolutionary rate and the rate of CD4+ T-cell decline, coupled with our HIV-1 sequence evolution model, explains previously conflicting observations of the relationships between the rate of HIV-1 quasispecies evolution and disease progression.