bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4209: Genotypic agreement between histological specimen and preoperative cytology in small lung adenocarcinoma.
Authors: Hirai Noriko , Takaaki Sasaki , Minami Yoshinori , Kitada Masahiro , Miyokawa Naoyuki , Ohsaki Yoshinobu 
Published: August 2014

Abstract
Background. Histological subtype and genotype is critical for making treatment decisions and improving patient outcomes in non-small cell lung cancer (NSCLC). Approximately 70% of lung cancers are diagnosed in advanced stages where small biopsies and cytological specimens are the only source of material for both diagnosis and genotyping. Patients with specific gene alterations in epidermal growth factor receptor (EGFR) or anaplastic lymphoma kinase (ALK) likely receive more benefit from EGFR TKI or ALK TKI therapy, respectively. Although, genotyping agreement from cytological and histological samples is critical, more investigational studies need to be explored to assess the concordance of genotype. Purpose. We performed a comparing investigation on concordance rate for pathological diagnosis and EGFR gene mutation status between surgical specimen and preoperative cytological specimen in small lung cancer. Additionally we reviewed immunohistochemical (IHC) staining with two different ALK specific antibodies. Materials and Methods. 55 patients who had surgically resected small (≦3cm) lung adenocarcinoma with known preoperative bronchial brushing cytology were examined retrospectively. IHC staining was conducted by mutation-specific antibodies using E746-A750 deletion and L858R for EGFR or 5A4 and D5F3 for ALK. DNA analysis was performed by PNA-RNA PCR clamp assay. Results. 1) Diagnostic concordance rate between cytological and histological specimen was 90.9%. Disagreement cases were included one case of squamous cell carcinoma, two cases of small cell carcinoma, one case of melanoma and one case of mucoepidermoid carcinoma by cytology. 2) In IHC positive for mutation-specific EGFR antibodies, the sensitivity was 83% in E746-A750 and 100% in L858R, respectively. In EGFR IHC positive cases, well to moderate differentiation were dominant. 3) In ALK IHC, one case was observed stronger cytoplasmic staining in D5F3 than 5A4. Furthermore, the cribriform pattern was observed in H&E staining. Distinctive cytological feature was not observed. Conclusion. Our results showed that high genotype concordance rates of histology and cytology agreement in small lung adenocarcinoma.
Citation Format: Noriko Hirai, Sasaki Takaaki, Yoshinori Minami, Masahiro Kitada, Naoyuki Miyokawa, Yoshinobu Ohsaki. Genotypic agreement between histological specimen and preoperative cytology in small lung adenocarcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4209. doi:10.1158/1538-7445.AM2013-4209
Abstract 4212: Deep sequencing analysis of the ALK kinase domain identifies resistant mutations in relapse patients following crizotinib treatment.
Authors: Huang Stephen 
Published: August 2014

Abstract
ALK resistance mutations conferring resistance to Xalkori vary widely within the tyrosine kinase domain. So far, nine different acquired resistant mutations have been identified in the clinic, including 1151Tins, L1152R, C1156Y, F1174C, L1196M, G1202R, D1203N, S1206Y, and, G1296A. We developed a deep sequencing method using semiconductor sequencing technology to quickly detect resistance mutations within the ALK kinase domain in tumor biopsies. By bar-coding, we were able to sequence multiple samples in a single run. We have also developed an algorithm to determine assay noisy level and call mutations automatically. The assay sensitivity to call close to 1% mutated allele demonstrated by a titration experiment with a cell line harboring a know mutation. Genomic DNA analysis from relapsed patients revealed several known mutations. Our assay demonstrates robust and sensitive detection of ALK kinase mutations in NSCLC tumor samples and aids in the elucidation of resistance mechanisms pertinent to the clinical setting.
Citation Format: Stephen Huang. Deep sequencing analysis of the ALK kinase domain identifies resistant mutations in relapse patients following crizotinib treatment. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4212. doi:10.1158/1538-7445.AM2013-4212
Abstract 4217: A real-time PCR assay for the detection of PIK3CA mutations in formalin-fixed paraffin embedded tissue (FFPET) specimens of breast cancer (BC).
Authors: Schlag Peter , Hoeppner Corey , Bristol Anona , Kaur Namneet , Quashnick Stephen , Ravirala Ramani , Kramer Joyce , Negash Minet , Brophy Victoria , Lee Sung , Soviero Stephen 
Published: August 2014

Abstract
Somatic mutations in the PIK3CA gene encoding the p110α catalytic subunit of the PI3K protein have been linked to human cancer and have been found to occur at a high frequency in BC (25-40%). Therapeutics that target key nodes in the PI3K signaling pathway are currently being developed and stratifying patients based on their PIK3CA mutation status is becoming more important. We describe the analytical performance of the cobas® PIK3CA Mutation Test (For Research Use Only), a multiplex allele-specific PCR assay designed to detect 17 mutations in exons 1, 4, 7, 9 and 20 in the PIK3CA gene in 3 PCR wells. The test detects ∼94% of known PIK3CA mutations found in BC.
The amount of DNA required for the assay (150 ng) can typically be isolated from a single 5 μm FFPET section with automated test results generated within 8 hours. The analytical sensitivity of the test, defined as ≥95% mutation detection rate, was found to be ∼5% mutant allele in BC FFPET tumor sections representing 4 prevalent PIK3CA mutations (H1047R, E545K, E542K, and Q546K). Additionally, the test was able to detect all 17 mutations at ≤ 5% mutant allele in plasmid/gDNA blends. The test was also compared to 2X bi-directional Sanger sequencing using 110 BC FFPET specimens. The PCR test detected mutations in 50 specimens that were Sanger (+) (100% positive agreement). Moreover, the test detected mutations in 4 Sanger (-) specimens and detected a second mutation in 1 Sanger (+) specimen that was not detected by Sanger. All 5 of the PCR (+)/Sanger (-) were confirmed mutant by 454 sequencing.
Sanger Sequencing Mutation Detected Mutation Not Detected Total cobas® PIK3CA Mutation Test Mutation Detected 50* 4 54 Mutation Not Detected 0 56 56 Total 50 60 110 *One specimen had an additional mutation.
When a panel of BC FFPET specimens was repeatedly tested over multiple days by 2 operators using 2 instruments and 2 reagent lots, a correct call was obtained in 99.5% (191/192) of tests. The results demonstrate that the cobas® PIK3CA Mutation Test is a fast, accurate and reproducible assay that is more sensitive than Sanger sequencing for the detection of PIK3CA mutations in BC tumors.
Citation Format: Peter Schlag, Corey Hoeppner, Anona Bristol, Namneet Kaur, Stephen Quashnick, Ramani Ravirala, Joyce Kramer, Minet Negash, Victoria Brophy, Sung Lee, Stephen Soviero. A real-time PCR assay for the detection of PIK3CA mutations in formalin-fixed paraffin embedded tissue (FFPET) specimens of breast cancer (BC). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4217. doi:10.1158/1538-7445.AM2013-4217
Abstract 4220: Establishment of a rapid and automated detection system for BRAF mutations in malignant melanoma.
Authors: Ide Masaru , Koba Shinichi , Nagano Yumi , Aragane-Sueoka Naoko , Sato Akemi , Inoue Takuya , Kobayashi Naomi , Misago Noriyuki , Narisawa Yutaka , Kimura Shinya , Sueoka Eisaburo 
Published: August 2014

Abstract
BRAF gene mutations have been observed in 30-70% of malignant melanoma patients. Recent development of therapeutic intervention using BRAF inhibitors requires an accurate and rapid detection system for BRAF mutations. In addition, there are only a few reports that investigated the clinical characteristics of the melanoma associated with BRAF mutations in Japanese patients on a large scale evaluation. We recently established quenching probe system (QP) for detection of an activating BRAF mutation, V600E and evaluated 113 melanoma samples diagnosed in Saga University Hospital from 1982 to 2011. The QP system includes fully automated genotyping, based on analysis of the probe DNA melting curve, which binds the target mutated site using a fluorescent guanine quenched probe. BRAF mutations were detected in 54 of 115 (47%) including 51 of V600E and 3 of V600K in Japanese melanoma cases. Among clinical subtypes of melanoma, nodular melanoma showed high frequency (12 of 15; 80%) of mutation followed by superficial spreading melanoma (13 of 26; 50%). The QP system is a simple and sensitive method to determine BRAF V600E mutation, and will be useful tool for patient-oriented therapy with BRAF inhibitors.
Citation Format: Masaru Ide, Shinichi Koba, Yumi Nagano, Naoko Aragane-Sueoka, Akemi Sato, Takuya Inoue, Naomi Kobayashi, Noriyuki Misago, Yutaka Narisawa, Shinya Kimura, Eisaburo Sueoka. Establishment of a rapid and automated detection system for BRAF mutations in malignant melanoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4220. doi:10.1158/1538-7445.AM2013-4220
Abstract 4225: PNA mediated real-time PCR clamping assay to detect IDH1 mutations .
Authors: Yoon Jihye , Choi jae jin , Choi Woohyung , Park Heekyung 
Published: August 2014

Abstract
The hotspot mutations in codon 132 of isocitrate dehydrogenase 1 (IDH1) is a frequent DNA alteration in gliomas and astrocytomas. IDH mutations are prognostic and diagnostic for tumors with mutation, associated with a proneural subclass, and have longer survival compared with those without the mutation.
We have developed a highly sensitive and simple method to detect hotspot mutations in codon 132 of IDH1 using PNA-mediated real-time PCR clamping, PNAClampTM.
PNAClampTM is based on unique properties of PNA probes that PNA oligomers are not recognized by DNA that can serve as sequence-selective clamps during PCR amplification. This method can also detect 5 mutations through only one tube reactions simultaneously, which requires only 10 ng of the target DNA each.
Data analysis was much faster and easier to perform than analysis of the sequencing data, and results could be obtained in 3hr from DNA extraction to analysis.
Furthermore, we could readily identify a mixture of 1% mutant allele vs. 99% wild type allele with our PNAClamp assay, in comparison to direct sequencing assay which have detection limit of approximately 20% mutant allele.
We performed the assay on 191 paraffin-embedded glioma specimens in Korea for diagnosing IDH mutation.
The results showed that the PNAClampTM IDH1 detected higher number of mutation (27.2%, 52/191) than of direct sequencing (20.9%, 40/191) in 191 giloma samples in Korea. The result was not in agreement with the sequencing in12 (6.3%) samples. This result was likely due to the high sensitivity of PNAClampTM.
PNAClampTM is a fast, sensitive and easy to perform method which can reliably detect common mutations of IDH genes in gliomas or other tumors.
Citation Format: Jihye Yoon, jae jin Choi, Woohyung Choi, Heekyung Park. PNA mediated real-time PCR clamping assay to detect IDH1 mutations . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4225. doi:10.1158/1538-7445.AM2013-4225
Abstract 4229: Study on the germline mutation and protein expression of hMLH1 and hMSH2 gene in Chinese HNPCC probands.
Authors: Sheng Xia 
Published: August 2014

Abstract
BACKGROUND&AIMS: Compare with sporadic colorectal cancer (SCRC), Hereditary nonpolyposis colorectal cancer (HNPCC) shows its own characteristcs associated with the molecular mechanism,clinical features,the methods for treatment and management of HNPCC kindreds. The molecular genetics basis of HNPCC was the mutation of mismatch repair (MMR) gene. Some HNPCC families which can found the mutation of MMR gene didn't fulfil any clinical criteria while more than fifty percent suspected HNPCC patients can't found mutation of MMR gene. Therefore, the tumorigenesis of HNPCC must be associated with other disease genes which have not been credited. The expression of hMLH1 and hMSH2 protein in 50 HNPCC probands fulfilling defferent clinical criteria and the germline mutation of hMLH1 and hMSH2 gene in 26 probands were analysed. Methods: The peripheral blood was collected from the probands of 26 HNPCC families fulfilling different clinical criterial, of which 7 families fulfilled AC, 19 kindreds fit BG. Genomic DNA was extracted following the manafacturer's protocol and used as the template to amplify 35 exons of the 2 genes by PCR. PCR products were purified and used as the template for direct DNA sequencing. The results of sequencing were analysed by different bioanalysis software. To further investigate the pathological effects of detected missense mutations, we analyse the same exon of hPMS2 gene using PCR-based sequencing in 130 healthy persons without family history. IHC envision two step method was performed.Results: 8 germline mutation of hMLH1 and hMSH2 was found in 26 HNPCC probands families. 4 fulfilled AC and 4 fulfilled BG..17 probands was found to be hMLH1 and hMSH2 protein deficient. Conclusion: The rate of germline mutation and protein expression was 30.8% and 34%. AC are the most sensitve clinical creteria to predict mutations. Immunohistochemical staining are reliable screening method with high predictive value for the detection of mutation. Some suspected HNPCC patients can't found mutation of MMR gene.
Citation Format: Xia Sheng. Study on the germline mutation and protein expression of hMLH1 and hMSH2 gene in Chinese HNPCC probands. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4229. doi:10.1158/1538-7445.AM2013-4229
Abstract 423: Metabolomic analysis of urine from patients undergoing total body irradiation.
Authors: Laiakis Evagelia C. , Mak Tytus D. , Anizan Sebastien , Amundson Sally A. , Barker Christopher A. , Wolden Suzanne L. , Brenner David J. , Fornace Albert J. 
Published: August 2014

Abstract
Development of biomarkers for the responses to radiation has relevance to assessment of patient course and outcome after radiation therapy, as well as to other radiologic events including accidental and terrorist. The purpose of this study was to extend the biomarker discovery to humans, as previous studies have focused on mice. Urine was collected from patients undergoing total body irradiation (TBI) at Memorial Sloan Kettering prior to bone marrow transplantation at 4-6h post irradiation (a single dose of 125cGy) and 24h (three fractions of 125cGy each). Patient diagnoses include leukemias (ALL, AML, and CML), non-hodgkins lymphoma, myelodysplastic syndrome, aplastic anemia, and essential thrombocytopenia. Global metabolomic profiling was obtained through analysis with Ultra Performance Liquid Chromatography (UPLC) coupled to time-of-flight mass spectrometry (TOFMS) (Waters). Peak alignment and deconvolution of the chromatographic data were conducted with MarkerLynx software (Waters, MA). Prior to further analysis, each sample was normalized to its respective creatinine. Ions with non-zero abundance values in at least 75% of samples in both groups were analyzed for statistical significance via the nonparametric Kolmogorov-Smirnov test for equality of probability distributions on the log-transformed dataset. Statistical significance for ions with non-zero abundance values in at least 75% of samples in only one group were analyzed categorically for presence (i.e. non-zero abundance) via the Fisher's exact test. Biomarker candidates were verified by tandem mass spectrometry (MS/MS) by comparison to pure chemicals and quantification of the markers was conducted with the triple quadrupole mass spectrometer XEVO TQ MS (Waters). Validated and quantified biomarkers include L-Octanoylcarnitine, Hypoxanthine, Trimethyl-L-Lysine, Acetyl-carnitine, Decanoylcarnitine, Pantothenic acid, Hippuric acid, Uric acid, and Xanthine, and thus contribute to the development of a human metabolomic signature following exposure to radiation, and can now be integrated with features including underlying disease status, gender, age, and outcome.
Citation Format: Evagelia C. Laiakis, Tytus D. Mak, Sebastien Anizan, Sally A. Amundson, Christopher A. Barker, Suzanne L. Wolden, David J. Brenner, Albert J. Fornace. Metabolomic analysis of urine from patients undergoing total body irradiation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 423. doi:10.1158/1538-7445.AM2013-423
Abstract 4230: A novel method for sequence- and strand-specific, genome-wide 5-hmC profiling.
Authors: Sun XueGuang , Petterson Adam , Chung Hunter , Jia Xi Yu , Van Eden Marc E. 
Published: August 2014

Abstract
5-Hydroxymethylcytosine (5-hmC) is a new epigenetic hallmark rapidly getting much interest as the subject of mapping and sequencing work. While the exact function of 5-hmC is not fully understood, it is likely to regulate gene expression via active DNA de-methylation. Previous studies have shown it may play an important role in cell differentiation and carcinogenesis. Cells that are more stem- and progenitor-like have greatly reduced levels of 5-hmC compared with more differentiated cells. Similarly, tumor cells display less 5-hmC than their normal counterparts. This was not associated with either grade or stage, suggesting that global loss of 5-hmC may be an early event in carcinogenesis. To date, several methods have been developed to profile 5-hmC at the genomic level: most are enrichment-based and utilize antibodies to 5-hmC or its modified forms or make use of bioorthogonal labeling and pull-down of glycosylated 5-hmC. The caveat is that these approaches are low resolution and that they require large amounts of input genomic DNA. Initial efforts for detection of 5-hmC at single-base resolution require several micrograms of DNA, require parallel or subtractive sequencing, and employ successive chemical treatments that can degrade DNA and hinder sequencing. Here we report on a new method that by combining modification-sensitive restriction enzymes with massively parallel (“next-generation”) sequencing approaches, genome-wide 5-hmC can be mapped at single site resolution from low (100 ng) DNA inputs. Importantly, this method can be used for strand-specific localization of 5-hmC as well as direct identification of single nucleotide polymorphisms (SNPs) within the sequencing reads. Data can also be compared directly with single-base resolution DNA methylation data from reduced-representation bisulfite sequencing (RRBS) for simultaneous 5-mC and 5-hmC profiling from the same sample. 5-mC and 5-hmC of human brain DNA using this combined method indicates unique distributions of the 5-hmC modification. This new method should provide a unique tool in enhancing our understanding of the interplay of genetic and epigenetic regulations in carcinogenesis.
Citation Format: XueGuang Sun, Adam Petterson, Hunter Chung, Xi Yu Jia, Marc E. Van Eden. A novel method for sequence- and strand-specific, genome-wide 5-hmC profiling. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4230. doi:10.1158/1538-7445.AM2013-4230
Abstract 4232: Increased sensitivity in whole-genome bisulfite sequencing (WGBS): A novel “post-bisulfite conversion” library construction method from sub-nanogram DNA inputs.
Authors: Sooknanan Roy , Hitchen John , Caruccio Nick 
Published: August 2014

Abstract
Genome-wide analysis of 5-methylcytosines is possible with whole-genome bisulfite sequencing (WGBS), where unmethylated cytosine residues are converted to uracil. However, a major challenge in WGBS is the degradation of DNA that occurs during bisulfite conversion under conditions required for complete conversion. Typically, ∼90% of input DNA is degraded and thus, is especially problematic with limited starting amounts of DNA. Additionally, regions that are rich in unmethylated cytosines are more sensitive to strand breaks. As a consequence, a majority of DNA fragments contained in di-tagged NGS DNA libraries treated with bisulfite “post-library construction” can be rendered inactive due to strand breaks in the DNA sequence flanked by the adapter sequences. These mono-tagged templates are then excluded during library enrichment resulting in incomplete coverage and bias when performing whole genome bisulfite sequencing.
Here, we describe a novel “post-bisulfite conversion” library construction method for preparing NGS libraries from genomic DNA prior to the addition of one or both adapters. This “post-bisulfite conversion” library construction method uses the resulting untagged or mono-tagged single-stranded DNA as template for the subsequent addition of adapter sequences required for NGS. Thus, single-stranded DNA fragments independent of size and position of strand breaks remain as viable templates for library construction, eliminating the loss of fragments and the selection bias associated with a “post-library construction” bisulfite conversion strategy. This novel “post-bisulfite conversion” library construction method exhibits high diversity, increased efficiency and sensitivity (500 picograms human genomic DNA input), and improved coverage required for WGBS.
Citation Format: Roy Sooknanan, John Hitchen, Nick Caruccio. Increased sensitivity in whole-genome bisulfite sequencing (WGBS): A novel “post-bisulfite conversion” library construction method from sub-nanogram DNA inputs. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4232. doi:10.1158/1538-7445.AM2013-4232