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• Linked Read Sequencing of Gastric Cancer Metastases for Complex SV Resolution

  In this study, linked read sequencing was performed on two ovarian metastases and matched normal tissue, from a patient with primary diffuse gastric cancer. Linked read sequencing is a DNA preparation technology whereby high molecular weight molecules of DNA are uniquely barcoded prior to fragmentation and sequencing, thus retaining information about genomic contiguity. This study performed an extended analysis of linked read sequencing data to resolve the complex structures of structural variants in the cancer genomes. Complex structural rearrangements were identified in the genomic region surrounding the known oncogene FGFR2, and the association between FGFR2 and gastric cancer metastasis was demonstrated in an organoid model.

  Study phs001362

• Whole genome sequencing (bam files) of 5 samples of myxofibrosarcoma and 5 matched pairs

  Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the whole genome sequence was performed.

  Study EGAS00001005444

• Whole exome sequencing (bam files) of 55 samples of myxofibrosarcoma and 44 matched pairs

  Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the whole exome sequence was performed.

  Study EGAS00001005442

• Targeted-capture sequencing (bam files) of 81 samples of myxofibrosarcoma and 44 matched pairs

  Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the Targeted-capture sequencing was performed.

  Study EGAS00001005443

• Assessment of de novo copy number variations in Italian patients with schizophrenia.

  We investigated de novo CNVs in the whole genomic DNA of schizophrenia patients and their parents and, specifically, in putative enhancer motifs.Study participants were part of a wider multicenter study, involving an Italian cohort of schizophrenia patients recruited by members of INRP - Italian Network for Research on Psychoses.Whole genomic DNA obtained from 46 family trios of schizophrenia probands was analyzed using the Enhancer Chip, a customized array CGH developed using the Agilent SurePrint G3 8X60K format, which is able to investigate the whole genome with a 300Kb resolution, specific disease loci at a tenfold higher resolution, and that was highly enriched in probes in more than 1.250 enhancer elements selected from the Vista Enhancer Browser (PLoS One. 2012;7(12):e52264).

  Study EGAS00001002159

• Pharmacogenomics of HIV Therapy - Atazanavir Bilirubin-related Side Effects

  This is an evaluation of genetic associations with atazanavir (ATV) discontinuation for bilirubin-related causes within 12 months of treatment. Patients were treated at an HIV primary care clinic in Nashville TN from 1998 to 2012. A previously known SNP in UGT1A1 (rs887829) was used to define metabolizer genotypes (extensive, intermediate, slow metabolizer). Over 500,000 SNPs from genome-wide genotyping were used to define MDS (Multidimensional Scaling) coordinates to account for population stratification. Patients were defined as cases if they discontinued ATV for bilirubin-related causes within 12 months of treatment, otherwise they were defined as controls if they did not stop treatment. Among 321 evaluable patients, 15 (4.6%) had bilirubin-related atazanavir discontinuation within 12 months. Homozygosity for rs887829 T/T was present in 28.1% of black, 21.4% of Hispanic, and 8.6% of white patients. Among all patients the hazard ratio (HR) for bilirubin-related discontinuation with T/T versus C/C genotype was 7.3 (95% C.I.: 1.7 to 31.5; p = 0.007). Among 152 white patients the HR was 14.4 (95% CI: 2.6 to 78.7; p = 0.002), but among 153 black patients the HR was 0.8 (95% C.I. 0.05 to 12.7; p = 0.87).

  Study phs001484

• CIDR: NCI Genome Wide Predictors of Survival in Colorectal Cancer

  CIDR/Molecular Correlates: This study genotyped archived blood samples from colorectal cancer cases participating in clinical trials. The goals of this project were to identify genetic variants associated with survival outcomes treatment and treatment-related severe adverse events among patients with colorectal cancer. Another goal was to examine the impact of adding information on germline genetic loci to existing prognostic models. MOSAIC: Multicenter International Study of Oxaliplatin/ 5FU-LV in the Adjuvant Treatment of Colon Cancer (MOSAIC). A randomized, open label efficacy trial to evaluate the FOLFOX regimen versus LV5FU2 in the adjuvant treatment of stage II and III colon cancer. The primary end point was disease-free survival. CPT.ES1.604: Randomized phase 3 study of weekly irinotecan plus high-dose 5-fluorouracil (FUIRI) versus biweekly irinotecan plus 5-fluorouracil/leucovorin (FOLFIRI) as first-line chemotherapy for patients with metastatic CRC. The aim of this study was to demonstrate that a regimen without leucovorin (LV) (FUIRI) is not inferior to the standard FOLFIRI (response rate). 03-TTD-01: The purpose of this phase III, multicenter, randomized, open-label study is to evaluate the safety and efficacy of combination therapy with capecitabine and oxaliplatin (XELOX) vs. oxaliplatin and 5-fluorouracil in continous infusion (5-FU CI) as first line treatment in advanced or metastatic colorectal cancer. The primary outcome measure is time to disease progression. Secondary outcome measures are to determine safety of combination, objective response rate, time to onset of response, duration of response, time to treatment failure, one year survival time, and overall survival time. 03-TTD-01: The purpose of this phase III, multicenter, randomized, open-label study is to evaluate the safety and efficacy of combination therapy with capecitabine and oxaliplatin (XELOX) vs. oxaliplatin and 5-fluorouracil in continous infusion (5-FU CI) as first line treatment in advanced or metastatic colorectal cancer. The primary outcome measure is time to disease progression. Secondary outcome measures are to determine safety of combination, objective response rate, time to onset of response, duration of response, time to treatment failure, one year survival time, and overall survival time. N0147: Randomized phase III clinical trial for adjuvant therapy in stage III colon cancer patients enrolled at institutions across North America. Originally designed to compare three different chemotherapy regimens, and then later expanded to evaluate adding cetuximab to each original arm (leading to six total arms). Further modification later added pre-screening for KRAS mutation status, with the resulting goal to assess the potential benefit of cetuximab added to the modified sixth version of the FOLFOX regimen (mFOLFOX6) in patients with resected stage III wild-type KRAS colon cancer. Main outcome of interest is disease-free survival in patients with wild-type KRAS, while secondary end points included overall survival and toxicity. N9741: Randomized phase III trial to compare the effectiveness of various combination chemotherapy regimens in treating patients who have advanced, recurrent, or metastatic colorectal cancer that cannot be treated with surgery or radiation therapy. C-08: A Phase III Clinical Trial Comparing Infusional 5-Fluorouracil (5-FU), Leucovorin, and Oxaliplatin (mFOLFOX6) Every Two Weeks With Bevacizumab to the Same Regimen Without Bevacizumab For the Treatment of Patients With Resected Stages II and III Carcinoma of the Colon. The primary aim of the trial was to compare the relative efficacy of mFOLFOX6 + bevacizumab with that of mFOLFOX6 alone in prolonging disease-free survival and the secondary aim was to compare the relative efficacy of mFOLFOX6 + bevacizumab with that of mFOLFOX6 alone in prolonging survival.

  Study phs001290

• Global Endometrial DNA Methylation Analysis Reveals Insights into mQTL Regulation and Associated Endometriosis Disease Risk and Endometrial Function

  Endometriosis is a common gynecological disorder affecting 11% of reproductive aged women and is a leading cause of pain and infertility. We investigated global DNA methylation (DNAm) profiles in endometrium associated with endometriosis, menstruation, and genetic variation. Endometrial samples were collected from 984 patients with confirmed endometriosis (n=637) and women without endometriosis (n=347). Patients were recruited through the University of California San Francisco, USA, University of Melbourne, Australia, Endometriosis CaRe Centre in Oxford, UK, and EXPPECT Centre, The University of Edinburgh, UK, using the World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project (WERF EPHect) standardized protocols for tissue collection and processing, and participant characteristics and clinical annotation. DNA was extracted from samples and was use to generate DNAm data using the Illumina Infinium MethylationEPIC Beadchip and genotype data using the Axiom Precision Medicine Research array. Estimates from this study suggest that 15.4% of the variation in endometriosis is captured by DNAm. DNAm analysis identified significant differences in DNAm profiles and DNAm networks, associated with endometriosis, endometriosis sub-phenotypes, and menstrual cycle phases. Integration of DNAm and genetic data in a DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis highlighting target genes contributing to disease risk. This study identified novel factors affecting epigenetic regulation in endometrium associated with endometriosis risk and disease heterogeneity and provides an important data resource for reproductive medicine. Genotype data generated as part of this study are available on dbGaP and methylation data are available on GEO.

  Study phs003307

• Wisconsin Longitudinal Study on Aging

  The Wisconsin Longitudinal Study (WLS) is a long-term study of a random sample of men and women, who graduated from Wisconsin high schools in 1957, and their siblings. The WLS panel started out with a panel of 10,317 members from the class of 1957. Over time a second panel of 8,734 randomly selected siblings of the original graduate panel were recruited for the study. Of these combined panel members, 9,027 survived and contributed saliva for genetic analysis. Survey data were collected from the original respondents or their parents in 1957, 1964, 1975, 1992, 2004, and 2011, and from a selected sibling in 1977, 1994, 2005, and 2011. WLS data provide a detailed record of educational, social, psychological, economic, mental and physical health characteristics of a relatively homogeneous population that is almost entirely of Northern and Western European ancestry. Saliva was first collected in 2007-2008 by mail. Additional samples were collected in the course of home interviews that began in March 2010.

  Study phs001157

• Idiopathic Pulmonary Fibrosis Network (IPFNet) Sildenafil Trial of Exercise Performance in Idiopathic Pulmonary Fibrosis (IPFNet-STEP-IPF-BioLINCC)

  Data Access NOTE: Please refer to the "Authorized Access" section below for information about how access to the data from this accession differs from many other dbGaP accessions. Objectives: The STEP-IPF study sought to evaluate whether treatment with sildenafil would improve walk distance, dyspnea, and quality of life in participants with advanced idiopathic pulmonary fibrosis (IPF).Background: IPF is a chronic, progressive lung disease of unknown cause that is characterized by the histopathologic pattern of usual interstitial pneumonia. Progression to end-stage respiratory insufficiency and death within 5 years after the onset of symptoms is characteristic. To date, no pharmacologic therapies have definitively been shown to improve survival or quality of life in participants with this disease.Participants with severe IPF have abnormalities of the pulmonary vasculature leading to decreased levels of resting and exercise-induced production of nitric oxide. Since nitric oxide is a potent pulmonary vasodilator, reduced levels are associated with pulmonary vasoconstriction and impaired gas exchange. Sildenafil (Revatio, Pfizer) is a phosphodiesterase-5 inhibitor that stabilizes the second messenger of nitric oxide, cyclic guanosine monophosphate, which leads to pulmonary vasodilatation. Such vasodilatation could improve ventilation–perfusion matching and thus gas exchange in with IPF.Design: STEP-IPF was a double-blind, randomized, placebo-controlled trial of oral sildenafil (20 mg three times daily). Participants meeting eligibility criteria were randomly assigned in a 1:1 ratio to receive sildenafil or matched placebo with the use of a permuted-block design, with stratification according to clinical center. The primary outcome was the presence or absence of an improvement of at least 20% in the 6-minute walk distance at 12 weeks, as compared with baseline. Key secondary outcomes included changes in the 6-minute walk distance, degree of dyspnea, and quality of life.Screening procedures included the taking of a detailed history, a physical examination, spirometry, echocardiography, CT imaging, and measurements of lung volume on plethysmography, carbon monoxide diffusion capacity, and arterial blood gases. Eligible participants returned for an enrollment visit within 6 weeks after screening. All participants received an initial dose of a study drug at this visit and were monitored for 60 minutes for adverse effects. Follow-up visits were scheduled at 1, 6, and 12 weeks. After completion of the 12-week visit, all participants were started on treatment with open-label sildenafil. Visits were scheduled at 13, 18, and 24 weeks; at 28 weeks, serious adverse events and vital status were documented. Testing of the 6-minute walk distance was performed with the use of a standardized protocol at the time of screening and enrollment and at study visits at 6, 12, 18, and 24 weeks. Participants with pulse oxygen saturation below 88% received supplemental oxygen. Conclusions: This study did not show a benefit for sildenafil for the primary outcome. The presence of some positive secondary outcomes creates clinical equipoise for further research. There were small but significant differences in arterial oxygenation, carbon monoxide diffusion capacity, degree of dyspnea, and quality of life favoring the sildenafil group.

  Study phs004085