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• National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK): Identification of VUR genes by exome sequencing

  Primary vesicoureteric reflux (PVUR), or non-syndromic VUR, is the most common type of congenital anomaly of the kidney and the urinary tract (CAKUT). PVUR is the single most important risk factor for pyelonephritis and renal parenchymal scarring in the pediatric age group. Renal parenchymal scarring due to PVUR is referred to as reflux nephropathy and is a major cause of end stage kidney disease requiring dialysis and kidney transplantation in children. PVUR shows familial aggregation; however, the specific genetic cause(s) of PVUR is unknown despite a number of linkage studies. Reasons for this include: variable expression of the disease, difficulty with case ascertainment, genetic heterogeneity and lack of large pedigrees that can facilitate locus identification. We have ascertained a large 97 member PVUR kindred spanning five generations. We performed a genome-wide linkage study (GWLS) on this family and obtained a significant genome-wide LOD score of 3.3 on chromosome 6p. We performed exome sequencing on affected individuals in the family and identified mutations in tenascin XB (TNXB) as a cause of familial VUR. The proposed studies have the following specific objectives: a) to define the role of tenascin genes in the etiology of PVUR, and b) to identify new PVUR causative genes. Our specific aims are (1) To perform mutation analysis in TNXB and other tenascins in a cohort of 200 individuals with familial and sporadic PVUR and define genotype/phenotype correlations. (2) To perform sequential genome wide linkage studies (GWLS) and whole exome/targeted sequencing in families with PVUR. Impact on public health: Identification of PVUR genes may provide a novel non-invasive diagnostic tool for a subset of children with PVUR. Furthermore, this research will provide insights into the pathogenesis of PVUR and further elucidate the pathways involved in the development of the kidney and genitourinary tract. Future studies will define the role of the genes in the etiology of other malformations of the kidney and urinary tract and also seek to unravel the mechanisms by which the identified gene causes PVUR and other malformations of the kidney and the urinary tract.

  Study phs000778

• Microbiomic and immunogenic biomarkers of adjuvant chemotherapy efficacy in stage III colorectal cancer

  The standard treatment for stage III colorectal cancer (CRC) is surgery, followed by adjuvant chemotherapy (AC). However, the efficacy of AC is limited, and approximately 30% of patients experience recurrence. Therefore, easily assessable molecular biomarkers that can predict response to AC are needed. Here, we aimed to identify predictive biomarkers of response to AC using tumor transcriptomic data. Tumor specimens from 253 patients who underwent surgery for stage III CRC between 1997 and 2019 were analyzed using RNA sequencing. Transcriptional subtyping and analyses of gut microbiome, immune cell fractions, and T-cell receptor (TCR) were performed to identify factors associated with recurrence-free survival (RFS) in patients treated with or without AC. Of 253 patients, 118 (46.6%) received AC. Twenty phyla and 799 species of the microbiomes were identified, among which Fusobacteria were identified in 247 patients (97.6%). Multivariable Cox proportional hazards regression analysis of patients who received AC showed that intratumoral Fusobacterium and M1 macrophage abundance and diversity of TCR alpha and delta (TRAD) were independently associated with RFS. Fusobacterium and M1 macrophage abundance, and TRAD diversity were associated with the response to AC, suggesting that these factors could serve as biomarkers for personalized treatment in stage III CRC.

  Study JGAS000875

• Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers

  Ovarian cancer is the leading cause of death from gynecological cancers worldwide. No effective screening methods exist, and tumors are commonly detected at advanced stages where treatment is much less effective. In this study, we used whole-genome cell-free DNA (cfDNA) fragmentome and protein biomarker (CA-125 and HE4) analyses to evaluate 591 women from the European Union or the United States with ovarian cancer, benign adnexal masses, or without ovarian lesions. Using a machine learning model that incorporated multi-analyte fragmentome data and protein measurements, we detected ovarian cancer with high specificity >99% and sensitivity of 72%, 69%, 87%, and 100% for stages I–IV, respectively (AUC=0.96, 95% CI: 0.94-0.99), including 90% of high grade serous ovarian cancers. At the same specificity, CA-125 alone detected 34%, 62%, 63%, and 100% of ovarian cancers for stages I–IV (p=0.001, two-sided test of equal proportions). Additionally, our approach distinguished benign masses from ovarian cancers with high accuracy (AUC of 0.88, 95% CI=0.83-0.92). These results were validated in an independent population. These findings show that integrated cfDNA fragmentome and protein analyses detect ovarian cancers with high performance, enabling a new accessible approach for noninvasive ovarian cancer screening and diagnostic evaluation.

  Study EGAS50000000484

• National Cancer Institute (NCI) Waldenstrom Macroglobulinemia Genome-wide Association Study

  A discovery GWAS is performed, consisting of genotyping 221 Waldenstrom macroglobulinemia (WM) cases on the Illumina Omni Express 12v1.1 platform and analyzing the genotypes together with those of 3798 previously genotyped controls in a model taking into account gender, age, and principal components of ancestry (i.e., significant eigenvectors). Directly genotyped data are supplemented by imputation using the Haplotype Reference Consortium.

  Study phs001284

• RP-1843 Arcagen - Gastrointestinal rare cancers (GI)

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting two datasets that contain NGS files from gastrointestinal rare cancers (n=119): - Dataset 1 (32 patients): Mesothelioma of the peritoneum (n=21) and Pseudomyxoma peritonei/mucinous adenocarcinoma of the appendix (n=11) - Dataset 2 (87 patients): Intra-hepatic cholangiocarcinoma (n=47), Extra-hepatic, cholangiocarcinoma (n=16), Not specified Cholangiocarcinoma (n=9), Small bowel adenocarcinoma (n=6) and other rare GI cancer (n=9)

  Study EGAS00001006299

• Genetic Neuroscience: How Human Genes and Alleles Shape Neuronal Phenotypes

  The goal of this collaborative, interdisciplinary project is to develop powerful, generalizable approaches for discovering how risk variants for psychiatric disorders shape neurobiological processes at multiple levels of analysis, and to identify the processes whose dysregulation underlies disease.Induced pluripotent stem cells (iPSCs) were used towards the development of these new experimental and inferential systems bridging gaps between human genetics and experimental biology. The largest publicly available collection of iPSCs (2607 lines) has been generated from 2184 donors by the California Institute for Regenerative Medicine (CIRM). To expand our donor collection, an additional 44 iPSC donors from the McLean_Levy cohort were identified. We wish to share the available SNP data for 2167 CIRM lines and whole genome sequence data generated at the Broad Institute for 473 of the CIRM and 44 McLean_Levy iPSC donors. These data can be used to identify (for experiments) lines with specific genotypes of interest and lines from donors with high or low polygenic risk scores for phenotypes of interest. The data can also be used to identify acquired mutations in the iPSC lines. The CIRM iPSC lines are available through Fujifilm Cellular Dynamics iPSC Repository (https://www.fujifilmcdi.com/cirm-ipsc-products/). The McLean_Levy lines are available through the NIMH Repository & Genomics Resource (https://www.nimhgenetics.org/).Additional project data registered with the study includes data from an iPSC line derived from an SMA patient (n=1), as well as single-cell RNA sequence data and supplemental processed genomic datasets in support of project publications.Molecular DatasetsSingle-cell RNA-seq: 10X Genomics, Illumina NovaSeqSupplemental "cell village" pooled genomic sequence data: Illumina NextSeqWhole Genome Genotyping: Infinium Global Screening Array-24 Kit, Illumina HumanCore chipWhole Genome Sequencing: Illumina NovaSeq

  Study phs002032

• Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients

  Background Despite advances in identification of genetic markers associated to severe COVID-19, the full genetic characterisation of the disease remains elusive. Imputation of low-coverage whole genome sequencing (lcWGS) has emerged as a competitive method to study such disease-related genetic markers as they enable genotyping of most common genetic variants used for genome wide association studies. This study aims at exploring the potential use of imputation in lcWGS for a highly selected severe COVID-19 patient cohort. Findings We generated an imputed dataset of 79 variant call format (VCF) patient files using the GLIMPSE1 tool, each containing, on average, 9.5 million single nucleotide variants. The validation assessment of imputation accuracy yielded a squared Pearson correlation of approximately 0.97 across sequencing platforms, showing that GLIMPSE1 can be used to confidently impute variants with minor allele frequency up to approximately 2% in Spanish ancestry individuals. We conducted a comprehensive analysis on the patient cohort, examining hospitalisation and intensive care utilisation, sex and age-based differences, and clinical phenotypes using a standardised set of medical terms specifically developed to characterise severe COVID-19 symptoms for this cohort. Conclusion This dataset highlights the utility and accuracy of lcWGS imputation in the study of COVID-19 severity, setting a precedent for other applications in resource-constrained environments. The methods and findings presented here may be leveraged in future genomic projects, providing vital insights for health challenges like COVID-19.

  Study EGAS00001007573

• Heart and Vascular Health Study (HVH)

  Objectives The Heart and Vascular Health Study (HVH) is a case-control study of risk factors for the development of myocardial infarction (MI), stroke, venous thrombosis (VT), and atrial fibrillation (AF). The study setting is Group Health, an integrated health care delivery system in Washington State. Background The HVH originated in 1988 with the examination of risk factors for MI. Over the ensuing years, the study has been funded by a series of grants, which have added case subjects with stroke, VT, and AF, and used a common control group. Study aims have focused on the associations of medication use with cardiovascular events. Starting in 1997, the study aims expanded to include genetic associations with cardiovascular disease. Participants recruited in 2009 or later and who provided blood samples for genetic analysis were asked for consent to deposit genetic and phenotype data in dbGaP. Design As part of the HVH study, case subjects were identified by searching for ICD-9 codes consistent with MI, stroke, VT, or AF, and medical records were reviewed to confirm the diagnosis. Control subjects were identified at random from the Group Health enrollment and were matched to MI cases. All subjects have an index date. For cases, the index date was assigned as the date that the cardiovascular event (MI, stroke, VT, or AF) came to clinical attention. For controls, the index date was a random date within the range of the case index dates. For both cases and controls, information was collected from the inpatient and outpatient medical record, by telephone interview with consenting survivors, and from the Group Health pharmacy and laboratory databases. Consenting participants provided a blood specimen. Genetic Research Genetic factors underlying cardiovascular disease are studied using DNA isolated from the blood samples.

  Study phs001013

• RNA-Seq in Patients with Primordial Dwarfism

  Transcriptome studies in patients with rare genetic diseases can potentially aid in the interpretation of likely causal genetic variation through identification of altered transcript abundance and/or structure. RNA-Seq is the most sensitive assay for both investigating transcript structure and abundance The primary aim of this pilot project is to investigate to what degree integrating exome-Seq and RNA-Seq data on the same individual can accelerate the identification of causal alleles for rare genetic diseases. There are two main strands to this: (i) identifying which variants discovered in exome-seq appear to be having a functional impact on transcripts, and (ii) identifying transcript outliers, especially among known causal genes, that may not necessarily have a causal variant identified from exome sequencing. The latter may identify the presence of causal variants that lie far from coding regions (e.g. the formation of cryptic splice sites deep within introns, or loss of long range regulatory elements), which can be confirmed with further targeted genetic assays. Just over 50% of all disease-causing variants recorded in the Human Gene Mutation Database (HGMD) affect transcript structure and abundance (e.g. nonsense SNVs, essential splice site SNVs, frameshifting indels, CNVs). This pilot project will study RNA from lymphoblastoid cell-lines from 12 patients with primordial dwarfism syndromes, for 10 of these samples we have previously generate exome data as part of our collaboration with the group of Prof Andrew Jackson. The two remaining samples are positive controls where the causal mutation is known, and is known to affect transcript structure and/or abundance. Primordial dwarfism is a prime candidate for these RNA-seq studies because all known causal mutations to date have key roles in DNA replication and thus, unsurprisingly, the products of the causal genes are typically ubiquitously expressed. Each RNA will be sequenced, with two technical replicates (independent RT-PCR and libraries) per sample, and each replicate run in 1/2 of a HiSeq lane using 100bp paired reads. Samples preparation was as follows :The cells were grown to confluency, then pellets frozen at -80. RNA samples were prepared using the Qiagen RNeasy kit, then nanodropped and analyzed using the bioanalyzer to determine concentration and purity. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001000640

• Transdisciplinary Studies of Genetic Variation in Colorectal Cancer(CORECT): Meta-analysis

  This study is part 2 of 2 for Schumacher et al, Nat Communication. 2015 Jul 7;6:7138. Part 2 is the pooled meta-analysis of 29 different studies of 37,955 European (18,299 Cases/19,656 Controls) participants using eight different genotyping platforms/variations. table, th, td { border: 1px solid black; border-collapse: collapse; } Study Name Participants Platform CFR-1 2976 Illumina 1M, 1M Duo, Omni1 CFR-2 3053 Affymetrix Axiom MECC 1 982 Illumina Omni 2.5 MECC2 1940 Affymetrix Axiom Kentucky 2172 Affymetrix Axiom ACS/CAPII 1086 Affymetrix Axiom Melbourne 1008 Affymetrix Axiom Newfoundland 672 Affymetrix Axiom ASTERKSI 1895 Illumina 300K COLO23 212 Illumina 300K DACHS1 3417 Illumina 300K DACHS2 1173 Illumina OmniExpress DALS1 1416 Illumina 550k/610K DALS2 874 Illumina 300K HPFS1 457 Illumina OmniExpress HPFS2 348 Illumina OmniExpress HPFS AA 658 Illumina OmniExpress MEC 674 Illumina 300K NHS1 1168 Illumina OmniExpress NHS2 340 Illumina OmniExpress NHSAA 1091 Illumina OmniExpress OFCCR 1172 Affymetrix 100k/500K PHS 771 Illumina OmniExpress PMH 402 Illumina 300K PLCO1 2509 Illumina 550k/610K PLCO2 901 Illumina 300K VITAL 573 Illumina 300K WHI1 1999 Illumina 550k/610K WHI2 573 Illumina 300K Since this study is a meta-analysis no corresponding phenotype, pedigree, sample, subjects, or primary molecular data are available. Each contributing study/platform will have fulfilled its own DBGAP submission commitment. This DBGAP entry is for European participants in the the pooled meta-analysis exclusively.

  Study phs001499