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• Ghana Prostate Study

  Participants were recruited through the Ghana Prostate Study-a population-based component, and a clinical component. The population-based component was a probability sample designed using the 2000 Ghana Population and Housing Census data in an attempt to recruit approximately 1,000 men aged 50-74 years in the Greater Accra region (~3 million people), which successfully recruited 1,037 healthy men between 2004 and 2006 with a response percentage of 98.8 %. Consented individuals underwent an in-person interview, and within 7 days had a digital rectal examination (DRE) and provided an overnight fasting blood sample for prostate-specific antigen (PSA) testing, biomarker assays, and genetic analysis. Subjects who had a positive screen by PSA (>2.5 ng/ml) or DRE underwent a transrectal ultrasound-guided biopsy. A total of 73 histologically confirmed prostate cancer cases were identified through the population-based screening component of the Ghana Prostate Study and were included in the case population in the published GWAS (Cook et al., Human genetics, 2013). From the remaining 964 screen-negative individuals, 836 had at least 20 μg DNA extracted and available for analysis, and 500 of these were matched to cases for analysis by age (in 5-year categories). In the Ghana Prostate Study, we recruited 676 prostate cancer cases at Korle Bu Teaching Hospital in Accra, Ghana, between 2008 and 2012. All consented cases were interviewed and provided an overnight fasting blood sample. At the time of selection for this analysis we had recruited 582 prostate cancer cases, from which we selected 427 for analysis. Combined with the 73 cases diagnosed through the population-based component of the study, this yielded 500 available prostate cancer cases for analysis.

  Study phs000838

• Genomics and Methylation of Neuroendocrine Prostate Cancer from cfDNA (Cornell/Trento 2019)

  A subset of castration resistant prostate cancers develop small cell neuroendocrine prostate cancer (NEPC) as a mechanism of treatment resistance. Metastatic tissue biopsies to evaluate for NEPC transformation are invasive and challenging to perform serially. We performed whole exome and whole genome bisulfite sequencing of plasma cfDNA and matched tumor biopsy samples from 62 patients with metastatic prostate cancer along the disease spectrum to evaluate for NEPC associated genomic and epigenomic features. Multiple tissue biopsies and/or plasma time points were included for a subset of patients to characterize disease heterogeneity and dynamic changes. Computational analysis of clonality and allele specific quantification allowed for detailed comparison of matched tumor tissue and cfDNA data (CLONET v2). Methylation profiles detected from tissue and plasma data were compared and NEPC specific alterations were evaluated in cfDNA. The study supports the feasibility of a plasma based assay for the detection of NEPC.

  Study phs001752

• Human Companion Data for 'A Transcriptomic Atlas of Mouse Cerebellar Cortex Reveals Novel Cell Types'

  In this study, we used single-nucleus RNA-seq to comprehensively define the cell specialization of the mouse cerebellar cortex and vermis. We focused in particular on two interneuron populations—the unipolar brush cells (UBCs) and the molecular layer interneurons (MLIs), identifying continuous variation within the former population, and a new discrete axis of variation in the latter. Human postmortem tissue was used to demonstrate that these specializations are evolutionarily conserved in primates. Together, these findings provide the first comprehensive cellular atlas of the cerebellar cortex, and outline a methodological and conceptual framework for the integration of molecular, morphological, and physiological ontologies for defining brain cell types.

  Study phs002414

• FHS-Net Social Networks

  Note: Data Use Restrictions: The data must only be used for genetic research projects solely in the area of health-related social-network research. This study compiles detailed information on family and social ties linked to participants in the offspring cohort of the Framingham Heart Study. The investigators took computerized information from self-report data used by the FHS for over 30 years to facilitate health exam scheduling. These tracking sheets asked participants to identify people close to them, which were assumed by the investigators to indicate a social tie. Individuals are listed as "egos" (if the ties are from their perspective) and/or "alters" (if they are linked as a friend or family members to one of the other participants). All egos were FHS offspring participants while alters could be FHS participants in any cohort or non-participants. This information was combined with internal FHS pedigree data on family ties to list family member alters (as well as the nature of their relationship). The resultant dataset therefore includes each ego-alter tie, the nature of their relationship and the start and end dates for their ties for each of seven waves for the offspring study. Due to privacy concerns, all exam dates for individuals are listed relative to the initial FHS exam date. The study investigators chose a random, confidential date, to which all initial exam dates are linked (by number of months from random date to initial exam date). With this information, researchers can have access to the temporal relationships among participants' exam dates while remaining unaware of the actual exam dates for individual participants. During each clinic exam cycle, the participants undergo a detailed examination including physical examination, medical history, laboratory testing, and electrocardiogram. Over the years, other tests (that may not be performed at every exam cycle) have included pulmonary function, lifestyle, physical function, cognitive function questionnaires, and various noninvasive cardiovascular tests including echocardiograms. This study involves phenotypic data from these exams including (when available) basic body measurements (height, weight, blood pressure), laboratory values (blood sugar levels, LDL levels), information on smoking and alcohol use, and tests of depression and cognitive functioning. Important links to apply for individual-level data Data Use Certification Requirements (DUC) Instructions to Request Authorized Access Apply here for controlled access to individual level data Participant Protection Policy FAQ In 1948, researchers recruited men and women from the town of Framingham, Massachusetts, beginning the first round of extensive physical examinations and lifestyle interviews that would later be analyzed for common patterns related to CVD development. Initially, the Framingham Heart Study enrolled 5,209 men and women from the Framingham area who were between the ages of 28 and 62 years. Beginning in 1971, the Framingham Heart Study enrolled 5,124 men and women, who were either offspring of the original cohort or spouses of those offspring. In 2002, 4,095 third generation participants (men and women) were enrolled.

  Study phs000153

• dbGaP Collection: Psychiatric Genomics Consortium (PGC) dbGaP Datasets

  This dbGaP Collection includes cases and controls used in the GWAS meta-analysis of neuropsychiatric phenotypes studied by investigators in the Psychiatric Genomics Consortium including major depression, bipolar disorder, attention deficit and hyperactivity disorder, schizophrenia, Tourette Syndrome, and obsessive-compulsive disorder. The consent type for data sets includes general research use as well as phenotype-specific restricted usage. This dbGaP collection was created to facilitate identification of datasets used in PGC analyses in order to expedite the application and ascertainment process for PGC members wishing to access data within the consortium. Non-PGC members may also apply for this dbGaP collection.

  Study phs001254

• Assessment of RNA-Seq Sample Preparation Methodology

  The goal of this study was two-fold, to determine if common purification techniques have any effect on downstream differential expression analysis and to evaluate combinations of alignment and differential expression software for reliability. To this end, blood was collected from three individuals and pooled during and after extraction. After pooling and mixing was completed, samples were divided into three aliquots for testing. The first aliquot was a control and not purified or concentrated. It was diluted to produce samples of varying concentrations for testing. The second aliquot was diluted to 20 ng/μL and used to test six different variations on the AMPure XP bead purification procedure. The last aliquot was also diluted to varying concentrations of 60, 30, and 9.6 ng/μL and purified using MinElute columns. Samples were submitted for total RNA-Seq library preparation and sequencing. Library preparation was performed using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (20020612, Illumina Inc.), and 2x150 bp PE sequencing was done on an Illumina NovaSeq 6000 with the S4 reagent kit. Comparisons were made between methods (AMPure vs. unpurified, AMPure vs. MinElute, MinElute vs. unpurified) to assess the effects of purification method on downstream differential expression. Comparisons were also made within methods using the varying concentrations tested for unpurified samples and for MinElute purified samples to assess the effects of concentration on differential expression. Variations of the AMPure procedure were also compared to assess the effectiveness of the variations tested in comparison to the unmodified procedure. A subset of samples was selected for use with alignment and differential expression package comparison. Unpurified high concentration samples eluted in RNAse-free water were compared to unpurified high concentration samples eluted in BR5, a buffer from the PAXgene blood miRNA kit, with the expectation that there should be no or very few differentially expressed genes. Unpurified high concentration samples eluted in RNAse-free water were also compared to unpurified low concentration samples also eluted in RNAse-free water, with possibly a small number of differentially expressed genes anticipated. A third dataset of simulated RNA-seq data was created with a known rate of differential expression. These files were aligned using Bowtie2, HISAT2, kallisto, RSEM, Rsubread, Salmon, and STAR. Results were then analyzed for differential expression using ALDEx2, baySeq, DEGseq, DESeq2, edgeR, limma, NOISeq, PoissonSeq, and SAMseq. Differential expression results of all three comparisons were evaluated to determine which combinations provided the most reliable results for both real and simulated data.

  Study phs003001

• Development and Validation of Patient-Derived Xenografts from Fibrolamellar Carcinoma Human Tissue

  We developed and validated Patient-Derived Xenografts (PDX) of Fibrolamellar Carcinoma human tissue from surgical resections. Human tissues from primary liver tumor, recurrent liver, and liver metastases were implanted into NOD-SCID-Gamma (NSG) mice (Jackson laboratories) and monitored for tumor growth. Some of the original tissues were frozen for further analysis including RNA sequencing. Tumors that grew were then harvested and passaged into additional mice. Some tumor tissues from the PDX samples were frozen for RNA-Seq analysis. The PDX was validated by histologic, transcriptomic and proteomic analysis. The RNA-Seq analysis was performed on original tissue samples including primary liver tumor, recurrent liver, liver metastases, normal liver, and the derived PDX.

  Study phs002435

• Resident memory CD8 T cells persist for years in human small intestine

  Resident memory CD8 T cells (Trm) have been shown to provide effective protective responses in the small intestine (SI) in mice. A better understanding of the generation and persistence of SI CD8 Trm cells in humans may have implications for intestinal immune-mediated diseases and vaccine development. Analyzing normal and transplanted human SI we demonstrated that the majority of SI CD8 T cells were bona fide CD8 Trm cells that survived for over 1 year in the graft. Intraepithelial and lamina propria CD8 Trm cells showed a high clonal overlap and a repertoire dominated by expanded clones, conserved both spatially in the intestine and over time. Functionally, lamina propria CD8 Trm cells were potent cytokine-producers, exhibiting a polyfunctional (IFN-γ+ IL-2+ TNF-α+) profile, and efficiently expressed cytotoxic mediators after stimulation. These results suggest that SI CD8 Trm cells could be relevant targets for future oral vaccines and therapeutic strategies for gut disorders.

  Study EGAS00001003676

• A standardised framework for robust fragmentomic feature extraction from cell-free DNA sequencing data

  Fragmentomic features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. However, a lack of systematic evaluation of biases in feature quantification has hindered the adoption of such applications. We compared features derived from whole-genome sequencing of ten healthy donors using nine library kits and ten data-processing routes, and validated them in 1,182 plasma samples from published studies. Our results clarify the variations resulting from library preparation and feature quantification methods. We designed the Trim Align Pipeline and the cfDNAPro R package as unified interfaces for data pre-processing, feature extraction, and visualisation, aiming to standardise multimodal feature engineering and integration for machine learning.

  Study EGAS00001008051

• Whole Exome Sequencing for Colorectal Cancer

  This project was designed to use next generation sequencing technology to screen the protein coding regions of the genome for low frequency variants in a panel of high-risk colorectal adenocarcinoma cases. Blood and cell-line DNA for colorectal cancer patients and a subset of quality control samples that had existing whole exome sequence data were analyzed using Illumina HiSeq sequencers. Samples from this project were from participants in the Women's Health Initiative (WHI) and the Diet, Activity, and Lifestyle Study (DALS).

  Study phs000410

• Genetic Causes of Congenital Anosmia

  The Genetic Causes of Congenital Anosmia study was designed to provide a list of candidate genes that are potentially causal for isolated congenital anosmia (ICA), a rare inherited disorder where individuals lack a sense of smell from birth in the absence of a known genetic syndrome (i.e. Kallman's syndrome). This study includes 193 participants from 18-87 years of age, divided into two cohorts: family and non-family. Genetic data from the family cohort was analyzed in a case-control family design to generate a list of 162 candidate genes for ICA. A targeted search for variants in this list of genes was then conducted in the non-family cohort to create a prioritized list of genes for further study. Ten unrelated families were recruited for the family cohort for a total of 52 participants, 25 of which had anosmia. The non-family cohort consisted of 141 anosmic individuals. 3 additional normosmic participants from incomplete families were collected, one of whom has a participating family member in the non-family cohort, and so has data provided here. Data collection was conducted remotely, resulting in 146 participants recruited from the United States, and 48 recruited internationally from ten different countries. Participants were interviewed for their anosmia status and to confirm that they had no known genetic syndromes. Participants also completed the University of Pennsylvania Brief Smell Identification Test (BSIT; Doty et al., 1984) to confirm their anosmic/normosmic status and provided a saliva sample for whole exome sequencing (WES). Participants who had family members with anosmia provided pedigree information via interview. Data submitted to dbGap include whole exome sequences from 194 individuals (163 anosmic) conducted with Illumina HiSeq2500 and Illumina NovaSeq next generation sequencing technologies. Family pedigree information for the 10 participating families and all participants in the non-family cohort who have non-participating anosmic family members was also included. Our goal was to provide a resource for further research into the genetics of isolated congenital anosmia and to aide in the understanding of this disorder, as well as human olfaction, in general. The WES data provided could be further analyzed for polygenic interactions, additional non-targeted analysis on the non-family cohort, or combined into databases of other anosmic populations for further gene targeting or selection.

  Study phs003328

• NHLBI TOPMed - NHGRI CCDG: Early-onset Atrial Fibrillation in the CATHeterization GENetics (CATHGEN) Cohort

  The CATHeterization GENetics (CATHGEN) biorepository collected biospecimens and clinical data on individuals age ≥18 undergoing cardiac catheterization for concern of ischemic heart disease at a single center (Duke University Medical Center) from 2000-2010; a total of N=9334 individuals were collected. Samples were matched at the individual level to clinical data collected at the time of catheterization and stored in the Duke Databank for Cardiovascular Diseases (DDCD). Clinical data included subject demographics, cardiometabolic risk factors, cardiac history including symptoms, age-of-onset of cardiovascular diseases, coronary anatomy and cardiac function at catheterization, laboratory data, and yearly follow-up for hospitalizations, vital status, medication use and lifestyle factors. AF cases were defined as individuals who had ever had AF based on any ECG available at Duke University or ICD-9 code for AF used for inpatient or outpatient billing.

  Study phs001600

• Genotype and exome data for an Australian Aboriginal population: a reference panel for health-based research

  Genetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalog of variants called after sequencing the exomes of 72 Aboriginal individuals to a depth of 20X coverage in 80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found 99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians.

  Study EGAS00001001585

• National Emphysema Treatment Trial (NETT-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. Available Data: The current release of the NETT study dataset includes follow-up data through May of 2013.Objectives: To compare lung-volume-reduction surgery with medical therapy for severe emphysema, and to identify participant selection criteria for lung volume reduction surgery.Background: Lung-volume-reduction surgery has been proposed as a palliative treatment for severe emphysema. Effects on mortality, the magnitude and durability of benefits, and criteria for the selection of participants have not been established.Participants: A total of 1,218 participants with severe emphysema underwent pulmonary rehabilitation and were randomly assigned at 17 centers to undergo lung-volume-reduction surgery (bilateral stapled wedge resection) or to receive continued medical treatment. Participants were randomized after a 6-10 week pulmonary rehabilitation period and participants with a forced expiratory volume in one second (FEV1) that was 20 percent or less of predicted and a homogeneous distribution of emphysema or carbon monoxide diffusing capacity 20 percent or less of predicted were not eligible for randomization due to poor post-surgery prognosis for death or functional improvement.Conclusions: Overall, lung-volume-reduction surgery increases the chance of improved exercise capacity but does not confer a survival advantage over medical therapy. It does yield a survival advantage for participants with both predominantly upper-lobe emphysema and low base-line exercise capacity. Participants previously reported to be at high risk and those with non-upper-lobe emphysema and high base-line exercise capacity are poor candidates for lung-volume-reduction surgery, because of increased mortality and negligible functional gain. (NEJM 2003;348:2059-2073).

  Study phs004077

• National Cancer Institute (NCI) Prostate Cancer Genome-Wide Association Study for Uncommon Susceptibility Loci (PEGASUS)

  This genome-wide association study was funded by the National Cancer Institute (NCI) to identify uncommon susceptibility loci for prostate cancer. A total of 4,600 prostate cancer cases and 2,840 controls of European ancestry from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial were genotyped using the Illumina HumanOmni2.5 and passed rigorous quality control filters. Additional genotype data (available in dbGap under other accession numbers) from 101 independent controls of European ancestry scanned with the HumanOmni2.5 were also included, resulting in a total of 4,600 cases and 2,941 controls for the published analysis. SNPs from the most promising regions, as determined by rank p-value, under multiple different models as well as select candidate genes were taken forward for replication using a custom Iselect chip in 6,575 cases and 6,392 controls of European ancestry. Results from the primary scan after imputation were then meta-analyzed with the Iselect results as well as results from previous GWAS. In a combined meta-analysis of the primary scan together with the custom Iselect replication and a previous GWAS, thirteen loci reached genome-wide significance (P < 5 x 10-8) for prostate cancer overall; however, each of them confirmed a previously reported locus. Although they did not reach genome-wide significance, we found evidence for two new suggestive loci at chromosome 16q22.2 (PKD1L3, rs12597458, P = 9.67 x 10-8) and 6p22.3 (CDKAL1, rs12198220, P = 2.13 x 10-7). In a combined case-only analysis of 12,518 prostate cancer cases, we identified two loci associated with Gleason score, a pathological measure of disease aggressiveness: rs35148638 at 5q14.3 (RASA1, P=6.49x10-9) and rs78943174 at 3q26.31 (NAALADL2, P=4.18x10-8). In a stratified case-control analysis, the SNP at 5q14.3 appears specific for aggressive prostate cancer (P=8.85x10-5) with no association for non-aggressive prostate cancer compared to controls (P=0.57). Only the cases and controls genotyped on the HumanOmni2.5 specifically for this study are included under this accession number. Controls (n=101) genotyped with the HumanOmni2.5 for another study are posted under a different accession number. Please note that the majority of prostate cancer cases and controls genotyped in CGEMS (and posted under a different accession number) are included in this study.

  Study phs000882

• Transcriptomic data of a discordant monozygotic twin pair for ALS

  The dataset contains bulk RNAseq data of a discordant monozygotic twin pair for ALS; in particular the matrix with gene names and TPM counts for each sample. For both healthy and ALS twin, RNA sequencing was performed on RNA samples collected at two different time points (T1 and T2), for a total of seven samples. RNA extracted from PBMCs was used for library preparation according to Illumina TruSeq Stranded mRNA kit and processed on Illumina NextSeq 550 sequencer. Reads were aligned to the reference human genome GRCh38/hg38 and annotations were provided by the Ensembl v100 database.

  Dataset EGAD50000001330

• Characterizing Individual Cells Obtained from Bone Marrow Biopsies of MPN Patients

  We profiled the transcriptomes of individual cells obtained from bone marrow aspirates of 7 treatment-naïve newly diagnosed JAK2-mutant myeloproliferative neoplasm (MPN) patients (3 polycythemia vera and 4 essential thrombocythemia patients), and 2 healthy controls. The submitted data corresponds to sequencing reads mapped to the human reference genome GhRC38 build using CellRanger for a total of 9 samples (one per patient). In addition, to reconstruct the lineage histories of single cells in MPN patients, we performed whole-genome sequencing of single-cell-derived colonies of hematopoietic stem and progenitor cells from 2 essential thrombocythemia (ET) patients: 22 JAK2-mutant colonies and 20 WT colonies for patient ET 1; and 13 JAK2-mutant colonies and 21 WT colonies for patient ET 2. The submitted data consists of sequencing reads aligned to the human reference genome GhRC38 build using bwa-mem. Each file corresponds to the whole-genome sequencing data for one colony.

  Study phs002308

• Sickle Cell Disease Natural History Data Resource (SCD NHDR)

  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. BackgroundThe NHLBI initiated the Sickle Cell Disease Natural History Data Resource (SCD NHDR) to leverage existing SCD studies to build a data resource to provide phenotypic data on contemporaneous control cohorts for gene therapy trials and other studies. The potential uses of the NHDR are broad, including providing matched controls for clinical trials, observing a cohort of untreated patients as part of a natural history study, or conducting comparative effectiveness research on a subpopulation with selected co-morbidities or drug treatment profiles. The SCD NHDR includes two multi-center SCD longitudinal cohort studies with extensive annual clinical data and patient surveys, the Sickle Cell Disease Implementation Consortium (SCDIC-I and SCDIC-II) and the Globin Research Network for Data and Discovery (GRNDaD). The SCDIC-I, initiated in 2017 and concluded in June 2022, enrolled over 2400 patients with SCD from 8 US treatment centers. The SCDIC-II reconsented 1220 of the SCDIC-I patients as well as enrolling an additional 450 new patients from the same 8 centers between September 2022 and October 2023, for a total of 1670 in SCDIC-II. Only two of the many GRNDaD centers are submitting data to the SCD NHDR for deposit into BDC (approximately 122 patients). Data submissions from the SCD NHDR to BDC will be annually starting in early 2024. Description of the Study Data All data obtained for the SCD NHDR are considered common data elements (CDEs) important for studies of SCD. These CDEs were identified from several workgroups of SCD experts convened under the NHLBI's Cure-SC Initiative (https://curesickle.org/cde-catalog). The following types of data elements were abstracted from the medical record – variables that describe the SCD diagnosis, SCD co-morbidities and other clinical complications, elements from the physical examination, medications and transfusions, insurance type, laboratory measurements, healthcare utilization, history of SCD-related procedures, and measurements from cardiac procedures. The following types of data were self-reported on the patient survey – demographics, diagnosis information, pain experience, social and mental health information, other patient reported outcome domains (e.g., sleep, fatigue), and alcohol and smoking history. Standard PRO measures were used from ASCQ-Me, PROMIS and Neuro-QoL. Patient surveys were completed approximately annually. Under SCDIC-I, two medical record abstractions and labs were reported at enrollment and approximately 3 years later. Under SCDIC-II and GRNDaD, all data are collected annually. Patients may refuse to complete the survey.

  Study phs003529

• CCG Multicentric Italian Lung Detection (MILD)

  For the CCG-MILD project, NCI will utilize whole genome sequencing and/or whole exome sequencing in conjunction with transcriptome sequencing to try to identify recurrent genetic alterations (mutations, deletions, amplifications, rearrangements) and/or gene expression signatures that would be important to the hypothesis(es) submitted by the investigators. The samples will be processed and submitted for genomic characterization using the established NCI Genome Characterization Pipeline. Subsequent genomic and clinical data will be hosted at the NCI Genomic Data Commons (GDC).

  Study phs002253

• Integrative_Oncogenomics_of_multiple_myeloma

  We used targeted capture and massively parallel sequencing of exomes of CD138 purified plasma cells and matched somatic DNA from 53 patients with Multiple Myeloma. 2281 variants were validated by 454 sequencing. The present study will validate an additional 5538 variants by targeted pull-down and sequencing. The normal and tumor samples will be indexed separately and pre-pooled in groups of 10 or 11. The sequence capture will use 5 reactions each for the normals and tumors. All normal samples will then be pooled and go thorugh one lane of HiSeq. Same for the tumors.

  Study EGAS00001000243

• Novel Factors for Unexplained Phenotypes of Subclinical Carotid Atherosclerosis

  The overall goal for this study was to determine the genetic factors associated with extreme phenotypes of subclinical atherosclerosis (protective and deleterious). Study participants were selected from the Northern Manhattan Study (NOMAS), a population based cohort study investigating stroke and stroke risk factors in Northern Manhattan. Cases and controls were individuals at the extreme ends of the distribution for carotid intima-media thickness and carotid plaque, with cases defined as individuals with subclinical atherosclerosis that could not be explained by traditional vascular risk factors (USAth) and controls defined as individuals with unexplained protection against atherosclerosis (UPAth).

  Study phs001560

• Single-cell gene expression data from CD8+ T cells from two Austrian COVID19 patients stimulated with wildtype and mutant SARS-Cov-2 peptides

  The data contains single-cell gene sequencing data (10x Genomics) from FACS-purified CD8 T lymphocytes from two Austrian patients. The cells were stimulated with one MHC class I peptides obtained from a common (wild type) variant and an emerging mutant variant of the SARS-Cov-2 virus. Then the samples were multiplexed using hashtag oligos. We provide the raw and aligned sequence data for: i. The single-cell experiments ii. The PCR-amplified samples for enrichment of the hashtag oligo multiplexing barcodes iii. The PCR-amplified samples for enrichment of the T Cell Receptor (TCR) VDJ region for immuno-profiling. The samples and libraries were processed and obtained in collaboration between St. Anna Children's Cancer Research Institute (CCRI), CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, and the Medical University of Vienna. The cell barcodes and processed data has been submitted to the GEO database with GEO accession GSE166651.

  Dataset EGAD00001006995

• Predictive value of chromosome 18q11.2-q12.1 loss for benefit from bevacizumab in metastatic colorectal cancer; a post-hoc analysis of the randomized controlled trial AGITG-MAX

  Patients and methods: We analyzed tumor samples of 256 patients enrolled in the AGITG-MAX 3-arm randomized controlled trial (RCT) who were randomly assigned to receive either capecitabine, or capecitabine and bevacizumab with- or without mitomycin. Chromosome 18q11.2-q12.1 copy number status was measured and correlated with PFS according to a predefined analysis plan with marker-treatment interaction as the primary end-point.Results: Chromosome 18q11.2-q12.1 losses were detected in 71% of patients (181/256) characteristic for mCRC. Consistent with the non-randomized study, significant PFS benefit of bevacizumab was observed in chromosome 18q11.2-q12.1 loss patients (P=0.009), and not in 18q no-loss patients (P=0.67). Although significance for marker-treatment interaction was not reached (Pinteraction = 0.28), hazard ratio and 95% confidence interval (HRinteraction 0.72, CI 0.39 - 1.32) show striking overlap with the non-randomized study cohorts (HRinteraction 0.41, CI 0.32 - 0.8) supported by a non-significant Cochrane chi-squared (P=0.11) for heterogeneity. Conclusions: PFS characteristics for marker positive- and negative patients randomized for treatment with- or without bevacizumab were consistent with those of the non-randomized discovery study, though the number of AGITG-MAX samples fell short to reach significance for marker-treatment interaction. Post-hoc analysis of the AGITG-MAX RCT provides supportive evidence for chromosome 18q11.2-q12.1 as a clinically relevant predictive marker for mCRC patients.

  Study EGAS00001005453

• Division of Cancer Epidemiology and Genetics (DCEG) Imputation Reference Dataset

  We have built a new resource for imputation of SNPs for existing and future genome-wide association studies (GWAS), known as the Division of Cancer Epidemiology and Genetics (DCEG) Reference Set. The first build of the data set includes 728 cancer-free individuals of European descent from three large prospectively sampled studies, 98 African-American individuals from the Prostate, Lung, Colon, and Ovary Cancer Screening Trial (PLCO), 74 Chinese individuals from a Chinese clinical trial in Shanxi, China (SHNX), and 349 unrelated individuals from the HapMap Project (see Molecular Data Section for details on arrays used). The final harmonized dataset includes 2.8 million autosomal polymorphic SNPs on 1,249 subjects after rigorous quality control metrics were applied.

  Study phs000396

• Ontario Familial Colon Cancer Registry Single Nucleotide Polymorphisms and CpG Methylation (OFCCR SNP-CpG)

  We profiled the methylation landscape of ~2100 DNA samples (~1100 cases of colorectal cancer and ~1000 controls) from the Ontario Familial Colon Cancer Registry (OFCCR) using the HumanMethylation450 array from Illumina. DNA was extracted from lymphocyte pellets, except for 99 samples for which DNA was extracted from lymphoblastoid cell lines. Samples were genotyped on the Affymetrix Human Mapping 100k and 500k arrays. The aim the study was to evaluate the interplay between genetic variation and methylation, including long-range epigenetic regulation.

  Study phs000779