Search Results - EGA European Genome-Phenome Archive

Illumina HumanOmniExpress genotyping data from the TEENAGE (TEENs of Attica: Genes and Environment) study.

The TEENAGE study is a cross-sectional study comprising healthy Greek adolescents. The study was conducted according to the guidelines specified in the Declaration of Helsinki and all procedures involving human subjects were approved by the Institutional Review Board of Harokopio University and the Greek Ministry of Education, Lifelong Learning and Religious Affairs. The TEENAGE study target population comprised adolescent students aged 13 to 15 years attending the first three classes of public secondary schools located in the wider Athens area of Attica. The regions across Attica from which students were recruited were physically similar and all urban in nature. Sampling of regions and schools selected to participate was random. Students were enrolled from the wider urban region to ensure that they were coming from families with varying educational background and socio-economic status. Moreover, in order to exclude any vast economic disparities, all participating schools were exclusively public schools, which are free of charge. A total of twenty-four schools participated in the study out of 285 junior secondary public schools in Attica. Anthropometric, medical and dietary information was obtained. DNA samples were genotyped using Illumina HumanOmniExpress BeadChips (Illumina, San Diego, CA, USA) at the Wellcome Trust Sanger Institute, Hinxton, UK. Genotype calling algorithm used was Illuminus (Teo et al., 2007).

Study EGAS00001000996

Copy number profiling of tissue and plasma samples from high grade serous epithelial ovarian cancer patients

This dataset includes 289 samples from 46 high grade serous epithelial ovarian cancer patients. Data are from both tissue samples (either primary tumor, or synchronous metastases) and circulating cell-free DNA (cfDNA) of plasma samples taken during therapy and follow-up.

Dataset EGAD00001006422

Diagnostic Genomic Analysis is Prognostic in AYA ALL Patients Treated on a MRD-Stratified Paediatric Protocol

Background: Over the last decade, next generation sequencing has enabled classification of multiple new recurrent genomic drivers of acute lymphoblastic leukemia (ALL). We provide a comprehensive genomic survey of adolescent and young adult (AYA) patients treated on the Australasian Leukaemia and Lymphoma Group (ALLG) ALL06 study. ALL06 clinical trial described the efficacy and tolerability of AYA ALL patients aged 15-39 years treated on a single minimal residual disease (MRD)-stratified platform. In this study we have taken the ALL06 cohort and retrospectively performed comprehensive genomic analyses assessing response of AYA patients with various genomic subtypes treated with a paediatric approach. Methods: Genomic risk classification of B- and T-ALL patients (n=57) enrolled to the study was based on mRNA-Sequencing, MLPA, immunophenotyping and cytogenetics. Results: Using this approach, 36/40 (90%) B- and 13/17 (76.5%) T-ALL patients were classified according to genomic risk. We have linked outcome data with each patient’s genomic risk and found a strong correlation between adverse genomic risk and MRD at the end of consolidation, translating to inferior overall and relapse free survival. Patients with adverse risk genomics who achieved negative MRD status had improved responses compared to those with persistent MRD. Patients with standard risk genomics had excellent responses regardless of their MRD status. Conclusion: Our data argue strongly for incorporation of a genomic risk classification into future ALL treatment paradigms at the time of diagnosis.

Study EGAS50000000752

Whole Genome Sequencing of clonal expansions of single healthy somatic cells (human, female)

HSC73_clone: Bone marrow mononuclear cells from the healthy 73 years old female were thawed and labeled with Alexa-Fluor 488-conjugated anti-CD34 (581, Biolegend), Alexa-Fluor 700-conjugated anti-CD38 (HIT2, eBioscience), a cocktail of APC-conjugated lineage antibodies consisting of anti-CD4 (RPA-T4), anti-CD8 (RPA-T8), anti-CD11b (ICRF44), anti-CD20 (2H7), anti-CD56 (B159, all BD Biosciences), anti-CD14 (61D3), anti-CD19 (HIB19) and anti-CD235a (HIR2, all eBiocience) and 1 micro-gram/ml propidium iodide (Sigma). Using a BD FACSAria cell sorter, single Lin-CD34+CD38-PI- cells were individually sorted into low-adhesion 96-well tissue culture plates (Corning) containing 100micro-litre of StemSpan Serum-Free Expansion Medium (Stemcell technologies) supplemented with 100ng/ml of human SCF and FLT-3L, 50ng/ml of human TPO, 20ng/ml of human IL-3, IL-6 and G-CSF (all cytokines from Peprotech) and 50U/ml of penicillin and 50μg/ml of streptomycin (Sigma). Cells were incubated at 37 degrees C in a humidified atmosphere with 5% CO2 in air. After 5 days in culture, another 100micro litres of cytokine-containing medium were added. 13 days after seeding, clones B6 and G2 had expanded to approx. 105 cells and were selected for whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) after tagmentation-based library preparation (see Extended Experimental Procedures) for clone B6 and standard library preparation for clone G2. For germline-control ~106 unsorted bone marrow mononuclear cells from the same donor were used for sequencing. An average of 30-fold sequence coverage for each the clones and the matching control were obtained.L4clone: A progenitor cell clone was raised from a peripheral blood sample of the 39 year old healthy female. Frozen peripheral blood mononuclear cells (PBMCs) were isolated from 2 ml heparinised peripheral blood via Ficoll Paque density centrifugation. A methylcellulose assay was performed as described earlier (Weisse et al., 2012). In brief, non-adherent mononuclear cells were incubated in the presence of the recombinant human cytokines IL-3, IL-5 and GM-CSF (R&D systems) over 14 days to induce colony formation. Colonies were detected under an inverted light microscope, and plucked by a pipette when colonies had approximately 10,000 cells/CFU. Each colony was washed three times in PBS and finally frozen as a cell pellet in -80 degrees C. Genomic DNA was isolated using the QIAamp DNA micro kit according to the instructions of the manufacturer (Qiagen, Hilden, Germany). Whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) was performed for colony 4 after tagmentation-based library preparation and resulted in 15-fold sequence coverage for each the colony and the matching whole blood.

Dataset EGAD00001000666

Whole genome sequencing of 108 epileptic patients from CENet cohort

Epileptic patients have been sequenced as part of the CENet cohort which is composed of patients with Genetic Generalized Epilepsy (GGE) or Non-Acquired Focal Epilepsy (NAFE) collected in CHUM Research Center in Montreal. Patients were diagnosed by epileptologists. The clinical epilepsy phenotype was classified according to the current classification by the International League against Epilepsy (ILAE). Libraries preparation and whole-genome sequencing: gDNA was cleaned up using ZR-96 DNA Clean & ConcentratorTM-5 Kit (Zymo) prior to being quantified using the Quant-iTTM PicoGreen dsDNA Assay Kit (Life Technologies) and its integrity assessed on agarose gels. Libraries were generated using the TruSeq DNA PCR-Free Library Preparation Kit (Illumina) according to the manufacturer‚Äôs recommendations. Libraries were quantified using the Quant-iTTM PicoGreen dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were denatured in 0.05N NaOH and diluted to 8pM using HT1 buffer. The clustering was done on a Illumina cBot and the flowcell was ran on a HiSeq 2500 for 2x125 cycles (paired-end mode) using v4 chemistry and following the manufacturer's instructions. A phiX library was used as a control and mixed with libraries at 0.01 level. Bioinformatics: The Illumina control software was HCS 2.2.58, the real-time analysis program was RTA v. 1.18.64. Program bcl2fastq v1.8.4 was used to demultiplex samples and generate fastq reads. The filtered reads were aligned to reference Homo_sapiens assembly b37. Each readset was aligned to create a .cram file.

Study EGAS00001007507

Combination pembrolizumab and radiotherapy induces systemic anti-tumor immune responses in immunologically-cold non-small cell lung cancer

The abscopal effects of radiation may sensitize immunologically “cold” tumors to immune checkpoint inhibition (ICI). We investigated the immunostimulatory effects of radiotherapy leveraging multi-omic analyses of serial tissue and blood biospecimens (n=293) from a phase 2 clinical trial of stereotactic body radiation therapy (SBRT) followed by pembrolizumab in metastatic non-small cell lung cancer (NSCLC; NCT02492568). Patients with immunologically-cold tumors (low tumor mutation burden, null PD-L1 expression, WNT-pathway mutated) in the SBRT arm had significantly longer progression-free survival compared to ICI alone (P<0.05). Induction of interferon-gamma, interferon-alpha, and antigen processing and presentation gene sets was significantly enriched post SBRT in non-irradiated tumor sites (FDR adjusted P<0.01). Significant on-therapy expansions of new and pre-existing TCR clones in both the tumor and blood compartments were noted in the SBRT arm (P<0.05). These findings support the systemic anti-tumor effects of immuno-radiotherapy and may open a therapeutic window of opportunity to overcome resistance to ICI.

Dataset EGAD50000000404

Diet, Genetic Factors, and the Gut Microbiome in Crohn's Disease

We investigate the hypothesis that consistent changes in the human gut microbiome are associated with Crohn's disease, a form of inflammatory bowel disease, and that altered microbiota contributes to pathogenesis. Analysis of this problem is greatly complicated by the fact that multiple factors influence the composition of the gut microbiota, including diet, host genotype, and disease state. For example, data from us and others document a drastic impact of diet on the composition of the gut microbiome. No amount of sequencing will yield a useful picture of the role of the microbiota in disease if samples are confounded with uncontrolled variables. We aim to characterize the composition of the gut microbiome while controlling for diet, host genotype, and disease state. Diet is controlled by analyzing children treated for Crohn's disease by placing them on a standardized elemental diet, and by testing effects of different diets on the gut microbiome composition in adult volunteers. Genotype is analyzed by large scale SNP genotyping, which is already underway and separately funded--team member Hakon Hakonarson is currently genotyping 50 children a week at ~half a million loci each and investigating connections with inflammatory bowel disease. Clinical status is ascertained in the very large IBD practice in the UPenn/CHOP hospital system. Effects of diet, host genotype, and disease state on the gut microbiome are summarized in a multivariate model, allowing connections between microbiome and disease to be assessed free of confounding factors. This project is divided into four sub-studies. In the Fecal Storage Methods (FSM) study, methods of stool storage and DNA extraction are compared to examine their impact on DNA sequence analysis results. The Controlled Feeding Experiment (CaFE) addresses the effects of controlled diets on the gut microbiome. In the Cross-sectional Study of Diet and Stool Microbiome Composition (COMBO), the effects of diet analyzed using surveys and deep sequencing of stool specimens. The fourth study, Pediatric Longitudinal Study of Elemental Diet and Stool Microbiome Composition (PLEASE), examines the effects of an elemental diet treatment on pediatric patients diagnosed with inflammatory bowel disease (IBD), particularly Crohn's disease. Fecal Storage Methods (FSM): Cross-sectional study Controlled Feeding Experiment (CaFE): Controlled trial Cross-sectional Study of Diet and Stool Microbiome Composition (COMBO): Cross-sectional study Pediatric Longitudinal Study of Elemental Diet and Stool Microbiome Composition (PLEASE): Longitudinal cohort study

Study phs000252

Plasma whole genome sequencing from patients with stage IV colorectal cancer and microsatellite instability

This dataset contains plasma WGS data from patients with stage IV colorectal cancer (CRC, n = 16) and healthy individuals (n = 21) used in the Pointy manuscript. Patients with CRC provided written consent and samples were collected as performed as described previously (Clinical-Trials.gov number NCT01876511; Georgiadis et al., 2019, Le et al., 2017). Plasma samples from 21 healthy control individuals were procured through BioIVT. Cell-free DNA (cfDNA) was extracted from plasma using the QIAamp Circulating Nucleic Acid Kit. Libraries were prepared with 5 to 250 ng of cfDNA using the NEBNext DNA Library Prep Kit. Libraries were sequenced on HiSeq2000/2500.

Dataset EGAD00001008999

Genomics Define Malignant Transformation in Myeloma Precursor Conditions

Multiple myeloma (MM) is consistently preceded by monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). While these precursor conditions are asymptomatic, they are not entirely benign and carry a lifelong risk of progression to MM. Unlike other cancers defined by pathology, malignant transformation from MGUS or SMM to MM has so far relied on demonstration of clinical end-organ damage as morphology and cytogenetics cannot reliably distinguish them. In this study, using genomic data from 374 patients with MGUS or SMM (277 training, 97 validation), to our knowledge, we demonstrate for the first time the ability to identify malignant transformation in MGUS and SMM. We introduce the concept of genomic MM and genomic MGUS to differentiate the subsets of MGUS and SMM that are biologically malignant with genomic features indistinguishable from MM from the subset that is premalignant and unlikely to progress to malignancy. Importantly, we find that most SMM has biological features of malignant transformation indistinguishable from MM. As expected, this subset that we consider having genomic MM is associated with a high risk of progression to MM although some patients remained progression-free beyond 5 years. Conversely, 60% of MGUS and 10% of SMM have no evidence of malignant transformation (genomic MGUS), with no progression during follow-up. Integration of genomic features with the 2/20/20 International Myeloma Working Group model significantly improved the prediction of progression among genomic MM. These findings support the use of genomic criteria to refine the classification and the risk stratification in myeloma precursor conditions.

Dataset EGAD00001015768

DNA methylation-based classification of sinonasal tumors [Proteomics data]

This dataset includes raw label-free mass spectrometry proteomics data of different sinonasal tumor entities as well as normal sinonasal tissue. 72 samples were processed on a Q Exactive HF-X instrument coupled to an easy nanoLC 1200 system using one microgram of peptides and an 110 minutes gradient.

Dataset EGAD00010002381

Aligned Low pass whole genbome sequencing of cell free and tumour DNA from 5 patients with high grade serous ovarian cancer. Samples have been aligned to hg19 and bam files uploaded

This is the aligned bam files of 5 patients, with sequential sampltes from patients comprising cfDNA and FFPE extracted tumour DNA

Dataset EGAD50000001632

A mathematical model of cell-free DNA fragment size reveals cancer-specific fragmentomic patterns

This study aim to test a mathematical model of cfDNA length distribution across multiple biodiy flulids. It try to investigate biological mechanisms of cfDNA fragmentation and release.

Study EGAS50000001560

Bulk RNA sequencing of day 2 and day 7 biopsies from the tuberculin skin test in people with latent tuberculosis, and of day 2 biopsies from saline controls

We used the tuberculin skin test (TST) as human challenge model to study the temporal evolution of the immune response to Mycobacterium tuberculosis (Mtb) antigens in vivo. Study participants comprised healthy HIV seronegative adults, 18-60 years of age. Latent tuberculosis (TB) infection was defined as immune memory for Mtb-specific antigens identified by positive peripheral blood IFNg release assays, but no clinical or radiological evidence of active TB. Two units tuberculin each were injected intradermally into the contralateral forearms of participants. After 2 days (n=216) or 7 days (n=158), 3 mm skin punch biopsies were taken from the injection sites and processed for whole genome transcriptional profiling by bulk RNA sequencing. The time points reflect maximum clinical inflammation (day 2) and maximum T cell infiltration (day 7) of the TST. TST samples were compared to skin biopsies taken two days after control injection of saline in a separate group of individuals (n=33), comprising healthy volunteers as well as patients with active or latent TB, ranging from 18-75 years of age. This dataset includes 407 samples from 256 individuals (n=33 saline, n=223 with Day 2 and/or Day 7 TST). Skin biopsies were collected into RNAlater (Qiagen) for RNA extraction. Total RNA was obtained with the Precellys Evolution homogenizer (Bertin Instruments) and Qiagen RNeasy mini kit. RNA was subjected to DNase treatment to remove contaminating genomic DNA using a TURBO DNA-free kit (Ambion, Life Technologies). The KAPA mRNA HyperPrep Kit (Roche Diagnostics) was used to construct stranded mRNA-Seq libraries from up to 500 ng intact total RNA. Paired-end sequencing was performed on the Illumina Nextseq using the Nextseq 500/550 High Output 75 cycle kit (Illumina). Runs were demultiplexed using bcl2fastq by Illumina.

Dataset EGAD50000001208

GDAP - Genome Diversity in Africa Project (2021-02-12)

The Genomic Diversity in Africa Project (GDAP) started with the plan to develop a genomic resource from African populations, characterise genomic diversity and population history, and facilitate clinical studies in Africa. Currently, 25 individuals from 24 ethnolinguistic groups have been whole-genome sequenced at high depth totalling 585 individuals. An additional 41 individuals have been sequenced with 10X Genomics libraries. At this stage, the initial curation of this dataset has been finished and we are performing the analysis in coordination with our collaborators. The current state of the GDAP represents a very diverse panel of African populations that maximizes geographical and ethnic variation and represents a great starting point to achieve the aforementioned goals. However, southern sub-Saharan countries, Bantu speakers and hunter gatherer groups are currently underrepresented, despite being crucial to understand the evolutionary history of the continent. After extensive effort to collate studies documentation, we finally have the opportunity to sequence 600 new individuals from these groups, including countries as Gabon, Rwanda and Zambia, and address these deficiencies. We aim to proceed with the same strategy: to sequence at high depth 25 individuals with standard PCR free libraries, with 2 additional individuals with 10X Genomics Chromium libraries per ethnolinguistic group. The former allows a good representation of variants down to low frequency in any given population, and the latter allows accurate phasing and the analysis of structural variation. By including these new populations, we want to investigate three crucial questions in African history in addition to the initial objectives: the Bantu expansion, the evolutionary history of hunter gatherers and the transatlantic slave trade. Additionally, the expanded dataset will help us better discover the genetic variation present in Africa and characterize the African pangenome. 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/ . This dataset contains all the data available for this study on 2021-02-12.

Dataset EGAD00001006965

Oncoarray Consortium - Lung Cancer Studies

The study was conducted under the auspices of the Transdisciplinary Research In Cancer of the Lung (TRICL) Research Team, which is a part of the Genetic Associations and MEchanisms in ONcology (GAME-ON) consortium, and associated with the International Lung Cancer Consortium (ILCCO). Ethics: All participants provided written informed consent. All studies were reviewed and approved by institutional ethics review committees at the involved institutions. Sequencing data are derived from four substudies. The substudies that contributed include Harvard, Liverpool, Toronto, and IARC. The Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study is a randomized primary prevention trial including 29,133 male smokers enrolled in Finland between 1985 and 1993. Participants ranged between ages of 50 to 69 at enrollment and were randomized in a factorial design to take either 50 milligrams of d-alpha tocopheryl acetate (Vitamin E), 20 mg of all-trans-beta-carotene, both or placebo. The study continued to monitor cancer incidence through 2012 and total mortality through December 2013. The CAncer de PUlmon en Asturias Study (CAPUA) is a hospital-based case-control study conducted in Asturias, Spain by the University of Oviedo. Lung cancer cases were recruited in three main hospitals of Asturias, following an identical protocol from 2002 to 2012. Eligible cases were incident cases of histologically confirmed lung cancer between 30 and 85 years of age and residents in the geographical area of each participating hospital. Controls were selected from patients admitted to those hospitals with diagnoses unrelated to the exposures of interest and individually matched by ethnicity, gender, age (± 5 years) and hospital. Epidemiologic data were collected personally through computer-assisted questionnaires by trained interviewers during the first hospital admission. Structured questionnaires collected information on sociodemographic characteristics, recent and prior tobacco use, environmental exposure (air pollution and passive smoking), diet, personal and family history of cancer, and occupational history from each participant. Peripheral blood samples (or mouthwash samples when they refused to donate blood) were collected from all participants. Coding of histology was based on 2001 WHO/IASLC. Genomic DNA was extracted based on standard protocol. The Canadian Screening Study includes the nested case-control samples from 3 screening programs: IELCAP-Toronto: Ever smokers of more than 10 pack-years age 50 and above were eligible for the I-ELCAP screening program since 2003, and a total of 4782 individuals have been enrolled in the Greater Toronto Area. Participants were administered a LDCT scan along with a standard study questionnaire at baseline. Blood samples were systematically collected at baseline since 2006. Participants who had an abnormality in a CT scan were followed up every 1 to 2 years. The screening program was organized by the Princess Margaret Hospital. PanCan: Ever smokers between the ages of 50-75 with no previous history of invasive cancer are eligible to participate in the study. The study was carried out across Canada in Vancouver, Calgary, Hamilton, Toronto, Ottawa, Quebec, Halifax, and St. John's. A total of 2537 smokers have been screened from 2008 to 2011. All study participants completed a detailed questionnaire, spirometry, collection of blood specimens for biomarker measurement and LDCT at baseline. All participants are followed for a minimum of 3 years. On yearly follow up, an updated shorter questionnaire is administered, blood is collected and CT scans are performed. Blood samples are available from all 2537 individuals. BCCA Screening Program: From 1990 to 2007, 4274 smokers above 40 years old who had smoked 20 pack-years or more were enrolled at BCCA. Upon enrollment, subjects completed a questionnaire for their lifestyle and medical history. Baseline spirometry was conducted using a flow-sensitive spirometer in accordance with the American Thoracic Society recommendations. Since 2000, a LDCT was obtained in 2440 individuals. The participants were followed prospectively to determine whether they developed lung cancer. A total of 9759 individuals participated in the CT screening program in Canada from these 3 programs. The samples included in this project is based on a subset of nested lung cancer case-control pairs based on 1:2 ratio. The Carotene and Retinol Efficacy Trial (CARET) was a randomized, double-blind, placebo-controlled trial of the cancer prevention efficacy and safety of a daily combination of 30 mg of beta-carotene and 25,000 IU of retinyl palmitate in 18,314 persons at high risk for lung cancer. CARET began in 1985, and the intervention was halted in January 1996, 21 months ahead of schedule, with the twin conclusions for definitive evidence of no benefit and substantial evidence of a harmful effect of the intervention on both lung cancer incidence and total mortality. CARET continued to follow and collect endpoints on their participants through 2005. Pathology reports and medical records were reviewed to confirm cancer endpoints, and death certificates obtained to capture cause of death. During the active intervention phase of CARET, serum, plasma, whole blood, and lung tissue specimens were collected on participants. These biospecimens make up the CARET Biorepository. For the OncoArray Project, CARET provided DNA extracted from whole blood of lung cancer cases and controls matched on age at baseline (± 4 years), sex, race, baseline smoking status, history of occupational asbestos exposure (asbestos vs heavy smoker), and year of enrollment (2-year intervals). The European Prospective Investigation into Cancer and Nutrition (EPIC) study is a multi-center cohort study involving 521,000 study participants from 10 European countries. The current study involved EPIC participants from 7 countries (Greece, Netherlands, UK, France, Germany, Spain, and Italy), including 1223 incident lung cancer cases and 1249 smoking matched controls. The Kentucky Lung Cancer Research Initiative is a study conducted by the Markey Cancer Center Cancer Center and the University of Kentucky using a population-based, case-control framework to study the extraordinarily high rates of lung cancer in Southeastern, Appalachian Kentucky. Cancer cases were recruited from the Kentucky Cancer Registry at the time of diagnosis and controls were recruited from a random digit dialing process from the same region. Study accrual began in January 5, 2012 and completed on September 5, 2014 and 520 subjects were recruited in a 4:1 ratio of controls: cases from Appalachian Kentucky. Of the 520 subjects recruited, 231 are included in the OncoArray analysis, including all 93 cancer cases, and 123 controls. Newly diagnosed lung cancer cases and controls underwent blood, toenail (for trace element analysis), urine, buffy coat, water, soil, and radon collection, residence GPS mapping, as well as an extensive epidemiologic, occupational, and health history questionnaire (Clinical Trials.gov Identifier: NCT01648166). The Harvard Lung Cancer Study (HLCS) is a case-control study based at Mass General Hospital (MGH) in Boston, Massachusetts from 1992 to 2004. Details of the study were described previously. Briefly, eligible cases included any person over the age of 18 years with a diagnosis of primary lung cancer that was further confirmed by an MGH lung pathologist. Controls were recruited from the friends or spouses of cancer patients or the friends or spouses of other surgery patients in the same hospital. Potential controls were excluded from participation if they had a diagnosis of any cancer (other than non-melanoma skin cancer). Interviewer-administered questionnaires, a modified version of the standardized American Thoracic Society respiratory questionnaire, collected information on demographics, medical history, family history of cancer, smoking history, and a detailed work history, including job titles and tasks. Genome-wide genotype data were first generated using Illumina Human 610-Quad BeadChips and then imputed by MACH against the 1000 Genome Project dataset (http://browser.1000genomes.org/index.html). The Institutional Review Board of MGH and the Human Subjects Committee of the Harvard School of Public Health approved the study. The Israel study (NICCC-LCA) is an ongoing case-control study of newly diagnosed lung cancer cases of any histology and population age/sex/ethnicity-matched "healthy" controls. All participants undergo face-to-face interviews, provide a venous blood sample (separated into DNA, Sera, lymphocytes) after signing an IRB-approved form. Histology reports, FFPE blocks and clinical follow-up are available for most cancer cases. The MD Anderson Cancer Center (MDACC) Study. Lung cancer cases and frequency-matched controls were ascertained from a large ongoing case-control study at the University of Texas MD Anderson Cancer Center (UTMDACC) since 1991. Detailed study description was provided previously (Spitz et al 2007). In brief, cases were newly-diagnosed and histologically confirmed lung cancer patients recruited from UTMDACC. Controls were healthy individuals without a history of cancer (except for nonmelanoma skin cancer) and recruited from the Kelsey-Seybold Clinics, the largest private multispecialty physician group in the Houston metropolitan area. Controls were frequency-matched to cases on age (±5 years), sex, and race/ethnicity. After providing written informed consent, each study participants completed an in-person interview by staff interviewers to collect information on demographics, smoking status, etc. Blood samples were also drawn from all the study participants. This study was approved by institutional review boards of UTMDACC and Kelsey-Seybold Clinics. The Malmö Diet and Cancer Study (MDCS) is a population-based prospective cohort study that recruited men and women aged at 44 to 74 years old of living in Malmö, Sweden between 1991 and 1996. The main goal of the MDCS is to study the impact of diet on cancer incidence and mortality. It consists of a baseline examination including dietary assessment, a self-administered questionnaire, anthropometric measurements and collection of blood samples. A total of 165 incident lung cancer cases and 174 individually smoking-matched controls were available for this analysis. The Multiethnic Cohort (MEC) Study includes 215,251 men and women aged 45-74 years at recruitment, primarily from five ethnic/racial groups - African Americans and Latinos mostly recruited from CA (mainly from Los Angeles County) and Japanese Americans, Native Hawaiians and whites (mostly recruited from HI). The cohort was assembled in 1993-1996 by mailing a self-administered questionnaire to persons identified primarily through driver's license files. The baseline questionnaire obtained information on demographics, anthropometry, smoking history, medical and reproductive histories, family history of cancer, diet and physical activity. Incident cancer cases are identified by regular linkage with the State of California Cancer Registry and the Hawaii Tumor Registry, both members of the SEER Program of the NCI. In 2001-2006, a prospective biorepository was assembled by collecting a pre-diagnostic blood specimen from 67,594 surviving MEC members. At the time of blood collection a short questionnaire was administered that included information on smoking during the previous 15 days. For this study, cases were all lung cancer cases incident to blood draw and diagnosed before December 2012. For each case, a control was selected among unaffected MEC participants who were alive at time of the case's diagnosis and matched on study site, sex, race/ethnicity, age (age at diagnosis for cases; age at blood collection for controls), and date of blood collection. The Mount-Sinai Hospital-Princess Margaret Study (MSH-PMH) was conducted in the greater Toronto area from 2008 to 2013. Lung cancer cases were recruited at the hospitals in the network of the University of Toronto. Controls were selected randomly from individuals registered in the family medicine clinics databases and were frequency matched with cases on age and sex. All subjects were interviewed, and information on lifestyle risk factors, occupational history and medical and family history was collected using a standard questionnaire. Tumors were centrally reviewed by the reference pathologist, a member of the International Association for the Study of Lung Cancer (IASLC) committee, and a second pathologist in the University Health Network. If the reviews conflicted, a consensus was arrived at after discussion. Coding of histology was based on 2001 WHO/IASLC. Genomic DNA was extracted based on standard protocol. The New England Lung Cancer Study (NELCS) is a population-based case-control study of lung cancer among residents of Northern and Central New Hampshire counties and the bordering region of Vermont. Cases with histologically confirmed primary incident lung cancer were identified from 2005 to 2007 using the New Hampshire State Cancer Registry and the Dartmouth-Hitchcock Medical Center (DHMC) Tumor Registry. Control participants were identified using a commercial database and matched to lung cancer cases within 5-year age groups, sex and county. Genomic DNA was isolated from blood or buccal specimens provided by consenting participants. The study complied with requirements of the Dartmouth College's Committee for Protection of Human Subjects. The Nijmegen Lung Cancer Study. The Netherlands patients with lung cancer were identified through the population-based cancer registry of the Netherlands Comprehensive Cancer Organisation in Nijmegen, the Netherlands. Patients who were diagnosed in one of three hospitals (Radboud University Medical Center, Canisius Wilhelmina Hospital in Nijmegen, and Rijnstate Hospital in Arnhem) since 1989 and who were still alive at April 15th, 2008 were recruited for a study on gene-environment interactions in lung cancer. 458 patients gave informed consent and donated a blood sample. This case series was expanded with 94 patients to a total of 552 by linking three other studies to the population-based cancer registry in order to identify new occurrences of lung cancer among the participants of these other studies. All three other studies (i.e., POLYGENE, the Nijmegen Biomedical Study, and the Radboudumc Urology Outpatient Clinic Epidemiology Study) were initiated to study genetic risk factors for disease and participants to these studies gave general informed consent for DNA-related research and linkage with disease registries. Information on histology, stage of disease, and age at diagnoses was obtained through the cancer registry. Lifestyle information was collected through a structured questionnaire and whole blood for DNA isolation was collected by the regional thrombosis services. The cancer-free controls (46% males) were selected from participants of the "Nijmegen Biomedical Study" (NBS), an age- and sex-stratified random sample of the general population of the municipality of Nijmegen, The Netherlands. All participants provided extensive lifestyle information by structured questionnaires and blood samples for DNA isolation, serum and plasma. All controls are of self-reported European descent. The study protocols of the NBS were approved by the Institutional Review Board of the Radboudumc and all study subjects signed a written informed consent form. The Northern Sweden Health and Disease Study (NSHDS) encompasses several prospective cohorts. The current study involves participants from the Västerbotten Intervention Project (VIP), a sub-cohort within NSHDS. VIP is an ongoing prospective cohort and intervention study intended for health promotion of the general population of the Västerbotten County in northern Sweden. VIP was initiated in 1985 and all residents in the Västerbotten County were invited to participate by attending a health check-up at 40, 50 and 60 years of age. Participants were asked to complete a self-administered questionnaire including various demographic factors such as education, smoking habits, physical activity and diet. In addition, height and weight were measured and participants were asked to donate a fasting blood sample for future research. A total of 243 incident lung cancer cases and 266 individually smoking-matched controls were available for this analysis. Norway National Institute of Occupational Health Study. Early-stage NSCLC cases and healthy controls at the time of enrollment were Caucasians of Norwegian origin and were recruited from the same geographical region (Western Norway). The patients were enrolled in the study, whenever practically feasible among patients admitted for lung cancer at the Haukeland University Hospital in Bergen, Norway. The informed written consents covering analysis of molecular and genetic markers was signed by the patients prior to surgery. Only patients with histologically confirmed early-stage NSCLC were included in our study. The subjects included in this project are a subgroup recruited into the project "lung cancer genetics" at NIOH. The controls were recruited from the same geographical region of Western Norway and frequency-matched with cases on cumulative smoking dose (pack-years). Pack-years smoked [( 20 cigarettes per day) x years smoked] were calculated to indicate the cumulative smoking dose. The Cases and controls were interviewed using similar questionnaires and were categorized as never smokers, ex-smokers or current smokers. Never smokers are subjects indicating having smoked less than 100 cigarettes in their life time. Ex-smokers were defined as those having quitted at least 1 year before sampling, and current smokers were those indicating that they were smokers at the time of sampling. The project has been approved by the Regional Committee for Medical and Health Research Ethics in Southern Norway in accordance with the WMA Declaration of Helsinki. The ethical approval covered access to the NSCLC databank. The Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) Study, a randomized trial aimed at evaluating the efficacy of screening in reducing cancer mortality, recruited approximately 155,000 men and women age 55 to 74 years from 1992 to 20014. Screening for lung cancer among participants in the intervention arm included a chest x-ray at baseline followed by either three annual x-rays (for current or former smokers at enrollment) or two annual x-rays (for never smokers); participants in the control arm received routine health care. Screening-arm participants provided data on sociodemographic factors, smoking behavior, anthropometric characteristics, medical history, and family history of cancer, as well as blood samples annually for the first 6 years of the study (baseline T0 and T1 through T5). Lung cancers were ascertained through annual questionnaires mailed to the participants, and positive reports were followed up by abstracting medical records or death certificates. Follow-up in the trial as of July 2009 was 96.7%. Patients were excluded because of missing baseline questionnaire, previous history of any cancer, diagnosis of multiple cancers during follow-up, missing smoking information at baseline, missing consent for utilization of biologic specimens for etiologic studies, or unavailability/insufficient quantity of serum or DNA specimens. The Resource for the Study of Lung Cancer Epidemiology in North Trent (ReSoLuCENT) is an ongoing study conducted in Sheffield from 2006 and due to complete recruitment in 2016. The study recruited pathologically confirmed lung cancer cases diagnosed at age 60 years or younger and family matched controls. Lung cancer cases diagnosed at ages older than 60 years were recruited if they reported a family history of lung cancer. The cases and matched controls were recruited through several major cancer treatment centers, however, the majority were recruited in North Trent. All participants completed a detailed lifestyle questionnaire which included questions about occupational exposures, education, medical history and family history of cancer and lung disease. Participants also donated blood samples for DNA extraction. The ReSoLuCENT study has been funded by the Sheffield Hospitals Charity, Sheffield ECMC and Weston Park Hospital Cancer Charity. First degree relatives were removed from the sample deposited to dbGaP. The Roy Castle Lung Study of Liverpool Lung Project (LLP) is a case-control and cohort study which has recruited over 11,500 individuals since 1996 from the Liverpool region in the UK. Detailed epidemiological and clinical data is collected with associated specimens (i.e. tumor tissue, blood, plasma, sputum, bronchial lavage and oral brushings). The participants have completed a detailed lifestyle questionnaire at recruitment, with repeat questionnaires at intervals; updated data on clinical outcome and hospital events are collected through the Health and Social Care Information Center (including Office of National Statistics mortality data, Cancer Registry and Health Episode Statistics). The project is registered on the UK National Institute for Health Research (NIHR) lung cancer portfolio and has all the required ethical approvals and sponsorship arrangements in place. The lung tumors were reviewed by the reference pathologist. The Seoul Bundang Lung Cancer Study was conducted between 2005 and 2010 to discover genetic and environmental factors related with lung cancer development. Lung cancer cases were recruited at the Seoul National University Hospital in Bundang. Controls were selected randomly from individuals participated in health check-up program and were frequency matched with cases on age and sex. All subjects were interviewed, and information on lifestyle risk factors, occupational history and medical and family history was collected using a standard questionnaire. Tumors were reviewed by the pathologists in the hospital. If the reviews conflicted, a consensus was arrived at after discussion. Coding of histology was based on 2001 WHO/IASLC. Genomic DNA was extracted based on standard protocol. The Shanghai Cohort Study (SCS) consisted of 18,244 men in Shanghai, China, who were 45-64 years old at the time of enrollment during 1986-1989. Approximately 80% of eligible men participated in the study. At the time of recruitment, each cohort subject was interviewed in-person by a trained nurse interviewer using a structured questionnaire that included background information, history of tobacco and alcohol use, current diet, and medical history. At the completion of the interview, the nurse collected a 10 ml blood and a single void urine specimen from the study participant. The buccal cell samples were collected from all surviving cohort members (~15,000) in the 2001-2002 follow-up interviews. The cohort has been followed for the occurrence of cancer and death through routine ascertainment of new cases from the population-based Shanghai Cancer Registry and Shanghai Vital Statistics Units. To maximize the cancer findings and minimize the loss of follow-up, we contacted each surviving cohort member annually. Retired nurses visit the last known address of each living cohort member and record details of the interim health history of the cohort member. As of December 31, 2014, cumulatively 612 (3.4%) original subjects were lost to follow-up, and 574 (3.1%) refused to our continued follow-up interview. A nested case-control study of incident lung cancer cases within the Shanghai Cohort Study was used to examine the association between serum levels of vitamin B6 and other compounds in the one-carbon metabolism pathway and risk of lung cancer. Briefly, 516 lung cancer cases were identified among cohort participants with available serum samples as of 12/31/2006. For each case, we randomly selected one control subject from all cohort members who were free of cancer and alive at the time of cancer diagnosis of the index case. Controls were matched to the index case by age at enrollment (±2 years), date of biospecimen collection (±1 month) and neighborhood of residence at recruitment, and smoking status (current, former and never smokers) as established previously for other studies. For former smokers, cases and controls were further matched by years since quitting smoking (<10 vs ≥10 years). One serum vial per subject was retrieved from biorepository and all serum samples were sent to the laboratory (B-vital) for measurements. DNA samples of 250 lung cancer cases and 250 matched controls were available for the present study. The Singapore Chinese Health Study (SCHS) cohort consisted of 63,257 Chinese men and women in Singapore when they were 45-74 years old at the time of enrollment between April 1993 and December 1998. At recruitment, each study subject was interviewed in person by a trained interviewer using a structured questionnaire that emphasized current diet assessed via a validated, 165-item food frequency questionnaire. The questionnaire also requested information on demographics, lifetime use of tobacco, incense use, current physical activity, usual sleep duration, reproductive history (women only), occupational exposure, medical history, and family history of cancer. Blood or buccal cell, and spot urine samples were collected first from a random 3% sample of cohort participants in April 1994, and extended to all surviving cohort participants starting in January 2000. Overall approximately 60% of eligible cohort participants donated biospecimens. The cohort has been passively followed for death and cancer occurrence through regular record linkage with the population-based Singapore Cancer Registry and the Singapore Registry of Births and Deaths. Migration out of Singapore, especially among housing estate residents, was negligible. As of latest update, only 55 individuals from this cohort were known to be lost to follow-up due to migration and other reason. A nested case-control study of incident lung cancer cases within the Singapore Chinese Health Study was used to examine the association between serum levels of vitamin B6 and other compounds in the one-carbon metabolism pathway and risk of lung cancer. As of 12/31/2011, 422 lung cancer cases were identified among cohort participants with available prediagnostic plasma samples. For each case, one control subject was randomly selected from all eligible cohort members who were alive and free of cancer on the date of cancer diagnosis of the index case. The control subject was individually matched to the index case by gender, dialect group (Hokkien, Cantonese), age at enrollment (±3 years), date of baseline interview (±2 year), date of biospecimen collection (±6 months), and smoking status (current, former, and never smokers). For current smokers, cases and controls were further matched by number of cigarettes per day (<15, ≥15 cigarettes/day). For former smokers, cases and controls were further matched by years since quitting smoking (<10, ≥10 years). One plasma aliquot per subject was retrieved from the biorepository and all plasma samples were sent to the laboratory (B-vital) for measurements, and one aliquot of DNA per subject for the present study. The International Agency for Research on Cancer (IARC) L2 Study. Lung cancer cases and controls were recruited through a multicentric case-control study coordinated by the IARC in Russia, Poland, Serbia, Czech Republic, and Romania from 2005 to 2013. Cases were incident cancer patients collected from general hospitals. Controls were recruited from individuals visiting general hospitals and out-patient clinics for disorders unrelated to lung cancer and/or its associated risk factors, or from the general population. Information on lifestyle risk factors, medical and family history was collected from subjects by interview using a standard questionnaire. All study participants provided written informed consent. The current study included 1,133 lung cancer cases and 1,117 controls genotyped on the Oncoarray. The Washington State University Lung Cancer Study is a hospital case-control study of 511 subjects with newly-diagnosed (within 1 year of diagnosis) lung cancer and 820 race-, sex- and age-matched controls. Lung cancer cases were recruited from lung cancer clinics within the H. Lee Moffitt Cancer Center while controls were recruited from the Lifetime Cancer Screening Center, a H. Lee Moffitt Cancer Center affiliate. None of the controls were diagnosed with any form of cancer at the time of screening. Detailed questionnaire data and oral buccal cells were collected for all subjects. The Total Lung Cancer (TLC) Study is a hospital-based study that included 458 lung cancer patients recruited for Moffitt Cancer Center's Total Cancer Care™ protocol between April 2006 and August 2010. Total Cancer Care™ is a multi-institutional observational study of cancer patients that prospectively collects self-reported demographic and clinical data, medical record information and blood samples for research purposes. All patients used in this cohort were recruited from the Thoracic Oncology Clinic at the Moffitt Cancer Center. The Vanderbilt Lung Cancer Study (BioVU) is a case-control study nested within the Vanderbilt University Medical Center biobank, BioVU. BioVU is a biorepository of DNA extracted from blood drawn from patients seeking routine clinical care at Vanderbilt University Medical Center and linked to de-identified electronic health records for research purposes. Lung cancer cases and controls were identified from BioVU participants in February 2014. Lung cancer cases were identified from the Vanderbilt tumor registry. All specimens undergo pathologic review for determination of morphology. Coding of histology was based on SEER Program Coding Guidelines. Controls were randomly selected from BioVU participants, excluding cancer patients, and were matched to cases on age (± 5 years), sex, and race. Relevant covariates were identified from electronic health records using natural language processing. Genomic DNA was extracted based on a standard protocol.

Study phs001273

Illumina HumanCoreExome genotyping data from the TEENAGE (TEENs of Attica: Genes and Environment) study.

The TEENAGE study is a cross-sectional study comprising healthy Greek adolescents. The study was conducted according to the guidelines specified in the Declaration of Helsinki and all procedures involving human subjects were approved by the Institutional Review Board of Harokopio University and the Greek Ministry of Education, Lifelong Learning and Religious Affairs. The TEENAGE study target population comprised adolescent students aged 13 to 15 years attending the first three classes of public secondary schools located in the wider Athens area of Attica. The regions across Attica from which students were recruited were physically similar and all urban in nature. Sampling of regions and schools selected to participate was random. Students were enrolled from the wider urban region to ensure that they were coming from families with varying educational background and socio-economic status. Moreover, in order to exclude any vast economic disparities, all participating schools were exclusively public schools, which are free of charge. A total of twenty-four schools participated in the study out of 285 junior secondary public schools in Attica. Anthropometric, medical and dietary information was obtained. DNA samples were genotyped using Illumina HumanCoreExome BeadChips (Illumina, San Diego, CA, USA) at the Wellcome Trust Sanger Institute, Hinxton, UK. Genotypes were called using GenCall (Illumina Genome Studio) followed by zCall and quality control (QC) was performed in two stages (pre- and post-zCall).

Study EGAS00001001001

HGSC WGS for the study Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

HGSC cases in the OvCaRe and CRCHUM Tumour Banks were selected according to the following criteria: (i) were administered platinum taxane based therapy; (ii) relapsed within 12 months (365 days) or had at least longer than 4.5 years (1642.5 days) follow-up data; (iii) had at least 50% tumour content by H&E staining and expert pathology review. All cases were re-reviewed by expert pathologists to confirm the diagnosis of HGSC. Germline BRCA1 and BRCA2 was determined for all patients through hereditary cancer screening programs. The design of cases selection as a discovery cohort was engineered to amplify biological differences by selecting cases from the extremes of the outcome distribution. All HGSC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome.

Dataset EGAD00001003268

ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA

Background Liquid biopsies, and the dynamic tracking of somatic mutations within circulating tumour DNA (ctDNA) can provide insight into the dynamics of cancer evolution and the intra-tumour heterogeneity that fuels treatment resistance. However, identifying and tracking dynamic changes in somatic copy-number alterations (SCNAs), which have been associated with poor outcome and metastasis, using ctDNA is challenging. Pancreatic adenocarcinoma is a disease which has been considered to harbour early punctuated events in its evolution, leading to an early fitness peak, with minimal further subclonal evolution. Methods To interrogate the role of SCNAs in pancreatic adenocarcinoma cancer evolution, we applied whole-exome sequencing of 55 longitudinal cell-free DNA (cfDNA) samples taken from 24 patients (including 8 from whom a patient-derived xenograft (PDX) was derived) with metastatic disease prospectively recruited into a clinical trial. We developed a method, Aneuploidy in Circulating Tumour DNA (ACT-Discover), that leverages haplotype phasing of paired tumour biopsies or PDXs to identify SCNAs in cfDNA with greater sensitivity. Results SCNAs were observed within 28 of 47 evaluable cfDNA samples. Of these events, 30% could only be identified by harnessing the haplotype-aware approach leveraged in ACT-Discover. The exceptional purity of PDX tumours enabled near-complete phasing of genomic regions in allelic imbalance, highlighting an important auxiliary function of PDXs. Finally, although the classical model of pancreatic cancer evolution emphasises the importance of early, homogenous somatic events as a key requirement for cancer development, ACT-Discover identified substantial heterogeneity of SCNAs, including parallel focal and arm-level events, affecting different parental alleles within individual tumours. Indeed, ongoing acquisition of SCNAs was identified within tumours throughout the disease course, including within an untreated metastatic tumour. Conclusions This work demonstrates the power of haplotype phasing to study genomic variation in cfDNA samples and reveals undiscovered intra-tumour heterogeneity with important scientific and clinical implications. Implementation of ACT-Discover could lead to important insights from existing cohorts, or underpin future prospective studies seeking to characterise the landscape of tumour evolution through liquid biopsy.

Study EGAS00001007077

Cell-free DNA analysis reveals POLR1D-mediated resistance to bevacizumab in colorectal cancer

Bevacizumab is an approved anti-angiogenic drug for patients with metastasized colorectal cancer (mCRC) targeting VEGF. The survival benefit of anti-VEGF therapy in mCRC patients is limited to a few months and acquired resistance mechanisms are greatly unknown. Using plasma DNA, we studied the evolution of tumor genomes in a cohort of patients with mCRC (n=150) and observed a recurrent focal amplification (8.7% of cases) on chromosome 13q12.2. Analysis of TCGA data (n=619) suggested an association with later stages, which we confirmed by longitudinal plasma analyses. We defined the minimally amplified region and studied the mechanistic consequences of copy number gain of the involved genes. The amplification of one gene, POLR1D, impacted cell proliferation, resulting in upregulation of VEGFA, an important regulator of angiogenesis which has been implicated in the resistance to bevacizumab. In several patients, we observed the emergence of this 13q12.2 amplicon under bevacizumab treatment, which was invariably associated with evolution of therapy resistance. Hence, we describe a novel resistance mechanism against a widely applied treatment in mCRC patients which will impact clinical management

Study EGAS00001003791

Poland Opole Voivodeship WGS

This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Genome Sequencing of 10 samples (5 female, 5 male of Opole Voivodeship, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

Dataset EGAD50000000124

Poland Podlaskie Voivodeship WGS

This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Genome Sequencing of 12 samples (6 female, 6 male of Podlaskie Voivodeship, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

Dataset EGAD50000000125

Poland Lubusz Voivodeship WGS

This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Genome Sequencing of 19 samples (8 female, 11 male of Lubusz Voivodeship, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

Dataset EGAD50000000127

Poland Holy Cross Voivodeship - WGS

This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Genome Sequencing of 6 samples (6 female of Holy Cross Voivodeship, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

Dataset EGAD50000000162

Poland Warmian-Mazurian Voivodeship WGS

This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Genome Sequencing of 15 samples (8 female, 7 male of Warmian-Mazurian Voivodeship, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

Dataset EGAD50000000128

Poland Lublin Voivodeship - WGS

This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Genome Sequencing of 24 samples (14 female, 10 male of Lublin Voivodeship, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

Dataset EGAD50000000155

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