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dbGaP phs000931 DMET Genes, Nicotine Metabolism and Prospective Abstinence - pht009405.v1.p1

- 27/11/24 - 7 formularios, 1 itemgroup, 7 items, 1 idioma

Itemgroup: pht009405

pht009401.v1.p1

1 itemgroup 7 items

Eligibility

1 itemgroup 7 items

pht009400.v1.p1

1 itemgroup 2 items

pht009402.v1.p1

1 itemgroup 2 items

pht009403.v1.p1

1 itemgroup 17 items

pht009404.v1.p1

1 itemgroup 11 items

dbGaP phs000942 Use of WGS for Diagnosis and Discovery in the Cancer Genetics Clinic - Eligibility

- 27/11/24 - 5 formularios, 1 itemgroup, 1 item, 1 idioma

Itemgroup: IG.elig

Principal Investigator: Theodora S. Ross, MD, PhD, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA, and Department of Cancer Genetics, UT Southwestern Medical Center, Dallas, TX, USA MeSH: Neoplasms,Breast Neoplasms,Ovarian Neoplasms,Peritoneal Neoplasms,Skin Neoplasms,Esophageal Neoplasms,Thyroid Neoplasms,Urinary Bladder Neoplasms,Endometrial Neoplasms,Fallopian Tube Neoplasms,Melanoma,Testicular Neoplasms,Bile Duct Neoplasms,Lung Neoplasms,Colonic Neoplasms,Adrenocortical Carcinoma,Carcinoma, Renal Cell,Colonic Polyps,Adenomatous Polyposis Coli,Lymphoma, Large B-Cell, Diffuse,Pheochromocytoma,Paraganglioma,Leiomyoma,Hemangioblastoma,Hyperparathyroidism,Pancreatic Neoplasms,Vulvar Neoplasms,Brain Neoplasms,Liver Neoplasms,Kidney Neoplasms,Prostatic Neoplasms,Glioblastoma,Oncocytoma, renal https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000942 Despite the potential of whole-genome sequencing (WGS) to improve patient diagnosis and care, the empirical value of WGS in the cancer genetics clinic is unknown. We performed WGS on members of two cohorts of cancer genetics patients: those with BRCA1/2 mutations (n = 176) and those without (n = 82). Initial analysis of potentially pathogenic variants (PPVs, defined as nonsynonymous variants with allele frequency 1% in ESP6500) in 163 clinically-relevant genes suggested that WGS will provide useful clinical results. This is despite the fact that a majority of PPVs were novel missense variants likely to be classified as variants of unknown significance (VUS). Furthermore, previously reported pathogenic missense variants did not always associate with their predicted diseases in our patients. This suggests that the clinical use of WGS will require large-scale efforts to consolidate WGS and patient data to improve accuracy of interpretation of rare variants. While loss-of-function (LoF) variants represented only a small fraction of PPVs, WGS identified additional cancer risk LoF PPVs in patients with known BRCA1/2 mutations and led to cancer risk diagnoses in 21% of non-BRCA cancer genetics patients after expanding our analysis to 3209 ClinVar genes. These data illustrate how WGS can be used to improve our ability to discover patients' cancer genetic risks. "Reprinted from doi:10.1016/j.ebiom.2014.12.003, with permission from EBioMedicine."

pht004834.v1.p1

1 itemgroup 5 items

pht004835.v1.p1

1 itemgroup 5 items

pht004836.v1.p1

1 itemgroup 16 items

pht004837.v1.p1

1 itemgroup 5 items

dbGaP phs000876 Transdisciplinary Research Into Cancer of the Lung (TRICL) - Eligibility

- 26/3/24 - 7 formularios, 1 itemgroup, 3 items, 1 idioma

Itemgroup: IG.elig

Principal Investigator: Christopher Amos, National Institutes of Health, Bethesda, MD, USA MeSH: Lung Neoplasms,Adenocarcinoma,Neoplasms, Squamous Cell https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000876 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 sub-studies. The sub-studies that contributed include Harvard, Liverpool, Toronto, and IARC. The IARC and Toronto studies are described above. A description of the Harvard and Liverpool studies is provided below. **Liverpool Lung Project:** The Liverpool Lung Project (LLP)1 is a case control and cohort study, which has over 11,500 individuals, with detailed epidemiological, clinical and outcome data with associated specimens (i.e. tumour tissue, blood, plasma, sputum, bronchial lavage, EBUS and oral brushings). The participants have completed a detailed lifestyle questionnaire and updated data on clinical outcome and hospital events are collected through the Office of National Statistics, Cancer Registry and from 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 LLP has detailed standard operating procedures (SOP) for all aspects of the recruitment, data, specimen collection as well as the data storage. The LLP Cohort study has 8,224 participants with blood and 7,761 with plasma samples. The LLP case-control samples have been incorporated into in a large number of international GWAS and molecular studies sup2,3/sup, methylation sup4-7/sup, microRNA sup8/supand next generation studies sup9-11/sup, resulting in high ranking publications, as well as forming the basis for the LLP risk prediction model sup12-14/sup which has been utilised in the UK lung cancer screening trial (UKLS) sup15-17/sup Patient and control DNAs were derived from EDTA-venous blood samples. *Harvard Samples.* David Christiani at the Harvard University School of Public Health has been directing research studies to investigate etiological factors influencing lung cancer development since 1983 and has amassed a collection of 2000 controls and 5055 lung cancer cases. He has been actively collecting and storing snap frozen tumor samples since 1992. Around 1500 tumor samples have been collected and the average wet tumor yield is about 30 grams of tumor, of which 631 cases have completely annotated clinical and survival information. Pathology confirmation is provided by two pathologists. At the time of surgery, a minimum of 30 grams of wet lung tumor tissue and 30 grams of non-involved tissue from the same lobe is sectioned, flash frozen and sent to Dr. Christiani's lab for logging and storage. A blood sample for DNA and serum is collected. A structured interview by trained research staff is conducted on each case, and clinical outcomes and treatments is extracted and entered into the molecular epidemiology data base at Harvard. Fresh frozen samples have been collected from 1451 lung cancer and are available for study. Samples from this collaborative study have played key roles in major studies, including the initial finding describing EGFR mutations in lung cancer sub22/sub. Participants in this study are patients, 18 years of age, with newly diagnosed histologically confirmed lung cancer. Samples that are included in the analysis have the following histologies: Adenocarcinoma: 8140/3, 8250/3, 8260/3, 8310/3, 8480/3 8560/3; LCC: 8012/3, 8031/3; squamous carcinoma: 8070/3, 8071/3, 8072/3, 8074/3; and other NSCLC: 8010/3, 8020/3, 8021/3, 8032/3, 8230/3. *The Toronto Study:* The Toronto study was conducted in the Great Toronto Area between 1997 and 2014. Cases were recruited at the hospitals in the network of University of Toronto and Lunenfeld- Tanenbaum Research Institute. At the time of recruitment in the clinical setting, provisional diagnoses of lung carcinoma were first assigned based on clinical criteria. Diagnoses for all cases included were histologically confirmed by the reference pathologist who is a specialist in pulmonary pathology, based on review of pathology reports from surgery, biopsy or cytology samples in 100% of cases. Diagnostic classification was done initially according to ICD-9, ICD-10, and ICD for oncology-2, and subsequently converted to ICD-O-3. Tumors were grouped into the major categories included in this analysis according to primary cancer type based on the ICD-3 definitions. Controls were randomly selected from individual visiting family medicine clinics and Ministry of Finance Municipal Tax Tapes. All subjects were interviewed using a standard questionnaire and information on lifestyle risk factors, occupational history, medical and family history was collected. Blood samples were collected from more than 85% of the subjects. *IARC:* The IARC data are derived from case-control studies conducted in Russia and include samples that have available tissue samples. Patient and control DNAs were derived from EDTA-venous blood samples. The lung cancer patients were classified according to ICD-O-3; SQ: 8070/3, 8071/3, 8072/3, 8074/3; AD: 8140/3, 8250/3, 8260/3, 8310/3, 8480/3, 8560/3, 8251/3, 8490/3, 8570/3, 8574/3; with tumous with overlapping histologies classified as mixed. *The Lung Cancer Transdisciplinary Research Cohort is utilized in the following dbGaP sub-studies.* To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" section of this top-level study page phs000876 Lung Cancer Transdisciplinary Research Cohort.- phs000877 Meta Analysis - phs000878 CIDR Lung Cancer - phs001681 Affy Axiom Array

pht005185.v2.p1

1 itemgroup 6 items

pht009909.v1.p1

1 itemgroup 5 items

pht009910.v1.p1

1 itemgroup 6 items

pht005542.v1.p1

1 itemgroup 9 items

pht005186.v1.p1

1 itemgroup 5 items

pht005184.v2.p1

1 itemgroup 5 items

dbGaP phs001075 Sequencing to Guide Cancer Care (CanSeq) - pht006108.v1.p1

- 23/6/23 - 4 formularios, 1 itemgroup, 3 items, 1 idioma

Itemgroup: pht006108

Principal Investigator: Levi Garraway, Dana Farber Cancer Institute, Boston, MA, USA MeSH: Neoplasms,Colonic Neoplasms,Lung Neoplasms,Adenocarcinoma of lung https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001075 The overall goal of the CanSeq U01 project is to study the impact of whole-exome sequencing (WES) on the clinical care of cancer patients and oncology provider practices. The aims of Project 1 are to implement and establish the feasibility of germline and somatic WES in patients with advanced solid tumors (lung and colon); to develop a framework for interpreting and reporting for exome sequencing data; to determine the proportion of patients with "actionable items" compared to existing technologies; and to report on the percentage of patients in whom unique WES findings led to a clinical action. The aims of Project 2 are to implement a production-scale platform for WES from archival (FFPE) material; to identify biologically relevant somatic and germline alterations existing in tumor/normal DNA from individual patients; to produce an evidence-based list of clinically "actionable" genetic alterations; and to develop inferential models that predict the utility of tumor genomic data within the larger clinical context. The goals of Project 3 are to describe the impact of information derived through WES on cancer patients; to test the hypothesis that patients will want to receive information about all potentially informative somatic and germline variants; to study patients' understanding of disclosed genomic information; and to describe the experiences of oncology providers as they implement WES into cancer care delivery.

pht006109.v1.p1

1 itemgroup 3 items

pht006111.v1.p1

1 itemgroup 3 items

pht006110.v1.p1

1 itemgroup 2 items

dbGaP phs001192 Thoracic Patient-Derived Xenografts - pht005690.v1.p1

- 1/6/23 - 3 formularios, 1 itemgroup, 5 items, 1 idioma

Itemgroup: pht005690

Principal Investigator: John Thomas Poirier, PhD, Memorial Sloan Kettering Cancer Center, New York, NY, USA MeSH: Lung Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001192 Targeted capture sequencing of 341 cancer associated genes in thoracic patient-derived xenografts.

Lung Neoplasms

pht005691.v1.p1

1 itemgroup 5 items

pht005692.v1.p1

1 itemgroup 9 items

dbGaP phs001210 NCI Lung Cancer and Smoking Phenotypes in African-American Subjects - pht005961.v1.p1

- 17/5/23 - 5 formularios, 1 itemgroup, 3 items, 1 idioma

Itemgroup: pht005961

Principal Investigator: Curtis C. Harris, National Institutes of Health, Bethesda, MD, USA MeSH: Lung Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001210 This is a two-stage case-control study designed to evaluate the association between common genetic variants and the risk of lung cancer. The stage 1 studies included 1737 cases and 3602 controls from the following studies: MD Anderson Lung Cancer Epidemiology Study, The Multiethnic Cohort Study (MEC), NCI-MD Lung Cancer-Case Control Study, Northern California Lung Cancer Study, Project CHURCH (Creating a Higher Understanding of Cancer Research δ Community Health), Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO), Southern Community Cohort Study (SCCS), and the Karmanos Cancer Institute at Wayne State University (KCI/WSU). The stage 2 studies included an independent set of 866 cases and 796 controls from the following studies: The Black Women's Health Study (BWHS), The Harvard-MGH Lung Cancer Susceptibility Study (HLCS), MD Anderson Lung Cancer Epidemiology Study, MD Anderson/LBJ Hospital Biorepository, NCI-MD Lung Cancer Case-Control Study, Northern California Lung Cancer Study, Philadelphia Lung Cancer Study on Gene Environment Interactions (Plus-Gene), Southern Community Cohort Study (SCCS), and KCI/WSU.

Lung Neoplasms

pht005962.v1.p1

1 itemgroup 3 items

pht005963.v1.p1

1 itemgroup 9 items

Eligibility

1 itemgroup 1 item

pht005964.v1.p1

1 itemgroup 5 items

dbGaP phs001273 Oncoarray Consortium - Lung Cancer Studies - pht006171.v2.p2

- 30/3/23 - 5 formularios, 1 itemgroup, 3 items, 1 idioma

Itemgroup: pht006171

Principal Investigator: Christopher Amos, PhD, National Institutes of Health, Bethesda, MD, USA MeSH: Lung Neoplasms,Adenocarcinoma,Neoplasms, Squamous Cell https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001273 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. *ATBC.* The Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study (ATBC) 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 (see http://atbcstudy.cancer.gov) *CAPUA.* The CAncer de PUlmon en Asturias (CAPUA study) 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.* It 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. *CARET.* 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). *EPIC.* The European Prospective Investigation into Cancer and Nutrition (EPIC) study. 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. *Kentucky Lung Cancer Research Initiative.* 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). 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. *Israel study* (NICCC-LCA). The NICCC-LCA study 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 M.D. Anderson Cancer Center Study (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).* The Malmö Diet and Cancer Study (MDCS) is a population-based prospective cohort study that between 1991 and 1996 recruited men and women aged 44 to 74 years of age living in Malmö, Sweden. 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).* The 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. bThe Mount-Sinai Hospital-Princess Margaret Study (MSH-PMH)./b 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. bThe New England Lung Cancer Study (NELCS)./b 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 bThe Nijmegen Lung Cancer Study./b 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 and 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. bNorthern Sweden Health and Disease Study Cohort (NSHDS)./b The Northern Sweden Health and Disease Study (NSHDS) encompasses several prospective cohorts, the current study involving study 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 (12). 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. bNorway National Institute of Occupational Health Study./b 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. bPLCO./b The 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. bThe Resource for the Study of Lung Cancer Epidemiology in North Trent (REsolucent)./b 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 centres, 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. bRoy Castle Lung Study./b 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. tumour 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 tumours were reviewed by the reference pathologist. bSeoul Bundang Lung Cancer Study./b 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. bShanghai Cohort Study (SCS)./b The SCS cohort 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 have recontacted 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. bSingapore Chinese Health Study (SCHS)./b Briefly, the 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. bThe IARC L2 study./b Lung cancer cases and controls were recruited through a multicentric case-control study coordinated by the International Agency for Research on Cancer 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. bThe Washington State University Lung Cancer Study./b This 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. bTotal Lung Cancer (TLC) Study./b Molecular Epidemiology of Lung Cancer Survival: 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. bThe Vanderbilt Lung Cancer Study (BioVU)./b The Vanderbilt Lung Cancer Study 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.

pht006172.v3.p2

1 itemgroup 3 items

pht006173.v2.p2

1 itemgroup 8 items

pht006174.v2.p2

1 itemgroup 5 items

Eligibility

1 itemgroup 5 items

dbGaP phs001249 Chemosensitive Relapse in Small Cell Lung Cancer Patient-Derived Xenografts - pht006175.v1.p1

- 23/3/23 - 3 formularios, 1 itemgroup, 5 items, 1 idioma

Itemgroup: pht006175

Principal Investigator: John Thomas Poirier, PhD, Memorial Sloan Kettering Cancer Center, New York, NY, USA MeSH: Lung Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001249 Genetic and epigenetic analysis of patient-derived xenograft models of acquired chemoresistance in small cell lung cancer.

Lung Neoplasms

pht006176.v1.p1

1 itemgroup 5 items

pht006177.v1.p1

1 itemgroup 11 items

dbGaP phs000716 GWAS of Lung Cancer Susceptibility in Never-Smoking Women in Asia - Eligibility

- 14/12/22 - 5 formularios, 1 itemgroup, 3 items, 1 idioma

Itemgroup: IG.elig

Principal Investigator: Qing Lan, MD, PhD, MPH, National Institutes of Health, Bethesda, MD, USA MeSH: Lung Neoplasms,Adenocarcinoma,Squamous Cell Carcinoma https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000716 To learn about the etiology of lung cancer among never-smoking women in Asia, we formed the Female Lung Cancer Consortium in Asia (FLCCA), which includes studies of lung cancer in Eastern Asia and conducted a GWAS. We analyzed a total of 5510 lung cancer cases and 4544 controls and identified 3 novel loci (Lan et al., 2012). Of these study subjects, 4922 lung cancer cases and 3959 controls are available for posting. Lan et al.., Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia. Nat Genet. 2012 Dec;44(12):1330-5. doi: 10.1038/ng.2456. Epub 2012 Nov 11. PubMed PMID: 23143601.

pht003705.v1.p1

1 itemgroup 3 items

pht003706.v1.p1

1 itemgroup 2 items

pht003708.v1.p1

1 itemgroup 4 items

pht003707.v1.p1

1 itemgroup 7 items

dbGaP phs000728 Lung Cancer Susceptibility in Smokers - pht003768.v1.p1

- 13/12/22 - 3 formularios, 1 itemgroup, 4 items, 1 idioma

Itemgroup: pht003768

Principal Investigator: Susan K. Dutcher, PhD, Washington University School of Medicine, St. Louis, MO, USA MeSH: Lung Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000728 Over 85% of all patients diagnosed with lung cancer report a history of tobacco use, though only 10% of tobacco smokers eventually develop lung cancer. Epidemiologic studies have shown that family members of patients with lung cancer have a higher risk of developing lung cancer than controls. In an effort to identify variants associated with tobacco induced lung cancer, we have sequenced germline DNA from affected and unaffected members of families with strong histories of tobacco related lung cancer.

Lung Neoplasms

pht003766.v1.p1

1 itemgroup 2 items

pht003767.v1.p1

1 itemgroup 3 items

dbGaP phs000559 PAGE: Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project - Eligibility

- 12/12/22 - 5 formularios, 1 itemgroup, 20 items, 1 idioma

Itemgroup: IG.elig

Principal Investigator: Dana Crawford, PhD, Vanderbilt University, Nashville, TN, USA MeSH: Neoplasms,Breast Neoplasms,Colorectal Neoplasms,Endometrial Neoplasms,Lung Neoplasms,Lymphoma, Non-Hodgkin,Ovarian Neoplasms,Melanoma,Prostatic Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000559 As part of Population Architecture using Genomics and Epidemiology PAGE study (Phase I), the Epidemiologic Architecture using Genomics and Epidemiology (EAGLE I) project accessed both epidemiologic- and clinic-based collections. The epidemiologic-based collection of EAGLE I included the National Health and Nutritional Examination Surveys (NHANES), ascertained between 1991-1994 (NHANES III), 1999-2002, and 2007-2008. NHANES is a population-based cross-sectional survey now conducted every year in the United States to assess the health status of Americans at the time of ascertainment and to assess trends over the years of survey. Genetic NHANES consists of 19,613 DNA samples linked to thousands of variables including demographics, health and lifestyle variables, physical examination variables, laboratory variables, and exposures. NHANES is diverse with almost one-half of the samples (46.4%) coming from self-reported Mexican Americans and non-Hispanic blacks. In contrast to NHANES, BioVU is a clinic-based collection of 150,000 DNA samples from Vanderbilt University Medical Center linked to de-identified electronic medical records (EMRs). Approximately 12% of BioVU's overall DNA sample collection is from African American, Hispanic, and Asian patients. The overall goals of PAGE I and EAGLE I were broad and several-fold:- Replicate genome-wide association study (GWAS)- identified variants in European Americans; - Identify population-specific and trans-population genotype-phenotype associations; - Identify genetic and environmental modifiers of these associations. NHANES is an excellent resource for the study of quantitative traits associated with common human diseases. However, given that the age range of NHANES spans childhood to late adulthood and not all diseases are surveyed, NHANES is less useful for the study of adult-onset diseases such as major cancers. Therefore, under American Recovery and Reinvestment Act (ARRA) funding, EAGLE as part of PAGE I defined eight major cancers sites for genetic analysis in BioVU, Vanderbilt's biorepository linked to de-identified EMRs. The eight major cancers defined for this study included melanoma, breast, ovarian, prostate, colorectal, lung, endometrial, and Non-Hodgkin's lymphoma (NHL). Cancer cases were defined using a combination of ICD-9 codes and tumor registry entries. Controls include BioVU participants without cancer and encompassing the age and gender distributions of cancer cases. Targeted genotyping of GWAS-identified variants for these diseases (124 SNPs) and ancestry informative markers (128 AIMs) was performed by the Center for Human Genetics Research Vanderbilt DNA Resources Core. After quality control, a total of 116 cancer-associated SNPs and 122 AIMs were available for downstream analyses.

pht003614.v1.p1

1 itemgroup 2 items

pht003615.v1.p1

1 itemgroup 3 items

pht003616.v1.p1

1 itemgroup 58 items

pht003617.v1.p1

1 itemgroup 5 items

dbGaP phs000753 High Density SNP Association Analysis of Lung Cancer - Eligibility

- 7/12/22 - 5 formularios, 1 itemgroup, 4 items, 1 idioma

Itemgroup: IG.elig

Principal Investigator: Chris Amos, PhD, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA MeSH: Lung Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000753 This research builds upon an extensive resource of a case-control study that has been ongoing at the UT MD Anderson Cancer Center since 1991. To identify risk variants for lung cancer, we conducted a genome-wide association study. Cases are newly diagnosed, histologically-confirmed patients presenting at MD Anderson Cancer and who had not previously received treatment other than surgery. Controls are healthy individuals seen for routine care at Kelsey-Seybold Clinics, the largest physician group-practice plan in the Houston Metropolitan area. This lung GWAS led to the identification of a susceptibility locus for lung cancer at 15q25.1. We used data from 315,450 tagging SNPs in 1,154 current and former (ever) smoking cases of European ancestry and 1,137 frequency-matched, ever-smoking controls from Houston, Texas in the discovery followed by the replication of the ten SNPs most significantly associated with lung cancer in an additional 711 cases and 632 controls from Texas and 2,013 cases and 3,062 controls from the UK. Two SNPs, rs1051730 and rs8034191, were significantly associated with risk of lung cancer with combined analysis yielded odds ratios of 1.32 (P 1X10-17) for both SNPs. These two SNPs mapped to a region of strong linkage disequilibrium within 15q25.1 containing PSMA4 and the nicotinic acetylcholine receptor subunit genes CHRNA3 and CHRNA5. (Nat Genet. 2008 May;40(5):616-22. PMID:18385676)

Lung Neoplasms

pht003874.v1.p1

1 itemgroup 5 items

pht003875.v1.p1

1 itemgroup 5 items

pht003876.v1.p1

1 itemgroup 6 items

pht003877.v1.p1

1 itemgroup 4 items

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