ID

45120

Description

Principal Investigator: Maria Teresa Landi, Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA MeSH: Lung Neoplasms,Smoking https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000336 Three genetic loci for lung cancer risk have been identified by genome-wide association studies (GWAS), but inherited susceptibility to specific histologic types of lung cancer is not well established. We conducted a GWAS of lung cancer and its major histologic types genotyping 515,922 single nucleotide polymorphisms (SNPs) in 5,739 incident lung cancer cases and 5,848 controls from one population-based case-control study and three cohort studies. Results were combined with summary data from 10 additional studies for a total of 13,300 cases and 19,666 controls of European descent. Four studies also provided histology data for replication resulting in 3,333 adenocarcinomas (AD), 2,589 squamous cell carcinomas (SQ), and 1,418 small cell carcinomas (SC). In analyses by histology, rs2736100 (*TERT*) on chromosome 5p15.33, was associated with risk of adenocarcinoma (OR=1.23, 95%CI=1.13-1.33, P=3.02x10sup-7/sup), but not other histologic types (OR=1.01, P=0.84, and OR=1.00, P=0.93, for SQ and SC, respectively). This finding was confirmed in each replication study and overall meta-analysis (OR=1.24, 95%CI=1.17-1.31, P=3.74x10sup-14/sup for AD and OR=0.99, P=0.69 and OR=0.97, P=0.48, for SQ and SC, respectively). Other previously reported association signals on 15q25 and 6p21 were also refined, but no additional loci reached genome-wide significance. In conclusion, a lung cancer GWAS identified a distinct hereditary contribution to adenocarcinoma. *Note: The lung study dataset to be released to dbGaP and caBIG excludes 47 individuals from the PLCO cohort who consented to participate only in cancer research projects and 22 individuals because of updated QC. Thus, the released dataset is derived from 11517 subjects, 5699 cases and 5818 controls. After the updated QC, the dataset to be released to dbGaP and caBIG includes 506062 SNPs.*

Link

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000336

Keywords

Versions (2)
  1. 9/10/22 9/10/22 - Simon Heim
  2. 10/12/22 10/12/22 - Adrian Schulz
Copyright Holder

Maria Teresa Landi, Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

Uploaded on

September 10, 2022

DOI

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License

Creative Commons BY 4.0
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dbGaP phs000336 DCEG Lung Cancer Study

English

Eligibility Criteria

4 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Lung cancer cases were included based on a lung cancer diagnosis established on clinical criteria and confirmed by pathology reports from surgery, biopsy, or cytology samples in approximately 95% of cases and on clinical history and imaging for the remaining 5%. Tumor histology was coded according to the International Classification of Diseases for Oncology.
Description

Lung cancer cases were included based on a lung cancer diagnosis established on clinical criteria and confirmed by pathology reports from surgery, biopsy, or cytology samples in approximately 95% of cases and on clinical history and imaging for the remaining 5%. Tumor histology was coded according to the International Classification of Diseases for Oncology.

Data type

boolean

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0242379
UMLS CUI [1,3]
C0679557
UMLS CUI [1,4]
C0332140
UMLS CUI [2,1]
C1512693
UMLS CUI [2,2]
C0019638
UMLS CUI [2,3]
C0009219
UMLS CUI [2,4]
C1512892
Of the eligible subjects, in the original analysis, 183 were excluded for issues related to genotyping quality control and 337 subjects were excluded with incomplete phenotype data resulting in a final dataset of 5739 lung cancer cases and 5848 controls. After the further exclusion of 47 individuals because of informed consent issues and 22 individuals for QC reasons, the dataset released in dbGap and caBIG includes 5699 cases and 5818 controls.
Description

Of the eligible subjects, in the original analysis, 183 were excluded for issues related to genotyping quality control and 337 subjects were excluded with incomplete phenotype data resulting in a final dataset of 5739 lung cancer cases and 5848 controls. After the further exclusion of 47 individuals because of informed consent issues and 22 individuals for QC reasons, the dataset released in dbGap and caBIG includes 5699 cases and 5818 controls.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0796344
UMLS CUI [1,3]
C0332306
UMLS CUI [2,1]
C0680251
UMLS CUI [2,2]
C0205257
UMLS CUI [2,3]
C0031437
UMLS CUI [2,4]
C1511726
UMLS CUI [3,1]
C0680251
UMLS CUI [3,2]
C0021430
UMLS CUI [3,3]
C0034378
The subjects included in the original analysis as reported in Landi et al., AJHG 2009, by study: Cases Controls EAGLE 1920 1979 ATBC 1732 1271 PLCO 1390 1924 CSP-II 697 674
Description

The subjects included in the original analysis as reported in Landi et al.,

Data type

boolean

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C2919603
UMLS CUI [1,3]
C1511726
The subjects included in the dataset to be released in dbGaP and caBIG, by study, after further exclusions for informed consent and QC reasons: Cases Controls EAGLE 1917 1978 ATBC 1732 1270 PLCO 1355 1896 CSP-II 695 674
Description

The subjects included in the dataset to be released in dbGaP and caBIG, by study, after further exclusions for informed consent and QC reasons

Data type

boolean

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0150098
Further details of genotyping exclusions are provided in Supplemental Table 2 of the AJHG Report (Landi et al.)
Description

Further details of genotyping exclusions are provided in Supplemental Table 2 of the AJHG Report (Landi et al.)

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C1285573
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Similar models

Eligibility Criteria

4 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
Lung cancer cases were included based on a lung cancer diagnosis established on clinical criteria and confirmed by pathology reports from surgery, biopsy, or cytology samples in approximately 95% of cases and on clinical history and imaging for the remaining 5%. Tumor histology was coded according to the International Classification of Diseases for Oncology.
Item
Lung cancer cases were included based on a lung cancer diagnosis established on clinical criteria and confirmed by pathology reports from surgery, biopsy, or cytology samples in approximately 95% of cases and on clinical history and imaging for the remaining 5%. Tumor histology was coded according to the International Classification of Diseases for Oncology.
boolean
C1512693 (UMLS CUI [1,1])
C0242379 (UMLS CUI [1,2])
C0679557 (UMLS CUI [1,3])
C0332140 (UMLS CUI [1,4])
C1512693 (UMLS CUI [2,1])
C0019638 (UMLS CUI [2,2])
C0009219 (UMLS CUI [2,3])
C1512892 (UMLS CUI [2,4])
Of the eligible subjects, in the original analysis, 183 were excluded for issues related to genotyping quality control and 337 subjects were excluded with incomplete phenotype data resulting in a final dataset of 5739 lung cancer cases and 5848 controls. After the further exclusion of 47 individuals because of informed consent issues and 22 individuals for QC reasons, the dataset released in dbGap and caBIG includes 5699 cases and 5818 controls.
Item
Of the eligible subjects, in the original analysis, 183 were excluded for issues related to genotyping quality control and 337 subjects were excluded with incomplete phenotype data resulting in a final dataset of 5739 lung cancer cases and 5848 controls. After the further exclusion of 47 individuals because of informed consent issues and 22 individuals for QC reasons, the dataset released in dbGap and caBIG includes 5699 cases and 5818 controls.
boolean
C0680251 (UMLS CUI [1,1])
C0796344 (UMLS CUI [1,2])
C0332306 (UMLS CUI [1,3])
C0680251 (UMLS CUI [2,1])
C0205257 (UMLS CUI [2,2])
C0031437 (UMLS CUI [2,3])
C1511726 (UMLS CUI [2,4])
C0680251 (UMLS CUI [3,1])
C0021430 (UMLS CUI [3,2])
C0034378 (UMLS CUI [3,3])
The subjects included in the original analysis as reported in Landi et al.,
Item
The subjects included in the original analysis as reported in Landi et al., AJHG 2009, by study: Cases Controls EAGLE 1920 1979 ATBC 1732 1271 PLCO 1390 1924 CSP-II 697 674
boolean
C1512693 (UMLS CUI [1,1])
C2919603 (UMLS CUI [1,2])
C1511726 (UMLS CUI [1,3])
The subjects included in the dataset to be released in dbGaP and caBIG, by study, after further exclusions for informed consent and QC reasons
Item
The subjects included in the dataset to be released in dbGaP and caBIG, by study, after further exclusions for informed consent and QC reasons: Cases Controls EAGLE 1917 1978 ATBC 1732 1270 PLCO 1355 1896 CSP-II 695 674
boolean
C1512693 (UMLS CUI [1,1])
C0150098 (UMLS CUI [1,2])
Further details of genotyping exclusions are provided in Supplemental Table 2 of the AJHG Report (Landi et al.)
Item
Further details of genotyping exclusions are provided in Supplemental Table 2 of the AJHG Report (Landi et al.)
boolean
C0680251 (UMLS CUI [1,1])
C1285573 (UMLS CUI [1,2])
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