ID

45523

Description

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.

Link

dbGaP study = phs000716

Keywords

Versions (1)
  1. 12/14/22 12/14/22 - Simon Heim
Copyright Holder

Qing Lan, MD, PhD, MPH, National Institutes of Health, Bethesda, MD, USA

Uploaded on

December 14, 2022

DOI

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License

Creative Commons BY 4.0
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dbGaP phs000716 GWAS of Lung Cancer Susceptibility in Never-Smoking Women in Asia

English

Eligibility Criteria

5 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
Participants (all non-smoking female) were drawn from studies in Eastern Asia. Cases were histologically confirmed lung cancer.
Description

Participants (all non-smoking female) were drawn from studies in Eastern Asia. Cases were histologically confirmed lung cancer.

Data type

boolean

Alias
UMLS CUI [1,1]
C4554048
UMLS CUI [1,2]
C0086287
UMLS CUI [1,3]
C0337672
UMLS CUI [1,4]
C0947630
UMLS CUI [1,5]
C0015631
UMLS CUI [1,6]
C0019638
UMLS CUI [1,7]
C0521091
UMLS CUI [1,8]
C0242379
Exclusions included: (i) samples with low completion rates; (ii) samples with extreme mean heterozygosity rates. The thresholds were chosen based on the sample completion rates or sample mean heterozygosity distribution by each QC group; and (iii) discordant expected duplicate samples. The average genotype concordance rate for the expected duplicates was great than 99.9%. Further QC at the individual level led to the following exclusions: (i) gender discordance; (ii) subjects with Asian ancestry less than 86%; (iii) subjects with first degree relatives in dataset; (iv) subjects with incomplete phenotype, ever smoked, unknown histology or ineligibility.
Description

Exclusions included: (i) samples with low completion rates; (ii) samples with extreme mean heterozygosity rates. The thresholds were chosen based on the sample completion rates or sample mean heterozygosity distribution by each QC group; and (iii) discordant expected duplicate samples. The average genotype concordance rate for the expected duplicates was great than 99.9%. Further QC at the individual level led to the following exclusions: (i) gender discordance; (ii) subjects with Asian ancestry less than 86%; (iii) subjects with first degree relatives in dataset; (iv) subjects with incomplete phenotype, ever smoked, unknown histology or ineligibility.

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0205251
UMLS CUI [1,3]
C1554962
UMLS CUI [1,4]
C1521828
UMLS CUI [1,5]
C0444504
UMLS CUI [1,6]
C0019425
UMLS CUI [1,7]
C0449864
UMLS CUI [1,8]
C1517001
UMLS CUI [1,9]
C0332597
UMLS CUI [1,10]
C0370003
UMLS CUI [1,11]
C4553529
UMLS CUI [1,12]
C0017431
UMLS CUI [1,13]
C0079399
UMLS CUI [1,14]
C0034378
UMLS CUI [1,15]
C1257906
UMLS CUI [1,16]
C1517194
UMLS CUI [1,17]
C0205257
UMLS CUI [1,18]
C0031437
UMLS CUI [1,19]
C3475470
UMLS CUI [1,20]
C1512714
In addition, data from the GELAC study that was scanned using non-NIH Taiwan resources before Taiwan joined the FLCCA GWAS are not being posted. These data were scanned on the Ilumina 317 and 610. Further, data from 5 subjects from the Singapore study are not being posted, since these subjects indicated on their informed consent that they did not wish their data to be used by any other investigators except those in the Singapore study.
Description

In addition, data from the GELAC study that was scanned using non-NIH Taiwan resources before Taiwan joined the FLCCA GWAS are not being posted. These data were scanned on the Ilumina 317 and 610. Further, data from 5 subjects from the Singapore study are not being posted, since these subjects indicated on their informed consent that they did not wish their data to be used by any other investigators except those in the Singapore study.

Data type

boolean

Alias
UMLS CUI [1,1]
C0947630
UMLS CUI [1,2]
C0039260
UMLS CUI [1,3]
C0035201
UMLS CUI [1,4]
C2350277
UMLS CUI [1,5]
C0681850
UMLS CUI [1,6]
C0021430
UMLS CUI [1,7]
C1524063
UMLS CUI [1,8]
C1511726
UMLS CUI [1,9]
C2346578
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Similar models

Eligibility Criteria

5 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
C1512693 (UMLS CUI [1,1])
C0680251 (UMLS CUI [1,2])
Participants (all non-smoking female) were drawn from studies in Eastern Asia. Cases were histologically confirmed lung cancer.
Item
Participants (all non-smoking female) were drawn from studies in Eastern Asia. Cases were histologically confirmed lung cancer.
boolean
C4554048 (UMLS CUI [1,1])
C0086287 (UMLS CUI [1,2])
C0337672 (UMLS CUI [1,3])
C0947630 (UMLS CUI [1,4])
C0015631 (UMLS CUI [1,5])
C0019638 (UMLS CUI [1,6])
C0521091 (UMLS CUI [1,7])
C0242379 (UMLS CUI [1,8])
Exclusions included: (i) samples with low completion rates; (ii) samples with extreme mean heterozygosity rates. The thresholds were chosen based on the sample completion rates or sample mean heterozygosity distribution by each QC group; and (iii) discordant expected duplicate samples. The average genotype concordance rate for the expected duplicates was great than 99.9%. Further QC at the individual level led to the following exclusions: (i) gender discordance; (ii) subjects with Asian ancestry less than 86%; (iii) subjects with first degree relatives in dataset; (iv) subjects with incomplete phenotype, ever smoked, unknown histology or ineligibility.
Item
Exclusions included: (i) samples with low completion rates; (ii) samples with extreme mean heterozygosity rates. The thresholds were chosen based on the sample completion rates or sample mean heterozygosity distribution by each QC group; and (iii) discordant expected duplicate samples. The average genotype concordance rate for the expected duplicates was great than 99.9%. Further QC at the individual level led to the following exclusions: (i) gender discordance; (ii) subjects with Asian ancestry less than 86%; (iii) subjects with first degree relatives in dataset; (iv) subjects with incomplete phenotype, ever smoked, unknown histology or ineligibility.
boolean
C0680251 (UMLS CUI [1,1])
C0205251 (UMLS CUI [1,2])
C1554962 (UMLS CUI [1,3])
C1521828 (UMLS CUI [1,4])
C0444504 (UMLS CUI [1,5])
C0019425 (UMLS CUI [1,6])
C0449864 (UMLS CUI [1,7])
C1517001 (UMLS CUI [1,8])
C0332597 (UMLS CUI [1,9])
C0370003 (UMLS CUI [1,10])
C4553529 (UMLS CUI [1,11])
C0017431 (UMLS CUI [1,12])
C0079399 (UMLS CUI [1,13])
C0034378 (UMLS CUI [1,14])
C1257906 (UMLS CUI [1,15])
C1517194 (UMLS CUI [1,16])
C0205257 (UMLS CUI [1,17])
C0031437 (UMLS CUI [1,18])
C3475470 (UMLS CUI [1,19])
C1512714 (UMLS CUI [1,20])
In addition, data from the GELAC study that was scanned using non-NIH Taiwan resources before Taiwan joined the FLCCA GWAS are not being posted. These data were scanned on the Ilumina 317 and 610. Further, data from 5 subjects from the Singapore study are not being posted, since these subjects indicated on their informed consent that they did not wish their data to be used by any other investigators except those in the Singapore study.
Item
In addition, data from the GELAC study that was scanned using non-NIH Taiwan resources before Taiwan joined the FLCCA GWAS are not being posted. These data were scanned on the Ilumina 317 and 610. Further, data from 5 subjects from the Singapore study are not being posted, since these subjects indicated on their informed consent that they did not wish their data to be used by any other investigators except those in the Singapore study.
boolean
C0947630 (UMLS CUI [1,1])
C0039260 (UMLS CUI [1,2])
C0035201 (UMLS CUI [1,3])
C2350277 (UMLS CUI [1,4])
C0681850 (UMLS CUI [1,5])
C0021430 (UMLS CUI [1,6])
C1524063 (UMLS CUI [1,7])
C1511726 (UMLS CUI [1,8])
C2346578 (UMLS CUI [1,9])
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