ID

45214

Descripción

Principal Investigator: Stephen J. Chanock, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute and Core Genotyping Facility, Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA MeSH: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000396 We have built a new resource for imputation of SNPs for existing and future genome-wide association studies (GWAS), known as the Division of Cancer Epidemiology and Genetics (DCEG) Reference Set. The first build of the data set includes 728 cancer-free individuals of European descent from three large prospectively sampled studies, 98 African-American individuals from the Prostate, Lung, Colon, and Ovary Cancer Screening Trial (PLCO), 74 Chinese individuals from a Chinese clinical trial in Shanxi, China (SHNX), and 349 unrelated individuals from the HapMap Project (see Molecular Data Section for details on arrays used). The final harmonized dataset includes 2.8 million autosomal polymorphic SNPs on 1,249 subjects after rigorous quality control metrics were applied.

Link

dbGaP study = phs000396

Palabras clave

Versiones (2)
  1. 2/8/22 2/8/22 - Simon Heim
  2. 12/10/22 12/10/22 - Adrian Schulz
Titular de derechos de autor

Stephen J. Chanock, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute and Core Genotyping Facility, Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

Subido en

12 de octubre de 2022

DOI

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Licencia

Creative Commons BY 4.0
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dbGaP phs000396 DCEG Imputation Reference Dataset

Inglés

Eligibility Criteria

3 formularios  
Inclusion and exclusion criteria
Descripción

Inclusion and exclusion criteria

An established quality control (QC) process was applied to samples by study (Referred to as "QC Groups") to ensure that only high-quality genotypes were retained for the analytic data set. QC metrics included completion rates by sample or locus, sample heterozygosity rate and duplicate concordance rate and standard thresholds for exclusion of data generated per array were applied. The results of 198 arrays from 153 different individuals were excluded.
Descripción

An established quality control (QC) process was applied to samples by study (Referred to as "QC Groups") to ensure that only high-quality genotypes were retained for the analytic data set. QC metrics included completion rates by sample or locus, sample heterozygosity rate and duplicate concordance rate and standard thresholds for exclusion of data generated per array were applied.

Tipo de datos

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C0796344
We also excluded individuals and loci with discordance rates greater than 1% after merging the genotypes generated from different arrays, resulting in exclusion of 5 individuals (2 ATBC, 1 CPSII and 2 PLCO). Assays from Illumina Hap1, Omni1, Omni2.5 arrays were harmonized based on the locus meta-data of 1000 Genomes June 2010 release and HapMap 3 February 2009 release. An additional 763 loci were excluded due to incompatible alleles (either matching directly or by reverse complementing) between our data and the public reference data.
Descripción

We also excluded individuals and loci with discordance rates greater than 1% after merging the genotypes generated from different arrays, resulting in exclusion of 5 individuals (2 ATBC, 1 CPSII and 2 PLCO). Assays from Illumina Hap1, Omni1, Omni2.5 arrays were harmonized based on the locus meta-data of 1000 Genomes June 2010 release and HapMap 3 February 2009 release.

Tipo de datos

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C3639994
UMLS CUI [1,3]
C0017431
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Similar models

Eligibility Criteria

3 formularios
Name
Tipo
Description | Question | Decode (Coded Value)
Tipo de datos
Alias
Item Group
Inclusion and exclusion criteria
An established quality control (QC) process was applied to samples by study (Referred to as "QC Groups") to ensure that only high-quality genotypes were retained for the analytic data set. QC metrics included completion rates by sample or locus, sample heterozygosity rate and duplicate concordance rate and standard thresholds for exclusion of data generated per array were applied.
Item
An established quality control (QC) process was applied to samples by study (Referred to as "QC Groups") to ensure that only high-quality genotypes were retained for the analytic data set. QC metrics included completion rates by sample or locus, sample heterozygosity rate and duplicate concordance rate and standard thresholds for exclusion of data generated per array were applied. The results of 198 arrays from 153 different individuals were excluded.
boolean
C0680251 (UMLS CUI [1,1])
C0796344 (UMLS CUI [1,2])
We also excluded individuals and loci with discordance rates greater than 1% after merging the genotypes generated from different arrays, resulting in exclusion of 5 individuals (2 ATBC, 1 CPSII and 2 PLCO). Assays from Illumina Hap1, Omni1, Omni2.5 arrays were harmonized based on the locus meta-data of 1000 Genomes June 2010 release and HapMap 3 February 2009 release.
Item
We also excluded individuals and loci with discordance rates greater than 1% after merging the genotypes generated from different arrays, resulting in exclusion of 5 individuals (2 ATBC, 1 CPSII and 2 PLCO). Assays from Illumina Hap1, Omni1, Omni2.5 arrays were harmonized based on the locus meta-data of 1000 Genomes June 2010 release and HapMap 3 February 2009 release. An additional 763 loci were excluded due to incompatible alleles (either matching directly or by reverse complementing) between our data and the public reference data.
boolean
C0680251 (UMLS CUI [1,1])
C3639994 (UMLS CUI [1,2])
C0017431 (UMLS CUI [1,3])
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