The discovery GWAS included genotyped as well as imputed SNPs for better coverage. Sample genotypes were phased and missing markers were imputed using the software IMPUTE2 (ref. 54 (link)). Phased data of 1,094 samples from the 1000 Genomes Project (www.1000genomes.org) were used as the reference data set. These samples are from African, African American, Asian, Caucasian and Native American populations. We excluded SNPs with an information coefficient value <0.5 and minor allele frequency <1%. For markers in the MEC data, we conducted additional stringent quality-control analyses to exclude SNPs with different minor allele frequencies in controls typed on or imputed from different genotyping platforms. SNPs that exhibited differences in minor allele frequencies between the controls genotyped with the Illumina Infinitum 660 W-Quad or Omni 2.5 M platforms at P<0.01, and/or had ORs >10 or <0.1 were excluded. The final GWAS analysis included 7,229,558 SNPs.
Fejerman L., Ahmadiyeh N., Hu D., Huntsman S., Beckman K.B., Caswell J.L., Tsung K., John E.M., Torres-Mejia G., Carvajal-Carmona L., Echeverry M.M., Tuazon A.M., Ramirez C., Gignoux C.R., Eng C., Gonzalez-Burchard E., Henderson B., Marchand L.L., Kooperberg C., Hou L., Agalliu I., Kraft P., Lindström S., Perez-Stable E.J., Haiman C.A, & Ziv E. (2014). Genome-wide association study of breast cancer in Latinas identifies novel protective variants on 6q25. Nature Communications, 5, 5260.
AfricanAfrican american Asian Caucasian Genomes Gwas Native american Populations Snps
Corresponding Organization :
Other organizations :
University of California, San Francisco, University of Minnesota, Cancer Prevention Institute of California, Instituto Nacional de Salud Pública, University of California, Davis, University of Tolima, Centro Dermatológico Federico Lleras Acosta, Instituto Nacional de Cancerología, Hospital Universitario de Neiva, University of Nariño, Foscal Hospital, Palo Alto University, Stanford University, University of Southern California, University of Hawaiʻi at Mānoa, University of Hawaii System, Fred Hutch Cancer Center, Northwestern University, Albert Einstein College of Medicine
Phased data of 1,094 samples from the 1000 Genomes Project as the reference data set
Exclusion of SNPs with information coefficient value < 0.5 and minor allele frequency < 1%
Exclusion of SNPs with different minor allele frequencies in controls typed on or imputed from different genotyping platforms
positive controls
Not specified
negative controls
Not specified
Annotations
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