NIGMS Collection - Genotypes and Copy Number Resources

The NIGMS Human Genetic Cell Repository at Coriell is genotyping the genomes of selected cell lines in the Repository using the Affymetrix SNP 6.0 GeneChip at the Coriell Genotyping and Microarray Center. The genotype data are available for download to the scientific community.

FAQ 1: How do I get these genotypes?
These genotypes will soon be available on dbGaP. The genotypes that are available will be linked to the sample pages and will be announced here.

FAQ 2: What formats are available?
The samples were genotyped with the Affymetrix SNP 6.0 GeneChip and the .cel files will be available.

FAQ 3: What samples are available?
The samples currently completed are from the Human Variation Collection. The genotypes of the human variation panels are listed by ethnicity, which is self-reported. The samples have been available in the Human Variation collection for several years. Publications using these samples are available in the web catalog.

Panel Description
HD100CAU Individuals of self declared Caucasian ancestry
HD100AA Individuals of African-American heritage
HD100MEX Individuals of Mexican-American heritage
HD100CHI Individuals of Han ancestry

FAQ 4: Will these genotypes be placed in the NCBI Data Repositories?
Currently they are being transferred to dbGaP.. At that time the research intent will be reviewed by the NIGMS Data Access Committee (DAC) and will be made available on the dbGAP website.

FAQ 5: What methods and quality control were used to prepare the genotypes?
Sample Preparation: Genomic DNA (~500 ng) was processed according to the Affymetrix Genome-Wide SNP Nsp/Sty 6.0 protocol. Samples were subjected to quality control following the PCR, quantification, and fragmentation steps. The genotype calls were calculated using the Affymetrix Command Console v2.0 software. All samples were initially QC genotyped, and only those with a QC call rate of greater than 85% were fully genotyped using the Birdseed algorithm. These files are available in the download.

FAQ 6: How do I cite the use of these genotypes?
Please indicate the Reference numbers of the samples, panels or populations and state that the genotypes were downloaded from dbGaP and give the dbGaP Accession number.

FAQ 7: How do I find more information about handling cel and chp file formats?
Go to the Affymetrix Genotyping Console Software.

FAQ 8: What additional samples are being genotyped?
We are currently genotyping a set of samples from the Chromosomally Aberrant Collection. When new genotypes from these samples are available, it will be announced on this page in FAQ3.