Microarray Genotyped Samples

Samples with Microarray Genotyping Data

The NIGMS Human Genetic Cell Repository has genotyped more than 1000 Repository cell lines with the Affymetrix Genome-Wide Human SNP Array 6.0 platform. The Affymetrix SNP 6.0 array detects approximately 940,000 SNPs and provides copy number information for more than 900,000 additional locations across the genome. The genotyping data has been deposited at the Database of Genotypes and Phenotypes (dbGaP). Investigators can view study information on the dbGaP website and must apply through dbGaP for access to controlled data (e.g., cel files containing raw genotyping data).

Genotyping data for NIGMS Repository samples resides in the following three studies in dbGaP:

National Institute of General Medical Sciences (NIGMS) Human Genetic Cell Repository Human Variation Panels including 100 African-Americans (HD100AA), 100 Caucasians (HD100CAU), 100 Han People of Los Angeles (HD100CHI) and 100 Mexican American Community of Los Angeles (HD100MEX) (Study Accession: phs000211.v1.p1)
This study comprises 400 samples from the NIGMS Human Genetic Cell Repository Human Variation Panels. The populations genotyped included Americans of African, Caucasian, Mexican, and Han Chinese ancestry, with each population contributing 100 samples.

Genotyping NIGMS Chromosomal Aberration and Inherited Disorder Samples (Study Accession: phs000269.v1.p1)
716 samples derived from 697 individuals from the Chromosomal Aberrations and Inherited Disorders collections of the NIGMS Human Genetic Cell Repository were genotyped and analyzed for CNV determination by the Microarray Center at the Coriell Institute for Medical Research. Karyotyping is performed on all cell cultures in the Repository with reported chromosome abnormalities. The samples chosen for genotyping in this study are intended to represent a diverse set of copy number variants, but the selection was also weighted to over-sample commonly manifested types of aberrations.

Genotyping NIGMS CEPH Samples from the United States, Venezuela, and France (Study Accession: phs000268.v1.p1)
The CEPH Reference Family collection contributed by the Centre d'Etude du Polymorphisme Humain (CEPH), Foundation Jean Dausset, Paris, France, includes families collected by R. White (Utah), J. Dausset (French), J. Gusella (Venezuelan), and J. Egeland (Amish). There are a total of 809 individuals accounting for 832 pedigree positions in the reference families. Family relationships for the 61 reference families were verified at the Coriell Institute for Medical Research and approved by CEPH. In an effort to enhance the value of this cell culture resource available from the NIGMS Human Genetic Cell Repository, the Coriell Genotyping and Microarray Center used the Affymetrix Genome-Wide Human SNP Array 6.0 platform to genotype 181 samples from the NIGMS HGCR CEPH collection. Included are thirteen families from the United States (Amish Pedigree 884 and Utah Pedigrees 1331, 1356, 1400, 1416, 1424, 1427, 1477, and 1582), France (Pedigrees 35 and 66), and Venezuela (Pedigrees 102 and 104). Twelve of the families consist of 3 generations and one family consists of 2 generations. Pedigree charts and sample descriptions are available on the CEPH Resources here . Additional data regarding these samples are available on the CEPH website: http://www.cephb.fr/

An Excel spreadsheet listing all NIGMS Repository microarray genotyped samples is available here. The first tab on the spreadsheet shows Human Variation Panel samples, the second tab shows Chromosomal Aberration and Inherited Disorder samples, and the third tab shows the CEPH Reference Family collection samples.

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 Genotyping Console software.

Citing the Use of These Genotypes
Please indicate the Catalog ID numbers of the samples, panels, and/or populations; state that the genotypes were downloaded from dbGaP; and give the dbGaP Accession number.

Finding More Information About Handling cel and chp File Formats
Go to the Affymetrix Genotyping Console Software.