Genotyping 400 Samples from the NIGMS Human Variation Panels

The Human Genetic Cell Repository is sponsored by the National Institute of General Medical Sciences (NIGMS) with the mission of supplying scientists with the materials for accelerating disease gene discovery and functional studies. The resources available include highly-characterized, contaminant-free cell cultures and high quality, well-characterized DNA samples derived from these cultures, both subjected to rigorous quality control. The Repository was established in 1972 at Coriell and contains more than 9,500 cell lines, primarily fibroblasts and transformed lymphoblasts. The Repository has a major emphasis on inherited diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, Human Variation and many apparently healthy controls. The Human Variation collection provides cell lines and DNA samples from a variety of populations. The panels of African-Americans (HD100AA) and Caucasians (100CAU) used for this study are comprised of samples present in the Repository that were originally collected over the years from apparently healthy people to be used as "controls", for example, unaffected family members of persons with identified mono-genetic diseases. The samples for the Han people of Los Angeles (HD100CHI) and the Mexican American Community of Los Angeles (HD100MEX), however, were collected relatively recently from volunteers, identified as member of these communities, specifically for use in these panels. The Coriell Genotyping and Microarray Center in conjunction with the NIGMS repository used the Affymetrix Genome-Wide Human SNP 6.0 platform to genotype 400 samples from the NIGMS human variation panels. The populations genotyped included Americans of African, Caucasian, Mexican, and Han Chinese ancestry. 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.]]>
Ethnicities for the African American and Caucasian panels are self-identified as reported in physician records. Inclusion in the Han People of Los Angeles Panel requires that all four grandparents were born in Taiwan, China, or Hong Kong. Inclusion in the Mexican-American Community of Los Angeles Panel requires that at least three grandparents were born in Mexico.]]>
1972-1997: Samples from patients seen by clinical geneticists were submitted to the NIGMS Human Genetic Cell Repository as unaffected family members of patients with documented, mono-genetic diseases. 1997-2000: Human Variation panels were developed in response to requests for sets of cell lines and DNA samples identified by ethnicity. The current African American and Caucasian panels were created at that time from cell lines in the collection that were identified by ethnicities stated in the clinical information supplied by submitting geneticists. They are not samples specifically collected for ethnic panels. The ID numbers for the panel members can be linked to the original reference numbers in the Repository catalog. The African American and Caucasian panels were first shipped in 2000. 2003: Samples from Chinese Americans and from Mexican Americans were collected in structured efforts involving community consultations in Los Angeles, California to provide samples for the respective panels. The cell lines and panels were created and first distributed in 2003. 2008: Genotyping data from the Affymetrix GeneChip 6.0 for the four panels was made available though Coriell and the NIGMS Human Genetic Cell Repository pending availability in dbGaP through an NIGMS DAC. More than 6,000 cell cultures and 100,000 DNA samples have been distributed from these four sets of samples to hundreds of investigators in the US and overseas since the inception of the collection.]]>