Genotyping technology is advancing at a rapid pace, and we hope that the resource weare constructing
will have some durable value, which means we should seek to use the best available technology within
reach of the fmancial resources available. The RC4 proposed using a then-state-of-the-art Illumina
lmillion SNP platform, the Omnil-quad (lllumina is the preferred chip manufacturer for DNA samples
based on saliva, as ours are). Since that time Illumina has released a new chip with coverage of 2.5
million SNPs. The 150% increase in number of SNPs translates to coverage of SNPs with a 2%
population frequency of allele variation, compared with 5% for the Omni-l chip. As genetics moves
away from (unsuccessful) models of common single gene variants with large effects on phenotypic traits
and toward models of rare variants and gene-gene interactions, the coverage of rarer variations becomes
increasingly important.
A key strength of the HRS sample for genetic analysis is its substantial representation of African-
Americans. Nearly one quarter of the 7,000 participants covered under the RC4 are African-Americans.
This population benefits greatly from the technology behind the new 2.5m chip. Earlier generations of
chips were designed based on the HapMap sample, which had weaker than expected representation of
the actual variation in genomes of populations of recent African origin. The 1000 Genome Project that
forms the basis for the new generation chips captures much more of the genomic variation seen in
individuals with significant recent African ancestry, and has led to the inclusion of many thousands of
additional SNPs that better represent the spectrum of genetic variation among African-Americans. My
understanding is that there may be ARRA funds available dedicated to the study of minority health, and
we feel that using the improved chip technology on samples from African Americans in the HRS would
be a fitting use for some of this money.
Funding:
Health and Human Services, Department of-National Institutes of Health
Funding Period:
09/30/2010 to 08/31/2013