The International HapMap Project is a resource for researchers containing genotype, sequencing, and expression information for EBV-transformed lymphoblastoid cell lines derived from populations across the world. The expansion of the HapMap beyond the four initial populations of Phase 2, referred to as Phase 3, has increased the sample number and ethnic diversity available for investigation. However, differences in the rate of cellular proliferation between the populations can serve as confounders in phenotype-genotype studies using these cell lines. Within the Phase 2 populations, the JPT and CHB cell lines grow faster (p < 0.0001) than the CEU or YRI cell lines. Phase 3 YRI cell lines grow significantly slower than Phase 2 YRI lines (p < 0.0001), with no widespread genetic differences based on common SNPs. In addition, we found significant growth differences between the cell lines in the Phase 2 ASN populations and the Han Chinese from the Denver metropolitan area panel in Phase 3 (p < 0.0001). Therefore, studies that separate HapMap panels into discovery and replication sets must take this into consideration.
Bibliographical noteFunding Information:
This work was supported by the Pharmacogenetics of Anticancer Agents Research (PAAR) Group, funded by the National Institutes of Health (NIH)/National Institute of General Medical Sciences grant GM61393, NIH/National Cancer Institute Breast SPORE P50 CA125183 and RO1 CA136765. The authors would also like to thank the PAAR cell line core at the University of Chicago for its assistance in ordering and receiving these cell lines. Christine M. Beiswanger is an employee of the Coriell Institute for Medical Research, a nonprofit 501(c)(3) biomedical research foundation. The Coriell Institute for Medical Research is contracted by the National Human Genome Research Institute (NHGRI) to establish, maintain, and distribute the HapMap cell lines to the research community. Fees collected for the distribution of the cell lines are returned to the NHGRI in a cost-reimbursement arrangement.