Next generation genome-wide association tool: Design and coverage of a high-throughput European-optimized SNP array

Thomas J. Hoffmann, Mark N. Kvale, Stephanie E. Hesselson, Yiping Zhan, Christine Aquino, Yang Cao, Simon Cawley, Elaine Chung, Sheryl Connell, Jasmin Eshragh, Marcia Ewing, Jeremy Gollub, Mary Henderson, Earl Hubbell, Carlos Iribarren, Jay Kaufman, Richard Z. Lao, Yontao Lu, Dana Ludwig, Gurpreet K. MathaudaWilliam McGuire, Gangwu Mei, Sunita Miles, Matthew M. Purdy, Charles Quesenberry, Dilrini Ranatunga, Sarah Rowell, Marianne Sadler, Michael H. Shapero, Ling Shen, Tanushree R. Shenoy, David Smethurst, Stephen K. Van den Eeden, Larry Walter, Eunice Wan, Reid Wearley, Teresa Webster, Christopher C. Wen, Li Weng, Rachel Whitmer, Alan Williams, Simon C. Wong, Chia Zau, Andrea Finn, Catherine Schaefer, Pui Yan Kwok, Neil Risch

Research output: Contribution to journalArticlepeer-review

133 Scopus citations


The success of genome-wide association studies has paralleled the development of efficient genotyping technologies. We describe the development of a next-generation microarray based on the new highly-efficient Affymetrix Axiom genotyping technology that we are using to genotype individuals of European ancestry from the Kaiser Permanente Research Program on Genes, Environment and Health (RPGEH). The array contains 674,517 SNPs, and provides excellent genome-wide as well as gene-based and candidate-SNP coverage. Coverage was calculated using an approach based on imputation and cross validation. Preliminary results for the first 80,301 saliva-derived DNA samples from the RPGEH demonstrate very high quality genotypes, with sample success rates above 94% and over 98% of successful samples having SNP call rates exceeding 98%. At steady state, we have produced 462 million genotypes per week for each Axiom system. The new array provides a valuable addition to the repertoire of tools for large scale genome-wide association studies.

Original languageEnglish (US)
Pages (from-to)79-89
Number of pages11
Issue number2
StatePublished - Aug 1 2011
Externally publishedYes


  • Coverage
  • Genome-wide association study
  • Microarray
  • Single nucleotide polymorphism
  • Throughput

ASJC Scopus subject areas

  • Genetics


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