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Combined coverage of IBCv1 with the 500 K and one million SNP products for Group1 loci in HapMap populations.

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posted on 2008-10-31, 02:15 authored by Brendan J. Keating, Sam Tischfield, Sarah S. Murray, Tushar Bhangale, Thomas S. Price, Joseph T. Glessner, Luana Galver, Jeffrey C. Barrett, Struan F. A. Grant, Deborah N. Farlow, Hareesh R. Chandrupatla, Mark Hansen, Saad Ajmal, George J. Papanicolaou, Yiran Guo, Mingyao Li, Stephanie DerOhannessian, Paul I. W. de Bakker, Swneke D. Bailey, Alexandre Montpetit, Andrew C. Edmondson, Kent Taylor, Xiaowu Gai, Susanna S. Wang, Myriam Fornage, Tamim Shaikh, Leif Groop, Michael Boehnke, Alistair S. Hall, Andrew T. Hattersley, Edward Frackelton, Nick Patterson, Charleston W. K. Chiang, Cecelia E. Kim, Richard R. Fabsitz, Willem Ouwehand, Alkes L. Price, Patricia Munroe, Mark Caulfield, Thomas Drake, Eric Boerwinkle, David Reich, A. Stephen Whitehead, Thomas P. Cappola, Nilesh J. Samani, A. Jake Lusis, Eric Schadt, James G. Wilson, Wolfgang Koenig, Mark I. McCarthy, Sekar Kathiresan, Stacey B. Gabriel, Hakon Hakonarson, Sonia S. Anand, Muredach Reilly, James C. Engert, Deborah A. Nickerson, Daniel J. Rader, Joel N. Hirschhorn, Garret A. FitzGerald

For the combined coverage of IBCv1 with the 500 K SNP products (A–F): coverage (y axis) was assessed using Max r2 (× axis), at an MAF cutoff of 0.02, for the HapMap 22 release in CEPH (CEU) (A), Chinese (CHB) plus Japanese (JPT) (B), and Yoruba (YRI) HapMap individuals (C). Coverage was also assessed at an MAF cutoff of 0.05 in CEU (D), CHB+JPT (E), and YRI individuals (F). For combined coverage with the one million SNP products (G–L): Coverage (y axis) was also assessed using Max r2 (× axis), at an MAF cutoff of 0.02, for the HapMap 22 release in CEPH (CEU) (G), Chinese (CHB) plus Japanese (JPT) (H), and Yoruba (YRI) HapMap individuals (I) and coverage with an MAF cutoff of 0.05 in CEU (J), CHB+JPT (K), and YRI individuals (L). IBCv1 refers here to the version1 ITMAT-Broad-CARe array using 45,237 SNPs that passed manufacturers criteria. Affy_5.0 refers to the Affymetrix 5.0 array and ILMN_HapMap550 refers to the Infinium 550 K HumanHap array which contains 500,568 and 555,352 SNPs respectively. Affy_6.0 refers to the Affymetrix 6.0 array and ILMN_1M refers to the Illumina Infinium one million SNP array containing ∼906,600 and ∼1,050,000 SNPs respectively.

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