PCA analysis of the study participants.

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posted on 2012-03-08, 00:04 authored by Eimear E. Kenny, Itsik Pe'er, Amir Karban, Laurie Ozelius, Adele A. Mitchell, Sok Meng Ng, Monica Erazo, Harry Ostrer, Clara Abraham, Maria T. Abreu, Gil Atzmon, Nir Barzilai, Steven R. Brant, Susan Bressman, Edward R. Burns, Yehuda Chowers, Lorraine N. Clark, Ariel Darvasi, Dana Doheny, Richard H. Duerr, Rami Eliakim, Nir Giladi, Peter K. Gregersen, Hakon Hakonarson, Michelle R. Jones, Karen Marder, Dermot P. B. McGovern, Jennifer Mulle, Avi Orr-Urtreger, Deborah D. Proctor, Ann Pulver, Jerome I. Rotter, Mark S. Silverberg, Thomas Ullman, Stephen T. Warren, Matti Waterman, Wei Zhang, Aviv Bergman, Lloyd Mayer, Seymour Katz, Robert J. Desnick, Judy H. Cho, Inga Peter

(A) PCA showing the first (X-axis) and second (Y-axis) eigenvectors plotting all 3,252 study participants (907 CD cases and 2,345 controls) across ∼22 K unlinked SNPs indicated by light blue open circles. Also included and color-coded in the graph are the four HapMap (www.hapmap.org) reference samples as solid triangles; CEPH-Utah (CEU; green), Yoruban-Nigeria (YRI; red), Han Chinese (CHB; orange) and Japanese (JPT; dark grey); and seven Jewish samples from the Jewish Hapmap project [2] as solid circles, consisting of Ashkenazi Jews (AJ; blue), one European (Italian; purple), three Middle Eastern (Syrian; fuchsia, Iraqi; teal and Iranian; turquoise) and two Sephardic Jewish cohorts (Turkey; brown and Greek; orange). (B) The same analysis excluding the YRI and CHB+JPT reference panels. (C) A histogram of PC1 values for study participants (light blue) near the AJ cluster and intermediate between the AJ and CEU clusters. The histogram of PC1 values for the included samples show three distinct modes (Groups 1–3), with AJ reference (blue) and CEU (green) indicated.

PCA analysis of the study participants.

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