Changes

We selected a grid of 3,380 markers (distributed approximately one per megabase, across the autosomes and the X chromosome) that showed strong differentiation between African- and European-ancestry samples sequenced by the 1000 Genomes Project. Markers previously genotyped on the Illumina Omni 2.5M array were favored and markers with A/T or G/C alleles were avoided.

We selected a grid of 3,380 markers (distributed approximately one per megabase, across the autosomes and the X chromosome) that showed strong differentiation between African- and European-ancestry samples sequenced by the 1000 Genomes Project. Markers previously genotyped on the Illumina Omni 2.5M array were favored and markers with A/T or G/C alleles were avoided.

For the Native American vs. European SNPs:  AIMs were also excluded if they were in LD with another AIM (R2 > 0.1 in Native American populations, to be conservative), if they were physically within 250 kbases of another SNP (to ensure they were well-distributed throughout the genome), or if they was within-continent heterogeneity. The ancestral populations include CEU, TSI, and a population of Spaniards for European ancestry, and six populations of Native Americans: Mayan, Nahuan, Zapoteca, Tepehuano, Quechuan and Aymaran.

 

A grid of 1,000 markers selected to be informative for Native American vs. European ancestry. These AIMs were selected to be in low linkage disequilibrium of one another (defined as R2 <= 0.1 in Native American populations, to be conservative) and widely separated (by requiring that they should be at least 250 kbases from other European vs Native American ancestry AIMs. SNPs with significant within continent heterogeneity were excluded.

 

The ancestral populations include CEU, TSI, and a population of Spaniards for European ancestry, and six populations of Native Americans: Mayan, Nahuan, Zapoteca, Tepehuano, Quechuan and Aymaran.

 

Among these SNPs, 998 could be designed into Illumina assays.

== Scaffold for Identity by Descent ==

== Scaffold for Identity by Descent ==