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Abstract

The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and nonmedical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome and mitochondrial DNA (mtDNA), the current phase focuses on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism (SNP) genotyping, they were designed for medical genetic studies and contain medically related markers that are inappropriate for global population genetic studies. GenoChip, the Genographic Project's new genotyping array, was designed to resolve these issues and enable higher resolution research into outstanding questions in genetic anthropology. The GenoChip includes ancestry informative markers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all known Y-chromosome and mtDNA haplogroups. The chip was carefully vetted to avoid inclusion of medically relevant markers. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. The chip performances are illustrated in a principal component analysis for 14 worldwide populations. In summary, the GenoChip is a dedicated genotyping platform for genetic anthropology. With an unprecedented number of approximately 12,000 Y-chromosomal and approximately 3,300 mtDNA SNPs and over 130,000 autosomal and X-chromosomal SNPs without any known health, medical, or phenotypic relevance, the GenoChip is a useful tool for genetic anthropology and population genetics.

Keywords: AimsFinder; GenoChip; Genographic Project; genetic anthropology; haplogroups; population genetics.

Figures

F<sc>ig</sc>. 1.—
Fig. 1.—
Worldwide distribution of population from which AIMs were obtained. AIMs from over 450 world populations were harvested from the literature (green) and calculated based on genotyped data from public and private collections (red) including over 30 Jewish populations (blue).
F<sc>ig</sc>. 2.—
Fig. 2.—
SNP density in the Genochip. The average numbers of GenoChip SNPs per 100,000 nucleotides across the genome are color coded. Gaps in the assembly are shown in gray.
F<sc>ig</sc>. 3.—
Fig. 3.—
Success rate in identifying Y-chromosomal (left) and mtDNA (right) haplogroups. The plots depict all known basal haplogroups (columns), the number of known subgroups in each haplogroup (top of each column), and the proportion of subgroups that were validated with the GenoChip.
F<sc>ig</sc>. 4.—
Fig. 4.—
MAF distributions for autosomal (a) and X-chromosomal (b) HapMap SNPs. MAF distributions are shown for HapMap SNPs and two subsets that overlap with the Illumina Human660W and GenoChip SNPs.
F<sc>ig</sc>. 5.—
Fig. 5.—
Distribution of locus-specific FST in three continental populations. FST values were obtained for (a) autosomal and (b) X-chromosomal HapMap SNPs. FST distributions are shown for HapMap SNPs and two subsets that overlap with the Illumina Human660W and GenoChip SNPs. The histograms show bin distribution as indicated on the x axis and the cumulative distribution (line).
F<sc>ig</sc>. 6.—
Fig. 6.—
PCA plots of genetic diversity across 14 worldwide populations. Each figure represents the genetic diversity seen across the populations considered, with each sample mapped onto a spectrum of genetic variation represented by two axes of variations corresponding to two eigenvectors of the PCA. Individuals from each population are represented by a unique color. (A) Analysis of all populations. The insets magnify European, Asian, and the cluster of Amerindian and Indian individuals. (B) Analysis of East Asian individuals. (C) Analysis of European individuals. (D) Analysis of Amerindian and Indian individuals. A polygon surrounding all or most of the individuals belonging to a group designation highlights the population groups.

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