An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels

Nassir, Rami; Kosoy, Roman; Tian, Chao; White, Phoebe A; Butler, Lesley M; Silva, Gabriel; Kittles, Rick; Alarcon-Riquelme, Marta E; Gregersen, Peter K; Belmont, John W; De La Vega, Francisco M; Seldin, Michael F

doi:10.1186/1471-2156-10-39

Table 2 Ascertainment of Continental Ancestry Using 93 SNP AIM Panel

From: An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels

	STRUCTURE Criterion^a					Eigenvector Criterion
	EUR	EAS	AFR	OCEAN	AMI	EUR	EAS	AFR	OCEAN	AMI
European (643) ^b	91.9%	0.0%	0.0%	0.0%	0.0%	87.1%	0.0%	0.0%	0.0%	0.0%
Ashkenazi (40)	97.5%	0.0%	0.0%	0.0%	0.0%	95.0%	0.0%	0.0%	0.0%	0.0%
Palestinian (26)	73.1%	0.0%	0.0%	0.0%	0.0%	80.8%	0.0%	0.0%	0.0%	0.0%
Bedouin (47)	78.7%	0.0%	0.0%	0.0%	0.0%	80.9%	0.0%	0.0%	0.0%	0.0%
Russian (13)	92.3%	0.0%	0.0%	0.0%	0.0%	84.6%	0.0%	0.0%	0.0%	0.0%
CEU (48)	93.8%	0.0%	0.0%	0.0%	0.0%	93.8%	0.0%	0.0%	0.0%	0.0%
EURA (399)	94.2%	0.0%	0.0%	0.0%	0.0%	88.2%	0.0%	0.0%	0.0%	0.0%
OEUR (70)^c	90.0%	0.0%	0.0%	0.0%	0.0%	78.6%	0.0%	0.0%	0.0%	0.0%
East Asian (250)	0.0%	88.5%	0.0%	0.0%	0.0%	0.0%	90.6%	0.0%	0.0%	0.0%
CHB (43)	0.0%	97.7%	0.0%	0.0%	0.0%	0.0%	88.4%	0.0%	0.0%	0.0%
JPT (43)	0.0%	93.0%	0.0%	0.0%	0.0%	0.0%	88.4%	0.0%	0.0%	0.0%
Chinese American (44)	0.0%	84.1%	0.0%	0.0%	0.0%	0.0%	84.1%	0.0%	0.0%	0.0%
Yakut (15)	0.0%	20.0%	0.0%	0.0%	0.0%	0.0%	66.7%	0.0%	0.0%	0.0%
Mongolian (9)	0.0%	88.9%	0.0%	0.0%	0.0%	0.0%	77.8%	0.0%	0.0%	0.0%
Filipino American (42)	0.0%	73.8%	0.0%	0.0%	0.0%	0.0%	88.1%	0.0%	0.0%	0.0%
OEAS (54)	0.0%	64.8%	0.0%	0.0%	0.0%	0.0%	85.2%	0.0%	0.0%	0.0%
Sub-Saharan AFR (221)	0.0%	0.0%	99.1%	0.0%	0.0%	0.0%	0.0%	87.3%	0.0%	0.0%
YRI (56)	0.0%	0.0%	100.0%	0.0%	0.0%	0.0%	0.0%	87.5%	0.0%	0.0%
Nilo-Saharan (23)	0.0%	0.0%	95.7%	0.0%	0.0%	0.0%	0.0%	91.3%	0.0%	0.0%
Mbuti (15)	0.0%	0.0%	100.0%	0.0%	0.0%	0.0%	0.0%	80.0%	0.0%	0.0%
Biaki (32)	0.0%	0.0%	100.0%	0.0%	0.0%	0.0%	0.0%	100.0%	0.0%	0.0%
Mandeka (24)	0.0%	0.0%	100.0%	0.0%	0.0%	0.0%	0.0%	100.0%	0.0%	0.0%
OSSAFR (71)	0.0%	0.0%	98.6%	0.0%	0.0%	0.0%	0.0%	94.4%	0.0%	0.0%
South Asian (104)	7.7%	0.0%	0.0%	0.0%	0.0%	18.3%	0.0%	0.0%	0.0%	0.0%
Indian (64)	1.6%	0.0%	0.0%	0.0%	0.0%	9.4%	0.0%	0.0%	0.0%	0.0%
Burusho (7)	0.0%	0.0%	0.0%	0.0%	0.0%	14.3%	0.0%	0.0%	0.0%	0.0%
Balochi (15)	13.3%	0.0%	0.0%	0.0%	0.0%	20.0%	0.0%	0.0%	0.0%	0.0%
Kalash (18)	27.8%	0.0%	0.0%	0.0%	0.0%	50.0%	0.0%	0.0%	0.0%	0.0%
Amerindian (136)	0.0%	0.0%	0.0%	0.0%	86.8%	0.0%	0.0%	0.0%	0.0%	80.1%
Maya-Kachiquel (50)^c	0.0%	0.0%	0.0%	0.0%	98.0%	0.0%	0.0%	0.0%	0.0%	98.0%
Maya HGDP (13)	0.0%	0.0%	0.0%	0.0%	46.2%	0.0%	0.0%	0.0%	0.0%	46.2%
Quechuan (26)	0.0%	0.0%	0.0%	0.0%	76.9%	0.0%	0.0%	0.0%	0.0%	88.5%
OAMI (47)	0.0%	0.0%	0.0%	0.0%	91.5%	0.0%	0.0%	0.0%	0.0%	66.0%
Oceana (32)	0.0%	0.0%	0.0%	96.8%	0.0%	0.0%	0.0%	0.0%	93.5%	0.0%
OTHER (234)	1.7%	0.0%	9.8%	0.0%	1.3%	2.1%	0.0%	4.7%	0.0%	3.8%
Mozabite (30)	3.3%	0.0%	0.0%	0.0%	0.0%	3.3%	0.0%	0.0%	0.0%	0.0%
Mexican (66)	1.5%	0.0%	0.0%	0.0%	4.5%	1.5%	0.0%	0.0%	0.0%	13.6%
African American (100)	1.0%	0.0%	23.0%	0.0%	0.0%	1.0%	0.0%	11.0%	0.0%	0.0%
Uygur (10)	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%	0.0%
Puerto Rican (28)	3.6%	0.0%	0.0%	0.0%	0.0%	7.1%	0.0%	0.0%	0.0%	0.0%

a. For STRUCTURE, the criterion was >0.85 membership in a particular cluster using K = 6. For PCA the criterion was mean +/- 2 SD for each of the first four PCs where the mean was determined based on the self-identified ethnic group.
b. The continental group is shown in bold and selected individual ethnic groups presented below each continental heading. For presentation purposes many of the individual ethnic groups were placed together: other European (OEUR), other East Asian (OEAS), other sub-Saharan African (OSSAFR) and other Amerindian (OAMI).
c. The Maya-Kachiquel were Maya from the Kachiquel language group as previously described[7] and is from a collection distinct from the HGDP Maya group.

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