Lack of direct evidence for natural selection at the candidate thrifty gene locus, PPARGC1A

BMC Medical Genetics

Table 1 Populations, genotyping platforms and analyses used to evaluate evidence of association and selection in PPARGC1A

		Phenotype
Population	Genotyping Platform	Gout (n)	Control (n)	Analysis
NZ Caucasian	TaqMan SNP Assay	647	360	Single Marker GLM + F_ST on rs8192678
NZ Māori	TaqMan SNP Assay	137	176	Single Marker GLM + F_ST on rs8192678
CI Māori	TaqMan SNP Assay	71	64	Single Marker GLM + F_ST on rs8192678
Samoan	TaqMan SNP Assay	144	76	Single Marker GLM + F_ST on rs8192678
Tongan	TaqMan SNP Assay	73	41	Single Marker GLM + F_ST on rs8192678
Māori	AXIOM SNP chip	35	36	F_ST, Fay and Wu’s H, Tajima’s D, iHS and XP-EHH
Samoan	OMNIexpress chip	48	48	F_ST, Fay and Wu’s H, Tajima’s D, iHS and XP-EHH
		Unknown Phenotype
1KGP CEU	WGS	99		F_ST, Fay and Wu’s H, Tajima’s D, iHS and XP-EHH
1KGP CHB	WGS	103		F_ST, Fay and Wu’s H, Tajima’s D, iHS and XP-EHH
1KGP CHS	WGS	108		F_ST, Fay and Wu’s H, Tajima’s D, iHS and XP-EHH
1KGP GBR	WGS	92		F_ST, Fay and Wu’s H, Tajima’s D, iHS and XP-EHH
1KGP YRI	WGS	109		F_ST, Fay and Wu’s H, Tajima’s D, iHS and XP-EHH

All individuals in the Māori AXIOM and Samoan OMNIexpress datasets were also genotyped by the TaqMan® assay, and included in their respective population groups. NZ = New Zealand. CI = Cook Islands. WGS = whole genome sequencing. 1KGP = 1000 genomes project (http://www.1000genomes.org/home). Populations used were Utah, USA residents with Northern and Western European ancestry (CEU, Han Chinese in Beijing, China (CHB), Southern Han Chinese (CHS), China, British in England and Scotland (GBR) and Yoruba in Ibadan, Nigeria YRI. For a complete description of the 1000 Genomes project samples see http://www.1000genomes.org/data#DataAvailable. No phenotypic data were available for these populations

ISSN: 1471-2350