Data on common variants associated with coronary artery disease/myocardial infarction in ethnic Arabs.

The data shows results acquired in a large cohort of 5668 ethnic Arabs involved in a common variants association study for coronary artery disease (CAD) and myocardial infarction (MI) using the Affymetrix Axiom Genotyping platform ("A genome-wide association study reveals susceptibility loci for myocardial infarction/coronary artery disease in Saudi Arabs" Wakil et al. (2015) [1] ). Several loci were described that conferred risk for CAD or MI, some of which were validated in an independent set of samples. Principal Component (PCA) analysis suggested that the Saudi Cohort was close to the CEU and TSI populations, thus pointing to similarity with European populations.

Specifications table

Value of the data

Genomic distribution of risk variants for CAD/MI in ethnic Arabs.

Comparative analysis of the genomic distribution of the associated loci for CAD/MI between the Arab population and other ethnic groups.

Regional association plots demonstrate loci on 2q33, 8q13, 9p31 for CAD and on 21q22.11 for MI.

Principal component analysis comparison with 11 other MApMAp3 populations shows variations and clustering of ethnic populations.

The Saudi Arab cohort show similarities with the Caucasian populations.

Data

The summary puts together the clinical features of the studied cases versus controls, the genomic distribution of the implicated variants and the principal component analysis of the data, as well as comparison of the Saudi population with other ethnic groups(Fig. 1, Fig. 2, Fig. 3)(Table 1).

Fig. 1

Regional association plots for coronary artery disease and myocardial infarction.

Fig. 2

Principal Component Analysis.

Fig. 3

Principal component analysis.

Table 1

Important clinical features and demographics of the coronary artery disease cases (CAD) versus angiographed controls

	CAD controls			CAD cases
	All	Male	Female	All	Male	Female
Gender	3000	1590(0.53)	1410(0.47)	2668	2028(0.76)	640(0.24)
Age	49.8±0.30	50.3±0.40	49.2±0.40	59.8±0.20	59.3±0.25	61.6±0.40
BMI	29.4±0.12	28.3±0.15	30.6±0.19	29.3±0.10	28.5±0.10	31.9±0.23
MI	933	589(0.63)	344(0.37)	2495	1919(0.77)	576(0.23)
T2DM	1207	646(0.54)	561(0.46)	1848	1354(0.73)	494(0.27)
HTN	1846	963(0.52)	883(0.48)	2187	1631(0.75)	556(0.25)
lHDLC	907	592(0.65)	315(0.35)	1353	1115(0.82)	238(0.18)
hLDLC	312	166(0.53)	146(0.47)	346	251(0.73)	95(0.27)
hTG	1846	963(0.52)	883(0.48)	2187	1631(0.75)	556(0.25)
hChol	710	365(0.51)	345(0.49)	1177	876(0.74)	301(0.26)
FH	679	378(0.56)	301(0.44)	500	397(0.79)	103(0.21)
OBS	1228	533(0.43)	695(0.57)	1087	710(0.65)	377(0.35)
Smokers	882	820(0.93)	62(0.07)	1251	1219(0.97)	32(0.03)
VD
One	0	0	0	973	718(0.74)	255(0.26)
Two	0	0	0	529	408(0.77)	121(0.23)
>Two	0	0	0	1164	910(0.78)	254(0.22)

The numbers in brackets give the percentages of the total (all) values of the group. BMI, body mass index; FH, family history of CAD; MI, myocardial infarction; hLDLC, high low density lipoprotein-cholesterol level; lHDLC, low high density lipoprotein-cholesterol level; hTG, hypertriglyceridaemia; hChol, hypercholesterolaemia; HTN, hypertension; T2DM, type 2 diabetes mellitus; VD, number of diseased vessels.

The figure shows the loci on loci 2q33, 8q13, 9p31 associated with coronary artery disease and locus 21q22.11.associated with and myocardial infarction.

The figure shows the first and second principal component plot for the Saudi Arab samples (4431 samples: 2165 cases and 2266 controls) with eleven other HapMap3 populations (ASW, African ancestry in Southwest USA; CEU, Utah residents of European ancestry; CHB, Han Chinese in Beijing, China; CHD, Chinese in Metropolitan Denver, Colorado; JPT, Japanese in Tokyo, Japan; GIH, Gujarati Indians in Houston, Texas; LWK, Luhya in Webuye, Kenya; MKK, Maasai in Kinyawa, Kenya; TSI, Tuscans in Italy; YRI, Yoruba in Ibadan, Nigeria; MEX, Mexicans).

The figure displays the first and second principal component plot of the Saudi Arab samples (4431 samples: 2165 cases and 2266 controls) without Hapmap3 populations.

Experimental design, materials and methods

The discovery study involved 5668 Saudi Arabs who were subjected to genotyping using Affymetrix Axiom Genome-Wide ASI Array (Asian population). Genotyping data were generated using the Axiom GT1 algorithm and an IBS/IBD analysis in PLINK [2]. Analyses of the genome-wide association (GWA) were based on a linear mixed model method using FASTLMM-Select with Principal Component (PCs) as in Lippert et al. [3] and Widmer et al. [4]. Heritability estimation was performed according to Yang et al. [5] implemented in Genome-wide Complex Trait analysis (GCTA) software and extended in REACTA. The population substructure was examined by Principal Component Analysis (PCA) using the GCTA as described by Yang and colleagues [5] to eliminate the outliers that do not conform to the main cluster of samples that form the Saudi cohort, and may therefore lead to false positive results.

Subject area	Genetics
More specific subject area	Genetics of complex cardiovascular diseases
Type of data	Tables and figures
How data was acquired	Data table was acquired using statistical methods by SPSS,
Data format	Raw and analyzed data
Experimental factors	None
Experimental features	Genome-wide association experiments were performed using Affymetrix platform; analysis performed using PLINK, GTCA, FASTLMM and principal Component Analysis
Data source location	All regions of Saudi Arabia
Data accessibility	Data is with this article