Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population

BMC Genomics

Table 3 Regions of the genome with excess San ancestry in TB cases relative to controls

Length			Mean San ancestry
Region	Begin-end SNP	(Nr SNPs)	TB cases	Control	Genes
1p31	rs12144711-rs7554551	671230 (123)	0.2902	0.1615	GADD45A, GNG12, DIRAS32
9q21	rs2309428-rs1847503	2080640 (323)	0.2909	0.1609	FAM189A, APBA1, PTAR1, C9orf135, MAMDC2, SMC5, KLF9
22q12	rs16986925-rs6006426	1290997 (152)	0.2850	0.1745	C22orf31, KREMEN1, EWSR1, RHBDD3, EMID1, AP1B1, RASL10A, GAS2L1, NEFH, RFPL1, NF2, NIPSNAP1, THOC5, UQCR10, CABP7, ZMAT5, ASCC2, MTMR3, HORMAD2, LIF, OSM

This table summarizes regions of the genome with excess San ancestry, found in TB cases relative to controls, after adjusting for age, gender and genome-wide San ancestry. Ancestry segments that are associated with increased San ancestry in cases compared to controls were identified and contiguous segments were merged. P-values for each of the individual ancestry segments are available in Additional file 1: Table S1. The mean RFMix genome-wide San ancestry estimates are 0.2304 and 0.1847 for cases and controls respectively, and the standard deviation of San local ancestry deviations is 0.0258 and 0.0321 in cases and controls respectively. Only regions of 500 000 base pairs or longer are shown (two short regions on chromosome 5 were excluded).

ISSN: 1471-2164