The population structure of the primary scan families was inferred using the model-based clustering software STRUCTURE [37].
Six microsatellites that were positive for linkage in the primary scan, as well as the 6 additional microsatellites added for the refined mapping, were genotyped in 26 of the additional 79 multicase families that were Muslim.
For Chromosomes 2 (7 markers) and 11 (7 markers), microsatellites that were positive for linkage in the primary scan, as well as the 7 additional microsatellites added for the refined mapping, were genotyped in the 79 additional multicase families.
Instead, for markers DXS6799 and DXS8020 (Figure S2) used in the primary scan (see Table 4), the primary binary decision and splitting function clustered families east of the UTM easting 322,321 m, with 16 families living west of this split contributing to LOD scores of 1.14 and 1.15, respectively.
For Chromosomes 6 (5 markers) and 8 (5 markers) microsatellites that were positive for linkage in the primary scan, as well as the 4 additional microsatellites added for the refined mapping, were genotyped in 52 of the additional 79 multicase families that were Hindu.
Unrelated individuals from the primary scan families were tested for K = 1 to 4 subpopulations using three different ancestry models and assuming that the allele frequencies are fairly similar across this Indian population: (i) Admixture/Correlated frequencies, (ii) No admixture/Correlated frequencies and (iii) Linkage/Correlated frequencies.
The primary scan provided evidence (≥2 adjacent markers allele-sharing LOD≥0.59; nominal P≤0.05) for linkage on Chromosomes 2, 5, 6, 7, 8, 10, 11, 20 and X, with peaks at 6p25.3-p24.3 and 8p23.1-p21.3 contributed to largely by 31 Hindu families and at Xq21.1-q26.1 by 27 Muslim families.
This analysis will be referred to as the primary scan.
The primary scan forms the basis of the analysis, whereas the secondary scan is used to correct the intensities of spots with saturation in the primary scan.
