Supporting information for Heredity original article
Population-specific recombination sites within human MHC region.
Tze Hau Lam . Meixin Shen . Jer-Ming Chia . Soh Ha Chan . Ee Chee Ren
Figure Legends
Supplementary Figure 1 Recombination site within the sperm-typed recombination region between STR markers
3-7 to BAT2-GT. (a) EHH plot of HLA-C-B haplotypes across the LTA-BAT2 recombination region (42kb). (b) The
allelic calls of the Illumina GoldenGate MHC genotyped SNPs on HLA-B*40-01, B*46:01, B*38:02 and B*58:01
haplotypes telomeric and centromeric of the recombination interval. (c) Re-sequencing across an 7kb segment
(position 31,676,401 to 31,683,255) that overlaps with the SNPs recombination interval. The HLA haplotypes are
derived from SNPs ascertained through re-sequencing. Positions highlighted in green correspond to SNPs in the
Illumina GoldenGate MHC panel and their allelic calls are highlighted in red while the others are polymorphic sites
revealed by re-sequencing. (d) Location of 1703bp recombination site refined by re-sequencing and the repetitive
elements in close proximity to the site.
Supplementary Figure 2 Recombination site within the sperm-typed recombination region between STR markers
RING-CA to DPB2A2. (a) EHH plot of HLA-DRB1 haplotypes across the BDR2-HLA-DPB1 recombination region
(102kb). (b) The allelic calls of the Illumina GoldenGate MHC genotyped SNPs on HLA-DRB1*09-01,
DRB1*15:01 and
DRB1*04:05 haplotypes telomeric and centromeric of the recombination interval. (c) Re-
sequencing acrossan 4.5kb segment (position 33,129,124 to 33,133,678) that overlaps with the SNPs recombination
interval. The HLA haplotypes are derived from SNPs ascertained through re-sequencing. Positions highlighted in
green correspond to SNPs in the Illumina GoldenGate MHC panel and their allelic calls are highlighted in red while
the others are polymorphic sites revealed by re-sequencing. (d) Location of 1677bp recombination site refined by resequencing and the repetitive elements in close proximity to the site.
Supplementary Figure 3 Extended haplotype homozygosity (EHH) plots of SNP haplotypes for common HLA-A
haplotypes. (a) CHSG, (b) CEU and (c) YRI. Dots in the panels above each plot indicate the SNPs interval where
haplotypes break, with each color denoting a specific HLA-A haplotype. Positions of recombination sites and their
relative sizes are mapped onto the plots as follows: recombination segments identified by sperm recombinants
(highlighted in pink columns) and HapMap-inferred sites that coincide with EHH drops (highlighted in blue
columns).
Supplementary Figure 4 Extended haplotype homozygosity (EHH) plots of SNP haplotypes for common HLA-CB haplotypes. (a) CHSG, (b) CEU and (c) YRI. Dots in the panels above each plot indicate the SNPs interval where
haplotypes break, with each color denoting a specific HLA-C-B haplotype. Positions of recombination sites and
their relative sizes are mapped onto the plots as follows: recombination segments identified by sperm recombinants
(highlighted in pink columns) and HapMap-inferred sites that coincide with EHH drops (highlighted in blue
columns).
Table Legends
Supplementary Table 1 List of oligonucleotide primers. (a) used to amplify the recombination site intervals for resequencing, (b) used for the recombination site telomeric to HLA-F, (c) used for the recombination site between LTA
- BAT2 and (d) used for the recombination site between BRD2 - HLA-DPA1.
Supplementary Table 2 HLA allele frequencies. (a) HLA-A, (b) HLA-B , (c) HLA-C and (d) HLA-DRB1.
Supplementary Table 3 Common HLA haplotype frequencies. (a) 3-locus HLA-A-C-B haplotype, (b) 3-locus
HLA-C-B-DRB1 haplotype and (c) 4-locus HLA-A-C-B-DRB1 haplotype.
Supplementary Table 4 Number of common and population-specific recombination sites identified in the CHSG,
CEU and YRI across HLA-A and –B region.