Evaluating Parental Population Sex Biased Gene Flow in African Americans

Supplementary Table 1. TaqMan SNP Genotyping Assays for the Y chromosome and mtDNA

Marker / ID/Locus / DNA / Polymorphism a / PCR Primer / Probe / TM / SNP region /
m9 / rs3900 / Y / C / G / F: ACCCTGAAATACAGAACTGCAAAGA
R: ACTAAGTATGTAAGACATTGAACGTTTGAACA / ATGGTTGAATGCTCTTTA
AAGATGGTTGAATCCTCTTTA / 60 / CAGGACCCTGAAATACAGAACTGCAAAGAAACGGCCTAAGATGGTTGAAT[C/G]CTCTTTATTTTTCTTTAATTTAGACATGTTCAAACGTTCAATGTCTTACA
m45 / rs2032631 / Y / G / A / F: AGAGAGGATATCAAAAATTGGCAGTGAA
R: GGCCTGGACCTCAGAAGGA / AAATTATAGATAAGCAAAAAG
AATTATAGATAGGCAAAAAG / 60 / TAACTCTAGGAGAGAGGATATCAAAAATTGGCAGTGAAAAATTATAGATA[G/A]GCAAAAAGCTCCTTCTGAGGTCCAGGCCAGGAGATAGTAGGATTTAAGAA
m60 / rs2032623 / Y / - / T / F: CAGACTCTGTCTTTACATTTCAAAATGCA
R: GACACAGACCAACATTGAGTAACCA / TGTGCCTGATCTTTA
TGTGCCTGATACTTTA / 60 / ATAAACACATACAGACTCTGTCTTTACATTTCAAAATGCATGACTTAAAG[▬/T]ATCAGGCACACAGTGGTTACTCAATGTTGGTCTGTGTCTCTGTAACGTAA
m69 / rs2032673 / Y / T / C / F: GCCTGTTCAAATCCAAAAGCTTCAG
R: TTGGATCTTTATTCCCTTTGTCTTGCT / CTCCTGAAACAAAATA
CACTCCTGAAATAAAATA / 60 / GTAGCCTGTTCAAATCCAAAAGCTTCAGGAGGCTGTTTACACTCCTGAAA[T/C]AAAATATATTTCAGCAAGACAAAGGGAATAAAGATCCAAAAAAACAGGAG
m89 / rs2032652 / Y / C / T / C___2259382_1Y b / 60 / GCTCAGCTTCCTGGATTCAGCTCTCTTCCTAAGGTTATGTACAAAAATCT[T/C]ATCTCTCACTTTGCCTGAGTTGCAGCTACCTTTGCTGGTGATCCTGGACC
m96 / rs9306841 / Y / G / C / F: TGTAAAGGACCATATATTTTGCCATAGGTTT
R: GCTGTGATGTGTAACTTGGAAAACA / CTCATAATACGATAAAAC
TCTCATAATAGGATAAAAC / 60 / GACCATATATTTTGCCATAGGTTTTTAATATTATACCTGAGTGTTTTATC[G/C]TATTATGAGAGACCTGTTTTCCAAGTTACACATCACAGCTCACTTTAAAG
m170 / rs2032597 / Y / A / C / F: GCTCTTATTAAGTTATGTTTTCATATTCTGTGCA
R: GTGAGACACAACCCACACTGA / AAATCATTGTTCCTTTTTT
AAATCATTGTTCATTTTTT / 60 / TTCTGTGCATTATACAAATTACTATTTTATTTACTTAAAAATCATTGTTC[A/C]TTTTTTTCAGTGTGGGTTGTGTCTCACTGTAAAATGAGGACCTGTTTTTG
m203 / rs2032653 / Y / G / C / F: CAACAGCGGCGGTAGTGA
R: CGTGGGACTTGGAAATTTGTTGTT / CATGAAATCGTGCGCAGT
TCCATGAAATCCTGCGCAGT / 60 / TTTGCCTCATCACCGAAGGCAACAGCGGCGGTAGTGAGCGACACTGCGCA[G/C]GATTTCATGGAAACAACAAATTTCCAAGTCCCACGACGATACCCAACCTT
m207 / rs2032658 / Y / A / G / C___2307221_1Y b / 60 / GGAAAAAACGTTACAACTATGGGGCAAATGTAAGTCAAGCAAGAAATTTA[A/G]AAAGAGAATAACAATACCTTTTGAATAATCTTCCAACAAGAGGTTGAAGT
m216 / rs2032666 / Y / C / T / F: CAACCAGTTTTTATGAAGCTAGAAAAAAATTCC
R: GGTTCTAAATCTGAATTCTGACACTGCTA / ATACCTGTTGAATATTACATTT
CCTGTTGAATGTTACATTT / 60 / AACCAGTTTTTATGAAGCTAGAAAAAAATTCCTTTATTAAAGAAATGTAA[C/T]ATTCAACAGGTATACATAACTAGCAGTGTCAGAATTCAGATTTAGAACCA
+3594 / MTND1 / mtDNA / T / C / F: CAAAGGCCCCAACGTTGTAG
R: GCTAGGCTAGAGGTGGCTAGAAT / AGGTTGAGGTTAACCAG
CTAGGTTGAGGTTGACCAG / 58 / ACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGT[T/C]AACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGT
+1018 / MTRNR1 / mtDNA / A / G / F: CCCTCCCCAATAAAGCTAAAACTCA
R: GGGTCTTAGCTATTGTGTGTTCAGA / TGACACAAAATAAACTAC
TTGACACAAAATAGACTAC / 56 / TAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATA[A/G]ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAA
+10400 / MTND3 / mtDNA / C / T / F: GAAATTGCCCTCCTTTTACCCCT
R: CTAAGAGGGAGTGGGTGTTGAG / TATATACCAATTCAGCTCAGTC
ACCAATTCGGCTCAGTC / 58 / CTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAAC[C/T]GAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTA
+15043 / MTCYB / mtDNA / G / A / F: CCAATGGCGCCTCAATATTCTTTAT
R: CCGATGTTTCAGGTTTCTGAGTAGA / CATCGGACGAGGCC
ATCGGGCGAGGCC / 60 / CACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGG[G/A]CGAGGCCTATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGG
+9540 / MTCO3 / mtDNA / C / T / F: GCAGGATTTTTCTGAGCCTTTTACC
R: GATGTGTTTAGGAGTGGGACTTCT / CCCCCCAATTAGGAG
CCCCCCAACTAGGAG / 60 / CAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAA[C/T]TAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA
+10873 / MTND4 / mtDNA / C / T / F: ACAACCACCCACAGCCTAATTATT
R: GGCTTGCCATGATTGTGAGG / ATCATCCCCCTACTATT
CATCATCCCTCTACTATT / 58 / ATAATTTGAATCAACACAACCACCCACAGCCTAATTATTAGCATCATCCC[C/T]CTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCCAAC

SNP polymorphism detection was performed using PCR with a program consisting of 3 minutes denaturing at 95˚C followed by 50 cycles for the Y chromosomes SNPs and 30 cycles for the mtDNA SNPs (except +10400 = 35 cycles and +3594 = 40 cycles). Cycles consisted of 15 s denaturing at 92˚C and 1 minute at the specific temperature listed in the table. The product was genotyped in a 7900HT DNA sequence detector (AB).

aThe ancestral allele is shown on the left.

bThe assay number from Applied Biosystems is provided since the probe and PCR primer sequences were not available