PCR and Minisequencing Primers for the Y-Chromosomal SNP Markers
| Locus | Primer[ii] [iii] | Sequence, 5′ to 3′[iv] | Size of PCR product (bp) | Nucleotide variation[v] | References |
| DYS271[i] | 5′ PCR primer | GCT CCC CTG TTT AAA AAT GTA GG | 136 | A/G | Seielstad et al. 1994 |
| (M2) | 3′ PCR primer | TAC AGC TCC CCC TTT ATC CTC C | |||
| ms primer | CCT TTA TCC TCC ACA GAT CTC A | ||||
| 92R7[i] | 5′ PCR primer | TGC ATG AAC ACA AAA GAC GTA | 100 | C/T | Mathias et al. 1994 |
| 3′ PCR primer | GCA TTG TTA AAT ATG ACC AGC | Hurles et al. 1999 | |||
| ms primer | TTA AAT ATG ACC AGC AAA GAC AA | ||||
| SRY4064[i] | 5′ PCR primer | CCA GCC CTT CGA GAG GTC AA | 106 | G/A | Whitfield et al. 1995 |
| 3′ PCR primer | CAG GAT GGT CTC AAT CTC TTC | ||||
| ms primer | CTC TTC ACC CTG TGA TCC GCT | ||||
| SRY9138 | 5′ PCR primer | GTT GAT ATG ATA TTA TAG AGG C | 118 | C/T | Whitfield et al. 1995 |
| 3′ PCR primer | ACC TAC ATG CAA AAA TAA GGA TG | ||||
| ms primer | GAG GCA AAT TTA ATG CTC TCG G | ||||
| SRY10831[i] | 5′ PCR primer | TGG CCT CTT GTA TCT GAC TTT TT | 112 | A/G | Whitfield et al. 1995 |
| (SRY-1532) | 3′ PCR primer | CAA GGC ACC ACA TAG GTG AAC | Kwok et al. 1996 | ||
| ms primer | CAT AGG TGA ACC TTG AAA ATG TTA | Veitia et al. 1997 | |||
| DYS199 | 5′ PCR primer | AAT AGG TTG ACC TGA CAA TGG | 113 | C/T | Underhill et al. 1996 |
| (M3) | 3′ PCR primer | TCA TTT TAG GTA CCA GCT CTT | |||
| ms primer | AAT GGG TCA CCT CTG GGA CTG A | ||||
| PN1 | 5′ PCR primer | AGG AAC AAG GGT CTT GAG AGG | 98 | C/T | Hammer et al. 1997 |
| 3′ PCR primer | TAT CTC TTC CCC TTT AAG ACA A | ||||
| ms primer | AAG GGT CTT GAG AGG GAG AGC | ||||
| PN2[i] | 5′ PCR primer | CTT CAT GCT GGT TAA AGG AGC A | 145 | C/T | Hammer et al. 1997 |
| 3′ PCR primer | ACC TCA GAA TCA GCT CCA | ||||
| ms primer | AGG TGC CCC TAG GAG GAG AA | ||||
| PN3 | 5′ PCR primer | AGC ATC TGA GAA AAC TGC CTC | 104 | A/G | Hammer et al. 1997 |
| 3′ PCR primer | CAA TGC TCC TAA CTC TAA TTT AC | ||||
| ms primer | TCT GAG AAA ACT GCC TCT GCT TGA | ||||
| Tat[i] | 5′ PCR primer | CTC TGA GTG TAG ACT TGT GA | 146 | T/C | Zerjal et al. 1997 |
| 3′ PCR primer | GAA GGT GCC GTA AAA GTG TGA A | ||||
| ms primer | CTC TGA AAT ATT AAA TTA AAA CAA C | ||||
| SRY2627 | 5′ PCR primer | CGC AGT TTG GCT TCC GGG CC | 121 | C/T | Veitia et al. 1997 |
| 3′ PCR primer | TTC ACC CTG TAG GGC ATG GG | Bianchi et al. 1997 | |||
| ms primer | CCA AGG AAG CCC CAC AGG GTG C | ||||
| M4[i] | 5′ PCR primer | TCC TAG GTT ATG ATT ACA GAG CG | 319 | A/G | Underhill et al. 1997 |
| (DYS234) | 3′ PCR primer | GCA GAA CAT TTG TAC TGT TCC | |||
| ms primer | ACT AGA TAT AGA TCT TAG ATA TGA TTA | ||||
| M6 | 5′ PCR primer | ACC ACA TTT CTG GTT GGC TTG T | 132 | C/T | Underhill et al. 1997 |
| 3′ PCR primer | CCC TAC TTT GAT GGC TAA TAC TA | ||||
| ms primer | TGG TTG GCT TGT AGT TCT TTC T | ||||
| M7 | 5′ PCR primer | GCA TCA CCA AAG GGC ATG TAA TC | 116 | C/G | Underhill et al. 1997 |
| 3′ PCR primer | TGA GTT ACT GTT CTT CTT GTT GTT | ||||
| ms primer | AAA GGG CAT GTA ATC ATT CCT CT | ||||
| M8[i] | 5′ PCR primer | CCC ACC CAC TTC AGT ATG AA | 318 | G/T | Underhill et al. 1997 |
| 3′ PCR primer | ACT CGA GGC TGA CAG AC | ||||
| ms primer | GAC CAA TAG AAG AAC TGC CCA A | ||||
| M9 | 5′ PCR primer | GTA AGA CAT TGA ACG TTT GAA CA | 154 | C/G | Underhill et al. 1997 |
| 3′ PCR primer | GCA GCA TAT AAA ACT TTC AGG A | ||||
| ms primer | GAA ACG GCC TAA GAT GGT TGA AT | ||||
| M11 | 5′ PCR primer | GCA TAA ACA AGA ACT TAC TGA G | 270 | A/G | Underhill et al. 1997 |
| 3′ PCR primer | TAT CTC TCT GTC TGT CTC TC | ||||
| ms primer | CCC TCT CTC CTT GTA TTC TAA C | ||||
| M12[i] | 5′ PCR primer | CTC CCG AGT AGC TGG GAA | 155 | G/T | Underhill et al. 1997 |
| DYS260 | 3′ PCR primer | AGC AGT CCA AGA CTA GCC TGA G | |||
| ms primer | TGA GCA ACA TAG TGA CCC CCA T | ||||
| M13 | 5′ PCR primer | GCC ATG ATT TTA TCC AAC C | 142 | C/G | Underhill et al. 1997 |
| 3′ PCR primer | GGG CAG TAG GTA GGT TAA GGG | ||||
| ms primer | GTA GGT TAA GGG CAA GAC GGT TA | ||||
| M14 | 5′ PCR primer | TGT TAA AAC TGA GCT TCA TTA AC | 204 | T/C | Underhill et al. 1997 |
| 3′ PCR primer | GGT TGG ATA AAA TCA TGG CT | ||||
| ms primer | ATT ATA AAT GAA AAA ATC AGT AAC ATG | ||||
| M17 | 5′ PCR primer | CAA ACT GAT GTA GAG ACA TCT | 175 | G/T[vi] | Underhill et al. 1997 |
| 3′ PCR primer | ACT CAC CAG AGT TTG TGG TTG | ||||
| ms primer | GTG GTT GCT GGT TGT TAC GGG | ||||
| M19 | 5′ PCR primer | CAA ACT GAT GTA GAG ACA TCT | 175 | A/T | Underhill et al. 1997 |
| 3′ PCR primer | ACT CAC CAG AGT TTG TGG TTG | ||||
| ms primer | AAA CTA TTT TTG TGA AGA CTG TTG TA | ||||
| M20 | 5′ PCR primer | TCT ACA TGT TCA GTG CAA ATG CA | 211 | A/G | Underhill et al. 1997 |
| 3′ PCR primer | GAT TGG GTG TCT TCA GTG CT | ||||
| ms primer | GTC AAC CAA CTG TGG ATT GAA AAT | ||||
| M21[i] | 5′ PCR primer | ATT TGA GCA GGC AGA AGA ATC A | 197 | A/T | Underhill et al. 1997 |
| 3′ PCR primer | TTG TGG GTA ATA GGC ATG TCT | ||||
| ms primer | CTG GAA GCT AAG TCA ACT GAA AC | ||||
| M22[i] | 5′ PCR primer | TCC CTA TTT GTT TTA AGG TGC CA | 121 | A/G | Underhill et al. 1997 |
| 3′ PCR primer | GCA GAC TAA GGC CCA TAT GGG | ||||
| ms primer | TAT GGG CAC TGG GGG AAG GAG G |
[i] Detection from complementary DNA strand compared to reference.
[ii] PCR primers contained the nonspecific universal sequences TTC TAA TAC GAC TCA CTA TAG GGA GA and GCG GTC CCA AAA GGG TCA GT in the 5′ end of either the forward or the reverse primers. The minisequencing primers contained a spacer-sequence of 15 T-residues in their 5′ ends.
[iii] ms = Minisequencing.
[iv] Primer sequences shown in bold were designed for this study; unbolded primer sequences are from the reference.
[v] The nucleotide variation is given as in the reference.
[vi] M17 is a deletion of G; T is the next nucleotide detected in the minisequencing reaction.