Title: A study of the Bodrogköz population in North-Eastern Hungary by Y chromosomal haplotypes and haplogroups
Journal name:Molecular Genetics and Genomics
Authors: H. Pamjav, Á. Fóthi, T. Fehér and E. Fóthi
Corresponding author: Horolma Pamjav
Email:
Email:

Primers and Taqman probes are generally used.

Haplogroup and mutation name / Mutation / Forward primer / Reverse primer / Reporter 1 / Reporter 2 / Reference
KT-M9 / C->G / - / - / - / - / TaqMan SNP Genotyping Assay: rs3900; hCV11691379
J2b-M12 / G->T / GCCACCACCCCTAGCTAATTTT / CCAAGACTAGCCTGAGCAACATAG / CCCCCATCTCTACAAAT / CCCCCATATCTACAAAT / Custom TaqMan SNP Genotyping Assay
E1b1b1-M35 / G->C / CTCAGTGTCCCAATTTTCCTTTGG / GAACAACTAATCCATGCAGACTTTCG / CCTGTGTCCCAGTGTC / TGTGTCGCAGTGTC / Custom TaqMan SNP Genotyping Assay
C2-M38 / T->G / GCAATGGTATGTAGGCAATGAAAAATCTT / CTTCCACAATCTTTTAAAAACCTTACAACACA / CTTACTGAATAAAAAAGTTGG / CTTACTGAATAAAACAGTTGG / Custom TaqMan SNP Genotyping Assay
PR-M45 / G->A / - / - / - / - / TaqMan SNP Genotyping Assay: rs2032631; hCV2414552
J2a1-M47 / G->A / CCTGAATTTAATAGGTAAATCTGTTTTTAATTAGAGCTATATCA / CCAGAAGAAGGCTGAAATCAATCCA / AATGTCTTAACATAGAAGTTT / ATGTCTTAACATAAAAGTTT / Custom TaqMan SNP Genotyping Assay
H1-M52 / A->C / TCCCTGGCCAATAAAGGTGTTTT / GACGAAGCAAACATTTCAAGAGAGAA / CCTGCAAGGATGTTT / CTGCACGGATGTTT / Custom TaqMan SNP Genotyping Assay
J1a-M62 / T->C / ATGAAAAGTTTTACACATAGTTAAAAATACTAAAACACCATTA / AGATGGCAATTTTTTTTCAATGTTTGTTGG / CCATGGAAAGAGAAAG / CATGGAGAGAGAAAG / Custom TaqMan SNP Genotyping Assay
J2a2-M67 / A->T / CGTGTCCTAAAAGAAAAATGAGATTGTGA / TGATTATAGAAGCAAAGAGTCTTTTCACTTGT / CCCCTCTATATTTGTTTTT / CCCCTCTATATATGTTTTT / Custom TaqMan SNP Genotyping Assay
T-M70 / A->C / GCCCACTATACTTTGGACTCATGT / GCTGGACTATAGGGATTCTGTTGTG / CTCCATGAGAACTAAGAC / TCCATGAGACCTAAGAC / Custom TaqMan SNP Genotyping Assay
E1b1b1a-M78 / C->T / GTTCGACATGAACACAAATTGATACACT / AGCAAGTACTATGACCAGCTTATTTTGAA / ACTTCTTTCCGCCCTTC / ATACTTCTTTCTGCCCTTC / Custom TaqMan SNP Genotyping Assay
E1b1b1b-M81 / C->T / ACTATCATACTCAGCTACACATCTCTTAACA / GCGTAGGTATGTAGTAGATTGTTTCTTCTT / TGAGTATACTCTATGACGTTCA / AGTATACTCTATGACATTCA / Custom TaqMan SNP Genotyping Assay
H1a-M82 / -2bp / AGATCCAAAAAAACAGGAGAGCTAAGG / AGATTATAAAATAATGTTTAATACCTACTGAAGAAACAAACCTA / CTGGAAACATATGAAAAT / CTGGAAACATGAAAAT / Custom TaqMan SNP Genotyping Assay
FT-M89 / C->T / TGGATTCAGCTCTCTTCCTAAGGTT / AGCAAAGGTAGCTGCAACTCA / AAGTGAGAGATGAGATTT / AAAGTGAGAGATAAGATTT / Custom TaqMan SNP Genotyping Assay/ TaqMan SNP Genotyping Assay: rs2032652; hCV2259382
J2b-M102 / G->C / GGTAAATCTTTGAAATTTATTAAATGAAGTATAGATTGAATACAAGT / TTTATTCCTATGTTTGTTTTCCTTAATCTCTAGGG / CAATGGTGAGTAAGATG / CAATGGTGACTAAGATG / Custom TaqMan SNP Genotyping Assay
C1-M105 / C->T / GGTGAAAAGAGTAGACAATAAGGAAGGT / CACCTACTCCTTGCTGACTTGAG / ACCCATAGCATTTCT / ATTACCCATAACATTTCT / Custom TaqMan SNP Genotyping Assay
M1-M106 / A->G / CAAGCATAGCTTTGTTACTGGGAAA / CTTCCTTATTGTCTACTCTTTTCACCTCTT / CTATGACAGTATCAAAGAAA / TGACAGTATCGAAGAAA / Custom TaqMan SNP Genotyping Assay
O1a-M119 / A->C / GATGTAGAAAAATGTTATGGGTTATTCCAATTCA / CCGCAGTGCTATGTGTTTATTTGG / CATACAGGCTAAAATA / ACAGGCGAAAATA / Custom TaqMan SNP Genotyping Assay
O3-M122 / T->C / TGCTCTGTGTTAGAAAAGATAGCTTTATTCAG / TTGCCTTTTGGAAATGAATAAATCAAGGT / CCTGAGAGCATGAATT / CTGAGAGCGTGAATT / Custom TaqMan SNP Genotyping Assay
E1b1b1c-M123 / G->A / GTTGCCCAGGAATTTGCATTTCTA / ACAGAGCAAGTGACTCTCAAAGTC / CTAGCATATCAGCATCGC / TAGCATATCAACATCGC / Custom TaqMan SNP Genotyping Assay
R2-M124 / C->T / GCAAAGTTGAGGTTGCACAAACTC / GCAACACCAGAATCTAACAAAGCAA / TTATTAAACCGACTTCCC / TTATTAAACCAACTTCCC / Custom TaqMan SNP Genotyping Assay
CT-M168 / C->T / - / - / - / - / TaqMan SNP Genotyping Assay: rs2032595; hCV1083229
I-M170 / A->C / GCTCTTATTAAGTTATGTTTTCATATTCTGTGCA / GTGAGACACAACCCACACTGA / AAATCATTGTTCATTTTTT / AAATCATTGTTCCTTTTTT / Custom TaqMan SNP Genotyping Assay
J2-M172 / T->G / CCTCTCAGTATCAACAGGTAAAAAGGATT / GCCAGGTACAGAGAAAGTTTGGA / CATTTTGATGCTTTACTTAAA / TTGATGCTTGACTTAAA / Custom TaqMan SNP Genotyping Assay
R1-M173 / A->C / - / - / - / - / TaqMan SNP Genotyping Assay: rs2032624; hCV2292796
D-M174 / T->C / TCCTTTTTAATGTATCAAATCGCTTCTCTGA / CAAATGCACCCCTCACTTCTG / TTCTGGAGTGCCCTAGTG / CTGGAGTGCCCCAGTG / Custom TaqMan SNP Genotyping Assay
O-M175 / -5bp / TGAATCAGGCACATGCCTTCTC / AGAATATTAATGATACCTTTTTTTCTACTGATACCTTTGT / CATTCTTGAGAAGAGAAGT / CTGTTCATTCTTGAGAAGT / Custom TaqMan SNP Genotyping Assay
R1a1-M198 / C->T / CCAGTCATGATGAGGTGGAATGTAT / ACTCCCTAAACATTACATGAGAAATTGCT / ACCTAAAAGAGCTCTTTC / ACCTAAAAGAACTCTTTC / Custom TaqMan SNP Genotyping Assay
G-M201 / G->T / GCAATAGTTACTACTTGAGTTACTATATTAGTGCA / CAGCTTCATCCAACACTAAGTACCT / ACTGAGGGTTTTCG / ACTGAGGTTTTTCG / Custom TaqMan SNP Genotyping Assay
R-M207 / A->G / - / - / - / - / TaqMan SNP Genotyping Assay: rs2032658; hCV2307221
C-M216 / C->T / - / - / - / - / TaqMan SNP Genotyping Assay: rs2032666; hCV1017491
C3-M217 / A->C / GGTTAAGATTCTTTAACTTGTGAAGGAGAATG / GCTGCTGTGGCTTTCATCAAAATAA / CTTCTGAAGAGTTTGTGTCAC / CTGAAGAGTTGGTGTCAC / Custom TaqMan SNP Genotyping Assay
N-M231 / T->A / ATCATCATTCAATTAATACCTAAAAAACAACATTTACTGT / TTTGACACCACAGAAATTACAGGTATGA / TTCTACTGCTTTCGAATTG / TACTGCTTTCAAATTG / Custom TaqMan SNP Genotyping Assay
I2b -M223 / C->T / TGCCGCTATAAAAATTAGACTCTGTGTT / GCTGGAGTCTGCACATTGATAAATT / TGATGCAATTTATTTACGACTGT / ATGCAATTTATTTACAACTGT / Custom TaqMan SNP Genotyping Assay
I1-M253 / C->T / GATGCTCAGCTAACTAGTCCTGTTTATAG / GCAAGCATCATAGTAAACAAGGACTCA / CCTGGAGAAGTCAACT / CCTGGAGAAATCAACT / Custom TaqMan SNP Genotyping Assay
J-M304 / A->C / CAGTATGTGGGATTTTTTTAGATGTGTTCAA / AGAAATAAACAAATAACTTTCAAAACGTCTTATACCAAAA / TCACCAGTTGTTTCACAAG / ACCAGTTGTGTCACAAG / Custom TaqMan SNP Genotyping Assay
G2a-P15 / C->T / AGCCAATGCTTGAGGTTCTGAAT / CCACTTGTGGACTTTATCTAAATATGGGA / TGCCTTCAGGCGTAAG / CTGCCTTCAGACGTAAG / Custom TaqMan SNP Genotyping Assay
G2a-L156 / A->T / - / - / - / - / TaqMan SNP Genotyping Assay:
rs35190095
G1-M285 / G->C / - / - / - / - / TaqMan SNP Genotyping Assay:
rs13447378
G1a-P20 / C deletion / CCCATGGTTGGGATTGTGACT / CGCACATGAATCCTGGTTTTGT / CTTCGACCCAACTCA / TACTTCGACCAACTCA / Custom TaqMan SNP Genotyping Assay
R1b1-P25 / C->A / GGACCATCACCTGGGTAAAGTG / TGGACCGAGATACGAGACACAAT / TGCCTGCAAATAGA / CTGCCTGAAAATAGA / Custom TaqMan SNP Genotyping Assay
I2a1-P37.2 / T->C / CAAGCATAGTGATAGGGTGGGATT / CTGGCAAAGGCGGGAATC / TTTGGTTTACACTATGAACC / TGGTTTACACTGTGAACC / Custom TaqMan SNP Genotyping Assay
R1a1*-M198 (xM458xZ280xZ93) / C->T / CCAGTCATGATGAGGTGGAATGTAT / ACTCCCTAAACATTACATGAGAAATTGCT / ACCTAAAAGAGCTCTTTC / ACCTAAAAGAACTCTTTC / Custom TaqMan SNP Genotyping Assay
R1a1-M458 / T->C / GCTCAGGTGCCAGGGAATAAATT / TCACTTCTTGCTTTGAAAGACATTCCT / CCTGGCTCTCTTATCAAA / TGGCTCTCTCATCAAA / Custom TaqMan SNP Genotyping Assay
R1a1-Z280 / C->T / GCATAATTACTGCTGTCATCTTCCTGAA / CAAAGGTCTTTACTTGTGCAATATCATAAATGA / AGCTTTTAGTTAGATCCATTCTA / AGCTTTTAGTTAGATCTATTCTA / Custom TaqMan SNP Genotyping Assay
R1a1-Z93 / G->A / TCCCCAAATGAGTTAAAAGACATGAATGT / GCATGTCAGGGATTCAGGAAAAGA / ACTTCCTTTGGCTTCCA / ACTTCCTTTAGCTTCCA / Custom TaqMan SNP Genotyping Assay
E-SRY4064 / G->A / CTGTAATCCCAGCCCTTCGA / CCAGGATGGTCTCAATCTCTTCAC / ATCCGCTCGCCTTGA / ATCCGCTTGCCTTGA / Custom TaqMan SNP Genotyping Assay
M2a-SRY9138 / C->T / CCTGGTTGAGAGATTAAAATGTGTTGATATGA / GTGTTGGTTCTCCTGTAAAGTAATAAACCT / CTCTCGGCCCCCCTG / CTCTCGGTCCCCCTG / Custom TaqMan SNP Genotyping Assay
C,FT (xDE)-P143 / G->A / GATCCCAACTTCGGTTTTTGGTAAAA / ATCCAAGGAGCAACACAGTGT / AGCTCTTCATAACCCCA / CTCTTCACAACCCCA / Custom TaqMan SNP Genotyping Assay
N1c-Tat / T->C / - / - / - / - / TaqMan SNP Genotyping Assay: rs34442126; hCV61528117
N1c-L708 / C->A / GGTCCCAGAACAATAGGGAAAGATT / CCGCAGTCTCATTGTATTTGTGTAG / TTGCAAAGAGGGTTCAT / TTTGCAAAGAGTGTTCAT / Custom TaqMan SNP Genotyping Assay
R1b1-P312 / C->A / - / - / - / - / TaqMan SNP Genotyping Assay:
rs34276300
hCV61531537
R1b1-U106 / C->T / GTGCATAGGGATTCCTGAATAGCAA / GGAAGGCAGGTATTCAGAGAAGAAG / ATTGAACCCGTGGAGCT / AATTGAACCCATGGAGCT / Custom TaqMan SNP Genotyping Assay
R1b1-M412 / G->A / CCTGGGATAGAGAGTGTGAGAAGAAAT / GCACCTTCTATGTCATCTATCTTCATGT / ACCCTATCCATGCCTCAT / CCTATCCACGCCTCAT / Custom TaqMan SNP Genotyping Assay
R1b-M343 / C->A / - / - / - / - / TaqMan SNP Genotyping Assay: rs9786184
Q-M242 / C->T / - / - / - / - / TaqMan SNP Genotyping Assay:
rs8179021
I1-L22 / A->C / - / - / - / - / TaqMan SNP Genotyping Assay:
rs34626372
hCV61553744
J2-L24 / G->A / - / - / - / - / TaqMan SNP Genotyping Assay:
rs35248080
hCV61530225
N1b-P43 / G->A / GCCTGTAGTCCCAGCTACTTG / GGTGGGATCTTGGCTCACT / AATGGCGTGAACCC / AATGGCATGAACCC / Custom TaqMan SNP Genotyping Assay
J1-M267 / T->A / - / - / - / - / TaqMan SNP Genotyping Assay:
rs9341313

1