Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations

Naidoo, Thijessen; Schlebusch, Carina M; Makkan, Heeran; Patel, Pareen; Mahabeer, Rajeshree; Erasmus, Johannes C; Soodyall, Himla

doi:10.1186/2041-2223-1-6

Table 2 Single base extension (SBE) primer sequences and final concentrations used in the study, grouped by assay.

From: Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations

SNP		SBE primer (5' - 3')	Size (mers)	Concentration (μM)	Assay
SRY10831	FW	(C)₃CTCTTGTATCTGACTTTTTCACACAGT	30	0.10	YSNP1
M168	FW	(C)₁₂TGGAGTATGTGTTGGAGGTGAGT	35	0.40
M89	RV	(GACT)₂(C)₁₀CAACTCAGGCAAAGTGAGAGAT	40	0.40
M201	FW	(GACT)₂(C)₉AGATCTAATAATCCAGTATCAACTGAGG	45	0.40
M69	FW	(GACT)₄(C)₁₁GGAGGCTGTTTACACTCCTGAAA	50	0.40
M170	FW	(GACT)₄(C)₉ACTATTTTATTTACTTAAAAATCATTGTTC	55	0.80
M172	FW	(GACT)₇(C)₁₂CCAAACCCATTTTGATGCTT	60	0.40
M9	FW	(GACT)₈(C)₁₁AAACGGCCTAAGATGGTTGAAT	65	0.40
M207	FW	(GACT)₈(C)₁₁GCAAATGTAAGTCAAGCAAGAAATTTA	70	0.80
M198	FW	(GACT)₉(C)₉TCAGTATACCAATTAATATTTTTGAAAGAG	75	0.80
M343	FW	(GACT)₁₃(C)₉AGAGTGCCCTCGTGTTCCA	80	0.40
M91	FW	CCTACATTGCTATTCTGTTTTTTTT	25	0.60	Hg-A
M31	RV	(C)₈CCACTGCTGTTCTGTCTACCA	29	0.60
M14	RV	(C)₅CTTCATTAACTTTTTTAAACTGCTTATA	33	0.60
M114	RV	(C)₁₅AGCTGTACAAGGCTCTTCAAAT	37	0.60
P28	FW	(C)₁₄GGTTAAAAGAAAAAAGCTCTCAGATAG	41	0.40
M28	RV	(C)₂₇TCGAGGTCCTCTGGCATC	45	0.50
M51	RV	(C)₂₉CTCTGATCCCTGTTGGAAGC	49	0.50
M13	FW	(C)₃₁GTAGGTTAAGGGCAAGACGGTTA	54	0.60
M171	RV	(C)₃₂AGGTCTCTGACTGTTCAGTTTTATT	57	0.50
M118	RV	(C)₃₅CAGCTGACACTTGTGTTTTCTTTATA	61	0.20
M60	FW	(C)₃TTACATTTCAAAATGCATGACTTAAAG	30	0.40	Hg-B
M146	RV	(C)₁₁CTAAAACCCAGTGTTAATTACCCG	35	0.80
M182	FW	(C)₁₃CTTAAAGCAGTGGTTAATGTAAACAAA	40	0.80
M150	FW	(C)₂₂TGCCCACACACACAGATAGAAGT	45	0.80
M152	FW	(C)₂₃GCTTTCTCCTGATAATGTTCTTCTTCT	50	0.80
M108	RV	(C)₂₇CTTTTCTCTGACATTCAGGTATAGTTTC	55	0.30
M43	FW	(C)₃₉CTCTTTCCATGGCCAACAAAC	60	0.40
M112	FW	(C)₃₈AAAGAGGTGAGATAAAAACAAAGCAGT	65	0.40
P6	FW	(C)₃TCAATAGAGGTTTCCACAGTTAAGTCT	30	0.10	Hg-B2b
M115	FW	(C)₃CAGAGTTTAAATTAGTATTTGATTTCACATTA	35	0.80
M30	FW	(C)₁₄ATCATGTTTTAAGTCCTGACATCTGT	40	0.10
P7	FW	(C)₂₁CCATCACCTGGGTAAAGTGAATTA	45	0.40
P8	FW	(C)₂₇GCAGCTCACCTTTCATTTAGGTC	50	0.20
M211	FW	(C)₃₀TAGGCAAAAGGATGTTAACAACAAG	55	0.80
M40	RV	(C)₁₀TCTTCACCCTGTGATCCGCT	30	0.60	Hg-E
M33	FW	CGATCTGTTCAGTTTATCTCATAAGTTACTAGTTA	35	0.30
M44	RV	(C)₁₁AGGAAATCTCCTAACCTTCTAGTACACTG	40	0.40
M75	FW	(C)₂₀AAAAGACAATTATCAAACCACATCC	45	0.10
M41	FW	(C)₃₀TGGCCAACATGGTGAAACTG	50	0.50
M85	RV	(C)₂₄GCTTGTGTTCTATTAAGTGTAGTTTTGTTAG	55	0.20
P2	RV	(GACT)₈(C)₈AGGTGCCCCTAGGAGGAGAA	60	0.40
M2	RV	(GACT)₉(C)₆CCCTTTATCCTCCACAGATCTCA	65	0.60
M35	RV	(GACT)₁₀(C)₉TTCGGAGTCTCTGCCTGTGTC	70	0.80
M58	FW	(C)₅ATTTATTGTCTTCTGCAGAATTGGC	30	0.10	Hg-E1b1a
M116	FW	(C)₅GCTTTCTGAAAAAATAATTTCAAACTGATA	35	0.40
M149	FW	(C)₉CTAACAAAACTACACTTAATAGAACACAAGC	40	0.10
M154	RV	(C)₁₆GTGTTACATGGCCTATAATATTCAGTACA	45	0.40
M155	RV	(C)₂₃AATTCAGAATATTTCATCTCTGGTCAC	50	0.40
M10	FW	(C)₂₆AATTTTTTTGTTTATTCCCAATGATCTTA	55	0.50
M191	FW	(GACT)₅(C)₁₀ATTTACATTTTTTTCTTTACAACTTGACTA	60	0.40
M78	FW	AATTGATACACTTAACAAAGATACTTCTTTC	31	0.80	Hg-E1b1b1
M148	RV	(C)₇TTTCTAGGTAACGTATGTAGACATTTCTG	36	0.80
M81	FW	(C)₁₅AGAGGTAAATTTTGTCCTTTTTTGAA	41	0.80
M107	FW	(C)₁₈TAAGCCAACGTATTAACCTTCTAATTTC	46	0.20
M165	RV	(C)₂₀AAATATTTCAGGTAAAACCACTCTATTAGTA	51	0.40
M123	FW	(C)₂₇AAAGTCACAGTATCTGAACTAGCATATCA	56	0.80
M34	FW	(GACT)₇(C)₁₃GCCTGGCTTCCACCCAGGAG	61	0.20
M136	RV	(GACT)₈(C)₁₂GGTGAGCAGCATTGAGGAAGAC	66	0.10
M281	RV	(GACT)₈(C)₁₁AGGTTGCACAAACTCAGTATTATTAAAC	71	0.80

SNP, single nucleotide polymorphism; FW, forward orientation; RV, reverse orientation

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ISSN: 2041-2223

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