Y-SNP 35plex Assay

A Y-Chromosome SNP Assay for Co-amplification of 25 DNA Fragments and Simultaneous Detection of 35 Human Y-SNPs

Juan J. Sanchez et al. (2003) Forensic Sci. Int., 137(1):74-84; Email address: juan.sanchez@forensic.ku.dk

Table 1: Y Chromosome single nucleotide polymorphisms (SNPs) and primer sequences for PCR amplification

Locus	GenBank or dbSNPs accesion	Mutation	PCR Primers Forward Primer	(5’ à 3’) Reverse Primer	mM	Amplicon Size (bp)
M2/sY81	Rs3893	A/G	acggaaggagttctaaaattcagg	aaaatacagctccccctttatcct	0.15	128
M9*	Rs3900	C/G	aggaccctgaaatacagaactg	aaatatttcaacatttcacaaaggaa	0.36	186
M17*	Rs3908	4G/3G	cctggtcataacactggaaatc	agctgaccacaaactgatgtaga	0.09	170
M18*	Rs3909	2 bp insertion	cctggtcataacactggaaatc	agctgaccacaaactgatgtaga	0.09	170
M19*	Rs3010	T/A	cctggtcataacactggaaatc	agctgaccacaaactgatgtaga	0.09	170
M32*	AC009977	T/C	tgaccgtcataggctgagaca	ttgaagcccccaagagagac	0.07	160
M33*	AC009977	A/C	tgaccgtcataggctgagaca	ttgaagcccccaagagagac	0.07	160
M35	Rs1179188	G/C	agggcatggtccctttctat	tccatgcagactttcggagt	0.42	96
M40/SRY₄₀₆₄	AC006040	G/A	tggtctcaatctcttcaccctgt	catttcagtaaatgccacacaaga	0.18	119
M45*	Rs2032631	G/A	gagagaggatatcaaaaattggcagt	tgacagtggcaccaaaggtc	0.03	138
M46/Tat	AC002531	T/C	tatatggactctgagtgtagacttgtga	ggtgccgtaaaagtgtgaaataatc	0.46	115
M52	AC009977	A/C	cctcaacttcccagagtgttg	gacgaagcaaacatttcaagagag	0.03	152
M78*	AC010889	C/T	tgcattactccgtatgttcgac	tggaagcttaccatctttttatga	0.08	132
M81*	Rs2032640	C/T	catctcttaacaaaagaggtaaattttgtcc	cattgtgttacatggcctataatattcagt	0.24	179
M89	Rs2032652	C/T	tggattcagctctcttcctaaggttat	ctgctcaggtacacacagagtatca	0.03	135
M96	AC010889	G/C	tgccctctcacagagcactt	ccacccactttgttgctttg	0.27	143
M123	AC010889	G/A	gttgcccaggaatttgcat	cacagagcaagtgactctcaaag	0.02	88
M139*	AC010137	5G/4G	ccccgaaagttttattttattcca	ttctcagacaccaatggtcctatc	0.06	113
M151*	AC010889	G/A	catctcttaacaaaagaggtaaattttgtcc	cattgtgttacatggcctataatattcagt	0.24	179
M153*	AC010137	T/A	ccccgaaagttttattttattcca	ttctcagacaccaatggtcctatc	0.06	113
M154*	AC010889	T/C	catctcttaacaaaagaggtaaattttgtcc	cattgtgttacatggcctataatattcagt	0.24	179
M157*	AC010889	A/C	gagagaggatatcaaaaattggcagt	tgacagtggcaccaaaggtc	0.03	138
M163*	AC009977	A/C	aggaccctgaaatacagaactg	aaatatttcaacatttcacaaaggaa	0.36	186
M167/SRY₂₆₂₇	AC006040	C/T	cggaaccactaccagcttca	agttaaggccccacgcagt	0.03	113
M170	Rs2032597	A/C	cagctcttattaagttatgttttcatattctgtg	gtcctcattttacagtgagacacaac	0.07	119
M172	Rs2032604	T/G	tgagccctctccatcagaag	gccaggtacagagaaagtttgg	0.16	179
M173	Rs2032624	A/C	ttttcttacaattcaagggcatttag	ctgaaaacaaaacactggcttatca	0.10	81
M175	Rs2032678	-5bp	gatttaaactctctgaatcaggcacat	ttctactgatacctttgtttctgttcattc	0.02	79
M212*	Rs2032664	C/A	ccatataaaaacgcagcattctgtt	tggagagaacttgagaaaaagtagagaa	0.12	176
M213*	Rs2032665	T/C	ccatataaaaacgcagcattctgtt	tggagagaacttgagaaaaagtagagaa	0.12	176
M224*	AC010889	T/C	tgcattactccgtatgttcgac	tggaagcttaccatctttttatga	0.08	132
SRY₁₀₈₃₁/SRY₁₅₃₂	Rs2534636	A/G	tcatccagtccttagcaaccatta	ccacataggtgaaccttgaaaatg	0.06	150
12f2	AC005820	present/absent	cactgactgatcaaaatgcttacagat	ggatcccttccttacaccttataca	0.06	90
92R7	Rs2535813	GA/A	ttaaatccctcctatttgtgctaacc	aatgcatgaacacaaaagacgtaga	0.04	89
P25	Rs150173	C/CA	tggaccatcacctgggtaaagt	ggcagtataaggttgtcacatcacat	0.01	109

*SNP markers on the same DNA fragment: (M9 and M163), (M17, M18 and M19), (M32 and M33), (M45 and M157), (M78 and M224), (M81, M151 and M154), (M139 and M153), (M212 and M213). All primers were redesigned compared to previously published primers.

Table 2: Minisequencing primer sequences of 35 Y chromosome SNP markers

PCR Primers

Forward Primer

Reverse Primer

Amplicon