Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes

Martínez-Cruz, Begoña; Ziegle, Janet; Sanz, Paula; Sotelo, Graciela; Anglada, Roger; Plaza, Stéphanie; Comas, David

doi:10.1186/2041-2223-2-13

Investigative Genetics

Table 1 Genetic markers analysed in the OpenArray, the Y haplogroup they define, the alleles and their call rates (successful genotype calls)

From: Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes

List of genetic markers analysed				List of genetic markers analysed (continuation)				List of genetic markers analysed (continuation)
Marker	Haplogroup^a	Alleles^b	Call rate (%)	Marker	Haplogroup^a	Alleles^b	Call rate (%)	Marker	Haplogroup^a	Alleles^b	Call rate (%)
M216	C	C/T	95.8	P259	I1d	T/G	96.6	M231	N	G/A	94.7
M168	CT	C/T	98.1	P215	I2	A/G	95.1	M128	N1a	2-bp del	97.0
M174	D	T/C	97.7	P37.2	I2a	T/C	96.6	P43	N1b	G/A	96.6
M145^c	DE	G/A	96.6	P41.2	I2a1	T/C	97.3	P105	N1c	G/A	96.2
M203^c	DE	G/C	96.6	M26	I2a2	G/A	95.5	M214	NO	G/C	96.6
M96	E	G/C	98.1	M223	I2b	C/T	96.2	M119	O1a	A/C	99.2
P147	E1	T/A	97.7	M284	I2b1	ACAA/del	96.2	P31	O2	T/C	95.8
M33	E1a	A/C	95.5	M379	I2b2	GT/del	97.0	M122	O3	T/C	98.9
P177	E1b	C/T	93.6	P95	I2b4	G/T	95.1	M45	P	G/A	96.2
P2	E1b1	C/T	97.3	P123	IJ	T/C	94.3	M242	Q	C/T	97.3
M2	E1b1a	A/G	97.0	M304	J	A/C	94.3	M207	R	A/G	95.5
M215	E1b1b	A/G	97.3	M267	J1	T/G	95.5	M173	R1	A/C	93.2
M35	E1b1b1	G/C	95.8	M62	J1a	T/C	95.5	SRY10831.2	R1a	G/A	99.6
M78	E1b1b1a	C/T	98.1	M365	J1b	A/G	Failed	M56	R1a1a	A/T	97.7
V12	E1b1b1a1	A/G	97.3	M390	J1c	A/ins	Failed	M157	R1a1b	A/C	98.1
V13	E1b1b1a2	G/A	97.0	P56	J1d	A/G	96.6	M204	R1a1c	T/G	95.8
V22	E1b1b1a3	T/C	97.7	P58	J1e	T/C	95.5	P98	R1a1d	C/T	Failed
V65	E1b1b1a4	G/T	96.2	M172	J2	T/G	96.6	PK5	R1a1e	C/T	95.8
M81	E1b1b1b	C/T	89.8	M410	J2a	A/G	95.5	M343	R1b	C/A	97.3
M123	E1b1b1c	G/A	97.7	M47	J2a1	G/A	96.6	M18	R1b1a	2-bp ins	96.6
M281	E1b1b1d	G/A	97.0	M340	J2a10	G/C	94.7	P297	R1b1b	G/C	95.8
V6	E1b1b1e	G/C	99.6	M419	J2a11	AAAAG/del	95.8	M73	R1b1b1	2-bp del	96.2
P72	E1b1b1f	G/A	98.1	P81	J2a12	C/T	Failed	M269	R1b1b2	C/T	96.2
M329	E1b1c	G/C	98.1	P279	J2a13	G/A	98.1	L23	R1b1b2a	A/G^e	84.8
P75	E1b2	G/A	Failed	M67	J2a2	A/T	95.1	P311	R1b1b2a1	A/G	97.0
M75	E2	G/A	97.7	M92	J2a2a	T/C	96.2	U106	R1b1b2a1a	C/T	97.3
M89	F	C/T	97.7	M68	J2a3	A/G	91.3	U198	R1b1b2a1a1	G/A	98.5
M201	G	G/T	95.5	M137	J2a4	T/C	97.7	P107	R1b1b2a1a2	G/A	Failed
M285	G1	G/C	96.6	M158	J2a5	G/A	97.7	P312	R1b1b2a1b	A/C^e	97.3
P20	G1a	C/del	95.8	M289	J2a6	G/A	96.6	M65	R1b1b2a1b1	A/T	96.6
P76	G1b	G/C	98.9	M318	J2a7	T/C	97.3	M153	R1b1b2a1b2	T/A	97.7
P287	G2	G/T	96.6	M319	J2a8	T/A	97.7	SRY2627	R1b1b2a1b3	C/T	97.3
P15	G2a	C/T	97.7	M339	J2a9	T/G	97.7	U152	R1b1b2a1b4	C/T	97.0
M287	G2b	A/T	97.0	M12	J2b	G/T	97.0	M126	R1b1b2a1b4a	4-bp del	97.3
M377	G2c	A/G	94.7	M205	J2b1	T/A	98.1	M160	R1b1b2a1b4b	A/C	96.2
M69	H	T/C	97.0	M241	J2b2	G/A	Failed	L21	R1b1b2a1b5	C/G	97.7
M52	H1	A/C	95.5	M9a^d	K	C/G	97.3	M37	R1b1b2a1b5a	C/T	87.9
Apt	H2	G/A	92.8	M9b^d	K	C/G	97.3	M222	R1b1b2a1b5b	G/A	97.7
M170	I	A/C	97.0	M20	L	A/G	94.3	P66	R1b1b2a1b5c	G/A	98.1
M253	I1	C/T	97.0	M27	L1	C/G	94.7	M335	R1b1c	T/A	96.2
M21	I1a	A/T	96.2	M317	L2	GA/del	94.3	M124	R2	C/T	98.1
M72	I1b1	A/G	98.1	M357	L3	C/A	97.3	M70	T	A/C	97.0
P109	I1c	G/A	95.8	P256	M	G/A	97.7

^aHaplogroups are based upon data published by Karafet et al. [8] and on the Internal Society of Genetic Genealogy (ISOGG) 2009 Y-DNA SNP Index website (http://isogg.org/tree/ISOGG_YDNA_SNP_Index09.html).
^bThe two alleles of each marker (ancestral or derived) are shown.
^cBoth markers (M145 and M203) define the same branch of the human Y-chromosome phylogeny (haplogroup DE).
^dMarker M9 was genotyped with two independent assays, with TaqMan probes labelled with different fluorophores (see "SNP selection" inside the Material and Methods section).
^eAncestral allele not available.

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ISSN: 2041-2223

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