TIA: algorithms for development of identity-linked SNP islands for analysis by massively parallel DNA sequencing

BMC Bioinformatics

Table 1 Identity-Linked SNP Island Identification within the Human Genome using Computational Algorithms

	Target Identification Filter			Sequence Repetition Rejection Filter			Primer Design Feasibility Filter
Chromosome	5-SNP	4-SNP	3-SNP	5-SNP	4-SNP	3-SNP	5-SNP	4-SNP	3-SNP
1	311	1231	4557	126	478	1689	3	0	2
2	350	1185	4666	131	444	1759	2	0	1
3	288	1085	3973	116	417	1530	0	0	6
4	368	1218	4306	137	463	1699	0	0	4
5	256	939	3546	80	328	1314	0	1	0
6	289	987	3717	104	374	1414	1	1	3
7	255	933	3393	79	326	1244	0	2	0
8	203	748	3015	83	297	1229	1	1	2
9	167	581	2333	55	192	902	1	0	0
10	230	819	2891	76	300	1143	1	0	0
11	228	754	2878	96	299	1197	0	0	2
12	201	732	2593	62	261	967	1	0	2
13	181	608	2179	62	221	797	0	0	2
14	120	469	1748	32	168	641	1	0	1
15	129	446	1653	44	152	617	0	0	0
16	140	416	1630	41	144	589	0	1	1
17	123	446	1654	37	151	566	0	1	2
18	123	444	1597	54	164	587	0	0	1
19	126	411	1399	36	99	362	0	0	0
20	108	377	1372	38	139	521	0	0	3
21	93	302	993	28	111	370	0	0	2
22	60	199	751	23	68	275	1	0	0
X	119	485	2027	41	154	722	0	1	0
Y	0	0	0	0	0	0	0	0	0
TOTAL	4468	15,815	58,871	1581	5750	22,134	12	8	34
Remaining Target Islands	79,154			29,465			54

The human reference genome (version GRCh37.p13) was computationally filtered for unique, identity-linked SNP islands, containing a minimum of 5, 4, or 3 identity-relevant SNPs. SNP islands amenable to analysis by Illumina sequencing chemistries and to targeted amplification from the genome were located using a target identification filter, a sequence repetition rejection filter, and a primer design feasibility filter

ISSN: 1471-2105