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

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

  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
  1. 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