A Microsphere-Based Assay for Multiplexed Single Nucleotide Polymorphism Analysis Using Single Base Chain Extension

Table 2.

Calculated MESF Values for Multiplexed Analysis

DNA sample ddNTP terminator reaction SNP analyzed
503 504 505 506 507 509 510 511 512 513 514 515
CEPH1 A −40 989 15,415 2,866 1,727 23,113 1,800 2,051 2,986 4,750 2,114 37,943
C 1,118 3,062 2,341 4,263 3,128 3,060 22,545 26,298 4,676 34,825 2,862 2,502
G 30,260 17,380 10,218 40,707 44,653 854 1,713 2,077 18,400 3,360 31,014 2,052
T 1,677 2,997 766 4,868 2,630 3,428 1,862 3,097 2,139 31,556 1,350 3,399
CEPH2 A 24,324 1,281 1,158 36,042 2,001 14,220 2,671 2,695 3,273 5,775 31,821 20,874
C 682 2,983 1,701 6,047 56,597 1,108 23,931 27,097 4,258 35,886 2,979 813
G 13,750 8,003 20,345 19,321 19,224 616 1,348 2,082 2,544 3,418 15,880 1,400
T 2,681 10,827 781 3,629 2,011 24,111 2,846 3,200 17,666 36,343 3,463 30,878
CEPH3 A −300 1,404 31,515 8,101 1,950 13,979 2,155 3,071 3,236 5,454 1,392 41,198
C 852 2,574 616 5,550 8,467 1,321 11,044 22,882 1,511 4,293 2,145 1,331
G 27,595 15,679 1,128 41,843 43,402 288 886 1,563 10,563 3,606 31,904 1,612
T 1,154 2,407 1,681 4,091 1,661 22,340 10,387 3,386 13,856 63,945 1,021 3,665
CEPH4 A 21,336 1,409 14,919 3,654 1,707 29,352 2,341 2,062 2,487 5,333 1,090 39,260
C 747 1,235 992 5,141 2,310 1,788 30,619 12,469 2,622 5,754 2,299 1,856
G 14,173 8,235 10,605 49,175 49,640 1,174 2,042 2,679 10,182 4,703 31,362 1,152
T 1,843 10,360 1,424 5,601 3,083 4,322 3,176 10,497 11,547 57,578 1,695 3,436
CEPH5 A 667 1,509 16,122 3,563 1,332 27,454 1,379 2,370 4,242 5,533 2,124 38,337
C 621 3,295 −225 7,332 2,046 3,560 30,488 22,694 3,809 32,136 2,506 2,943
G 30,852 17,229 10,238 48,006 48,465 1,235 2,052 2,901 3,591 4,860 32,230 2,980
T 2,125 2,449 2,170 5,201 2,163 3,127 3,233 3,685 25,453 34,144 2,932 3,118
CEPH6 A 21,077 1,331 14,439 37,356 1,884 12,900 2,253 2,886 3,023 5,775 1,520 33,546
C 2,873 2,006 1,083 6,681 57,081 2,337 30,141 22,979 4,060 7,013 2,746 3,118
G 13,735 7,809 10,383 25,831 22,917 900 1,996 2,685 4,185 4,661 30,584 2,295
T 1,939 10,925 516 5,166 2,234 22,665 2,799 4,301 27,736 69,067 2,289 2,794
CEPH7 A 466 1,012 31,337 37,161 2,412 12,493 2,495 3,040 3,820 6,882 1,848 39,483
C 1,154 2,472 2,215 5,889 54,698 2,098 37,761 23,440 3,622 7,953 2,947 3,590
G 33,017 18,848 1,344 25,874 22,774 1,346 2,650 3,494 4,091 5,444 32,169 1,363
T 2,428 1,276 1,304 5,636 1,828 21,973 2,774 4,218 26,748 67,520 1,186 2,820

  • ↵Twelve SNPs (SNP503–SNP515) were amplified separately and pooled. The pooled samples were then analyzed in a multiplexed single base chain reaction as described in Methods. MESF values indicating the presence of a particular allele are indicated in boldface type. Sequences of PCR primers and capture oligonucleotides will be provided upon request.

This Article

  1. Genome Res. 10: 549-557

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