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Detection of indels in iPS cells

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Akio Miyao edited this page Jun 21, 2019 · 2 revisions

Detection of indels in iPS cells

In a comparison between a male sample in the Personal Genome Project Caucasian, PGP1 (NA20431) and iPS cells from the same person based on the bidirectional method, we detected 81 indels.

Sequence: PGP1 https://www.ncbi.nlm.nih.gov/sra/?term=SRX337951, PGP1-iPS https://www.ncbi.nlm.nih.gov/sra/?term=SRR101449

Reference: Gore, A. et al. Somatic coding mutations in human induced pluripotent stem cells. Nature 471, 63–67 (2011).

Junction by 5' to 3' alignment Junction by 3' to 5' alignment Type Size PGP1 PGP1iPS Genotype Sequence between junction
Chromosome Position Chromosome Position Ref Alt Ref Alt
1 93,576,235 1 93,576,230 insertion 2 8 0 6 9 H AC
1 156,700,590 1 156,700,596 deletion -8 6 0 22 13 H T
1 173,873,700 1 173,873,691 insertion 1 6 1 14 8 H TTTTTTT
1 200,575,544 1 200,575,524 deletion -2 6 0 18 17 H ACACACACACACACACACACA
2 48,713,934 2 48,713,934 deletion -1 5 1 31 22 H
2 61,869,659 2 61,869,653 deletion -4 6 0 5 7 H TTTCTTTCT
2 68,513,777 2 68,513,776 deletion -6 5 0 8 8 H ATAGAG
2 102,665,093 2 102,665,081 insertion 1 5 1 11 6 H TTTTTTTTTT
2 110,164,502 2 110,164,488 deletion -1 5 0 13 7 H AAAAAAAAAAAAAA
2 113,723,239 2 113,723,235 insertion 3 6 0 6 8 H
2 186,828,802 2 186,828,795 deletion -1 6 1 5 6 H AAAAAAA
2 186,844,689 2 186,844,679 deletion -1 10 0 8 9 H AAAAAAAAAA
3 188,609,147 3 188,609,138 insertion 1 11 0 15 8 H TTTTTTT
3 198,076,934 3 198,076,934 deletion -1 6 1 30 38 H
4 48,175,996 4 48,175,986 insertion 8 6 0 21 12 H A
4 68,234,426 4 68,234,419 insertion 1 5 1 14 9 H AAAAA
4 87,891,813 4 87,891,804 insertion 8 6 0 6 10 H
4 174,310,773 4 174,310,771 deletion -2 10 1 17 11 H TGT
5 98,856,463 5 98,856,463 deletion -3 5 1 25 19 H AG
5 129,023,616 5 129,023,604 insertion 1 7 0 5 10 H TTTTTTTTTT
5 146,509,136 5 146,509,125 deletion -1 5 1 8 7 H TTTTTTTTTTT
5 157,753,934 5 157,753,922 insertion 1 5 1 5 5 H TTTTTTTTTT
5 176,494,153 5 176,494,152 deletion -3 5 0 16 17 H GTT
6 43,454,257 6 43,454,254 deletion -2 5 0 7 8 H AGAG
6 53,498,695 6 53,498,693 deletion -4 5 0 10 17 H GGCTG
6 69,333,105 6 69,333,117 deletion -12 5 0 9 7 H C
6 73,787,521 6 73,787,514 insertion 1 6 0 9 5 H TTTTT
6 80,200,914 6 80,200,906 deletion -1 5 1 16 11 H TTTTTTTT
6 80,200,917 6 80,200,906 deletion -1 5 1 16 11 H TTTTTTTTTTT
6 85,194,133 6 85,194,126 insertion 1 5 1 5 8 H AAAAA
6 97,231,672 6 97,231,659 deletion -1 5 0 13 10 H GGGGGGAAAAAAA
6 124,823,398 6 124,823,381 deletion -2 5 1 9 6 H ACACACACACACACACAC
6 138,278,351 6 138,278,350 insertion 1 5 0 11 14 H A
7 16,674,383 7 16,674,365 insertion 4 8 1 14 12 H TATTTATTTATTT
7 16,697,138 7 16,697,113 insertion 4 5 0 10 7 H TTTGTTTGTTTGTTTGTTTG
7 83,469,119 7 83,469,112 insertion 1 8 1 19 19 H TTTTT
7 90,346,829 7 90,346,826 deletion -3 5 1 32 20 H TTCTT
8 24,501,623 8 24,501,614 deletion -2 5 1 16 13 H TTTTTTTTTT
8 39,082,637 8 39,082,625 deletion -1 7 0 27 12 H TTTTTTTTTTTT
8 66,793,604 8 66,793,591 insertion 1 7 0 6 3 H TTTTTTTTTTT
8 81,829,343 8 81,829,341 insertion 1 7 1 7 7 H
8 86,477,337 8 86,477,335 deletion -2 14 1 21 17 H ACA
9 5,812,762 9 5,812,754 insertion 4 5 1 6 7 H AGT
9 74,630,434 9 74,630,433 deletion -1 7 1 27 20 H G
9 86,310,622 9 86,310,621 deletion -2 6 0 17 15 H TG
9 86,325,309 9 86,325,303 deletion -1 8 0 16 13 H GGGGGG
9 107,485,929 9 107,487,025 deletion -1,101 6 0 30 42 H ACCT
9 107,485,930 9 107,487,025 deletion -1,101 6 0 30 41 H ACCTG
9 107,485,931 9 107,487,025 deletion -1,101 6 0 30 40 H ACCTGT
10 50,203,578 10 50,203,581 insertion 14 5 0 9 7 H ATCCTATGGTGAAGAGGG
10 88,275,227 10 88,275,226 deletion -1 6 1 1 5 M T
10 96,576,869 10 96,576,856 insertion 1 5 0 12 9 H AAAAAAAAAAA
10 122,332,347 10 122,332,340 insertion 1 8 0 21 10 H GGGGG
11 34,931,553 11 34,931,541 insertion 1 5 1 18 14 H TTTTTTTTTT
11 73,679,516 11 73,679,515 insertion 3 6 1 6 6 H TAT
12 13,608,898 12 13,608,896 deletion -1 5 0 9 7 H AA
12 20,711,556 12 20,711,547 insertion 1 6 0 22 16 H AAAAAAA
12 69,739,696 12 69,739,692 deletion -1 5 0 5 4 H GGGG
12 82,357,287 12 82,357,286 deletion -3 7 0 13 11 H ATC
13 28,292,291 13 28,292,284 deletion -1 6 1 9 9 H AAAAAAA
13 45,252,868 13 45,252,859 insertion 1 10 1 45 29 H TTTTTTT
13 60,528,447 13 60,528,444 deletion -3 7 1 38 27 H ATAAT
13 110,208,752 13 110,208,751 deletion -2 6 0 35 35 H TA
14 71,073,540 14 71,073,525 insertion 2 5 0 36 28 H CTCTCTCTCTCT
14 71,073,541 14 71,073,525 insertion 2 5 0 36 27 H CTCTCTCTCTCTC
14 71,073,542 14 71,073,525 insertion 2 5 0 36 26 H CTCTCTCTCTCTCT
14 81,503,993 14 81,503,992 deletion -1 7 0 8 4 H T
15 50,490,248 15 50,490,238 deletion -1 9 1 13 6 H TTTTTTTTTT
15 51,768,473 15 51,768,460 insertion 1 5 1 5 4 H TTTTTTTTTTT
15 70,984,149 15 70,984,144 deletion -3 5 0 36 27 H CAACAAC
16 19,544,939 16 19,544,938 deletion -2 5 1 17 10 H AT
16 50,320,132 16 50,320,132 deletion -4 8 0 8 7 H AAA
16 84,022,721 16 84,022,722 deletion -2 6 0 14 14 H
16 84,977,819 16 84,977,818 deletion -1 6 0 7 10 H A
17 40,766,480 17 40,766,468 deletion -2 6 0 11 5 H TCTCTCTCTCTCT
18 697,378 18 697,379 deletion -2 5 0 15 13 H
18 12,027,943 18 12,027,943 deletion -1 7 0 10 8 H
18 26,460,007 18 26,460,001 deletion -1 5 1 5 6 H TTTTTT
18 42,923,785 18 42,923,771 deletion -1 6 0 9 6 H AAAAAAAAAAAAAA
18 74,081,925 18 74,081,919 insertion 1 10 0 25 20 H TTTT
19 9,126,030 19 9,126,022 insertion 5 7 0 22 16 H AT
20 488,781 20 489,779 deletion -1,001 12 0 45 21 H CT
20 21,382,069 20 21,382,066 deletion -1 5 0 10 8 H AAA
21 10,570,672 21 10,570,665 deletion -1 6 0 28 14 H AAAAAAA
21 29,066,644 21 29,066,632 deletion -1 5 0 8 4 H TTTTTTTTTTTT
X 55,146,313 X 55,159,135 deletion -12,819 6 0 16 20 H AGTG
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