Kun:LabNotes/ExonomeSeq/2009-11-22
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Additional Sanger confirmation of mutations[edit]
- I used the reads that came from the CV-fibroblast library Alice made on 10/09/09 as the reference to call variants in the HL022 CV-iPS data. The CV-fibroblast library was suboptimal, so I filtered out all synonymous variants, and manually check each candidate in the HuRef database. Eventually I found 12 candidates, for which the PCR primers were designed and ordered.
- Athurva also performed variant calling independently, and found three additional candidates that were not in my list. These three candidates were also included in the Sanger validation.
Primer ID | Sequence | Primer ID | Sequence | Amplicon Info |
USP54-S252F-LP | TAGGCAGCCCAGAGTTTAAG | USP54-S252F-RP | TTGTGCTTCACTGTCCTGAT | >chr10:74946544+74946945 402bp |
PSMG1-M88T-LP | CCTACCGAGGGATTGGATTT | PSMG1-M88T-RP | TATTACCCCGTGAGCATGTG | >chr21:39474076+39474498 423bp |
CDKN2AIP-S330L-LP | CACGGTTCTGCATCATTTGT | CDKN2AIP-S330L-RP | GCTGCTCTTGGAAGCTAGTA | >chr4:184604546+184604959 414bp |
GSG1-V252I-LP | AGATGCCTACCTCCATTCTT | GSG1-V252I-RP | ATTCTCCCCTTCTCAGATGC | >chr12:13131979+13132379 401bp |
SPEN-L929*-LP | GAGAGCAAAGCCCTGAAAAG | SPEN-L929*-RP | TCCAGATCCACAGCACTTAC | >chr1:16127853+16128258 406bp |
PBLD-R81*-LP | ACTAGGCTCAGGTTTGATTCT | PBLD-R81*-RP | CTAGACCTCAGCAACCCAAA | >chr10:69721742+69722146 405bp |
OR6Q1-L305V-LP | AGACTGTGGATTTCCTGGTG | OR6Q1-L305V-RP | ATATCCAAGGCAAGGAAACT | >chr11:57555599+57555992 394bp |
KIAA0564-I963L-LP | CACAACCACACACTGTGAAA | KIAA0564-I963L-RP | TTCAGTCACCCAGTGAAGTT | >chr13:41156992+41157383 392bp |
ZWILCH-N56H-LP | TTCCATTGACTTGCATAGAACT | ZWILCH-N56H-RP | AGAACTCATTTTCACCGATGC | >chr15:64593287+64593586 300bp |
TIAM1-K1469R-LP | TTCACGGACTCACAGAACTC | TIAM1-K1469R-RP | ATGCTCCATGACAGATTGGT | >chr21:31414786+31415195 410bp |
DSP-M2819I-LP | GCTATGCCAAAATCCTGACC | DSP-M2819I-RP | CAAGCACCGGGATTTTCTTT | >chr6:7530800+7531199 400bp |
RNF20-R415K-LP | AGTCACAGTTCTCCGTCTTG | RNF20-R415K-RP | TCTCACATACACGTAAGCTCT | >chr9:103352770+103353351 582bp |
STK33-V270L-LP | TGGCAAAAATTGTTCAAGCTG | STK33-V270L-RP | GAACCCCAGAATTCAATGCAA | >chr11:8430558+8431132 575bp |
OR13F1-S229G-LP | CTGCCATGGTGGAAATGATG | OR13F1-S229G-RP | AGGATTCAACATGGGGGTTT | >chr9:106306828+106307225 398bp |
GOLGA4-G1943D-LP | ACAGGCTTTACAACAGATGGA | GOLGA4-G1943D-RP | TGGGTTGGTGAAACTTATCC | >chr3:37344033+37344432 400bp |