Skip to main content

Table 3 Translocations confirmed by published RNA sequencing data

From: Whole genome sequence analysis of BT-474 using complete Genomics’ standard and long fragment read technologies

ChrA GeneA ChrA start ChrA end GeneA strand ChrB GeneB ChrB start ChrB end GeneB strand Paper Supported by SV data Supported by raw reads
1 AHCTF1 247,002,400 247,094,726 - 4 NAAA 76,831,808 76,862,166 - Kangaspeska et al. yes SV_ID37 yes
17 STARD3 37,793,333 37,820,454 + 20 DOK5 53,092,266 53,267,710 + Edgren et al. no yes
20 VAPB 56,964,175 57,026,157 + 17 IKZF3 37,913,968 38,020,441 - Edgren et al. yes SV_ID124 yes
20 TRPC4AP 33,590,207 33,680,618 - 17 MRPL45 36,452,989 36,479,101 + Kangaspeska et al. no yes
20 RAB22A 56,884,771 56,942,563 + 19 MYO9B 17,186,591 17,324,104 + Edgren et al. yes SV_ID145 yes
  1. Translocations identified in the standard and LFR libraries were compared to RNA sequencing identification of translocations in BT-474 from publications of Edgren et al. [7] and Kangaspeska et al. [8]. An explanation of the fields are as follows: chrA, the chromosome for the A side of the translocation; geneA, the gene affected on the A side of the translocation; chrA start, the start of the breakpoint region for the chrA side; chrA end, the end of the breakpoint region for the chrA side; geneA strand, the coding direction of the gene on the A side of the translocation; chrB, the chromosome for the B side of the translocation; geneB, the gene affected on the B side of the translocation; chrB start, the start of the breakpoint region for the chrB side; chrB end, the end of the breakpoint region for the chrB side; geneB strand, the coding direction of the gene on the B side of the translocation; paper, the publication in which the translocation was identified; supported by SV data (if there is evidence from at least one of our libraries to support this translocation a “yes” will appear in the table followed by the SV ID for our translocation, otherwise a “no” will appear); supported by raw reads (if there is evidence from at least one mate-pair read in one of our libraries to support this translocation a “yes” will appear in the table followed by the SV ID for our translocation, otherwise a “no” will appear)