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

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Table 3 Translocations confirmed by published RNA sequencing data

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

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)

ISSN: 2047-217X