jmcdani
commented
2 months ago Deletion event appears correct
Evidence of non-clonal? In ~200X region, at deletion coverage drops to ~175X potentially only on one haplotype and maybe only in some cells.
Nearby germline small variants Ribbon shows a number of reads that do no have deletion. The reads that indicate deletion all seem to have nearby small insertions, 11 and 24bp, these are not see on reads that span the deleted region. These small insertions do appear in some portion of the normal reads. Looking in IGV germline variants support this region is diploid, het germline variants seen in normal remain het in tumor.
Occurs inside deletion --> 8 bp deletion in normal in half reads, implying on one haplotype however deleted region in tumor seem to have 3 kinds of read
only a small fraction of reads are the clipped reads, does this support a non-clonal population?
Nearby large germline event not associated with this deletion
Normal has nearby large germline event that appears to occur in one haplotype. This deletions DOES NOT appear to be on the same halplotype as the large germline event. HOWEVER, this event is less apparent in ONT reads.
Breakpoints appear to be exact when left aligned
homologous sequence at left end in deleted region with 5 bases post deletion on right.
QUESTION Does any of the evidence support non-clonal? I think the deletion is in MOST of the cells but is there evidence for a sub clone with other variants I noted?
jzook
chr3 101703348 Minda_95 N <DEL> . PASS SVLEN=3190;SVTYPE=DEL;SUPP_VEC=PB_ID_51866_2,PB_d_315,ONT_ID_11133_2,ONT_d_150,ILL_MantaDEL:64089:0:1:0:0:0,PB_severus_DEL4753,ONT_severus_DEL5502,PB_Sniffles2.DEL.235M2,ONT_Sniffles2.DEL.251M2,ILL_2050296736:2,ILL_gridss59fb_9329hhttps://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr3:101703348#ribbon