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jzook / testHG008curation

This repository is primarily for the Genome in a Bottle Consortium to curate structural variants in HG008
https://www.nist.gov/programs-projects/cancer-genome-bottle
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[chr17:31977413-32004128][DEL][SVLEN=26715bp] #264

Open jzook opened 1 month ago

jzook commented 1 month ago

chr17 31977413 Minda_52 N <DEL> . PASS SVLEN=26715;SVTYPE=DEL;SUPP_VEC=PB_r_167,ILL_MantaDEL:233235:1:2:0:0:0,PB_severus_DEL2746,ONT_severus_DEL3107,PB_ID_32124_2,ILL_2432545328:2,ILL_gridss252fb_8676h,ONT_ID_60507_2,PB_Sniffles2.DEL.1C1M10,ONT_Sniffles2.DEL.1F5M10

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr17:31977413#ribbon

aganezov commented 1 month ago

Appears as a true somatic deletion.

Screenshot 2024-10-11 at 09 49 47

Screenshot 2024-10-11 at 09 49 33

True left breakpoint appears to be at chr17:31,977,414, 1 bp to the right of the reported one. Assembly fails to capture the deletion. Left breakpoint appears to fall into both a SINE repeat and an annotated seg dup.

Screenshot 2024-10-11 at 09 52 02

Right breakpoint appear to be correct at chr17:32,004,128. Right breakpoint is outside of a nearby SINE repeat, but does fall into an annotated seg dup (distinct from the left frebapoint seg dup).

Screenshot 2024-10-11 at 09 54 16

Read phasing fails in this area, but from the coverage changes across all technologies, it appears a true clonal somatic deletion, affecting 1 haplotype across all cells.

Has a, what appears to be a somatic duplication, ~300Kbp downstream.

jzook commented 1 month ago

Since this is in an LOH region with ~100x coverage of surrounding regions, this seems likely subclonal and exact breakpoints with homology