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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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[chr15:79431718-79432727][DEL][SVLEN=1009bp] #257

Open jzook opened 1 week ago

jzook commented 1 week ago

chr15 79431718 Minda_45 N <DEL> . PASS SVLEN=1009;SVTYPE=DEL;SUPP_VEC=ONT_ID_71992_2,ONT_severus_DEL2557,ONT_Sniffles2.DEL.1E2ME,PB_ID_20108_2,PB_severus_DEL2292,PB_d_126,ONT_d_53

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr15:79431718#ribbon

aquaskyline commented 1 week ago

Correct deletion. Breakpoints should be revised to chr15:79431718-79432733 to match the Dragen result. Likely clonal. Screenshot 2024-10-13 at 22 56 31 Screenshot 2024-10-13 at 22 58 02 Screenshot 2024-10-14 at 08 50 35

Left-end breakpoint: Screenshot 2024-10-14 at 09 17 41

Right-end breakpoint: Screenshot 2024-10-14 at 09 18 26

Attention needed that there is 15bp deletion on another haplotype overlapping at the middle of this deletion. Screenshot 2024-10-14 at 09 20 53

aquaskyline commented 5 days ago

Deletion in MINAR1, a gene that found to be in inhibiting angiogenesis.

I quote from OMIM:

Using human and porcine cell culture studies, as well as mouse and zebrafish angiogenesis assays, Ho et al. (2018) found that MINAR1 inhibited angiogenesis. MINAR1 expression was downregulated in human breast cancer compared with normal breast, and its reexpression in breast cancer MDA-MB-231 cells inhibited cell proliferation. Coimmunoprecipitation and pull-down assays revealed that human MINAR1 and NOTCH2 interacted directly, and binding of NOTCH2 to MINAR1 increased the stability of MINAR1.