What LOH means in CANVAS
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6 weeks ago
ManuelDB ▴ 30

Context:

I am developing a program that analyse CNV. The first thing this program does is filter and take only CNVs. I do this selecting variants which 5th column contains <CNV>

 1 753816 Canvas:GAIN:1:753816:813096 N <CNV> 10 PASS SVTYPE=LOH;END=813096 RC:BC:CN:MCC 87:18:2:2
3 26664139 Canvas:GAIN:3:26664139:32101159 N <CNV> 61 PASS SVTYPE=CNV;END=32101159 RC:BC:CN:MCC 1
18:6520:4:2
5 1000000 Canvas:REF:3:1000000:2000000 N . 61 PASS END=2000000 RC:BC:CN:MCC 118:6520:2:1


The application at the end tells me many things but one important value is if the CNV is GAIN or LOSS. I have been confused because I got some REF in the column where only should be GAIN or LOSS. I have been checking my application looking for errors until I have ensured that everything is ok. I have checked the VCF file and I have seen that there are variants like this

 chr13 26478278 Canvas:REF:chr13:26478279:38482776N <CNV> 40 PASS SVTYPE=LOH


I have been reading CANVAS documentation and don't find what is LOH

What is the difference between these two CNVs

 753816 Canvas:GAIN:1:753816:813096 N <CNV> 10 PASS SVTYPE=LOH;END=813096 RC:BC:CN:MCC 87:18:2:2
26664139 Canvas:GAIN:3:26664139:32101159 N <CNV> 61 PASS SVTYPE=CNV;END=32101159 RC:BC:CN:MCC 1
18:6520:4:2


Why some SVTYPE=LOH don't tell you if this is LOSS or GAIN

If I don't find out what that means. I am thinking on filter CNV based on the 7th column because I think that when SVTYPE is equal to CNV, the GAIN/LOSS is always given

CANVAS • 204 views
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LOH = loss of heterozygosity

The reference was heterozygous at the position, the sample is not anymore, so you have an LOH event. This can of course be anything, from starting from a SNV point mutation, it doesn't need to be a structural variant.