LOH determined

[Jingjiao-ma]

Hi

 I run FACETS and get the results:

chrom	seg	num.mark	nhet	cnlr.median	mafR	segclust	cnlr.median.clust	mafR.clust	start	end	cf.em	tcn.em	lcn.em
1	1	479	79	0.0965351900685901	0.0403774889537343	14	0.0486443901051894	0.0403774889537343	10583	581900	1	2	1
1	2	223937	35564	-0.260170210987769	0.240391887957227	3	-0.279420057298134	0.250369380666881	58230069426214	0.394624061086929	1	0
1	3	17560	2102	-0.369619979099715	0.252093019901172	2	-0.361566996656013	0.255944278101722	69426589	74757300	0.394624061086929	1	0
1	4	90955	13571	-0.31368627544908	0.253806864037177	3	-0.279420057298134	0.250369380666881	74757454	102153700	0.394624061086929	1	0

the ten.em=2 and lcn.em=0 is copy-neutral LOH state the ten.em=1 and lcn.em=0 is LOH or heterozygous deletions?

Best Regards~ Thank you !

[veseshan]

Heterozygous deletion is LOH i.e. what once was a het is no longer so.

[Jingjiao-ma]

Thank you, I kown the tcn.em=1 and lcn.em=0 is in LOH state.

[dariober]

...I just happened to see this thread... Maybe the table here helps to classify the CNV state into LOH, DEL, DUP etc...? (Scroll down a bit in the thread)

[kobejamescurry]

Heterozygous deletion is LOH i.e. what once was a het is no longer so. your LOH definition is not complete