Loh Analysis Of Ngs(Exome) Data

Question

[Jane]

I have Next gen sequencing(exome) data. After analysis using samtools, I have a annotated snp file. Example:

Reference Name Reference Position Type of variation Reference Base SNP Consensus Quality SNP Quality Mapping Quality Read Depth SNP Ratio Zygosity DBannotation DBSNP ID DBSNP Alleles DBSNP Strand Gene Symbol GeneID Function class refallele frame residue aaposition mrnaacc prot_acc

chr10 91498127 SNP T C 30 96 60 16 C(16) Homozygous Annotated rs1886996 C/T + KIF20B 9585 missense;reference C;T 1 R;C 1137 NM016195.2 NP057279.2

I also have data from normal(non-tumor) samples. How can I make LOH calls on these files?

Answer 1

[Sean Davis]

LOH means Loss of Heterozygosity. If you have the calls in the tumor and the calls in the normal, where the normal is heterozygous and the tumor is homozygous, that is called LOH. How one calculates LOH is still an area of research and requires some knowledge of the experimental setup. In particular, one must be aware of tumor heterogeneity and normal admixture as well as ploidy.

If you want a software package that can make calls of LOH, consider looking at varScan. It may or may not be the right approach for your data, but I wanted to suggest just one possible solution.

Answer 2

[Larry_Parnell]

Seems very similar to this very similar question - also by you? Again, I would suggest you look at the work of Don Conrad, including his guest post to teh Genomes Unzipped blog for advice. He is an expert in this area.