I manually sequenced and covered a wide genomic region for one specific patient and all it's SNPs within this region are homozygous. While in the other hand all the other samples have shown heterozygosity for the same SNP's and same genomic region. I was wondering whether this patient could have a LOH or not and if there is any way to predict it.
You can use softwares -GTC of Affymetrix (it's free) or SVS of GoldenHelix that will show LOH in every SNP loci and segments with numbers of SNPs and sizes of lengths
why not doing insted copy number analysis (CNV) (RT-qPCR or dPCR) and get the real answer (and not a prediction)?
Dear Santos Alonso,
What do you exactly mean? Transfect cells and express this specific DNA sample and then check the gene expression levels by RT-qPCR? How would You know then that is missing one chromosomal region or one of the two copies of the gene?
Dear Ivan
Not quite. I mean analyzing the "copy number" of that particular genomic region (using genomic DNA). If the region is homozygous due to loss of a chromosome region, then the copy number for that region should be 1 (instead of 2 for a nomal reference region).
(by RT-qPCR I meant Real-Time quantitative PCR, not Reverse Transcription! Sorry!)
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