I am doing targeted next generation sequencing targeting a number of somatic mutations. One of the mutations is a point mutation. Now in a sample if I have total 1000 reads, 10 reads are point mutation that I am targeting, how will this be interpreted? would this be a positive result? What is the minimum number of mutated reads in order to label a sample positive?
Dear Saima Qayum, I think that in the case or ctDNA, microdissected and even 4-6 different samples of the same tumor you have to consider 10 from 1000 because of heterogeneity (minor clones etc.). Of course in the case of polymorphysm (1-5% and more in the population) you have to be carefull with 10/1000. In any case the best way is Sanger sequencing or in the case of 10/1000 ddPCR to improve sensitivity and validate your data.
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