I'm not a big fan of using pooling but we are actively discussing it as a mutation screening approach. The benefit would be reduced cost but with the drawback of limited depth per chromosome. The key issue here is to allow detection of single nucleotide variants even in heterozygous form from each individual within the pool. What is your experience? Ion Torrent, Illumina. Best /Hans
@hans -2 to 3 samples(best if 2) per lane on illumina HiSeq should give you enough coverage per exome for mutation detection. You get an average coverage of about 150X(PE sequencing). Exome -Agilent 44Mb
Hope I answered your question
The problem would not be coverage, but variant calling. Consider the number of false positives/negatives when calling a heterozygous variant in one of the samples with a theoretical number of reads equalling 25%.
Also, to sufficiently call a heterozygous variant you need 33x on target coverage, preferably x80, meaning one would probably miss a lot even with an average of x160 times coverage.
@Joakim- We could confirm mutations with confidence with two human exomes per lane in cancer samples. For really low frequency mutations we did targeted sequencing(much smaller size compared to exome)
Confirming known positions I can agree with, pre-library pooling to detect novel variants, especially heterozygous in dominant disorders, I'm just worried you will miss a lot.
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