Low Coverage using target enrichment on Ion Torrent

reggiardo.anselmo · 04-25-2016, 07:50 PM

Hi everybody.
Hope you can help troubleshooting this issue.
I used to carry our BRCA1/BRCA2 target enrichment using Ampliseq paneles. However, I´ve recently changed to GeneRead panels by QIAGEN with very similar results.
I´ve carried out about 12 runs but the last three samples I've run when I analyzed them using the QIAGEN web portal turned out to have a low coverage (around 40X) and a lot of previously unreported variantes. In previous samples the coverage was higher than 500X and variants were almost always the same for both genes.
Do you have any suggestion of why the depth has decreased and how this is related to an increased number of variants?
Could it be due to a wrong dilution of original library prior to OT2?

thanks!

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04-25-2016, 07:50 PM	#1
reggiardo.anselmo Junior Member Location: Argentina Join Date: Mar 2015 Posts: 2	Low Coverage using target enrichment on Ion Torrent Hi everybody. Hope you can help troubleshooting this issue. I used to carry our BRCA1/BRCA2 target enrichment using Ampliseq paneles. However, I´ve recently changed to GeneRead panels by QIAGEN with very similar results. I´ve carried out about 12 runs but the last three samples I've run when I analyzed them using the QIAGEN web portal turned out to have a low coverage (around 40X) and a lot of previously unreported variantes. In previous samples the coverage was higher than 500X and variants were almost always the same for both genes. Do you have any suggestion of why the depth has decreased and how this is related to an increased number of variants? Could it be due to a wrong dilution of original library prior to OT2? thanks!