Nextseq 500 base calling

[Paulfrobbins]

Does anyone have any suggestions about how to filter out the mis-called variants on Nextseq? Also, has anyone used the v2 kits? Is the fidelity significantly improved?

[Brian Bushnell]

We are about to run a test on the NextSeq v2 chemistry, so I'll probably have some data in a week or two.

[Paulfrobbins]

Thank you. We are anxious to see if we can improve the reliability of our Nextseq data. Our group at the National Cancer Institute is attempting to identify mutated gene products expressed in cancer cells that can be recognized by patient immune cells that will allow us to develop effective cancer therapies. We purchased a Nextseq because we needed to get our data quickly in order to develop treatments for patients with advanced cancer, and we have already identified many targets using this approach. Enhancing the accuracy of the variant calls would make this process simpler, as it would help to eliminate many of the false positives. Some of these are easy to identify as they appear in repeated tumor samples - I presume these are regions of the genome that are difficult to sequence. We also merge whole exome with RNAseq, which helps to validate the calls.