I have performed human whole-genome sequencing using NovaSeq6000 and analyzed the data using Basespace. Now I got some results for breast cancer 28 genes list which has been assembled in an excel file. Anybody can help me regarding how I should go further to come up with good findings? Which software I can use for the analyses. My target is to find a novel gene that is responsible for breast cancer disease.
Hello Shahina Akter I am not sure what you are asking Since baseSpace gave you the final vcf and list of breast cancer mutations detected! I assume you want to focus on identifying mutations in BC gene unidentified samples. If you are looking for novel genes, then match the mutations you found in known BC genes to the samples and exclude these samples as cause identified and focus on the samples without a known cause. Prioritize the detected variants in those samples based on consequence (nonsense mutations first, missense second) utilize mutation prediction software to help you with these since some are harmless, and exclude common missense variants of frequencies more than 0.05 in genome databases (genome AD, 1000 genome project). Then when you have a shortlist, go through literature to identify functions of these genes or whether they were reported before in sporadic reports. Good luck.
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