Sat, Mar 7, 2015 at1:54 pm
Customer asks about analysis options for resequencing data besides SNP analysis.
Sun, Mar 8, 2015 at 12:18 PM
AccuraScience LB: Could you tell us whether this is whole-genome sequencing data, exome sequencing or targeted resequencing (e.g., cancer panel sequencing)? Besides SNP calling and Indel calling (the latter is typically done together with SNP calling), other analysis options might include would CNV (copy number variation) calling, recurrent mutation analysis, analysis of functional consequences of the mutations (i.e., is it missense, nonsense or frameshift, whether the mutation is expected to produce deleterious functional effects), pathway analysis (i.e., identification of biological pathways (e.g., in terms of Gene Ontology terms) that are highly over-represented in the genes carrying the SNP mutations.
For high-coverage cancer panel data with potentially heterogonous samples (that is, mixture of normal and tumor samples or tumor samples with multiple subclones, you might also be interested in estimating occurring frequencies of the variants. There are also methods available to dissect the subclonal structures of tumor samples based on analysis of the mutation profiles.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
Disclaimer: This text was selected and edited based on genuine communications that took place between a customer and AccuraScience data analysis team at specified dates and times. The editing was made to protect the customer’s privacy and for brevity. The edited text may or may not have been reviewed and approved by the customer. AccuraScience is solely responsible for the accuracy of the information reflected in this text.