Development of a new method to accurately identify single nucleotide variants using small FFPE breast samples

Most tissue collections of neoplasms are composed of formalin-fixed paraffin-embedded (FFPE) excised tumor samples used for routine diagnostics. DNA sequencing is becoming increasingly important in cancer research and clinical management; however, it is difficult to sequence DNA from FFPE samples accurately. In this project, we aim to reduce this problem by developing and validating a new bioinformatic algorithm to robustly identify somatic single nucleotide variants using small amounts of DNA extracted from archival FFPE samples of human breast cancers. For this, we use 28 pairs of technical replicates--the same DNA sample sequenced twice independently. The resulting algorithm is expected to provide a crucial improvement in detecting SNVs in FFPE samples, and therefore in the genomic analysis of most FFPE clinical tissue collections.