Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples

High quality tumour DNA is essential for any personalised treatment strategy based on next generation sequencing (NGS). Here we show that methanol fixation is superior to formalin, greater DNA yield, longer fragment size and more accurate copy number calling using shallow whole genome sequencing. We also show provide a new approach to understand fixation artefacts using non-negative matrix factorization.

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