Bioinformatics Seminar
Time:
Venue: Na
3 May 2016
NaCopy number analysis by low coverage whole genome sequencing using low-input DNA from formalin-fixed paraffin embedded tumour tissue
David GoodePeter Mac
Copy number alterations (CNAs) are major genetic drivers in many malignancies ; and their accurate detection is crucial in both research and clinical settings. Molecular Inversion Probe (MIP) microarrays are the standard method for detecting CNAs from formalin-fixed paraffin embedded (FFPE) tumour samples ; but it is often difficult to obtain DNA of sufficient quantity and quality for use with MIP arrays. Low-coverage whole genome sequencing (LC-WGS) presents a potentially cheaper ; faster and more flexible method for CNA analysis on wider range of clinical specimens.
We tested several methods for pre-treatment and preparation of libraries from DNA from FFPE samples. With the right protocol and data filters ; CNAs can be detected with accuracy and sensitivity comparable to MIP arrays from as little as 5ng of input DNA ; at sequencing coverages of 1X or lower. We found average read depth had a bigger influence on signal-to-noise ratio that did amount of starting material or choice of analysis method (Control-FREEC or QDNAseq) and proper genome masking is important for reducing false positive CNA calls.
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