Tools & Techniques

To enable integrated analysis of DNA and RNA from clinical specimens, we have developed a suite of protocols for collecting tissues and blood, generating slides for pathology review, and co-isolation of nucleic acids.

To enable benchmarking and comparison of tools for detecting copy number variants, we developed Bamgineer, a tool for Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

Our laboratory and computational methods for generation and analysis of DNA sequence from circulating tumour DNA.

Library construction for hybrid capture (panel listed in brackets)

Cell-free DNA extraction from blood plasma

Co-isolation of DNA and RNA from already isolated cell or frozen tissue sections

We are one of the core software development teams for cbioportal.org and maintain a fork of the code from which we periodically merge components back to the main development code base.

A fairly generic tracking system, designed to be connected to some kind of persistent storage and some other kind of authentication system, allow a kind of spreadsheet view with the data persisted, and different users seeing different data.

Genomic DNA extraction from buffy coat or cultured cells

Sectioning, staining, and co-isolation of DNA/RNA from FFPE tissues

VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number variants (CNVs) from targeted next-generation sequencing data.