Demonstrated Protocol, Last Modified on March 17, 2017, Permalink
The Chromium™ Genome Protocols generate long-range information across the length of individual DNA molecules. Starting the process with High Molecular Weight (HMW) genomic DNA (gDNA) will typically result in better application performance, such as increased haplotype phase block length and ability to call structural variants. Optimal performance has been characterized on input gDNA with a mean length >50 kb.
This Demonstrated Protocol outlines a method for HMW gDNA extraction from fresh frozen tissue. This Protocol can produce gDNA with an average size of >200 kb when analyzed on a pulsed-field gel, and typically >80 kb after the Chromium Genome Protocols. There are many variables that will affect gDNA quality in sample types, including sample age, transportation methods, type of tissue, additives, freezing method, etc.
This Protocol outlines HMW gDNA extraction from fresh frozen breast tumor tissue. While results are expected to be similar across many tissue types, this Protocol has not yet been extensively tested. Importantly, there are tissue types for which HMW gDNA extraction is universally difficult (e.g. liver, due to high enzyme activity) and also yield sub-optimal results with this Protocol.