Whole exome sequencing (WES) is ideal for unbiased detection of somatic mutations and copy number changes in tumor samples. Analysis can be performed on genomic DNA, fresh frozen tissue, FFPE scrolls or slides, blood, stool, saliva, cell pellets, or buffy coats that preferably yield >250ng of DNA at a concentration of 5ng/uL or higher.
The DFCI CIMAC/Broad’s process includes hybrid capture (Illumina Rapid Capture Enrichment – 37Mb target), sequencing (Illumina, 76bp paired reads), and a sample identification quality control check, as well as data storage (5 years). Our hybrid selection libraries for deep somatic exomes typically meet or exceed 85% of targets at 50X, and for standard exomes, meet or exceed 80% at 20x. The DFCI/Broad CIMAC has the ability to process up to 188 samples per week with no minimum batch size. Processing times vary and depend on current demand.
The MD Anderson CIMAC uses Agilent SureSelect (Human All Exon V6) for hybrid capture. Prior to whole exome sequencing, individual libraries are prepared, hybridizations, and captures are performed. Depending on the target size of the SureSelect capture, multiple samples can be pooled and sequenced in a single lane using the 8-bp SureSelectXT Low Input multiplex indexes. The SureSelectXT Low Input Library preparation is compatible with both high-quality gDNA prepared from fresh or fresh frozen samples and lower quality DNA prepared from FFPE samples, using a DNA input range to 10 to 200 ng DNA. MD Anderson uses the Illumina sequencing platforms (NovaSeqs and HiSeqs) and Agilent’s automated library preparation system (Bravo B) with the capacity to process 192 samples per week. The quality of the raw data conforms to Illumina’s standards.
WES is available at MD Anderson and Dana Farber CIMAC sites.