Comparison of Whole-Genome Sequencing Strategies for the Detection of Somatic Mutations in Cancer

May 4, 2016
Comparison of Whole-Genome Sequencing  Strategies for the Detection of Somatic Mutations in Cancer
“Just the place for sequencing a Snark! I have sequenced it twice: That alone should encourage the crew. Just the place for sequencing a Snark! I have sequenced it thrice: What I sequence three times is true.” — Adapted from The Hunting of the Snark (An Agony, in Eight Fits) by Lewis Carroll [Wikicommons / Henry Holiday's cover of the first edition of The Hunting of the Snark]

Stephen C. Peiper, M.D., Erica Johnson, Ph.D., and Zi-Xuan Wang, Ph.D.

The diagnostic work up of most malignant tumors is not complete unless the work up includes genomic characterization. At the time of diagnosis this may consist of a panel of prognostic and/or predictive analyses performed using cytogenetics, fluorescence in situ hybridization, standard molecular technologies, and next-generation sequencing (NGS). Whereas genomic interrogation of early-stage tumors using NGS is typically in the form of a multigene panel designed for the particular malignancy, the genomic analysis of advanced-stage cancers may be based on aggressive examination using a large panel of genes, only some of which encode targets for molecularly directed therapies.

Based on the significant advances in NGS technologies and the decreasing costs, the technocrati have advocated increasingly broad sequencing panels to characterize the mutational landscape of recurrent tumors and rare types of malignancies, as illustrated by the NCI-Molecular Analysis for Therapy Choice (MATCH) trial. The seduction of comprehensive genomic analysis has led to enthusiasm for performing whole exome and whole genome sequencing in oncology, as promoted by NantHealth. Whole genome sequencing (WGS) also is coming into its own as a front-line diagnosis tool for neurogenetic disorders, as convincingly discussed in another article in Clinical OMICs (http://www.clinicalomics.com/articles/exome-sequencing-beginning-to-displace-common-genetic-tests-in-clinic/603).

While NGS technology for high-throughput sequencing is advancing rapidly, the bioinformatics support required for precision interpretation has lagged behind. Potential challenges in data interpretation are illustrated in two recent publications, one focusing on the assessment of somatic mutations in oncology specimens analyzed by WGS, and the second on disparities in results of “recreational genetic studies” in the direct-to-consumer market.

Alioto et al., compared the WGS findings from a medulloblastoma cancer sample sequenced by eight laboratories in the International Cancer Genome Consortium, all using the same sequencing platform HiSeq (Alioto TS, et. al. Nature Communications 2015; 6:10001). The initial observation was that the quality of the libraries prepared using different protocols (with or without PCR amplification and with varied reagent suppliers) had a significant impact on average coverage depth and evenness of coverage. Two of the eight sites did not meet the minimal requirement (30X) for average coverage depth, and their data were excluded. Even among the remaining six sites, the percentage of the genome sequenced with at least 25X coverage depth ranged from approximately 75% to less than 50%. This could significantly limit the identification of mutations in the latter case.

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