Clinically actionable mutation profiles in patients with cancer identified by whole-genome sequencing

Abstract

Next-generation sequencing (NGS) efforts have established catalogs of mutations relevant to cancer development. However, the clinical utility of this information remains largely unexplored. Here, we present the results of the first eight patients recruited into a clinical whole-genome sequencing (WGS) program in the United Kingdom. We performed PCR-free WGS of fresh frozen tumors and germline DNA at 75× and 30×, respectively, using the HiSeq2500 HTv4. Subtracted tumor VCFs and paired germlines were subjected to comprehensive analysis of coding and noncoding regions, integration of germline with somatically acquired variants, and global mutation signatures and pathway analyses. Results were classified into tiers and presented to a multidisciplinary tumor board. WGS results helped to clarify an uncertain histopathological diagnosis in one case, led to informed or supported prognosis in two cases, leading to de-escalation of therapy in one, and indicated potential treatments in all eight. Overall 26 different tier 1 potentially clinically actionable findings were identified using WGS compared with six SNVs/indels using routine targeted NGS. These initial results demonstrate the potential of WGS to inform future diagnosis, prognosis, and treatment choice in cancer and justify the systematic evaluation of the clinical utility of WGS in larger cohorts of patients with cancer.

Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma

“…The DLBCL patient was recruited as part of a large-scale clinical sequencing study utilizing the Illumina short read platform, details of which have been previously published 10 . This patient was selected for subsequent Nanopore sequencing on the basis that this tumour type has long been recognized to harbor chromosomal abnormalities, such as loss of chromosomal SHORT VS LONG-READ GENOME SEQUENCING FOR SOMATIC VARIANT DETECTION 5 17p, which can influence clinical prognosis and management.…”

“…2446 of the somatic variants were located within genes. We filtered the short-read somatic small variant calls for clinical relevance using a number of different sources, including COSMIC Cancer Genes Census (v71) 37 , "My Cancer Genome" (www.mycancergenome.org) and ClinicalTrials.gov (http://clinicaltrials.gov), as previously described 10 . This resulted in 13 SNVs, 3 of which were located on chr17 (Supplementary Table 1).…”

“…The patient was consented as part of a local clinical WGS programme for analysis of tumor and constitutional DNA (as previously described in 10 SHORT VS LONG-READ GENOME SEQUENCING FOR SOMATIC VARIANT DETECTION 22…”

“…Whole Genome Sequencing (WGS) is among these and is the most comprehensive approach for characterising and analysing an individual's genetic variation 6 . Substantial reductions in cost mean that WGS has become an increasingly important tool for clinical diagnosis and targeted treatment of rare disease and cancer 4,[7][8][9][10][11] . Of particular importance to precision oncology is the ability of WGS to identify driver mutations (including those in non-coding regions) 12,13 , detect mutational signatures [14][15][16] , characterise structural variation and chromosomal rearrangements 17,18 , and pinpoint the genomic integration sites of oncoviruses, such as human papillomavirus 19 .…”

Differential genomic and transcriptomic events associated with high-grade transformation of Chronic Lymphocytic Leukemia

“…Variants which were predicted as having HIGH impact by VEP, or which were flagged as deleterious by SIFT or probably damaging by PolyPhen were kept for further analysis. Copy number analyses were carried out as described inSchuh et al (2018) 42 .…”