Clinical-grade whole-genome sequencing and 3′ transcriptome analysis of colorectal cancer patients

Abstract

Background Clinical-grade whole-genome sequencing (cWGS) has the potential to become the standard of care within the clinic because of its breadth of coverage and lack of bias towards certain regions of the genome. Colorectal cancer presents a difficult treatment paradigm, with over 40% of patients presenting at diagnosis with metastatic disease. We hypothesised that cWGS coupled with 3′ transcriptome analysis would give new insights into colorectal cancer. Methods Patients underwent PCR-free whole-genome sequencing and alignment and variant calling using a standardised pipeline to output SNVs, indels, SVs and CNAs. Additional insights into the mutational signatures and tumour biology were gained by the use of 3′ RNA-seq. Results Fifty-four patients were studied in total. Driver analysis identified the Wnt pathway gene APC as the only consistently mutated driver in colorectal cancer. Alterations in the PI3K/mTOR pathways were seen as previously observed in CRC. Multiple private CNAs, SVs and gene fusions were unique to individual tumours. Approximately 30% of patients had a tumour mutational burden of > 10 mutations/Mb of DNA, suggesting suitability for immunotherapy. Conclusions Clinical whole-genome sequencing offers a potential avenue for the identification of private genomic variation that may confer sensitivity to targeted agents and offer patients new options for targeted therapies.

Bile acids as carcinogens in the colon and at other sites in the gastrointestinal system

“…68 Mutation frequency, measured by whole genome sequencing in 54 colon cancers, found single nucleotide variants to occur between 2459 and 1,601,093 times in the cancers, somatic insertions or deletions occurred between 360 and 464,252 times in the cancers, and structural variants (inversions and balanced translocations or genomic imbalances) occurred between 6 and 681 times in the cancers. 69 This is much higher than the mutation frequency of 30-70 per diploid genome found in a parent to child generation. Among the thousands of mutations in colon cancers, some alter the protein products of genes.…”

“…68 Mutation frequency, measured by whole genome sequencing in 54 colon cancers, found single nucleotide variants to occur between 2459 and 1,601,093 times in the cancers, somatic insertions or deletions occurred between 360 and 464,252 times in the cancers, and structural variants (inversions and balanced translocations or genomic imbalances) occurred between 6 and 681 times in the cancers. 69…”

Reference gene selection for clinical chimeric antigen receptor T-cell product vector copy number assays

“…Since patients with the same type of cancer may have different chromosomal abnormalities, it may be worthwhile to either use multiple reference controls to make sure the reference controls work properly and there are no structural chromosome alterations. Clinical-grade whole-genome sequencing has been studied on colorectal cancer patients [ 32 ] and it has the potential to become the standard of care within the clinic. Chromosome karyotyping and clinical-grade whole-genome sequencing may be needed before we start copy number analyses.…”

PI3K/mTOR is a therapeutically targetable genetic dependency in diffuse intrinsic pontine glioma

“…software component counts the coverage of each target interval on the panel, performs normalization, calculates fold change values for each gene, a quality control Q-score and determines the CNV status for each CNV target gene. Illumina Annotation Engine Nirvana software performed annotation of small variants, calculating tumor mutational burden and microsatellite instability for each sample (32). Finally, the MANTA fusion caller was utilized to discover, assemble, and score large-scale gene fusions (33).…”