ArticleGenome medicine2021
Clinical-grade whole-genome sequencing and 3' transcriptome analysis of colorectal cancer patients.
Article in Genome medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 7 citations in OpenAlex.
- Recurrent deletions and regulatory disruption of the Y chromosome in cancer.Communications biology · 2026Article
- Integrating next-generation sequencing and artificial intelligence for the identification and validation of pathogenic variants in colorectal cancer.Frontiers in oncology · 2025Article
- Multiparametric magnetic resonance imaging (MRI)-based radiomics model explained by the Shapley Additive exPlanations (SHAP) method for predicting complete response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer: a multicenter retrospective study.Quantitative imaging in medicine and surgery · 2024Article
- Proteogenomic characterization of primary colorectal cancer and metastatic progression identifies proteome-based subtypes and signatures.Cell reports · 2024Article
- Reference gene selection for clinical chimeric antigen receptor T-cell product vector copy number assays.Cytotherapy · 2023Article
- Bile acids as carcinogens in the colon and at other sites in the gastrointestinal system.Experimental biology and medicine (Maywood, N.J.) · 2023Review
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Authors and funding
14 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundClinical-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.
methodsPatients 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.
resultsFifty-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.
conclusionsClinical 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.