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Cancer Genomics and Diagnostics
Research Guide
What is Cancer Genomics and Diagnostics?
Cancer Genomics and Diagnostics is the study of DNA sequence variations, gene expression differences, and genomic alterations in tumor cells compared to normal cells to develop diagnostic tests, interpret variants, and enable precision oncology.
The field encompasses 97,070 works with tools like the cBioPortal providing access to multidimensional cancer genomics data from over 5,000 tumor samples across 20 studies. Richards et al. (2015) established standards for interpreting sequence variants, cited 30,174 times, guiding clinical genomic diagnostics. Siegel et al. (2020, 2021) report annual U.S. cancer incidence data through SEER, with over 20,000 and 17,000 citations respectively, linking genomics to population-level diagnostics.
Research Sub-Topics
ACMG Variant Interpretation Guidelines
Researchers refine ACMG/AMP frameworks for classifying germline variants as pathogenic, likely pathogenic, VUS, or benign using population frequency, computational predictions, and functional assays. Studies validate guidelines across cancer predisposition genes.
cBioPortal Cancer Genomics Analysis
This area develops and applies cBioPortal for visualizing multi-omic cancer data, identifying driver mutations, and correlating genomics with clinical outcomes across TCGA/ICGC cohorts. Methodological advances enable real-time pan-cancer queries.
Integrative Genomics Viewer IGV
Scientists enhance IGV software for interactive exploration of NGS alignments, copy number variations, and structural variants in cancer genomes. Benchmarking compares visualization accuracy across sequencing platforms.
Breast Cancer Comprehensive Genomic Profiling
Research integrates TCGA breast cancer multi-omics data to define PAM50 subtypes, ESR1/HER2 mutations, and homologous recombination deficiency signatures. Studies correlate genomics with immunotherapy responses.
Colorectal Cancer Genomic Evolution
This sub-topic traces adenoma-carcinoma progression through APC/KRAS/TP53 mutations using phylogenetic models on multi-region sequencing. Research identifies chromosomally unstable vs. microsatellite unstable pathways.
Why It Matters
Cancer Genomics and Diagnostics supports precision medicine by standardizing variant interpretation for clinical decisions, as in "Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology" (Richards et al., 2015), which provides frameworks adopted in labs worldwide. Platforms like cBioPortal, described in Cerami et al. (2012) and Gao et al. (2013), enable analysis of genomic data from thousands of samples, aiding oncologists in identifying actionable mutations. Recent applications include GRAIL's Galleri multi-cancer early detection test, with FDA Breakthrough Device designation since 2018 and a Premarket Approval application submitted in 2026, and Haystack's MRD liquid biopsy test, also FDA Breakthrough designated in 2025, detecting low-level circulating tumor DNA in advanced cancers.
Reading Guide
Where to Start
"Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology" (Richards et al., 2015) first, as it provides the foundational clinical standards for variant interpretation essential before exploring data tools or studies.
Key Papers Explained
Richards et al. (2015) establish variant interpretation standards, which Cerami et al. (2012) apply in cBioPortal for multidimensional data exploration from 5,000+ samples; Gao et al. (2013) build on this with integrative clinical-genomic analysis in cBioPortal. Siegel et al. (2020, 2021) contextualize with population statistics, while Robinson et al. (2011) in "Integrative genomics viewer" enable visualization of complex datasets like those in Koboldt et al. (2012) breast cancer portraits.
Paper Timeline
Most-cited paper highlighted in red. Papers ordered chronologically.
Advanced Directions
Recent preprints analyze whole-genome sequences from 1,364 breast cancers (2025) and comprehensive genomic profiling in 54,185 advanced solid tumors (2026). Liquid biopsy advancements include GRAIL's Galleri PMA submission (2026), Haystack MRD Breakthrough (2025), and DELFI's $225M funding (2025). Splicing dysregulation emerges as a frontier in precision medicine (Alatawi preprint).
Papers at a Glance
| # | Paper | Year | Venue | Citations | Open Access |
|---|---|---|---|---|---|
| 1 | Standards and guidelines for the interpretation of sequence va... | 2015 | Genetics in Medicine | 30.2K | ✓ |
| 2 | Cancer statistics, 2020 | 2020 | CA A Cancer Journal fo... | 21.0K | ✓ |
| 3 | The cBio Cancer Genomics Portal: An Open Platform for Explorin... | 2012 | Cancer Discovery | 17.7K | ✓ |
| 4 | AJCC Cancer Staging Manual | 2016 | — | 17.4K | ✕ |
| 5 | Cancer Statistics, 2021 | 2021 | CA A Cancer Journal fo... | 17.1K | ✓ |
| 6 | Integrative genomics viewer | 2011 | Nature Biotechnology | 15.7K | ✕ |
| 7 | Integrative Analysis of Complex Cancer Genomics and Clinical P... | 2013 | Science Signaling | 15.4K | ✓ |
| 8 | Integrating single-cell transcriptomic data across different c... | 2018 | Nature Biotechnology | 13.9K | ✓ |
| 9 | Comprehensive molecular portraits of human breast tumours | 2012 | Nature | 12.0K | ✓ |
| 10 | A genetic model for colorectal tumorigenesis | 1990 | Cell | 12.0K | ✕ |
In the News
GRAIL Submits FDA Premarket Approval Application for ...
Approval (PMA) application to the U.S. Food and Drug Administration (FDA) for its Galleri®multi-cancer early detection (MCED) test. The FDA designated the test as a Breakthrough Device in 2018.
FDA Grants Breakthrough Device Designation for Haystack ...
Haystack MRD is a highly sensitive and specific liquid biopsy test designed by cancer genomic pioneers and liquid biopsy experts to uncover low levels of circulating-tumor DNA (ctDNA)—tiny fragment...
Biomarx Attracts £700000 in Pre-Seed Funding for Lung ...
# Biomarx attracts £700,000 in pre-seed funding for lung cancer genomics Written by Editorial Team - MedTech World Tue, 06 Jan 2026
FDA Grants Breakthrough Device Designation to Haystack ...
1. FDA grants breakthrough device designation for haystack mrd circulating tumor dna test from quest diagnostics. News Release. Accessed August 29, 2025.
DELFI Diagnostics Announces $225 Million Series B Financing to Develop Globally Accessible Portfolio of Liquid Biopsy Tests - DELFI
Series B funding of $225 million.
Code & Tools
`muon`is a multimodal omics Python framework. Documentation | Tutorials | Publication
The cBioPortal for Cancer Genomics provides visualization, analysis, and download of large-scale cancer genomics data sets. For a short intro on cB...
The cBioPortal for Cancer Genomics provides visualization, analysis, and download of large-scale cancer genomics data sets. For a short intro on cB...
Recent Preprints
Cancer genomics - Latest research and news
Cancer genomics is the study of the totality of DNA sequence and gene expression differences between tumour cells and normal host cells. It aims to understand the genetic basis of tumour cell proli...
Cancer Genetics and Genomics - Springer Link
Uncover the latest and most impactful research in Cancer Genetics and Genomics. Explore pioneering discoveries, insightful ideas and new methods from leading researchers in the field. ## Latest res...
Whole-genome landscapes of 1,364 breast cancers
Breast cancer remains a major global health challenge 1 . Here, to comprehensively characterize its genomic landscape and the clinical significance of genomic characteristics, we analysed whole-gen...
Real-world clinical utility of comprehensive genomic profiling in advanced solid tumors
Comprehensive genomic profiling (CGP) is crucial in precision oncology, yet its real-world utility remains unclear. Here we analyzed data from the Japanese nationwide Center for Cancer Genomics and...
Liquid biopsies across the cancer care continuum
* Diagnostic markers * Tumour biomarkers ## Abstract
Latest Developments
Recent developments in cancer genomics and diagnostics include advancements in AI-powered interpretation of genomic data to facilitate personalized therapies (dailyreporter.esmo.org) and innovations in multi-cancer early detection using cell-free DNA fragmentomics analyzed through whole-genome sequencing and AI models (nature.com, nature.com). Additionally, research continues to explore the molecular landscape of cancer through comprehensive DNA sequencing, gene expression analysis, and the application of new technologies like CRISPR gene editing for targeted therapy (cancer.gov, nature.com). As of February 2026, these advances are shaping more precise and early diagnostic strategies in oncology.
Sources
Frequently Asked Questions
What standards exist for interpreting sequence variants in cancer genomics?
Richards et al. (2015) in "Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology" provide a joint framework classifying variants as pathogenic, likely pathogenic, uncertain, likely benign, or benign. These guidelines are used in clinical diagnostics to assess cancer risk from germline and somatic mutations. The paper has 30,174 citations, reflecting its foundational role.
How does cBioPortal support cancer genomics analysis?
Cerami et al. (2012) introduced the cBioPortal in "The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data," offering open access to data from over 5,000 tumor samples across 20 studies for interactive exploration. Gao et al. (2013) extended it in "Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal" to integrate genomic and clinical profiles. These tools facilitate visualization and download of large-scale datasets.
What do recent cancer statistics reveal about diagnostics needs?
Siegel et al. (2020) in "Cancer statistics, 2020" estimate U.S. new cancer cases and deaths using SEER data through 2016, with 20,975 citations. Siegel et al. (2021) in "Cancer Statistics, 2021" update through 2017 incidence, cited 17,063 times. These reports highlight the scale of cancer burden driving genomic diagnostics demand.
What is the role of liquid biopsies in cancer diagnostics?
Liquid biopsies detect circulating tumor DNA for early detection and monitoring, as in GRAIL's Galleri test with FDA Breakthrough designation since 2018 and PMA submission in 2026. Haystack's MRD test, FDA Breakthrough designated in 2025, identifies low ctDNA levels in solid tumors. DELFI Diagnostics raised $225 million in 2025 Series B for liquid biopsy development.
How has whole-genome sequencing advanced breast cancer diagnostics?
A 2025 preprint "Whole-genome landscapes of 1,364 breast cancers" analyzes sequences from 1,364 cases with transcriptome data, expanding genomic characterization. Koboldt et al. (2012) in "Comprehensive molecular portraits of human breast tumours" provided early molecular subtypes. These inform targeted diagnostics for breast cancer subtypes.
Open Research Questions
- ? How can splicing-driven post-translational dysregulation be targeted for precision cancer medicine and immunotherapy, as explored in recent preprints?
- ? What is the real-world clinical utility of comprehensive genomic profiling in 54,185 advanced solid tumor patients from the Japanese database?
- ? How do whole-genome sequences from 1,364 breast cancers reveal new diagnostic biomarkers?
- ? What integration challenges remain for single-cell transcriptomic data across cancer conditions and technologies?
- ? How can liquid biopsies be optimized across the cancer care continuum for minimal residual disease detection?
Recent Trends
Field works total 97,070; recent preprints include whole-genome analysis of 1,364 breast cancers and CGP utility in 54,185 Japanese patients (2026).
2025Liquid biopsy progress features GRAIL Galleri PMA submission , Haystack MRD FDA Breakthrough (2025), DELFI $225M Series B (2025), and Biomarx £700,000 funding for lung cancer genomics (2026).
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