ArticleNature communications2021
Mining mutation contexts across the cancer genome to map tumor site of origin.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Recurrence Patterns of Resected Ampullary Adenocarcinoma and Implications for Multimodal Therapy: A Hidden Genome-Derived Analysis from the Ampullary Cancer Collaborative.Annals of surgical oncology · 2026Article
- Genome-based classification of pancreatic acinar cell carcinoma reveals similarities to KRAS wild-type PDAC.Journal of translational medicine · 2025Article
- Rethinking cancer of unknown primary: from diagnostic challenge to targeted treatment.Nature reviews. Clinical oncology · 2025Review
- Histologic- and Genomic-Directed Adjuvant Therapy for Ampullary Adenocarcinoma: A Hidden Genome-Derived Analysis.Journal of the National Comprehensive Cancer Network : JNCCN · 2025Article
- Identifying somatic fingerprints of cancers defined by germline and environmental risk factors.Genetic epidemiology · 2024Article
- A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: The Hidden-Genome Classifier.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Article
- Topical hidden genome: discovering latent cancer mutational topics using a Bayesian multilevel context-learning approach.Biometrics · 2024Article
- Ampullary Adenocarcinoma: A Review of the Mutational Landscape and Implications for Treatment.Cancers · 2023Review
- Predicting Cancer Risk from Germline Whole-exome Sequencing Data Using a Novel Context-based Variant Aggregation Approach.Cancer research communications · 2023Article
- Complete genomic characterization in patients with cancer of unknown primary origin in routine diagnostics.ESMO open · 2022Article
- Machine-learning-enabled metasurface for direction of arrival estimation.Nanophotonics (Berlin, Germany) · 2022Article
- Genome-Derived Classification Signature for Ampullary Adenocarcinoma to Improve Clinical Cancer Care.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The vast preponderance of somatic mutations in a typical cancer are either extremely rare or have never been previously recorded in available databases that track somatic mutations. These constitute a hidden genome that contrasts the relatively small number of mutations that occur frequently, the properties of which have been studied in depth. Here we demonstrate that this hidden genome contains much more accurate information than common mutations for the purpose of identifying the site of origin of primary cancers in settings where this is unknown. We accomplish this using a projection-based statistical method that achieves a highly effective signal condensation, by leveraging DNA sequence and epigenetic contexts using a set of meta-features that embody the mutation contexts of rare variants throughout the genome.
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Registered trials
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.