ArticleGenome biology2024
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- Trial
- Article
- HisToSpatialCNV: an interpretable deep learning method predicting spatial copy number variations from histopathology images.Nature biomedical engineering · 2026Article
- Distinct genomic subgroups and mutational patterns in undifferentiated/dedifferentiated endometrial carcinoma.BMC cancer · 2025Article
- araCNA: somatic copy number profiling using long-range sequence models.NAR genomics and bioinformatics · 2025Article
- Tumor ploidy determination in low-pass whole genome sequencing and allelic copy number visualization using the Constellation Plot.Genome biology · 2025Article
- The Evolutionary Forest of Pancreatic Cancer.Cancer discovery · 2025Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics.Nature methods · 2024Article
Corrections and comments
- Update of
Authors and funding
7 authors.
Funding
Abstract
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this data analyze individual samples independently. We introduce HATCHet2, an algorithm to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 extends the earlier HATCHet method by improving identification of focal CNAs and introducing a novel statistic, the minor haplotype B-allele frequency (mhBAF), that enables identification of mirrored-subclonal CNAs. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 10 prostate cancer patients reveals previously unreported mirrored-subclonal CNAs affecting cancer genes.
Indexed as
Identifiers
What OpenQuestion holds
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.