Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations.

Oliver Priebe, Ron Solan, Conor Messer, Claudia Chu, Julian Hess, Gad Getz

Abstract read

In one paragraph

Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

Clustered structural variant hotspots enable oncogenic addiction and plasticity in osteosarcoma.bioRxiv : the preprint server for biology · 2026
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Oliver PriebeBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA.

Ron SolanBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA.

Conor MesserBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA.

Claudia ChuBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA.

Julian HessBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA. jhess@broadinstitute.org.

Gad GetzBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA. gadgetz@broadinstitute.org.

Funding

GDANII_DLBCL cohort analysis and cloud costsU24CA264024 · NCI · BROAD INSTITUTE, INC. · PI GAD A GETZ, Esther Rheinbay · 2021 to 2026

$2.1M

NIH HHS U24CA264024

6 · The paper itself

Abstract

Somatic copy number alterations (sCNAs) drive cancer initiation, progression, resistance, and metastasis. Furthering our understanding of sCNAs requires substantially larger cohorts. Most tumors available for sequencing are preserved with formalin-fixed, paraffin-embedding (FFPE), which causes DNA cross-linking that distorts coverage profiles and challenges current sCNA estimation methods. Traditional methods denoise data using large panels of similar normal samples, which are impractical to obtain for FFPE cohorts. Here, HapASeg overcomes this limitation by leveraging haplotype phasing and unique covariates to accurately estimate sCNA segments across FFPE, fresh frozen, whole genome sequencing and whole exome sequencing sample types, outperforming current methods without requiring panel-of-normal correction.

Indexed as

DNA Copy Number VariationsHaplotypesNeoplasmsHumansParaffin EmbeddingCancer GenomicsFFPESCNA estimation

Identifiers

PMID41689134

DOI10.1186/s13059-026-03971-w

PMCPMC12983724

What Socratic holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

None linked

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 Socratic graph.