ArticlebioRxiv : the preprint server for biology2025
Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes.
Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Somatic structural variants (SVs) play a crucial role in tumor development and evolution, yet their identification remains challenging, partly due to limitations in current reference genomes. We present a systematic evaluation of diploid donor-specific assemblies (DSAs)-generated based on hybrid long-read sequencing data-as the reference genome for detecting somatic SVs. We analyzed six tumor-normal cell line pairs, using the EchoSV tool we developed to consolidate haplotype-based SVs into a single DSA-based set and to compare SVs across reference genomes. Across Illumina, PacBio HiFi, and Oxford Nanopore Technology (ONT) data, DSA-based analysis improved read-mapping quality, identified over 20% additional SVs compared to GRCh38 and CHM13, and reduced germline artifacts. Most DSA-specific SVs were isolated deletions or insertions in repetitive elements, especially in satellite regions. By tracking sequence-context differences, we identified scenarios in which DSAs enabled detection of SVs missed on GRCh38/CHM13, and confirmed their functional impact with RNA-seq. These results highlight the value of integrating diploid DSAs into somatic SV analysis.
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.