Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic.

doi:10.1038/s41587-025-02839-x

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Article

Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic.

Nature biotechnology - 1 Sept 2026

Park Jimin, Cook Daniel E, Chang Pi-Chuan, Kolesnikov Alexey, Brambrink Lucas, Mier Juan Carlos, Gardner Joshua, McNulty Brandy, Sacco Samuel, Keskus Ayse G, Bryant Asher, Ahmad Tanveer, Shetty Jyoti, Zhao Yongmei, Tran Bao, Narzisi Giuseppe, Helland Adrienne, Yoo Byunggil, Pushel Irina, Lansdon Lisa A, Bi Chengpeng, Walter Adam, Gibson Margaret, Pastinen Tomi, Reiman Rebecca, Mankame Sharvari, Ranallo-Benavidez T Rhyker, Brown Christine, Robine Nicolas, Barthel Floris P, Farooqi Midhat S, Miga Karen H, Carroll Andrew, Kolmogorov Mikhail, Paten Benedict, Shafin Kishwar

Abstract excerpt

Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies offer potential advantages in repeat mapping and variant phasing. We present DeepSomatic, a deep-learning method for detecting somatic small nucleotide variations and insertions and deletions from both short-read and long-read data. The method has modes for...

Read the complete abstract on PubMed

Topics

Humans
Neoplasms
High-Throughput Nucleotide Sequencing

Methodology Data sources Editorial policy Privacy Delete account & data About Contact Helena Bioinformatics

Sequence Analysis, DNA

Deep Learning

Genetic Variation

Exome Sequencing

Cell Line, Tumor

Whole Genome Sequencing

Genomics

Source

Open in PubMed

Identifiers

PMID: 41102444
DOI: 10.1038/s41587-025-02839-x

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