Evidence map›Paper›PMID 41000705›Full record

ArticlebioRxiv : the preprint server for biology2025

A Universal Duplex Sequencing Approach for Accurate Detection of Somatic Mutations.

Shuvro P Nandi, Yuhe Cheng, Shams Al-Azzam, Safa Saeed, Audrey Kristin, Nadia Sunico, Isabella R Stuewe, Zichen Jiang, Luka Culibrk, Maria Zhivagui and 12 more

Abstract readPreprint
In one paragraph

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.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

22 authors.

Shuvro P NandiDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
Yuhe ChengDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
Shams Al-AzzamDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
Safa SaeedDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
Audrey KristinDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
Nadia SunicoDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
Isabella R StueweDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
Zichen JiangDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
Luka CulibrkDepartment of Pathology, Grossman Medical School, New York University, NY, USA.
Maria ZhivaguiKirk Kerkorian School of Medicine, University of Nevada, Las Vegas, NV, USA.
Xiaoxu YangDepartment of Neurosciences and Pediatrics, UC San Diego, La Jolla, CA, USA.ORCID 0000-0003-0219-0023
Rachel M WiseDepartment of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, USA.
Foster C JacobsMasonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
Bérénice ChavanelInternational Agency for Research on Cancer WHO, Epigenomics and Mechanisms Branch, Lyon, France.
Michael KorenjakInternational Agency for Research on Cancer WHO, Epigenomics and Mechanisms Branch, Lyon, France.
Mia PetljakDepartment of Pathology, Grossman Medical School, New York University, NY, USA.
Silvia BalboMasonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.ORCID 0000-0002-7686-0504
Laurie G HudsonDepartment of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, USA.
Ke Jian LiuStony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA.
Jiri ZavadilInternational Agency for Research on Cancer WHO, Epigenomics and Mechanisms Branch, Lyon, France.
Joseph G GleesonDepartment of Neurosciences and Pediatrics, UC San Diego, La Jolla, CA, USA.
Ludmil B AlexandrovDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.ORCID 0000-0003-3596-4515

Funding

Role of hypernutrition and metabolic stress in non-alcoholic steatohepatitis (NASH) driven hepatocellular carcinoma (HCC)P01CA281819 · NCI · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI Michael Karin · 2024 to 2026
$9.2M
Detecting Mutational Signatures of Environmental Mutagens in Heathy Individuals for Personalized Cancer PreventionR01ES032547 · NIEHS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ALEXANDROV, LUDMIL B · 2021 to 2025
$3.4M
Mapping immuno-genomic drivers of the head and neck precancer invasive-disease transitionU01CA290479 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ludmil B Alexandrov, Jorge Silvio Gutkind · 2023 to 2026
$3.1M
UC San Diego Genetics Training ProgramT32GM145427 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BRUCE A HAMILTON · 2022 to 2026
$2.6M
Comprehensive identification of germline-somatic interactionsR01CA269919 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ludmil B Alexandrov, Hannah Kathryn Carter · 2022 to 2026
$2.2M
The DNA adductome of lung carcinogenesisR01CA220376 · NCI · UNIVERSITY OF MINNESOTA · PI BALBO, SILVIA · 2018 to 2022
$1.7M
Understanding the origins of the mutational landscape in cancerR01ES036931 · NIEHS · UNIV OF ARKANSAS FOR MED SCIS · PI Ludmil B Alexandrov, Gunnar Boysen · 2025 to 2026
$1.5M
Exploring the Impact of Base Deaminase Deregulation on Precancer EvolutionR01CA296974 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Ludmil B Alexandrov, Catriona Helen Macleod Jamieson · 2025 to 2026
$890k
Understanding genomic stability between generations by assessing mutational burdens in single spermsR00HD111686 · NICHD · UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH · PI Xiaoxu Yang · 2025 to 2026
$498k
NCI NIH HHS P01 CA281819NCI NIH HHS R01 CA220376NCI NIH HHS R01 CA269919NCI NIH HHS R01 CA296974NCI NIH HHS U01 CA290479NICHD NIH HHS R00 HD111686NIEHS NIH HHS R01 ES032547NIEHS NIH HHS R01 ES036931NIGMS NIH HHS T32 GM145427
6 · The paper itself

Abstract

Ultra-accurate detection of rare somatic mutations is critical for understanding mutational processes in human disease, aging, and environmental exposures, yet current methods are limited by error rates, restricted genome coverage, and high DNA input. We present UDSeq, a duplex sequencing protocol combining random fragmentation, efficient UMI ligation, and quantitative input control to achieve near-complete genome/exome representation from as little as 100 pg DNA. Benchmarking in human sperm estimates a UDSeq error rate of ~2.5×10

Identifiers

PMID41000705
PMCPMC12458366

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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.