Evidence map›Paper›PMID 39554127›Full record

ArticlebioRxiv : the preprint server for biology2024

StableLift: Optimized Germline and Somatic Variant Detection Across Genome Builds.

Nicholas K Wang, Nicholas Wiltsie, Helena K Winata, Sorel Fitz-Gibbon, Alfredo E Gonzalez, Nicole Zeltser, Raag Agrawal, Jieun Oh, Jaron Arbet, Yash Patel and 2 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

12 authors.

Nicholas K WangDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0003-1043-3072
Nicholas WiltsieDepartment of Human Genetics, University of California, Los Angeles.ORCID 0009-0000-7683-5299
Helena K WinataDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0002-1001-5316
Sorel Fitz-GibbonDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0001-7090-5719
Alfredo E GonzalezDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0001-8963-3135
Nicole ZeltserDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0001-7246-2771
Raag AgrawalDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0001-8222-3117
Jieun OhDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0002-8961-8645
Jaron ArbetDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0003-4218-2458
Yash PatelDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0003-3113-7010
Takafumi N YamaguchiDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0003-1082-3871
Paul C BoutrosDepartment of Human Genetics, University of California, Los Angeles.ORCID 0000-0003-0553-7520

Funding

Women's CancersP30CA016042 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Robert Damoiseaux · 1985 to 2026
$134.5M
UCLA-Caltech Medical Scientist Training ProgramT32GM008042 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AJIJOLA, OLUJIMI A, DAWSON, DAVID WAYNE · 1985 to 2023
$29.9M
Training Grant in Genomic Analysis and InterpretationT32HG002536 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Valerie A Arboleda, Harold Pimentel · 2002 to 2026
$8.6M
UCLA-Caltech Medical Scientist Training ProgramT32GM152342 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Olujimi A Ajijola, David Wayne Dawson · 2024 to 2026
$5.3M
Advancing method benchmarking and data sharing through crowd-sourced competitions in cancer researchU24CA248265 · NCI · SAGE BIONETWORKS · PI BOUTROS, PAUL CHRISTOPHER, VARMA, SUSHEEL · 2020 to 2024
$4.1M
Virginia-UCLA-Toronto Biomarker Characterization CenterU2CCA271894 · NCI · OLD DOMINION UNIVERSITY · PI Paul Christopher Boutros, OLIVER John SEMMES · 2022 to 2026
$3.2M
Germline Determinants of Prostate Cancer EvolutionR01CA270108 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI PAUL T. SPELLMAN · 2023 to 2026
$2.9M
Predicting prostate cancer clinical outcomes with germline genomic biomarkersF31CA281168 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ZELTSER, NICOLE · 2024 to 2025
$83k
NCI NIH HHS F31 CA281168NCI NIH HHS P30 CA016042NCI NIH HHS R01 CA270108NCI NIH HHS U24 CA248265NCI NIH HHS U2C CA271894NHGRI NIH HHS T32 HG002536NIGMS NIH HHS T32 GM008042NIGMS NIH HHS T32 GM152342
6 · The paper itself

Abstract

Reference genomes are foundational to modern genomics. Our growing understanding of genome structure leads to continual improvements in reference genomes and new genome "builds" with incompatible coordinate systems. We quantified the impact of genome build on germline and somatic variant calling by analyzing tumour-normal whole-genome pairs against the two most widely used human genome builds. The average individual had a build-discordance of 3.8% for germline SNPs, 8.6% for germline SVs, 25.9% for somatic SNVs and 49.6% for somatic SVs. Build-discordant variants are not simply false-positives: 47% were verified by targeted resequencing. Build-discordant variants were associated with specific genomic and technical features in variant- and algorithm-specific patterns. We leveraged these patterns to create StableLift, an algorithm that predicts cross-build stability with AUROCs of 0.934 ± 0.029. These results call for significant caution in cross-build analyses and for use of StableLift as a computationally efficient solution to mitigate inter-build artifacts.

Identifiers

PMID39554127
PMCPMC11565985

What Socratic holds

Textmetadata
LicenceCC BY-NC
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.