Evidence map›Paper›PMID 41726899›Full record

ArticlebioRxiv : the preprint server for biology2026

scAmp analyzes focal gene amplifications at single-cell resolution.

Matthew G Jones, Natasha E Weiser, King L Hung, Xiaowei Yan, Sangya Agarwal, Jens Luebeck, Aditi Gnanasekar, Brooke E Howitt, Ellis J Curtis, Kevin Yu and 7 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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

17 authors.

Matthew G JonesCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Natasha E WeiserCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
King L HungCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Xiaowei YanCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Sangya AgarwalCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Jens LuebeckDepartment of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA.ORCID 0000-0003-4391-979X
Aditi GnanasekarDepartment of Pathology, Stanford University, Stanford, CA, USA.
Brooke E HowittDepartment of Pathology, Stanford University, Stanford, CA, USA.
Ellis J CurtisDepartment of Pathology, Stanford University, Stanford, CA, USA.
Kevin YuKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
John C RoseCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Katerina KraftCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.ORCID 0000-0002-2011-6946
Valeh Valiollah Pour AmiriDepartment of Genetics, School of Medicine, Stanford University, Stanford, CA, USA.
Leena SatpathyCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Vineet BafnaDepartment of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA.ORCID 0000-0002-5810-6241
Paul S MischelDepartment of Pathology, Stanford University, Stanford, CA, USA.
Howard Y ChangCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.

Funding

Computational methods for detecting patterns of complex genomic variationR01GM114362 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2022 to 2025
$906k
Software and algorithms for elucidating the structure, function, and evolution of extrachromosomal DNAU24CA264379 · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2025 to 2025
$731k
eDyNAmiC - UCSDOT2CA278635 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2022 to 2025
$654k
NCI NIH HHS OT2 CA278635NCI NIH HHS U24 CA264379NIGMS NIH HHS R01 GM114362
6 · The paper itself

Abstract

Oncogene amplification on extrachromosomal DNA (ecDNA) is a common driver of tumor progression and is associated with acquired drug resistance and poor patient survival. While whole genome sequencing (WGS) studies have revealed the landscape of genes amplified on ecDNA in tumors, it remains challenging to study the subclonal heterogeneity and functional (e.g., transcriptomic) consequences of ecDNA on tumors. To address this, we introduce

Identifiers

PMID41726899
PMCPMC12919090

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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.