Evidence map›Paper›PMID 38106141›Full record

ArticlebioRxiv : the preprint server for biology2024

Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes.

Wolu Chukwu, Siyun Lee, Alexander Crane, Shu Zhang, Sophie Webster, Ipsa Mittra, Marcin Imielinski, Rameen Beroukhim, Frank Dubois, Simona Dalin

Open access · greenAbstract 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, 1 citations in OpenAlex.

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

10 authors at 2 institutions in 3 countries.

Wolu ChukwuCancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0009-0004-5270-1586
Siyun LeeCancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0009-0005-5130-5212
Alexander CraneCancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0003-1930-279X
Shu ZhangCancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0009-0005-6592-118X
Sophie WebsterCancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Ipsa MittraCancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Marcin ImielinskiDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; Department of Pathology and Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.ORCID 0000-0002-2211-4741
Rameen BeroukhimCancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0001-6303-3609
Frank DuboisCancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0002-7654-6208
Simona DalinCancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0001-5024-9718
Broad Institute · USCornell University · US

Funding

Genetic evolution of glioblastomas during radiation and temozolomide therapyR01CA188228 · NCI · DANA-FARBER CANCER INST · PI BEROUKHIM, RAMEEN, CHAKRAVARTI, ARNAB · 2015 to 2025
$6.9M
Synthetic lethalities to cell cycle disruption in gliomaR01CA262462 · NCI · DANA-FARBER CANCER INST · PI RAMEEN BEROUKHIM, KEITH LLOYD LIGON · 2022 to 2026
$3.3M
MYB family alterations in pediatric gliomasR01CA215489 · NCI · DANA-FARBER CANCER INST · PI BEROUKHIM, RAMEEN, LIGON, KEITH LLOYD · 2017 to 2021
$2.8M
Characterizing TP53 and PPM1D mutations as resistance drivers to radiation therapy in Diffuse Intrinsic Pontine GliomasR01CA219943 · NCI · BROAD INSTITUTE, INC. · PI BEROUKHIM, RAMEEN, LIGON, KEITH LLOYD · 2017 to 2021
$2.5M
Differential resistance mechanisms to monofunctional vs bifunctional alkylating agents in gliomaF32CA261024 · NCI · BROAD INSTITUTE, INC. · PI DALIN, SIMONA · 2021 to 2023
$208k
NCI NIH HHS F32 CA261024NCI NIH HHS R01 CA215489NCI NIH HHS R01 CA219943
6 · The paper itself

Abstract

Although several recent studies have characterized structural variants (SVs) in germline and cancer genomes, the features of SVs in these different contexts have not been directly compared. We examined similarities and differences between 2 million germline and 115 thousand tumor SVs from a cohort of 963 patients from The Cancer Genome Atlas (TCGA). We found significant differences in features related to their genomic sequences and localization that suggest differences between SV-generating processes and selective pressures. For example, we found that transposon-mediated processes shape germline much more than somatic SVs, while somatic SVs more frequently show features characteristic of chromoanagenesis. These differences were extensive enough to enable us to develop a classifier - "the great GaTSV" - that accurately distinguishes between germline and cancer SVs in tumor samples that lack a matched normal sample.

Identifiers

PMID38106141
PMCPMC10723258
OpenAlexW4387607241

What OpenQuestion 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 OpenQuestion graph.