Evidence map›Paper›PMID 38522840›Full record

ArticleThe Journal of molecular diagnostics : JMD2024

Leveraging Off-Target Reads in Panel Sequencing for Homologous Recombination Repair Deficiency Screening in Tumor.

Markus Ball, Iordanis Ourailidis, Klaus Kluck, Michael Menzel, Martina Kirchner, Michael Allgäuer, Timothy Kwang Yong Tay, Fabian Schnecko, Anna-Lena Volckmar, Hannah Goldschmid and 6 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of molecular diagnostics : JMD, 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
0.3field-weighted citation impact, top 44% of its field
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

16 authors at 3 institutions in 2 countries.

Markus BallInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
Iordanis OurailidisInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
Klaus KluckInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
Michael MenzelInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
Martina KirchnerInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
Michael AllgäuerInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
Timothy Kwang Yong TayInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Department of Anatomical Pathology, Singapore General Hospital, Singapore; Department of Molecular Pathology, Singapore General Hospital, Singapore.
Fabian SchneckoInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
Anna-Lena VolckmarInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
Hannah GoldschmidInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
Olaf NeumanInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
Stefan FröhlingDepartment of Translational Medical Oncology, National Center for Tumor Diseases, Heidelberg, Germany; German Cancer Consortium, Heidelberg, Germany.
Peter SchirmacherInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Center for Personalized Medicine Heidelberg, Heidelberg, Germany.
Jan BudcziesInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; German Cancer Consortium, Heidelberg, Germany; Center for Personalized Medicine Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg, German Center for Lung Research, Heidelberg, Germany.
Albrecht StenzingerInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; German Cancer Consortium, Heidelberg, Germany; Center for Personalized Medicine Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg, German Center for Lung Research, Heidelberg, Germany. Electronic address: albrecht.stenzinger@med.uni-heidelberg.de.
Daniel KazdalInstitute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; German Cancer Consortium, Heidelberg, Germany; Translational Lung Research Center Heidelberg, German Center for Lung Research, Heidelberg, Germany. Electronic address: daniel.kazdal@med.uni-heidelberg.de.
Heidelberg University · DEGerman Cancer Research Center · DENational Center for Tumor Diseases · DE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Targeted tumor only sequencing has become a standard practice in cancer diagnostics. This study aims to develop an approach for robust copy number variant calling in tumor samples using only off-target region (OTR) reads. We also established a clinical use case for homologous recombination deficiency (HRD) score estimation (HRDest) using the sum of telomeric-allelic imbalance and large-scale state transition scores without the need for loss of heterozygosity information. A strong correlation was found between HRD score and the sum of telomeric-allelic imbalance + large-scale state transition in The Cancer Genome Atlas cohort (ρ = 0.99, P < 2.2 × 10

Indexed as

DNA Copy Number VariationsExome SequencingHigh-Throughput Nucleotide SequencingNeoplasmsAllelic ImbalanceHumansRecombinational DNA Repair

Identifiers

PMID38522840
PMCPMC12178388
OpenAlexW4393072605

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.