Evidence map›Paper›PMID 39501370›Full record

ArticleGenome biology2024

CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants.

Kazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Shafighi, Szymon M Kiełbasa, Hugo W van Kessel, Ruben A L de Groen, Joost S P Vermaat, Julieta H Sepúlveda Yáñez, Marcelo A Navarrete, Hendrik Veelken and 2 more

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Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

12 authors.

Kazimierz Oksza-Orzechowski *Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.
Edwin Quinten *Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.
Shadi ShafighiFaculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.
Szymon M KiełbasaDepartment of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands.
Hugo W van KesselDepartment of Hematology, Leiden University Medical Center, Leiden, Netherlands.
Ruben A L de GroenDepartment of Hematology, Leiden University Medical Center, Leiden, Netherlands.
Joost S P VermaatDepartment of Hematology, Leiden University Medical Center, Leiden, Netherlands.
Julieta H Sepúlveda YáñezDepartment of Hematology, Leiden University Medical Center, Leiden, Netherlands.
Marcelo A NavarreteEscuela de Medicina, Universidad de Magallanes, Punta Arenas, Chile.
Hendrik VeelkenDepartment of Hematology, Leiden University Medical Center, Leiden, Netherlands.
Cornelis A M van Bergen *Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.
Ewa Szczurek *Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland. szczurek@mimuw.edu.pl.ORCID 0000-0002-1320-6695

Funding

KWF Kankerbestrijding 13104Narodowe Centrum Nauki 2020/38/E/NZ2/00305
6 · The paper itself

Abstract

Tumours exhibit high genotypic and transcriptional heterogeneity. Both affect cancer progression and treatment, but have been predominantly studied separately in follicular lymphoma. To comprehensively investigate the evolution and genotype-to-phenotype maps in follicular lymphoma, we introduce CaClust, a probabilistic graphical model integrating deep whole exome, single-cell RNA and B-cell receptor sequencing data to infer clone genotypes, cell-to-clone mapping, and single-cell genotyping. CaClust outperforms a state-of-the-art model on simulated and patient data. In-depth analyses of single cells from four samples showcase effects of driver mutations, follicular lymphoma evolution, possible therapeutic targets, and single-cell genotyping that agrees with an independent targeted resequencing experiment.

Indexed as

Genetic HeterogeneityGenotypeLymphoma, FollicularReceptors, Antigen, B-CellHumansMutationSingle-Cell AnalysisReceptors, Antigen, B-CellCancer geneticsFollicular lymphomaStatistical methodsTumour heterogeneity

Identifiers

PMID39501370
PMCPMC11536712

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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.