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Oksza-Orzechowski, K.* ; Quinten, E.* ; Shafighi, S.* ; Kiełbasa, S.M.* ; van Kessel, H.W.* ; de Groen, R.A.L.* ; Vermaat, J.S.P.* ; Sepúlveda Yáñez, J.H.* ; Navarrete, M.A.* ; Veelken, H.* ; van Bergen, C.A.M.* ; Szczurek, E.

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

Genome Biol. 25:286 (2024)
Publ. Version/Full Text DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Cancer Genetics ; Follicular Lymphoma ; Statistical Methods ; Tumour Heterogeneity; Intratumor Heterogeneity; Phenotypic Heterogeneity; Clonal Evolution; Cell; Expression; Pathogenesis; Database
Language english
Publication Year 2024
HGF-reported in Year 2024
ISSN (print) / ISBN 1474-760X
e-ISSN 1465-6906
Journal Genome Biology
Quellenangaben Volume: 25, Issue: 1, Pages: , Article Number: 286 Supplement: ,
Publisher BioMed Central
Publishing Place Campus, 4 Crinan St, London N1 9xw, England
Reviewing status Peer reviewed
Institute(s) Institute of AI for Health (AIH)
POF-Topic(s) 30205 - Bioengineering and Digital Health
Research field(s) Enabling and Novel Technologies
PSP Element(s) G-540012-001
Grants Narodowe Centrum Nauki
DOI 10.1186/s13059-024-03417-1
WOS ID 001347989700001
Scopus ID 85208603013
PubMed ID 39501370
Erfassungsdatum 2024-11-07
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