Biology subjects

Harbers, L.

Publications and source records attributed to Harbers, L..

3 recordsLinked to original sources

bioRxiv2026

LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data

MotivationLong-read sequencing is increasingly used in cancer research and clinical genomics due to its ability to resolve complex genomic variation and previously inaccessible regions of the genome. However, dedidated workflows for comprehensive somatic variant analysis from long-read whole-genome data remain scarce, limiting uptake in cancer genomics. ResultsWe present LRSomatic, a Nextflow-based, nf-core-compliant pipeline supporting somatic SNV, indel, structural variant, and copy number calling from PacBio HiFi and ONT data. LRSomatic supports paired tumor-normal and tumor-only designs, as well as integration of epigenetic integration via Fiber-seq. Benchmarked on COLO829 and HG008 reference cell lines, LRSomatic achieves state-of-the-art performance across both platforms and variant types. Applied to a case of clear cell sarcoma, it recovers all identified driver alterations, including the pathognomonic EWSR1::ATF1 fusion, and resolves haplotype-specific chromatin accessibility via Fiber-seq. Availability and ImplementationFreely available at https://github.com/intgenomicslab/lrsomatic, implemented in Nextflow DSL2, supported via Docker and Singularity.

bioinformatics↗

bioRxiv2025

Long-read single-cell genome, transcriptome and open chromatin profiling links genotype to phenotypes.

Current single-cell multiomics methods typically provide limited genomic information, constraining genotype-phenotype studies. To address this gap, we developed SPLONGGET (Single-cell Profiling of LONG-read Genome, Epigenome, and Transcriptome), which integrates 10X Genomics barcoding with Oxford Nanopore sequencing to simultaneously profile genome, chromatin accessibility, and full-length transcriptomes in thousands of single cells. By retaining all tagmentation fragments during library preparation, SPLONGGET delivers whole-genome coverage, supports target enrichment for effective single-cell genotyping, and remains backwards compatible with existing short-read workflows. SPLONGGET enables comprehensive calling of small variants, structural variants, and copy number alterations. Applying SPLONGGET to paediatric B-cell acute lymphoblastic leukaemia revealed clonal dynamics and the phenotypic effects of somatic variants. Notably, we evidence parallel evolution of immune escape variants with four distinct splice site mutations and loss of heterozygosity in the CAR T-cell therapy CD19 target. In conclusion, SPLONGGET enables integrated high-throughput analysis of genetic variation and molecular phenotypes using off-the-shelf kits, offering a timely and powerful tool to study genetically heterogeneous samples, such as tumours but also ageing normal tissues.

genomics↗

bioRxiv2023

High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue

Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly characterized. Here, we performed multi-region, single-cell DNA sequencing to characterize the SCNA landscape across multiple tumor-rich and normal tissue regions ([~]125 mm3 tissue cubes) obtained from prostatectomy performed in two patients with localized prostate cancer. We identified two distinct populations of cells with abnormal karyotypes, one marked by sparse deletions or amplifications ( pseudo-diploid cells) and the second characterized by genome-wide copy number changes reminiscent of monster cells previously described in colorectal cancer. Pseudo-diploid cells formed numerous small-sized subclones ranging from highly spatially localized to broadly spread subclones mainly featuring (sub-)chromosomal arm deletions. In contrast, monster cells harbored whole-chromosome gains and losses and were mostly singular events detected throughout the prostate, including normal tissue regions. Targeted deep sequencing of cancer-associated genes revealed a more confined pattern of mutations overlapping with tumor-rich regions, although we also detected mutations in regions deemed normal based on morphological assessment and bulk RNA-seq. Highly localized pseudo-diploid subclones were confined within tumor-rich regions and typically carried deletions involving chromosome (chr) 6 and 13, resulting in simultaneous loss of multiple tumor-suppressor genes, including FOXO1 and FOXO3 encoding two transcription factors belonging to the Forkhead family previously implicated in prostate carcinogenesis. Tumor-rich regions also contained mutations in genes frequently mutated in prostate cancer, including FOXA1, LRP1B, SPOP, and SPTA1. Our study reveals that SCNAs are widespread in both normal and tumor regions across the prostate gland of patients with localized prostate cancer and suggests that a subset of pseudo-diploid cells harboring chromosomal deletions that result in the loss of specific tumor-suppressor genes drive tumorigenesis in the aging prostate.

cancer biology↗