Biology subjects

Furney, S. J.

Publications and source records attributed to Furney, S. J..

3 recordsLinked to original sources

bioRxiv2025

Whole genome sequencing of pre-treatment and post-treatment locally advanced rectal cancer using long and short read technologies

We performed Illumina short-read and nanopore (ONT) whole genome sequencing (WGS) on samples obtained from a 37-year-old patient with locally advanced rectal cancer who did not respond to neoadjuvant chemoradiotherapy (nCRT). Pre-treatment and post-nCRT tumour biopsy, adjacent normal tissue, and matched pre-treatment blood samples were sequenced to identify somatic alterations. We used DNA methylation from ONT WGS to detect changes in the tumour epigenomes compared to adjacent normal tissue. We employed established pipelines for the identification of somatic alterations to assess the concordance of SNV, short indel, copy number and structural variation from the short-read and long-read tumour genome data. Overall, 69.4% and 30.1% SNVs were concordant between technologies in the pre- and post-treatment tumours, respectively. A multinomial logistic regression was performed to further understand discordant SNV calls, highlighting tumour purity, presence in a repetitive region, strand bias, and germline variant allele frequency as factors contributing to discordance. Indel concordance was poor (26.8% and 9.2% in the pre- and post-treatment tumour, respectively). Copy number alteration profiles were highly similar while minimal concordance was reported for structural variants (2.4% and 0.3% for pre- and post-treatment tumours, respectively). Finally, we used the ONT data to detect DNA modifications (5-methylcytosine and 5-hydroxymethylcytosine) between tumour and matched adjacent normal tissue. Based on genome-wide average CpG modification rates, global hypomethylation was observed in tumours compared to adjacent normal tissues. Biologically relevant epigenomic changes related to epithelial-mesenchymal transition were detected in the post-treatment tumour, as well as potential radiation-induced changes in the post-treatment adjacent normal tissue.

genomics↗

bioRxiv2025

A multi-step filtering pipeline for human read removal enhances detection of Fusobacterium in WGS datasets with immunohistochemical confirmation in mucinous rectal cancer.

The study of tumour-associated microbiomes using whole-genome sequencing (WGS) has attracted considerable attention, but microbial signal detection remains controversial due to host contamination and methodological artefacts. As the necessity of human-read removal becomes increasingly evident, many groups now include this step in their data pre-processing workflows. In this work, we introduce an open-source tool designed for rigorous host-read removal and apply it to the reanalysis of WGS data from ten mucinous rectal adenocarcinoma cases originally published by Reynolds et al. The workflow integrates k-mer-based classification (Kraken2), quality and adapter trimming (Trim Galore), vector filtering (BBDuk/UniVec_Core), and duplicate-removal (FastUniq). After reducing data complexity, a multi-aligner, multi-reference approach (BWA-MEM/GRCh38, Bowtie2/T2T-CHM13, Minimap2/HPRC v1.1) removes remaining host sequences, collectively eliminating more than 99.9% of human-derived reads. Although the additional alignment steps eliminated only a small fraction of total reads, they consistently removed millions of residual sequences per sample, underscoring the importance of rigorous filtering in datasets where non-human reads are a small minority. Taxonomic profiling with PathSeq and MetaPhlAn revealed reproducible enrichment of Fusobacterium species in tumour versus matched normal tissues, with stricter filtering reducing overall microbial signal compared to prior results. Cross-validation with immunofluorescence analysis using pan-Fusobacterium (detecting both F. animalis and F. nucleatum) and F. nucleatum-specific antibodies showed a strong concordance with Fusobacterium subspecies detected by WGS. Compared to the unfiltered analysis, host depletion markedly reduced artificial microbial signals in normal samples while preserving tumour-associated Fusobacterium, resulting in a more reliable microbial profile. ImportanceWe developed an open-source tool that enables rapid removal of human-derived sequences and applied it to rectal cancer WGS data. This approach reduced false microbial signals while preserving true tumour-associated Fusobacterium, and we confirmed these findings in tissue using immunofluorescence staining. Our method provides a more reliable foundation for studying tumour-bacteria interactions.

bioinformatics↗

bioRxiv2019

Biological sex and age shape melanoma tumour evolution

Many cancer types display sex and age disparity in incidence and outcome. Here, we establish a mathematical approach using cancer mutational data to analyze how sex and age shape the tumour genome. We model how age-related (clock-like) somatic mutations that arise during cell division, and extrinsic (environmental) mutations accumulate in cancer genomes. As a proof-of-concept, we apply our approach to melanoma, a cancer driven by cell-intrinsic age-related mutations and extrinsic ultraviolet light-induced mutations, and show these mutation types differ in magnitude, chronology and by sex in the distinct molecular melanoma subtypes.\n\nOur model confirms age and sex are determinants of cellular mutation rate, shaping the final mutation composition. We show mathematically for the first time how, similar to non-cancer tissues, melanoma genomes reflect a decline in cell division during ageing. We find clock-like mutations strongly correlate with the acquisition of ultraviolet light-induced mutations, but critically, males present a higher number and rate of cell division-linked mutations. These data indicate the contribution of environmental damage to melanoma likely extends beyond genetic damage to affect cell division.

cancer biology↗