Biology subjects

Berry, G.

Publications and source records attributed to Berry, G..

3 recordsLinked to original sources

bioRxiv2026

Eco-Evolutionary Graph Theory: Regular Graphs can act as Amplifiers

The Moran model is celebrated for its analytical tractability, yet on network-structured populations it produces contradictory predictions dependent on a seemingly arbitrary choice of birth and death update rule, limiting its biological utility. Here we resolve this problem by decoupling birth and death processes and introducing vacant space. We show that this framework unifies existing models, finding that as the death rate tends to zero the ecological model converges to the death-Birth (dB) Moran process, while the Birth-death (Bd) fixation probability emerges as an upper bound in the limit of large fitness differentials. In this framework random regular and lattice graphs can increase the fixation probability of advantageous mutants and decrease the fixation probability of disadvantageous mutants. They are therefore amplifiers of selection, despite being neutral or suppressing in the Moran model, demonstrating how the introduction of vacant space alters evolutionary outcomes on population structures. This unifying approach is biologically motivated, with results varying continuously via scalar parameters rather than switching between discrete modelling choices. This enables its application in real-world scenarios and offers a better understanding of how population structures and connectivity promote or suppress evolution.

evolutionary biology↗

bioRxiv2026

The Genome In A Bottle HG002 assembly-based variant benchmark set enables comprehensive benchmarking of small and structural variants.

High-accuracy, high-resolution benchmark data are fundamental to improving the accuracy and generalizability of sequencing technologies and associated algorithms. Most existing benchmarks for DNA sequencing rely on mapping to a single linear reference, omitting inaccessible and highly repetitive complex genomic regions. Here, we present the Genome in a Bottle (GIAB) Consortium's HG002 v5.0q benchmark set, a more comprehensive variant benchmark derived from a fully phased, highly curated, and accurate diploid assembly of HG002. Our approach leverages recent advances in long-read sequencing and assembly to provide confident small- and structural-variant calls across previously inaccessible regions, including segmental duplications, homopolymers, tandem repeats, and complex immune loci. The v5.0 benchmark significantly expands the callable genome relative to v4.2.1, adding x200 Mbp of sequence and increasing variant detection by 18 % for small variants and 3-fold for structural variants compared to previous benchmarks. The benchmark regions include more variants in repetitive regions, including 1.2 x segmental duplications, 1.8 x tandem repeats, and 2.0 x homopolymers, compared to v4.2.1. Separate and combined small- and structural-variant benchmarks are available for three versions of the human reference genome (GRCh37, GRCh38, and CHM13). We validate the reliability of this benchmark set by comparing multiple sequencing technologies and variant calling pipelines and curating differences. The v5.0q benchmark provides a critical resource for the development and validation of next-generation sequencing technologies and analysis methods.

genomics↗

bioRxiv2018

Pisces: An Accurate and Versatile Variant Caller for Somatic and Germline Next-Generation Sequencing Data

MotivationNext-Generation Sequencing (NGS) technology is transitioning quickly from research labs to clinical settings. The diagnosis and treatment selection for many acquired and autosomal conditions necessitate a method for accurately detecting somatic and germline variants, suitable for the clinic.\n\nResultsWe have developed Pisces, a rapid, versatile and accurate small variant calling suite designed for somatic and germline amplicon sequencing applications. Pisces accuracy is achieved by four distinct modules, the Pisces Read Stitcher, Pisces Variant Caller, the Pisces Variant Quality Recalibrator, and the Pisces Variant Phaser. Each module incorporates a number of novel algorithmic strategies aimed at reducing noise or increasing the likelihood of detecting a true variant.\n\nAvailabilityPisces is distributed under an open source license and can be downloaded from https://github.com/Illumina/Pisces. Pisces is available on the BaseSpace SequenceHub as part of the TruSeq Amplicon workflow and the Illumina Ampliseq Workflow. Pisces is distributed on Illumina sequencing platforms such as the MiSeq, and is included in the Praxis Extended RAS Panel test which was recently approved by the FDA for the detection of multiple RAS gene mutations.\n\nContactpisces@illumina.com\n\nSupplementary informationSupplementary data are available online.

bioinformatics↗