Vincenza Colonna

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Scaling the PBWT for Long-Range Shared Ancestry Detection in Large Haplotype Panels

The paper introduces PBML, an algorithm for efficiently detecting long-range shared ancestry tracts in large haplotype panels by filtering short, uninformative matches.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

Identity-by-descent captures Shared Environmental Factors at Biobank Scale

This paper uses IBD-based clustering to reveal environmental and health disparities across subcommunities in a biobank dataset.

Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery

This study constructs a rat pangenome from linked-read data to enhance variant discovery and genotype-phenotype mapping in recombinant inbred strains.

The Biorepository and Integrative Genomics resource for inclusive genomics: insights from a diverse pediatric and admixed cohort

The paper analyzes genomic data from a diverse cohort to highlight genetic diversity and disparities in disease prevalence linked to ancestry and environment.

Building pangenome graphs

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The paper presents an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

A Draft Human Pangenome Reference

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice

The paper identifies a quantitative trait locus on chromosome 13 associated with STR expansion propensity in mice, implicating Msh3 in genome-wide mutation patterns.

A standardized approach for case selection and genomic data analysis of maternal exomes for the diagnosis of oocyte maturation and early embryonic developmental arrest in IVF

The paper develops a methodology for selecting IVF cases with oocyte maturation defects and preimplantation embryo lethality, using whole-exome sequencing and bioinformatics to identify causative genetic variants.

Deep sequencing of a large family of isogenic mice enables complex variants discovery and accurate phenotype mapping

The paper uses linked-read whole-genome sequencing to identify DNA variants in BXD mice and maps them to phenotypes, enabling systems genetics and precision medicine.

Prioritization of putatively detrimental variants in euploid miscarriages

The paper identifies potentially harmful genetic variants in euploid miscarriage embryos and highlights specific genes linked to miscarriage risk.

SVJAM: Joint Analysis of Structural Variants Using Linked Read Sequencing Data

SVJAM improves structural variant calling in linked-read data by jointly analyzing multiple samples, recovering missed variants and correcting incorrect types compared to LongRanger.

Succinct dynamic variation graphs

The paper introduces two C++ libraries for efficient manipulation of pangenomic graphs, showing improved performance over existing tools.

Inter-individual genomic heterogeneity within European population isolates

The paper analyzes genomic heterogeneity within European population isolates and finds that inter-individual variation is comparable to non-isolated populations, with some isolates showing higher levels due to recent introgression.

Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites.

The paper identifies 746k polymorphic sites in Capsicum species and finds four novel loci associated with fruit shape, including a mutation in the Longifolia 1-like gene.

Positive selection in Europeans and East-Asians at the ABCA12 gene

The paper confirms a positive selection signal at the ABCA12 gene in Europeans and East-Asians and refines its genomic location, finding no direct effect on gene expression but tracing the T allele's trajectory in human history.

Genomics and transcriptomics to unravel sex determination pathway and its evolution in sand flies

The paper identifies sex determination genes in sand flies using genomics and transcriptomics, proposes a model for their sex determination cascade, and characterizes a novel transformer homolog.

Purging of deleterious variants due to drift and founder effect in Italian populations with extended autozygosity

The paper analyzes whole-genome sequencing data from Italian founder populations to determine the cause of purging of deleterious variants, concluding that genetic drift and founder effect, not consanguinity, are responsible.

Genetic landscape of populations along the Silk Road: admixture and migration patterns

This study analyzes the genetic structure of six Central Asian populations along the Silk Road, revealing admixture patterns and migration events linked to historical expansions.

Human genomic regions with exceptionally high or low levels of population differentiation identified from 911 whole-genome sequences

The paper identifies genomic regions with high or low population differentiation using 911 whole-genome sequences, finding that highly differentiated sites are enriched for positive selection.