Claudia G. Gonzaga-Jauregui

A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

Genome-wide maps of highly-similar intrachromosomal repeats that mediate ectopic recombination in three human genome assemblies

The paper characterizes intrachromosomal repeats in three human genome assemblies, finding more repeats in the T2T-CHM13 assembly and identifying gene categories enriched for repeat-associated genomic disorders.

Centers for Mendelian Genomics: A decade of facilitating gene discovery

The paper describes the role of the Centers for Mendelian Genomics in advancing gene discovery through data sharing, collaboration, and resource development over the past decade.

NPRL3: Direct Effects on Human Phenotypic Variability, mTOR Signaling, Subcellular mTOR Localization, Cortical Lamination, and Seizure Susceptibility

The paper investigates NPRL3 variants' effects on mTOR signaling, cortical development, and epilepsy by using CRISPR/Cas9 knockout in cell lines and mice, showing mTOR hyperactivation and cortical dyslamination.

A de novo paradigm for male infertility

The paper identifies de novo mutations as a significant genetic cause of male infertility, finding several candidate genes and an enrichment of loss-of-function and missense mutations in intolerant genes.

Genomic analyses in a large clinical cohort reveal high prevalence of MECP2 variants associated with neuropsychiatric phenotypes in adulthood

The paper was withdrawn due to lack of full author consent.

Pathogenic variants in SMARCA5, a chromatin remodeler, cause a range of syndromic neurodevelopmental features

The paper identifies pathogenic variants in SMARCA5 as a cause of a neurodevelopmental syndrome with mild facial dysmorphia and developmental delay.

Rare variant analysis of 4,241 pulmonary arterial hypertension cases from an international consortium implicate FBLN2, PDGFD and rare de novo variants in PAH

This study identifies two new PAH risk genes, FBLN2 and PDGFD, through rare variant analysis of 4,241 PAH cases, with de novo variants contributing to ~15% of pediatric IPAH.

Mutation spectrum of NOD2 reveals recessive inheritance as a main driver of Early Onset Crohn’s Disease

The paper identifies recessive NOD2 inheritance as a major driver of early onset Crohn’s Disease in both pediatric and adult cohorts.

Validating gene-phenotype associations using relationships in the UMLS

The paper validates gene-phenotype associations by mapping genes to ICD codes using UMLS relationships, finding 249,764 gene-ICD mappings in a cohort of 92,455 samples.

Functional modeling of NMIHBA-causing PRUNE1 variants reveals a requirement for its exopolyphosphatase activity.

The paper investigates PRUNE1 variants causing NMIHBA, showing they disrupt exopolyphosphatase activity and lead to neurodevelopmental defects in mice.

Novel risk genes and mechanisms implicated by exome sequencing of 2,572 individuals with pulmonary arterial hypertension

The paper identifies two new risk genes for idiopathic pulmonary arterial hypertension through exome sequencing of 2,572 individuals.

Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank

Exomes of 49,960 UK Biobank participants reveal 231,631 predicted loss-of-function variants (>10-fold more than imputed data); burden tests implicate PIEZO1, MEPE, and COL6A1 in disease traits.

Profiling and leveraging relatedness in a precision medicine cohort of 92,455 exomes

The paper analyzes cryptic relatedness in a large exome cohort, identifies numerous close relationships, reconstructs pedigrees, and demonstrates their utility in improving mutation phasing and identifying de novo mutations.

KaryoScan: abnormal karyotype detection from whole-exome sequence

KaryoScan detects chromosomal anomalies from whole-exome sequencing, identifying aneuploidies and complex rearrangements in large cohorts.

Profiling copy number variation and disease associations from 50,726 DiscovEHR Study exomes

The paper identifies and analyzes exonic copy number variants (CNVs) in 50,726 DiscovEHR participants, linking them to clinical traits and phenotypes.