Joy Goffena

EpiSignaLR: an open resource for genome-wide episignature analysis from methylation-aware short- and long-read sequencing

The paper develops EpiSignaLR, a resource for genome-wide episignature analysis using methylation-aware sequencing data, identifying DMRs and classifiers for three neurodevelopmental disorders.

Accurate repeat expansion genotyping from whole-genome and real-time targeted nanopore sequencing with Mahi-mahi

Mahi-mahi accurately genotypes repeat expansions from nanopore sequencing data, matching orthogonal methods and identifying pathogenic alleles.

Long-read sequencing with targeted assembly of the opsin locus accurately evaluates genes in expressed positions

This paper evaluates long-read sequencing with targeted assembly for accurately analyzing the opsin gene cluster, showing high concordance and improved detection of color vision deficiencies and carrier status.

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.

Benchmarking long-read variant sensitivity across ONT and PacBio platforms using known clinically reported variants in a cohort of critically ill newborns

Determinants of haplotype phasing accuracy in long-read human genome sequencing

This study evaluates factors affecting haplotype phasing accuracy in long-read sequencing, showing that T2T reference genomes and longer reads improve performance.

Ultra-fast sample-to-sequencing workflow for clinical diagnostics using micropillars

This paper introduces an integrated microfluidic workflow for Oxford Nanopore sequencing that reduces hands-on time and sample loss while enabling high-quality library preparation from small sample volumes.

Concordance of whole-genome long-read sequencing with standard clinical testing for Prader-Willi and Angelman syndromes

This study evaluates whole-genome long-read sequencing for diagnosing Prader-Willi and Angelman syndromes, showing high accuracy in detecting genetic variants and methylation differences.

A Diagnostic Blind Spot: Deep intronic SVA_E Insertion identified as the most Common Pathogenic Variant Associated with Canavan Disease

The paper identifies a common intronic SVA_E insertion in ASPA as the most frequent pathogenic variant in Canavan disease using long-read sequencing.

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.

Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature

This study evaluates genome-wide DNA methylation analysis in genetically unsolved DEEs, identifying 10 causative or candidate genetic causes and refining a CHD2 episignature.