Emily Farrow

Genome-wide profiling of highly similar paralogous genes using HiFi sequencing

The paper develops Paraphase, a HiFi-based method to resolve highly similar paralogous genes, revealing genetic diversity and de novo events in segmental duplications.

Complex trait associations in rare diseases and impacts on Mendelian variant interpretation

This study quantifies polygenic liability in rare disease probands and finds associations between rare disease phenotypes and polygenic scores, supporting complex trait influences on Mendelian variant interpretation.

One-Sided Matching Portal (OSMP): a tool to facilitate rare disease patient matchmaking

The paper introduces OSMP, a tool for one-sided genomic matchmaking in rare disease patients, which efficiently filters variant occurrences to prioritize clinically relevant matches.

Pangenome graphs improve the analysis of rare genetic diseases

The paper uses pangenome graphs to improve detection of rare structural variants in a rare disease cohort, identifying novel diagnostic variants.

Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort

The paper uses HiFi sequencing to identify hypermethylation outliers in a rare disease cohort, finding allele-specific loss of regulatory elements linked to disease.

Resolving the unsolved: Comprehensive assessment of tandem repeats at scale

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.

Rapid and scalable preclinical evaluation of personalized antisense oligonucleotide therapeutics using organoids derived from rare disease patients

This paper describes a platform for generating patient-derived organoids to evaluate personalized antisense oligonucleotide therapeutics for rare diseases, showing reversal of disease phenotypes in Duchenne muscular dystrophy models.

Comprehensive SMN1 and SMN2 profiling for spinal muscular atrophy analysis using long-read PacBio HiFi sequencing

The paper develops Paraphase, a method using long-read sequencing to accurately determine SMN1 and SMN2 haplotypes and copy numbers, improving silent carrier detection in spinal muscular atrophy.

Deleterious, protein-altering variants in the X-linked transcriptional coregulator ZMYM3 in 22 individuals with a neurodevelopmental delay phenotype

The paper identifies ZMYM3 variants in 22 individuals with neurodevelopmental delay, showing recurrent mutations, phenotypic overlap, and functional effects, supporting ZMYM3 as a novel NDD gene.

Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes

The paper presents diagnostic analyses of 960 pediatric rare disease families using genomic sequencing and machine learning, finding higher diagnostic rates with long-read sequencing and highlighting challenges in variant interpretation.

De novo EIF2AK1 and EIF2AK2 variants are associated with developmental delay, leukoencephalopathy, and neurologic decompensation

The paper identifies de novo variants in EIF2AK1 and EIF2AK2 associated with neurodevelopmental disorders and leukoencephalopathy, showing similar pathogenic mechanisms to CACH/VWM.