Stephanie P. DiTroia

Systematic evaluation of incomplete penetrance in 4,325 rare disease families reveals divergent transcriptional networks in CHD8 pathology

The paper evaluates incomplete penetrance in 4,325 rare disease families, finding 1.6% of diagnosed cases involve inherited variants from unaffected parents and showing divergent transcriptional effects in CHD8-related cases.

Genomic Research as a Critical Pathway to Diagnosis for Individuals with Rare Disease

The Rare Genomes Project provides remote genomic sequencing to rare disease families, achieving a 23.3% diagnostic solve rate and highlighting the role of research in overcoming clinical diagnostic barriers.

Analysis of spliceosome-related coding and noncoding genes and pseudogenes reveals novel candidates

The paper identifies novel spliceosome-related genes and pseudogenes associated with rare diseases using variant analysis and prioritization methods.

Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing

This study evaluates the diagnostic yield of short-read and long-read sequencing in rare diseases, finding limited added value from long-read sequencing despite increased variant discovery.

Building an Interoperable Rare Disease Multi-omic Resource: The GREGoR Data Model and Dataset

The paper introduces a data model and dataset for rare disease research, enabling interoperable multi-omic data integration across clinical sites.

Systematic analysis of snRNA genes reveals frequent RNU2-2 variants in dominant and recessive developmental and epileptic encephalopathies

The paper identifies RNU2-2 variants as a frequent cause of neurodevelopmental disorders, both dominant and recessive, in a large cohort of individuals with rare disorders.

Integrating 730,947 exome sequences with clinical literature improves gene discovery

gnomAD v4 (730,947 exomes) brings LOFTEE-2 loss-of-function annotation (0.90 precision, strict mode), missense-aware constraint, and LLM-mined literature evidence combined with constraint to rank disease genes.

Mitochondrial DNA variant detection in over 6,500 rare disease families by the systematic analysis of exome and genome sequencing data resolves undiagnosed cases

The paper identifies mitochondrial DNA variants in undiagnosed rare disease families using exome and genome sequencing data, leading to diagnoses in 0.4% of cases.

The ClinGen Syndromic Disorders Gene Curation Expert Panel: Assessing the Clinical Validity of 111 Gene-Disease Relationships

The paper curates 111 gene-disease relationships for syndromic disorders, classifying their clinical validity and identifying gaps in knowledge.

Basic helix-loop-helix transcription factor BHLHE22 monoallelic and biallelic variants cause a neurodevelopmental disorder with agenesis of the corpus callosum, intellectual disability, tone and movement abnormalities

Considerations for reporting variants in novel candidate genes identified during clinical genomic testing

The paper develops criteria for identifying, sharing, and reporting novel candidate genes in clinical genomic testing to improve diagnostic yield for Mendelian conditions.

Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project

The paper evaluates variant prioritization methods for rare disease diagnosis using data from the Rare Genomes Project, finding that top models identify causal variants in most solved families and uncover potential candidates in unsolved ones.

Exome copy number variant detection, analysis and classification in a large cohort of families with undiagnosed rare genetic disease

The paper detects and classifies copy number variants in exome data from 6,633 families, identifying causal CNVs in 173 families and improving classification standards.

Heterozygous loss-of-function SMC3 variants are associated with variable and incompletely penetrant growth and developmental features

The paper identifies SMC3 loss-of-function variants associated with variable growth and developmental features, including some unexpected phenotypes like bone marrow failure and leukemia.

Unique Capabilities of Genome Sequencing for Rare Disease Diagnosis

This study evaluates genome sequencing's diagnostic yield in a cohort of undiagnosed rare disease patients, finding it solves 29.3% of cases with specific variant types not detectable by exome sequencing.

Loss-of-function variants in CUL3 cause a syndromic neurodevelopmental disorder

The paper reports a cohort of 35 individuals with CUL3 variants causing a syndromic neurodevelopmental disorder, showing loss-of-function variants disrupt protein homeostasis by impairing proteasomal degradation of CUL3 substrates.

seqr: a web-based analysis and collaboration tool for rare disease genomics

seqr is a web-based tool for analyzing rare disease genomic data, enabling variant filtering, annotation, and collaboration, with over 10,000 families analyzed and 300 novel disease genes discovered.

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.

The Importance of Automation in Genetic Diagnosis: Lessons from Analyzing an Inherited Retinal Degeneration Cohort with the Mendelian Analysis Toolkit (MATK)

The paper introduces MATK, an automated variant ranking tool for Mendelian disease diagnosis, showing it identifies most expert solutions and finds additional variants in unsolved cases.