Biology subjects

Havrilla, J. M.

Publications and source records attributed to Havrilla, J. M..

4 recordsLinked to original sources

bioRxiv2019

Phen2Gene: Rapid Phenotype-Driven Gene Prioritization for Rare Diseases

Human Phenotype Ontology (HPO) terms are increasingly used in diagnostic settings to aid in the characterization of patient phenotypes. The HPO annotation database is updated frequently and can provide detailed phenotype knowledge on various human diseases, and many HPO terms are now mapped to candidate causal genes with binary relationships. To further improve the genetic diagnosis of rare diseases, we incorporated these HPO annotations, gene-disease databases, and gene-gene databases in a probabilistic model to build a novel HPO-driven gene prioritization tool, Phen2Gene. Phen2Gene accesses a database built upon this information called the HPO2Gene Knowledgebase (H2GKB), which provides weighted and ranked gene lists for every HPO term. Phen2Gene is then able to access the H2GKB for patient-specific lists of HPO terms or PhenoPackets descriptions supported by GA4GH (http://phenopackets.org/), calculate a prioritized gene list based on a probabilistic model, and output gene-disease relationships with great accuracy. Phen2Gene outperforms existing gene prioritization tools in speed, and acts as a real-time phenotype driven gene prioritization tool to aid the clinical diagnosis of rare undiagnosed diseases. In addition to a command line tool released under the MIT license (https://github.com/WGLab/Phen2Gene), we also developed a web server and web service (https://phen2gene.wglab.org/) for running the tool via web interface or RESTful API queries. Finally, we have curated a large amount of benchmarking data for phenotype-to-gene tools involving 197 patients across 76 scientific articles and 85 patients de-identified HPO term data from CHOP.

bioinformatics↗

bioRxiv2018

Co-expression patterns define epigenetic regulators associated with neurological dysfunction

Coding variants in genes encoding for epigenetic regulators are an emerging cause of neurological dysfunction and cancer. However, a systematic effort to identify disease candidates within the human epigenetic machinery (EM) has not been performed, and it is unclear whether features exist that distinguish between variation-intolerant and variation-tolerant EM genes, and between EM genes associated with neurological dysfunction versus cancer. Here, we rigorously define a set of 295 human genes with a direct role in epigenetic regulation (writers, erasers, remodelers, readers). Systematic exploration of these genes reveals that while individual enzymatic functions are always mutually exclusive, readers often also exhibit enzymatic activity as well (dual function EM genes). We find that the majority of EM genes are very intolerant to loss-of-function variation, even when compared to the dosage sensitive group of transcription factors. Using this strategy, we identify 103 novel EM disease candidates. We show that the intolerance to loss-of-function variation is driven by the protein domains encoding the epigenetic function, strongly suggesting that disease is caused by a perturbed chromatin state. Unexpectedly, we also describe a large subset of EM genes that are co-expressed within multiple tissues. This subset is almost exclusively populated by extremely variation-intolerant EM genes, and shows enrichment for dual function EM genes. It is also highly enriched for genes associated with neurological dysfunction, even when accounting for dosage sensitivity, but not for cancer-associated EM genes. These findings prioritize novel disease candidate EM genes, and suggest that the co-expression itself may play a functional role in normal neurological homeostasis.

genomics↗

bioRxiv2018

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants

SV-plaudit is a framework for rapidly curating structural variant (SVs) predictions. For each SV, we generate an image that visualizes the coverage and alignment signals from a set of samples. Images are uploaded to our cloud framework where users assess the quality of each image using a client-side web application. Reports can then be generated as a tab-delimited file or annotated VCF. As a proof of principle, nine researchers collaborated for one hour to evaluate 1,350 SVs each. We anticipate that SV-plaudit will become a standard step in variant calling pipelines and the crowd-sourced curation of other biological results.\n\nCode available at https://github.com/jbelyeu/SV-plaudit\n\nDemonstration video available at https://www.youtube.com/watch?v=ono8kHMKxDs

bioinformatics↗

bioRxiv2017

A map of constrained coding regions in the human genome.

Deep catalogs of genetic variation collected from many thousands of humans enable the detection of intraspecies constraint by revealing coding regions with a scarcity of variation. While existing techniques summarize constraint for entire genes, single metrics cannot capture the fine-scale variability in constraint within each protein-coding gene. To provide greater resolution, we have created a detailed map of constrained coding regions (CCRs) in the human genome by leveraging coding variation observed among 123,136 humans from the Genome Aggregation Database (gnomAD). The most constrained coding regions in our map are enriched for both pathogenic variants in ClinVar and de novo mutations underlying developmental disorders. CCRs also reveal protein domain families under high constraint, suggest unannotated or incomplete protein domains, and facilitate the prioritization of previously unseen variation in studies of disease. Finally, a subset of CCRs with the highest constraint likely exist within genes that cause yet unobserved human phenotypes owing to strong purifying selection.

genomics↗