A5102891374- Genomics and Rare Diseases
- Cancer Genomics and Diagnostics
- Genomic variations and chromosomal abnormalities
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- Renal and related cancers
- Genetics, Bioinformatics, and Biomedical Research
- Renal cell carcinoma treatment
- Advanced Proteomics Techniques and Applications
- Biomedical and Engineering Education
- Artificial Intelligence in Healthcare and Education
- RNA modifications and cancer
- Health and Medical Research Impacts
- Biomedical Text Mining and Ontologies
- Hedgehog Signaling Pathway Studies
- Mobile Health and mHealth Applications
- Scientific Computing and Data Management
- Vaccine Coverage and Hesitancy
- Cardiomyopathy and Myosin Studies
- Gene expression and cancer classification
- RNA Research and Splicing
- Ethics in Clinical Research
University of California, Irvine
2023-2025
Invitae (United States)
2014-2024
Southern California Clinical and Translational Science Institute
2023
23andMe (United States)
2014
Harvard University
2010-2011
Center for Systems Biology
2010
National Institutes of Health
2002
National Cancer Institute
2002
In this overview to biomedical computing in the cloud, we discussed two primary ways use cloud (a single instance or cluster), provided a detailed example using NGS mapping, and highlighted associated costs. While many users new may assume that entry is as straightforward uploading an application selecting type storage options, illustrated there substantial up-front effort required before can make full of cloud's vast resources. Our intention was provide set best practices illustrate how...
Variant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes phasing all haplotypes of paralogous together. applied Paraphase to 160 long (>10 kb) duplication regions across the human genome with high (>99%) similarity, encoding 316 genes. Analysis five ancestral populations revealed variable copy numbers these regions. identified 23 paralog groups exceptionally low within-group...
Background Comparative genomics resources, such as ortholog detection tools and repositories are rapidly increasing in scale complexity. Cloud computing is an emerging technological paradigm that enables researchers to dynamically build a dedicated virtual cluster may represent valuable alternative for large computational bioinformatics. In the present manuscript, we optimize computation of large-scale comparative resource—Roundup—using cloud computing, describe proper operating principles...
Disease-specific genetic information has been increasing at rapid rates as a consequence of recent improvements and massive cost reductions in sequencing technologies. Numerous systems designed to capture organize this mounting sea data have emerged, but these resources differ dramatically their disease coverage depth. With few exceptions, researchers must manually search variety sites assemble complete set evidence for particular interest, process that is both time-consuming error-prone. We...
Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by Human Genome Variation Society (HGVS). Despite widespread use standard, no freely available comprehensive programming libraries available. Here we report an open-source easy-to-use Python library that facilitates parsing, manipulation, formatting validation according to HGVS specification. The current implementation...
Prior studies of the renal cell carcinoma (RCC) germline landscape investigated predominantly patients European ancestry. We examine frequency pathogenic and likely (P/LP) variants in 1,829 with RCC from various ancestries. Overall, P/LP are found 17% patients, among whom 10.3% harbor one or more clinically actionable potential preventive therapeutic utility. Patients African ancestry significantly FH compared to non-African controls Genome Aggregation Database (gnomAD). have CHEK2...
ABSTRACT Objective To conduct a retrospective analysis comparing traditional human-based consenting to an automated chat-based process. Materials and Methods We developed new consent using our IRB-approved forms. leveraged previously platform (Gia®, or “Genetic Information Assistant”) deliver the chat content candidate participants. The included information about study, educational information, quiz assess understanding. analyzed 144 families referred study during 6-month time period. A...
Abstract Objective We implemented a chatbot consent tool to shift the time burden from study staff in support of national genomics research study. Materials and Methods created an Institutional Review Board-approved script for automated chat-based consent. compared data prospective participants who used or had traditional conversations with staff. Results Chat-based consent, completed on user’s schedule, was shorter than conversation. This did not lead significant change affirmative...
Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum manifestations associated with loss-of-function has not been reported, leading to hypotheses alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, other resources identify individuals heterozygous,...
Petricoin, Emanuel F. III; Ardekani, Ali M.; Hitt, Ben A.; Levine, Peter J.; Fusaro, Vincent Steinberg, Seth Mills, Gordon B.; Simone, Charles; Fishman, David Kohn, Elise C.; Liotta, Lance A.
We evaluated the diagnostic yield using genome-slice panel reanalysis in clinical setting an automated phenotype/gene ranking system. analyzed whole genome sequencing (WGS) data produced from clinically ordered panels built as bioinformatic slices for 16 diverse, undiagnosed cases referred to Pediatric Mendelian Genomics Research Center, NHGRI-funded GREGoR Consortium site. Genome-wide was performed Moon™, a machine-learning-based tool variant prioritization. In five out of cases, we...
Abstract Introduction Advancements in sequencing technologies have significantly improved clinical genetic testing, yet the diagnostic yield remains around 30-40%. Emerging are now being deployed setting to address remaining gap. Methods We tested whether short-read genome could increase individuals enrolled into UCI-GREGoR research study, who had suspected Mendelian conditions and prior inconclusive testing. Two other collaborative cohorts, focused on aortopathy dilated cardiomyopathy,...
Abstract Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum manifestations associated with loss-of-function has not been reported, leading to hypotheses alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, other resources identify individuals...
Prior studies of the germline landscape renal cell carcinoma (RCC) have centered around predominantly white patients European ancestry. We examined frequency pathogenic and likely (P/LP) variants in 1,829 with RCC from various ancestries. Overall, P/LP were found 17%, among which 10.3% harbored ≥1 clinically actionable variant potential preventive or therapeutic utility. Patients African ancestry significantly more FH compared to had CHEK2 overall This work helps better understand underlying...