Marc Fiume
A5112877330- Genomics and Rare Diseases
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Ethics in Clinical Research
- Genomic variations and chromosomal abnormalities
- Autism Spectrum Disorder Research
- Genetics and Neurodevelopmental Disorders
- Molecular Biology Techniques and Applications
- Biomedical Text Mining and Ontologies
- Gene expression and cancer classification
- Environmental DNA in Biodiversity Studies
- Privacy-Preserving Technologies in Data
- Research Data Management Practices
- RNA modifications and cancer
- COVID-19 diagnosis using AI
- Machine Learning in Bioinformatics
- Semantic Web and Ontologies
- Genetic diversity and population structure
- BRCA gene mutations in cancer
- Chromosomal and Genetic Variations
- Biomedical Ethics and Regulation
- DNA and Biological Computing
- SARS-CoV-2 detection and testing
- Virology and Viral Diseases
- Identification and Quantification in Food
University Health Network
2018
University of Toronto
2009-2018
Ontario Genomics
2018
Ontario Institute for Cancer Research
2018
Open Group
2017
The development of Next Generation Sequencing technologies, capable sequencing hundreds millions short reads (25–70 bp each) in a single run, is opening the door to population genomic studies non-model species. In this paper we present SHRiMP - SHort Read Mapping Package: set algorithms and methods map genome, even presence large amount polymorphism. Our method based upon fast read mapping technique, separate thorough alignment for regular letter-space as well AB SOLiD (color-space) reads,...
We have developed PhenoTips: open source software for collecting and analyzing phenotypic information patients with genetic disorders. Our combines an easy-to-use interface, compatible any device that runs a Web browser, standardized database back end. The PhenoTips' user interface closely mirrors clinician workflows so as to facilitate the recording of observations made during patient encounter. Collected data include demographics, medical history, family physical laboratory measurements,...
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical genomic data through both harmonized aggregation federated approaches. decreasing cost sequencing (along with other genome-wide molecular assays) increasing evidence its utility will soon drive generation sequence from tens millions humans, levels diversity. In this perspective, we present GA4GH strategies addressing major challenges revolution. We...
The development of high-throughput sequencing (HTS) technologies has opened the door to novel methods for detecting copy number variants (CNVs) in human genome. While past CNVs have been detected based on array CGH data, recent studies shown that depth-of-coverage information from HTS can also be used reliable identification large copy-variable regions. Such methods, however, are hindered by biases lead certain regions genome over- or undersampled, lowering their resolution and ability...
High-throughput RNA sequencing (RNA-seq) promises to revolutionize our understanding of genes and their role in human disease by characterizing the content tissues cells. The realization this promise, however, is conditional on development effective computational methods for identification quantification transcripts from incomplete noisy data. In article, we introduce iReckon, a method simultaneous determination isoforms estimation abundances. Our probabilistic approach incorporates multiple...
A systematic way of recording data use conditions that are based on consent permissions as found in the datasets main public genome archives (NCBI dbGaP and EMBL-EBI/CRG EGA).
Abstract Motivation: The advent of high-throughput sequencing (HTS) technologies has made it affordable to sequence many individuals' genomes. Simultaneously the computational analysis large volumes data generated by new machines remains a challenge. While plethora tools are available map resulting reads reference genome, and conduct primary mappings, is often necessary visually examine results underlying confirm predictions understand functional effects, especially in context other...
<h3>BACKGROUND:</h3> The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. <h3>METHODS:</h3> Volunteers were screened for eligibility provided informed consent open sharing. Using blood DNA, we performed all possible classes DNA variants. A genetic counsellor explained implication results to each participant....
We promote a shared vision and guide for how when to federate genomic health-related data sharing, enabling connections insights across independent, secure databases. The GA4GH encourages federated approach wherein providers have the mandate resources share, but where cannot move legal or technical reasons. recommend connect national genomics initiatives into global network precision medicine resource.
The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase improve to requiring an agreement basic terms conditions, such as the use of DNA sequence health in research. A registered would enable range categories users gain access, starting with researchers clinical care professionals. It also facilitate general reuse but within bounds consent restrictions other ethical obligations. In piloting Scientific Demonstration sharing...
The Clinical Genome Resource (ClinGen)'s work to develop a knowledge base support the understanding of genes and variants for use in precision medicine research depends on robust, broadly applicable, adaptable technical standards sharing data information. To forward this goal, ClinGen has joined with Global Alliance Genomics Health (GA4GH) development open, freely-available regulatory frameworks secure responsible genomic health-related data. In its capacity as one 15 inaugural GA4GH "Driver...
The COVID-19 pandemic led to a large global effort sequence SARS-CoV-2 genomes from patient samples track viral evolution and inform the public health response. Millions of genome sequences have been deposited in repositories. Canadian Genomics Network (CanCOGeN – VirusSeq), consortium tasked with coordinating expanded sequencing across Canada early pandemic, created VirusSeq Data Portal, associated data pipelines procedures, support these efforts. goal was allow open access genomic...
Abstract The volume of genomics and health data is growing rapidly, driven by sequencing for both research clinical use. However, under current practices, the fragmented into many distinct datasets, researchers must go through a separate application process each dataset. This time-consuming stewards, it reduces velocity new discoveries that could improve human health. We propose to simplify this process, introducing standard Library Card identifies authenticates across all participating...
Background Early detection of autism can improve the quality life affected individuals [1]. Qualitative screening methods continue to improve, but still suffer from low sensitivity despite increasing specificity [2,3]. In collaboration with Hospital for Sick Children, we are sequencing exomes 1 000 in order discover genetic variants associated disorder. Discovery lead earlier diagnosis and treatment.
Abstract Fully understanding the genetic factors involved in Autism Spectrum Disorder (ASD) requires whole-genome sequencing (WGS), which theoretically allows detection of all types variants. With aim generating an unprecedented resource for resolving genomic architecture underlying ASD, we analyzed genome sequences and phenotypic data from 5,100 individuals with ASD 6,212 additional parents siblings (total n=11,312) Speaks MSSNG Project, as well other WGS cohorts. autism phenotyping were...