Embed Size (px)
DESCRIPTION
The success of whole exome sequencing (WES) for highly heterogeneous disorders, such as mitochondrial disease, is limited by substantial technical and bioinformatics challenges to correctly identify and prioritize the extensive number of sequence variants present in each patient. The likelihood of success can be greatly improved if a large cohort of patient data is assembled in which sequence variants can be systematically analysed, annotated, and interpreted relative to known phenotype. This effort has engaged and united more than 100 international mitochondrial clinicians, researchers, and bioinformaticians in the Mitochondrial Disease Sequence Data Resource (MSeqDR) consortium that formed in June 2012 to identify and prioritize the specific WES data analysis needs of the global mitochondrial disease community. Through regular web-based meetings, we have familiarized ourselves with existing strengths and gaps facing integration of MSeqDR with public resources, as well as the major practical, technical, and ethical challenges that must be overcome to create a sustainable data resource. We have now moved forward toward our common goal by establishing a central data resource (http://mseqdr.org/) that has both public access and secure web-based features that allow the coherent compilation, organization, annotation, and analysis of WES and mtDNA genome data sets generated in both clinical- and research-based settings of suspected mitochondrial disease patients. The most important aims of the MSeqDR consortium are summarized in the MSeqDR portal within the Consortium overview sections. Consortium participants are organized in 3 working groups that include (1) Technology and Bioinformatics; (2) Phenotyping, databasing, IRB concerns and access; and (3) Mitochondrial DNA specific concerns. The online MSeqDR resource is organized into discrete sections to facilitate data deposition and common reannotation, data visualization, data set mining, and access management. With the support of the United Mitochondrial Disease Foundation (UMDF) and the NINDS/NICHD U54 supported North American Mitochondrial Disease Consortium (NAMDC), the MSeqDR prototype has been built. Current major components include common data upload and reannotation using a novel HBCR based annotation tool that has also been made publicly available through the website, MSeqDR GBrowse that allows ready visualization of all public and MSeqDR specific data including labspecific aggregate data visualization tracks, MSeqDR-LSDB instance of nearly 1250 mitochondrial disease and mitochodnrial localized genes that is based on the Locus Specific Database model, exome data set mining in individuals or families using the GEM.app tool, and Account & Access Management. Within MSeqDR GBrowse it is now possible to explore data derived from MitoMap, HmtDB, ClinVar, UCSC-NumtS, ENCODE, 1000 genomes, and many other resources that bioinformaticians recruited to the project are organizing.
Citation preview
MseqDR consortium: a grass-roots effort to establish a global resource
aimed to empower genomic studies of mitochondrion diseases
Marcella Attimonelli Dept. of Biosciences, Biotechnology and Biopharmaceutics, University of Bari – IT
NGS and Mitochondrial diseases
A worldwide call for a great bioinformatics effort to correctly identify and prioritize the extensive number of sequence variants present in each patient affected by a suspected mitochondrial disease.
NGS, Mitochondrial diseasesand bioinformatics
The likelihood of success of the effort can be greatly improved if the large cohort of patient data is organized in a structured resource in which sequence variants can be systematically analysed, annotated and interpreted relatively to known phenotype.
The establishement of the MSeqDR consortium
To carry out this effort more than 100 international mitochondrial clinicians, researchers and bioinformaticians get engaged and united in the Mitochondrial Disease Sequence Data Resource (MSeqDR) consortium.
Through regular web-based meetings, we have familiarized ourselves with existing strengths and gaps facing• integration of MSeqDR with public resources• the major practical, technical, and ethical
challenges that must be overcome to create a sustainable data resource
Thanks to this effort a prototype of the MSeqDR central resource has been established
http://mseqdr.org/
The resource offers both public access and secure but web-based features allowing the analysis, annotation and organization of WES (Whole Exome Sequencing)
and mtDNA datasets of suspected mt disease patients generated in both clinical- and research-based
settings.
MSeqDR consortium structure• WG1 – Technology and BioinformaticsCoChair: Marni Falk (CHOP/Upenn), Xiaowu Gai PhD (MEEI) and Curt Sharfe (MD, PhD Stanford)Advisors: Lisa Brooks, Phd (NHGRI), Dehanna Church PhD (NCBI, NIH)
• WG2 – Phenotyping, Databases, IRB concerns and AccessCoChair: Patrick Chinnery MD, PhD (NewCastle), Lee-Jun Wong PhD (Baylor) and Peter White, PhD (CHOP/Pen)Advisors: Donna Maglott PhD (NCBI,NIH) and Yaffa Rubinstein PhD (NCATS, ORDR)
• WG3 – Mitochondrial DNA Specific concernsCoChair: Vincent Procaccio PhD (Angers) and Douiglas Wallace PhD (CHOP/Upenn)Advisors : Marie Lott PhD (CHOP), Marcella Attimonelli (DBBB)
MSeqDR major software components are:
o Data Capture software allowing capturing, annotation and integration of data derived from external resources.
o Gbrowse software allowing graphical display of the captured data
o MSeqDR-LSDB, the MSeQDR locus specific database designed by using LOVD
o MITO-BOX : a compendium of software allowing variants annotation and prioritization
o Account & Access Management.
MSeqDR LSDB
Data are organised according to the following classes:• Genes• Transcripts• Variants• Diseases• Individuals• Screenings
New data can be submitted by registered users
General Genomic
Platform Data Backend
• Ensembl Genes, UCSC Genes, NCBI Genes, HUGO genes nomenclature (HGNC)
• EVS, 1000 Genomes
MSeqDR Community
Genomic Resources
• Proprietary Exome (3500+) Data
• Mitomap: Expert Curation, 10K mitochondrial variants
• HmtDB: annotated complete mitochondrial genomes
• PhyloTree: Human mt Haplogroups classification
• Community data: Transgenomics Inc., POLG DB,
Mito-Phenome Resources
•OMIM, ClinVar, MedGen•Ensembl Phenotype•Mitomap disease names, HmtDB pathogenicity database, •HPO: the human Phenotype Ontology•Mito Dictionaries from NAMDC and UMDF
MSeqDR Gbrowse
Once selected a human genomic region and chosen the classes of data of interest, the user is allowed to browse among the available tracks and to move to metadata and
related tables
Example of a mtDNA region tracks
M:10,000-11,000
Mitochondrial Disease ToolsMSeqDR is collaborating with the community to bring
together various available and published tools.
Currently the following tools are fully implemented HBPCR, GEM.APP, MITOMASTER
On the way: MT.AT, MToolBox*, The Phenom Portal
* See Poster 21
The MSeqDR Prototype Development
Site 1. Xiaowu Gai , PhD , Lishuang Shen , PhD https://MSeqDR.org MEEI Common data upload and reannotationMSeqDR GBrowseMSeqDR-LSDBPhenome data
Site 2 Stephan Züchner, MD, PhDUniversity of Miami Miller School of Medicine Exome data set mining in individuals or families using the GEM.App tool
International group members of the consortium are contributing with software and databases.
MSeqDR will improve the prioritization of mitochondrial disease causing variants thanks to a self-training mechanism that will allow the identification of • rare cases whose genetic diagnosis may not have been
known• genetic links to "secondary" mitochondrial conditions
MSeqDR ParticipationInterested in joining MSeqDR consortium?
If you are interested in joining the MSeqDR consortium, please contact Dr. Marni Falk at [email protected].
Discussion about this MSeqDR Prototype Website and Development Effort?
Please contact Dr. Xiaowu Gai at [email protected], or comment at our online Feedback below. .
Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium
MSeqDR Consortium is supported by United Mitochondrial Disease Foundation (UMDF) and extramural program officers at NICHD, NIH and other institutions where the consortium participants are affiliated.
M.Attimonelli1, L.Shen11, M.Gonzalez2, D.C.Wallace3, M.Lott3, J.Leipzig3, F.Stassen4, M.Tarnopolsky5, R.Boles6,7, J.DaRe8, R.Bai9, M.Parisi10, D.Krotoski10, S.Zuchner2,
X.Gai11, M.J.Falk12
• 1Department of Biosciences Biotechnology and Biopharmaceutics, IT• 2 Human-Genetics Department, Miami • 3 Children’s Hospital Philadelphia, USA• 4Maastricht University, NL• 5 McMaster University, Canada• 6California University, USA• 8Transgenomic, USA• 9GeneDx, Gaithersburg, USA• 10 NICHD-NIH, Bethesda, USA• 11 Massachusetts-Eye-and-Ear-Infirmary, Harvard.Univ USA; • 12 University of Pennsylvania, USA
Acknowledgements to my coworkers
• Giuseppe Gasparre, Researcher at the Dept. of Medical and Surgical Sciences, University of Bologna , Italy
• Domenico Simone, Post-doctoral fellow at the Dept. of Biosciences, University of Milan, Italy (and now guest in my lab)
• Claudia Calabrese, Post-doctoral fellow at the Dept. of Medical and Surgical Sciences, University of Bologna , Italy (and now guest in my lab)
• Maria Angela Diroma, PhD student at the Dept. of Biosciences, Biotechnologies and Biopharmaceutics , University of Bari, Italy (and now guest at MEEI, Harvard University, Cambridge MA, USA)
• Mariangela Santorsola, PhD student at the Dept. of Sciences and Technologies, University of Sannio, Italy (and now guest in my lab)
• Rosanna Clima, PhD student at the Dept. of Medical and Surgical Sciences, University of Bologna , Italy (and now guest in my lab)
