Download Catalogue of Activities Work Product – Mendelian Genetic Disorders

Catalogue of Activities Work Product – Mendelian Genetic Disorders Sheet
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Rare Disease
Genomics
Genetic Variant
Genotype
Phenotype
Phenotype Ontology
Geographic Region:
• Africa
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• North America
• South America
• International
Name
1000 Genomes
Project
Type
Database
Topic
Genomics
Subtopic
Reference
Genome
Geographic
Region
Description
Recent improvements in sequencing technology ("next-gen" sequencing platforms) have
sharply reduced the cost of sequencing. The 1000 Genomes Project is the first project to
sequence the genomes of a large number of people, to provide a comprehensive resource on
human genetic variation.
International
As with other major human genome reference projects, data from the 1000 Genomes Project
will be made available quickly to the worldwide scientific community through freely
accessible public databases... The goal of the 1000 Genomes Project is to find most genetic
variants that have frequencies of at least 1% in the populations studied...
Website
Contact
http://www.
1000genom
es.org/
There is a considerable need and desire for networks of diagnostic laboratories/disease
consortia to be able to check each others databases for the presence of mutations they
observe in their own patients. But this is countered by the understandable reluctance and
impracticality of sharing the content of each group's database with other labs, or indeed with
the wider world.
Cafe Variome
Database,
Tool
Genetic
Variant,
Phenotype
Missing
Given the above, a way forward has been devised based upon enabling the 'open discovery'
of data (rather than data 'sharing') between networks of diagnostic laboratories or disease
consortia that know/trust each other and share an interest in certain causative genes or
diseases.
http://www.
cafevariom
e.org/
Tony Brookes:
[email protected]
http://care4
rare.ca/
Taila Hartley:
[email protected]
To that end, the Cafe Variome platform has been developed. We are reaching out to groups
and projects that could benefit from such a system, allowing them and their fellow labs to
securely share data between each other.
CARE for
RARE
(FORGE)
Consortiu
m/Collab
orative
Network
Rare Disease
North
America
CARE for RARE is a collaborative team of clinicians, informaticians, scientists and
researchers building upon the infrastructure and discoveries of the FORGE Canada (Finding
of Rare Disease Genes) project which identified more than 67 novel disease genes using
whole-exome sequencing (April 2011-March 2013). The goal of CARE for RARE is to
improve clinical care for patients and families affected by rare diseases by expanding and
improving diagnosis and treatment.
Centers for
Mendelian
Genomics
(CMGs)
Consortiu
m/Collab
orative
Network
ClinGen
Consortiu
m/Collab
orative
Network
Clinical
Sequencing
Exploratory
Research
(CSER)
Consortium
ClinVar
Consortiu
m/Collab
orative
Network
Database
The Centers for Mendelian Genomics (CMG) are co-funded by NHGRI and the National
Heart, Lung, and Blood Institute of National Institutes of Health (NHLBI). The CMG aim to
make major contributions to the discovery of the genetic basis of most or all Mendelian
disorders in two main ways. The first is to use genome-wide sequencing and other genomic
approaches to discover the genomic defects underlying as many Mendelian disorders as
possible, spanning the various Mendelian inheritance patterns, during the funding period.
The second is to accelerate the discovery by disseminating the obtained knowledge and
effective approaches, reaching out to individual investigators, and coordinating with other
rare disease programs worldwide.
Genomics
Genomics
Genetic
Variant,
Phenotype
http://www.
mendelian.
org/
Program contact - Lu
Wang:
[email protected]
http://www.
genome.go
v/27546192
CMG contact - Mike
Bamshad:
[email protected]
gton.edu
North
America
ClinGen is a National Institute of Health (NIH)-funded collaborative program dedicated to
harnessing both research data and the data from the hundreds of thousands of clinical
genetics tests being performed each year, as well as supporting expert curation to determine
the relevance of genes and variants to human health and disease.
http://www.
clinicalgen
ome.org
Heidi Rehm:
[email protected]
g
North
America
The National Human Genome Research Institute (NHGRI) and the National Cancer Institute
(NCI) have initiated a Clinical Sequencing Exploratory Research (CSER) program to support
multidimensional research in this area. CSER is a national consortium of projects that bring
together clinicians, scientists, laboratories, bioinformaticians, economists, legal scholars,
ethicists, and patients working together to develop and share innovations and best practices in
the integration of genomic sequencing into clinical care.
https://cserconsortium.
org/
Lucia Hindorff:
[email protected]
v
International
ClinVar is designed to provide a freely accessible, public archive of reports of the
relationships among human variations and phenotypes, with supporting evidence. By so
doing, ClinVar facilitates access to and communication about the relationships asserted
between human variation and observed health status, and the history of that interpretation.
ClinVar collects reports of variants found in patient samples, assertions made regarding their
clinical significance, information about the submitter, and other supporting data. The alleles
described in submissions are mapped to reference sequences, and reported according to the
HGVS standard. ClinVar then presents the data for interactive users as well as those wishing
to use ClinVar in daily workflows and other local applications. ClinVar works in
collaboration with interested organizations to meet the needs of the medical genetics
community as efficiently and effectively as possible.
https://ww
w.ncbi.nlm.
nih.gov/clin
var/
Melissa Landrum:
[email protected]
.gov
Database of
Genomic
Structural
Variation
(dbVar)
DatabasE of
genomiC
varIants and
Phenotype in
Humans Using
Ensembl
Resources
(DECIPHER)
Database of
Genotypes and
Phenotypes
(dbGaP)
Database of
Short Genetic
Variations
(dbSNP)
Deciphering
Developmental
Disorders
(DDD)
Database of genomic structural variation.
Database
Database,
Tool
Database
Genomics
Missing
Genetic
Variant,
Phenotype
International
Genomics
Missing
The overall aims of DECIPHER are to: 1. Aid in the interpretation of plausibly pathogenic
variants from genome- wide analyses by placing them in the context of known pathogenic
variants, other plausibly pathogenic variants and population variation 2. Annotate plausibly
pathogenic variants with their likely functional impact using Ensembl tools to compare
sequence and structural variants with the latest functional annotation of the current human
reference genome e.g define which genes are involved in a specific copy number variant
(microdeletion / microduplication) or for sequence variants, whether they are positioned
within a gene or regulatory element. 3. Facilitate research into the study of genes that affect
human health and development to improve diagnosis, management and therapy of rare
diseases.
The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute
the results of studies that have investigated the interaction of genotype and phenotype.
Short genetic variations.
Database
Consortiu
m/Collab
orative
Network
Genomics
Missing
Missing
Developm
ental
Disorders
Europe
The Deciphering Developmental Disorders (DDD) study aims to find out if using new
genetic technologies can help doctors understand why patients get developmental disorders.
To do this we have brought together doctors in the 24 Regional Genetics Services,
throughout the UK and Republic of Ireland, with scientists at the Wellcome Trust Sanger
Institute, a charitably funded research institute which played a world-leading role in
sequencing (reading) the human genome. The DDD study involves experts in clinical,
molecular and statistical genetics, as well as ethics and social science. Over the next few
years, we are aiming to collect DNA and clinical information from 12,000 undiagnosed
children in the UK with developmental disorders and their parents.
http://www.
ncbi.nlm.ni
h.gov/dbvar
/
http://decip
her.sanger.
ac.uk/
Helen Firth:
[email protected]
Matt Hurles:
[email protected]
http://www.
ncbi.nlm.ni
h.gov/gap
http://www.
ncbi.nlm.ni
h.gov/SNP/
http://www.
ddduk.org/
Helen Firth:
[email protected]
Matt Hurles:
[email protected]
Elements of
Morphology
EuRenomics
Gen2Phen
Gene Matcher
Tool –
nomenclat
ure
Phenotype
Ontology
Consortiu
m/Collab
orative
Network
Rare Disease
Database
Genetic
Variant,
Phenotype
Database,
Tool
http://eleme
ntsofmorph
ology.nih.g
ov/
John Carey:
[email protected].
edu
http://www.
eurenomics
.eu/
Franz Schaefer:
[email protected]
ni-heidelberg.de
International
The GEN2PHEN project aims to unify human and model organism genetic variation
databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and
to link this system into other biomedical knowledge sources via genome browser
functionality.
http://www.
gen2phen.o
rg/
Tony Brookes:
[email protected]
International
GeneMatcher is a freely accessible web site designed to enable connections between
clinicians and researchers from around the world who share an interest in the same gene or
genes. The principle goal for making GeneMatcher available is to help solve “unsolved”
exomes. This may be done with cases from research or clinical sources. No identifiable data
are collected. GeneMatcher was developed with support from the Baylor-Hopkins Center for
Mendelian Genomics as part of the Centers for Mendelian Genomics network.
https://gene
matcher.org
/
Ada Hamosh:
[email protected]
International
Kidney
Disease
An international group of clinicians working in the field of dysmorphology has initiated the
standardization of terms used to describe human morphology. The goals are to standardize
these terms and reach consensus regarding their definitions. In this way, we will increase the
utility of descriptions of the human phenotype and facilitate reliable comparisons of findings
among patients. Discussions with other workers in dysmorphology and related fields, such as
developmental biology and molecular genetics, will become more precise...
Europe
Our Consortium is devoted to improving the lives of patients affected by rare kidney
diseases. In line with the objectives of the International Rare Disease Research Consortium
(IRDiRC), we aim to develop novel tools that will allow to make more accurate diagnoses,
predict the disease course and the efficacy of available treatments, and help developing new
and better therapies for rare kidney diseases.
This project is receiving funding as part of the European Community’s commitment to the
IRDiRC initiative. In this quest we are joining forces with our FP7 partner project Neuromics
(for neuromuscular disorders) and the RD-CONNECT infrastructure platform.
Genetic
Variant,
Phenotype
Genomics
Management
Application
(GEM.app)
Database,
Tool
Genetic
Variant,
Phenotype
International
Genomes Management Application (GEM.app) is a software tool to annotate, manage,
visualize, and analyze large genomic datasets (https://genomics.med.miami.edu/). Currently,
~400 registered users from 36 countries are building dynamic communities centered around
phenotypic interests, with full control remaining with the PI of a study. GEM.app currently
contains >5000 whole exomes and genomes from 90 different phenotypes. The focus of
GEM.app is on user-friendly analysis for nonbioinformaticians to make next-generation
sequencing data directly accessible. Yet, GEM.app provides powerful and flexible filter
options, including single family filtering, across family/phenotype queries, nested filtering,
and evaluation of segregation in families. GEM.app has been used to successfully identify
>60 novel disease genes in the past 24 months.
https://geno
mics.med.
miami.edu/
Stephan Zuchner:
[email protected].
edu
http://www.
genomicme
dicineallian
ce.org/inde
x.php/2013
-02-19-1451-27/aims
George P. Patrinos:
[email protected] The Genomic Medicine Alliance aims to create collaboration ties between academics,
researchers, regulators, and the general public interested in all aspects of genomics and
personalized medicine. The Alliance provides the means to establish networks and to
encourage collaborative work towards advancing the Genomic Medicine discipline, focusing
in particular on translating results from academic research into clinical practice.
Genomic
Medicine
Alliance
Consortiu
m/Collab
orative
Network
Missing
International
In particular, the Genomic Medicine Alliance aims to:
• Encourage and catalyze multidisciplinary collaborative research between partner
institutions and scientists, particularly from emerging countries.
• Liaise among research organizations, clinical entities and regulatory agencies in areas
related to genomic medicine.
• Facilitate the introduction of pharmacogenomics and advanced omics technologies into the
mainstream clinical practice.
• Produce and propose guidelines and recommendations in all areas pertaining to genomic
medicine, always in close collaboration with other scientific academic entities, agencies and
regulatory bodies.
• Develop, independently or in close collaboration with partner institutions, and coordinate
educational activities in the area of genomic medicine.
Global Genomic
Medicine
Collaborative
(G2MC)
Consortiu
m/Collab
orative
Network
The Global Genomic Medicine Collaborative (G2MC) is an organization of global leaders in
the implementation of genomic medicine in clinical care, arising from an international
symposium in Washington, D.C. in January, 2014 convened by the National Human Genome
Research Institute and hosted by the US Institute of Medicine. It is an international genomic
medicine community formed to unite and catalyze the implementation of genomic tools and
knowledge into health care delivery globally. Specifically, it is intended to:
Genomics
International
• Serve as nexus, clearinghouse, and knowledge base for genomic medicine activities
globally;
Under
Constructio
n
Adam Berger:
http://www.
hgvs.org
Rania Horaitis:
[email protected]
http://www.
humanphenotypeontology.or
g/
Peter Robinson:
peter.robinson@charit
e.de
[email protected] • Develop opportunities for global genomic medicine demonstration projects
(implementation and outcomes research);
• Capture and disseminate best practices for genomic medicine (in bioinformatics, education,
evidence, pharmacogenomics, policy) across the global genomic medicine community; and
• Develop a financial model for sustained efforts.
Human Genome
Variation
Society (HGVS)
Human
Phenotype
Ontology (HPO)
Consortiu
m/Collab
orative
Network
Tool –
nomenclat
ure
Genomics
International
The Society aims to foster discovery and characterization of genomic variations including
population distribution and phenotypic associations. We will promote collection,
documentation and free distribution of genomic variation information and associated clinical
variations and endeavor to foster the development of the necessary methodology and
informatics...
To enhance human health through identification and characterization of changes in the
genome that lead to susceptibility to illness. To this end, to collate the genomic information
necessary for molecular diagnosis, research on basic mechanisms and design of treatments of
human ailments.
...The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of
phenotypic abnormalities encountered in human disease. Terms in the HPO describes a
phenotypic abnormality, such as atrial septal defect.
Phenotype
Ontology
International
The HPO was initially developed using information from Online Mendelian Inheritance in
Man (OMIM) and is now using information from OMIM and the medical literature and
contains approximately 10,000 terms. Over 50,000 annotations to hereditary diseases are
available for download or can be browsed using the PhenExplorer.
The Human Variome Project is working to ensure that all information on genetic variation
and its effect on human health can be collected, curated, interpreted and shared freely and
openly.
Human Variome
Project
Consortiu
m/Collab
orative
Network
Missing
International
In doing so, the Human Variome Project takes on four roles:
1) establishing and maintaining the standards, systems and infrastructure necessary for the
worldwide collection, curation, interpretation and sharing of information across the genome;
2) advocating and promoting ethical behaviour in the field of medical genetics and genomics;
3) sharing knowledge about our genome and its function in determining health; and 4)
assisting individuals and nations build their capacity to address the genetic aspects of
individual and global health.
http://www.
humanvario
meproject.o
rg/
Peter Robinson
(main):
peter.robinson@charit
e.de
International
Consortium for
Human
Phenotype
Terminologies
(ICHPT)
Tool –
nomenclat
ure
Phenotype
Ontology
International
Website forthcoming (a common set of terms are being mapped across all ontologies)
http://www.
ichpt.org/
Ségolène Aymé:
segolene.ayme@inser
m.fr
Ana Rath:
[email protected]
Ada Hamosh:
[email protected]
International
Rare Disease
Research
Consortium
(IRDiRC)
Consortiu
m/Collab
orative
Network
The International Rare Disease Research Consortium (IRDiRC) teams up researchers and
organizations investing in rare diseases research in order to achieve two main objectives by
the year 2020, namely to deliver 200 new therapies for rare diseases and means to diagnose
most rare diseases.
Rare Disease
International
A number of grand challenges are being addressed through collaborative actions to reach
these 2020 goals such as:
• establishing and providing access to harmonized data and samples,
• performing the molecular and clinical characterization of rare diseases,
• boosting translational, preclinical and clinical research,
• and streamlining ethical and regulatory procedures.
http://www.
irdirc.org/
Segolene Ayme:
segolene.ayme@inser
m.fr
Barbara Cagniard:
barbara.cagniard@irdi
rc.org
LOVD stands for Leiden Open (source) Variation Database.
Leiden Open
Variation
Database
(LOVD)
Database
Genetic
Variant,
Phenotype
International
Purpose: provide a flexible, freely available tool for gene variant and phenotype collection,
display and curation. On the Leiden server LOVD offers free hosting and support of LOVDpowered gene variant databases. LOVD is open source, released under the GPL license, and
is actively being improved. Several version of the software are available. LOVD 3.0 is
actively developed; currently we have releases every month.
http://
www.LOV
D.nl
The Winter-Baraitser Dysmorphology Database: The Winter-Baraitser Dysmorphology
Database (WBDD) currently contains information on over 4700 dysmorphic, multiple
congenital anomaly and mental retardation syndromes. It includes single gene disorders,
sporadic conditions, and those caused by environmental agents...
London
Dysmorphology
Database
Phenotype
Ontology
Missing
The Baraitser-Winter Neurogenetics Database: The Baraitser-Winter Neurogenetics Database
(BWND) currently contains information on over 4250 syndromes involving the central and
peripheral nervous system seen in adults and children...
The Photo Library: Now integrated into WBDD and BWND, the Photo Library is a superb
collection of over 20000 photographs that show the main dysmorphic features of the
syndrome and other relevant images, such as skeletal radiographs, hair microscopy, etc...
The London Ophthalmic Genetics Database (GENEEYE): The latest addition to the LMD
series, GENEEYE is a comprehensive database of over 2900 genetic ophthalmic conditions...
http://www.
lmdatabase
s.com/abou
t_lmd.html
Johann Den Dunnen:
LOVD@JohanDenDu
nnen.nl
MedGen
Neuromics
NHLBI Exome
Sequencing
Project (ESP)
and Exome
Variant Server
Tool –
nomenclat
ure
Consortiu
m/Collab
orative
Network
Tool
Phenotype
Ontology
Rare Disease
Genetic
Variant
North
America
Neurogen
etic
Disorders
Exome
Variant
Europe
MedGen is NCBI’s portal to information about human disorders and phenotypes having a
genetic component. The purpose of MedGen is to harmonize phenotype terminologies,
support computational access to phenotype data, and to add value through a variety of data
elements. MedGen aggregates terms from multiple vocabulary sources into a specific concept
and assigns a unique, stable identifier (Concept Unique Identifier; CUI) to that concept –
where possible, the same identifier used by UMLS. MedGen provides multiple types of
descriptors for concepts including names, synonyms, acronyms, semantic type, abbreviations,
sources of descriptors, attribution and identifiers (e.g., from OMIM, HPO and Orphanet),
textual definitions from multiple sources, hierarchical relationships between terms,
cytogenetic locations, causative genes and variants, mode of inheritance, tests in the NIH
Genetic Testing Registry (GTR), molecular resources, professional guidelines, reviews (e.g.
from GeneReviews and Medical Genetics Summaries), consumer resources, molecular
resources, clinical trials, and Web links to other related NCBI and non-NCBI resources.
MedGen serves as the terminology resource for ClinVar and GTR.
Neuromics is a research consortium which brings together the leading research groups in
Europe, five highly innovative SMEs as well as overseas experts in the relevant fields. Using
the most sophisticated -omics technologies, this consortium will revolutionize diagnostics
and develop new treatments for ten major neurodegenerative and neuromuscular diseases
affecting the cortex, basal ganglia, cerebellum, spinal cord, peripheral nerves, neuromuscular
junction, and muscle...
The Neuromics research efforts will interact closely with a similar project in the field of rare
kidney diseases – EURenOmics, sharing skills, experiences and infrastructure where
possible. Both will work closely with RD-Connect, a recently funded project which will
create an integrated platform connecting databases, registries, biobanks and clinical
bioinformatics for rare disease research.
North
America
The goal of the NHLBI GO Exome Sequencing Project (ESP) is to discover novel genes and
mechanisms contributing to heart, lung and blood disorders by pioneering the application of
next-generation sequencing of the protein coding regions of the human genome across
diverse, richly-phenotyped populations and to share these datasets and findings with the
scientific community to extend and enrich the diagnosis, management and treatment of heart,
lung and blood disorders.
http://www.
ncbi.nlm.ni
h.gov/medg
en
Wendy Rubinstein:
http://rdneuromics.
eu/
Olaf Riess:
[email protected]
http://evs.g
s.washingto
n.edu/EVS/
[email protected]
h.gov
Debbie Nickerson:
[email protected]
n.edu
Online
Mendelian
Inheritance in
Man (OMIM)
Database
Genotype,
Phenotype
International
OMIM is a comprehensive, authoritative compendium of human genes and genetic
phenotypes that is freely available and updated daily. The full-text, referenced overviews in
OMIM contain information on all known mendelian disorders and over 12,000* genes.
OMIM focuses on the relationship between phenotype and genotype. It is updated daily, and
the entries contain copious links to other genetics resources.
http://www.
omim.org/
Ada Hamosh:
[email protected]
http://www.
orpha.net/c
onsor/cgibin/index.p
hp
Ana Rath:
[email protected]
*As of August 2014, OMIM has over 14,700 genes.
Orphanet
Consortiu
m/Collab
orative
Network
Rare Disease
International
Orphanet is the reference portal for information on rare diseases and orphan drugs, for all
audiences. Orphanet’s aim is to help improve the diagnosis, care and treatment of patients
with rare diseases.Orphanet offers a range of freely accessible services:
• A multi-lingual inventory of rare diseases and a classification of diseases elaborated using
existing published expert classifications.
• An encyclopaedia of rare diseases in English, progressively translated into french, German,
Spanish, Portuguese, Italian, Dutch, Poland, Greek, and Finnish.
• An inventory of orphan drugs at all stages of development.
• A directory of expert resources, providing information on expert clinics, medical
laboratories, ongoing research projects, clinical trials, registries, networks, technological
platforms and patient organisations, in the field of rare diseases, in each of the 37 countries in
Orphanet’s consortium.
• An assistance-to-diagnosis tool allowing users to search by signs and symptoms.
• An encyclopaedia of recommendations and guidelines for emergency medical care and
anaesthesia.
• A fortnightly newsletter, OrphaNews, which gives an overview of scientific and political
current affairs in the field of rare diseases and orphan drugs, in English and French.
• A collection of thematic reports, the Orphanet Reports Series, focusing on overarching
themes, directly downloadable from the website.
Orphanet Rare
Disease
Ontology
(ORDO)
Tool –
nomenclat
ure
Phenotype
Ontology,
Rare Disease
International
The Orphanet Rare Disease ontology (ORDO) is jointly developed by Orphanet and the EBI
to provide a structured vocabulary for rare diseases capturing relationships between diseases,
genes and other relevant features which will form a useful resource for the computational
analysis of rare diseases. It derived from the Orphanet database (www.orpha.net ) , a
multilingual database dedicated to rare diseases populated from literature and validated by
international experts. It integrates a nosology (classification of rare diseases), relationships
(gene-disease relations, epiemological data) and connections with other terminologies
(MeSH, SNOMED CT, UMLS, MedDRA),databases (OMIM, UniProtKB, HGNC, ensembl,
Reactome, IUPHAR, Geantlas) or classifications (ICD10).
http://www.
orphadata.o
rg/cgibin/inc/ord
o_orphanet.
inc.php
Ana Rath (main):
[email protected]
Annie Olry:
[email protected]
The PharmGKB is a pharmacogenomics knowledge resource that encompasses clinical
information including dosing guidelines and drug labels, potentially clinically actionable
gene-drug associations and genotype-phenotype relationships. PharmGKB collects, curates
and disseminates knowledge about the impact of human genetic variation on drug responses
through the following activities:
Pharmacogeneti
cs Knowledge
Base
(PharmGKB)
Database
Genomics
Pharmaco
genetics
North
America
• Annotate genetic variants and gene-drug-disease relationships via literature reviews
• Summarize important pharmacogenomic genes, associations between genetic variants and
drugs, and drug pathways
• Curate FDA drug labels containing pharmacogenomic information
• Enable consortia examining important questions in pharmacogenomics
• Curate and participate in writing pharmacogenomic-based drug dosing guidelines
• Contribute to clinical implementation projects for pharmacogenomics through
collaborations
• Publish pharmacogenomic-based drug dosing guidelines, very important pharmacogene
summaries and drug-centered pathways
• Display all information on the website and provide comprehensive downloads
https://ww
w.pharmgk
b.org/
Teri E. Klein:
[email protected]
u
PhenoDB
Database,
Tool
Genetic
Variant,
Phenotype,
Rare Disease
International
To interpret whole exome/genome sequence data for clinical and research purposes,
comprehensive phenotypic information, knowledge of pedigree structure, and results of
previous clinical testing are essential. With these requirements in mind and to meet the needs
of the Centers for Mendelian Genomics project, we have developed PhenoDB
(http://phenodb.net), a secure, Web-based portal for entry, storage, and analysis of
phenotypic and other clinical information. The phenotypic features are organized
hierarchically according to the major headings and subheadings of the Online Mendelian
Inheritance in Man (OMIM®) clinical synopses, with further subdivisions according to
structure and function. Every string allows for a free-text entry. All of the approximately
2,900 features use the preferred term from Elements of Morphology and are fully searchable
and mapped to the Human Phenotype Ontology and Elements of Morphology. The PhenoDB
allows for ascertainment of relevant information from a case in a family or cohort, which is
then searchable by family, OMIM number, phenotypic feature, mode of inheritance, genes
screened, and so on. The database can also be used to format phenotypic data for submission
to dbGaP for appropriately consented individuals. PhenoDB was built using Django, an open
source Web development tool, and is freely available through the Johns Hopkins McKusickNathans Institute of Genetic Medicine. (Information on PhenoDB copied from:
http://www.ncbi.nlm.nih.gov/pubmed/23378291)
http://phen
odb.net
Ada Hamosh:
[email protected]
PhenomeCentral is a repository for secure data sharing targeted to clinicians and scientists
working in the rare disorder community. PhenomeCentral encourages global scientific
collaboration while respecting the privacy of patients profiled in this centralized database.
PhenomeCentral
Database,
Tool
Genetic
Variant,
Phenotype
International
Why is it useful?
• PhenomeCentral enables the discovery of multiple individuals affected by the same
unnamed disorder. Undiagnosed disorders may be present in only a handful of individuals
seen at different hospitals and sequenced by different centers. The PhenomeCentral
collaboration model enables effective and secure data-sharing techniques that allow
clinicians and scientists to learn about the existence of cases similar to theirs, which
eventually may help improve the understanding of disorder manifestations and confirm the
underlying cause.
• The matching algorithms are sensitive to atypical phenotypic manifestations of disorders.
The semantic model which is the basis of our matching process helps reveal subtle
similarities between disorder manifestations and may provide justification for reconsidering
diagnoses that were initially discarded due to atypical phenotypes.
https://phen
omecentral.
org/
Mike Brudno:
[email protected]
u
support@phenomecent
ral.org
PhenoTips
Tool –
nomenclat
ure
PhenoTips is an open source software tool for collecting and analyzing phenotypic
information for patients with genetic disorders. The user interface closely mirrors clinician
workflows so as to facilitate the recording of observations made during the patient encounter.
This easy-to-use front-end, compatible with any device that runs a Web browser, is coupled
with with a standardized database back-end where phenotypic information is represented
using the Human Phenotype Ontology (HPO).
Phenotype
Ontology
http://phen
otips.org/
Mike Brudno:
[email protected]
u
International
SNOMED CT is considered to be the most comprehensive multilingual health terminology in
the world. From abscess to zygote, SNOMED CT includes more than 311,000 unique
concepts. The concepts are organized in hierarchies, from the general to the specific. This
allows very detailed ("granular") clinical data to be recorded and later accessed or aggregated
at a more general level. "Concept descriptions" are the terms or names assigned to a
SNOMED CT concept. There are almost 800,000 descriptions in SNOMED CT, including
synonyms that can be used to refer to a concept.
http://www.
ihtsdo.org/s
nomed-ct/
Don Sweete:
[email protected]
International
TREAT-NMD is a network for the neuromuscular field that provides an infrastructure to
ensure that the most promising new therapies reach patients as quickly as possible. Since its
launch in January 2007 the network's focus has been on the development of tools that
industry, clinicians and scientists need to bring novel therapeutic approaches through
preclinical development and into the clinic, and on establishing best-practice care for
neuromuscular patients worldwide.
http://www.
treatnmd.eu/
Volker Straub:
volker.straub@newcas
tle.ac.uk
North
America
Collected data include demographics, medical history, family history, physical and
laboratory measurements, physical findings, and free-form notes.
In addition to data collection, PhenoTips automatically analyzes a wide range of
measurements and plots live the corresponding growth curves. It also supports accurate
diagnosis based on the entered data, and can suggest additional clinical investigations that
can improve the diagnosis.
SNOMED CT
Treat-NMD
Neuromuscular
Network
Tool –
nomenclat
ure
Consortiu
m/Collab
orative
Network
Phenotype
Ontology
Rare Disease
Neuromus
cular
Disease
Undiagnosed
Diseases
Network (UDN)
Consortiu
m/Collab
orative
Network
Rare
Disease,
Genomics
North
America
... Undiagnosed Diseases Network (UDN) is being established across the country to diagnose
both rare and new diseases. Furthermore, through the support of mechanistic studies, the
Network hopes to aid in management strategies for the patients. This program will advance
laboratory and clinical research, building upon the experience and expertise of the NIH
Intramural Undiagnosed Diseases Program (UDP) and similar programs, to enhance
coordination and collaboration among laboratory and clinical researchers across multiple
centers. The Network will benefit from having the capacity to share data and approaches
widely throughout the scientific community.
http://com
monfund.ni
h.gov/Disea
ses/index
Anastasia Wise:
[email protected]
v