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Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders.

Abstract Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis. This tool offers a user-friendly interface, and leads clinicians through simple steps by limiting the number of candidates to achieve a final diagnosis of a medical genetics case. A useful innovation is the "1-click" method, which enables listing all the relevant variants in genes present at OMIM for perusal by clinicians. Mendel,MD was experimentally validated using clinical cases from the literature and was tested by students at the Universidade Federal de Minas Gerais, at GENE-Núcleo de Genética Médica in Brazil and at the Children's University Hospital in Dublin, Ireland. We show in this article how it can simplify and increase the speed of identifying the culprit mutation in each of the clinical cases that were received for further investigation. Mendel,MD proved to be a reliable web-based tool, being open-source and time efficient for identifying the culprit mutation in different clinical cases of patients with Mendelian Disorders. It is also freely accessible for academic users on the following URL: https://mendelmd.org.
PMID
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Authors

Mayor MeshTerms

Databases, Genetic

Genetic Diseases, Inborn

Internet

Software

Keywords
Journal Title plos computational biology
Publication Year Start


 


PMID- 28594829
OWN - NLM
STAT- MEDLINE
DA  - 20170608
DCOM- 20170627
LR  - 20170627
IS  - 1553-7358 (Electronic)
IS  - 1553-734X (Linking)
VI  - 13
IP  - 6
DP  - 2017 Jun
TI  - Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the 
      diagnosis of patients with Mendelian disorders.
PG  - e1005520
LID - 10.1371/journal.pcbi.1005520 [doi]
AB  - Whole exome and whole genome sequencing have both become widely adopted methods
      for investigating and diagnosing human Mendelian disorders. As pangenomic
      agnostic tests, they are capable of more accurate and agile diagnosis compared to
      traditional sequencing methods. This article describes new software called
      Mendel,MD, which combines multiple types of filter options and makes use of
      regularly updated databases to facilitate exome and genome annotation, the
      filtering process and the selection of candidate genes and variants for
      experimental validation and possible diagnosis. This tool offers a user-friendly 
      interface, and leads clinicians through simple steps by limiting the number of
      candidates to achieve a final diagnosis of a medical genetics case. A useful
      innovation is the "1-click" method, which enables listing all the relevant
      variants in genes present at OMIM for perusal by clinicians. Mendel,MD was
      experimentally validated using clinical cases from the literature and was tested 
      by students at the Universidade Federal de Minas Gerais, at GENE-Nucleo de
      Genetica Medica in Brazil and at the Children's University Hospital in Dublin,
      Ireland. We show in this article how it can simplify and increase the speed of
      identifying the culprit mutation in each of the clinical cases that were received
      for further investigation. Mendel,MD proved to be a reliable web-based tool,
      being open-source and time efficient for identifying the culprit mutation in
      different clinical cases of patients with Mendelian Disorders. It is also freely 
      accessible for academic users on the following URL: https://mendelmd.org.
FAU - G C C L Cardenas, Raony
AU  - G C C L Cardenas R
AUID- ORCID: http://orcid.org/0000-0002-7496-0333
AD  - Laboratorio de Genomica Clinica, Faculdade de Medicina da UFMG, Universidade
      Federal de Minas Gerais, Belo Horizonte, Brazil.
FAU - D Linhares, Natalia
AU  - D Linhares N
AD  - Laboratorio de Genomica Clinica, Faculdade de Medicina da UFMG, Universidade
      Federal de Minas Gerais, Belo Horizonte, Brazil.
FAU - L Ferreira, Raquel
AU  - L Ferreira R
AUID- ORCID: http://orcid.org/0000-0003-3584-3633
AD  - Laboratorio de Genomica Clinica, Faculdade de Medicina da UFMG, Universidade
      Federal de Minas Gerais, Belo Horizonte, Brazil.
FAU - Pena, Sergio D J
AU  - Pena SDJ
AD  - Laboratorio de Genomica Clinica, Faculdade de Medicina da UFMG, Universidade
      Federal de Minas Gerais, Belo Horizonte, Brazil.
AD  - Departamento de Bioquimica e Imunologia, Instituto de Ciencias de Biologicas,
      Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
AD  - GENE-Nucleo de Genetica Medica, Belo Horizonte, Brazil.
LA  - eng
PT  - Journal Article
DEP - 20170608
PL  - United States
TA  - PLoS Comput Biol
JT  - PLoS computational biology
JID - 101238922
SB  - IM
MH  - *Databases, Genetic
MH  - *Genetic Diseases, Inborn/diagnosis/genetics
MH  - Genome
MH  - Genomics/*methods
MH  - High-Throughput Nucleotide Sequencing
MH  - Humans
MH  - *Internet
MH  - *Software
PMC - PMC5464533
EDAT- 2017/06/09 06:00
MHDA- 2017/06/28 06:00
CRDT- 2017/06/09 06:00
PHST- 2016/07/26 [received]
PHST- 2017/04/12 [accepted]
AID - 10.1371/journal.pcbi.1005520 [doi]
AID - PCOMPBIOL-D-16-01204 [pii]
PST - epublish
SO  - PLoS Comput Biol. 2017 Jun 8;13(6):e1005520. doi: 10.1371/journal.pcbi.1005520.
      eCollection 2017 Jun.