Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities. Falk MJ, et al. Mol Genet Metab. 2015 Mar;114(3):388-396.  Pubmed 25542617

Workshop Pictures:

  
    

Web Links and Demo Accounts

User ID: UMDF15  , Password: Mito15

Demo Account 2.(MSeqDR Phenotips server only):

User ID: UMDF16  , Password: umdf16

Demo Account 3.(MSeqDR Phenotips server only):

User ID: DemoMSeqDR, Password: DemoMSeqDR

LinkedIn Login:  Use your LinkedIn Account to login

MSeqDR server https://mseqdr.org  and  https://mseqdr.org/clinical

Backup site: https://mseqdr.org/demo  and  https://mseqdr.org/demo/clinical

MSeqDR Phenotips server:

MSeqDR PhenoTips  http://mseqdr.org:8080/phenotips/

Or

MSeqDR PhenoTips Demo1:  http://mseqdr.org:8090/

Part I Variant Submission Example, in HGVS format, for mtDNA, genomic DNA, genes and transcript notations:

m.15800C>T

1:g.215821999G>A

AARS2:c.1774C>T

NM_178857.5:c.134G>A

19:g.54621653_54621662del

Phenotype tools and patient input example:

Mutations inFBXL4, Encoding a Mitochondrial Protein, Cause Early-Onset Mitochondrial Encephalomyopathy

http://www.sciencedirect.com/science/article/pii/S0002929713003364#tblfn1

Subject 5 (S5):

��Subject 5 (S5) is a 9 yo girl, the only child from nonconsanguineous parents of European origin. She was born at the 39^th week, small for gestational age (2,410 g). Apgar scores were 7�C9. She has chronic lactic acidosis and RTA, global developmental delay (she is nonverbal) with truncal hypotonia, ataxia, and choreoathetoid movements, neutropenia, frequent infections, and severe GI dysmotility and swallowing difficulty, requiring PEG. She had several generalized seizures. She has dismorphic features of face and limb malformations (Figures 1A and S1A), with moderate microcephaly; her BMI is 17.4 (Underweight BMI < 18.5)

Finding:

Subjects 5 and 8 were compound heterozygous carrying both a nonsense mutation together with a missense variant. Subject 5 harbored a c.1067del (p.Gly356Alafs∗15) nonsense mutation in the maternal FBXL4 allele and a c.1790A>C (p.Gln597Pro) missense mutation in the paternal FBXL4 allele; 

Input VCF from WES whole exome sequencing: FBXL4_patient_exome.vcf  (~142K variants)

Input HPO from above: HP:0003593,HP:0001518,HP:0001263,HP:0001999,HP:0003128,HP:0002059,HP:0002134,HP:0007042,HP:0000297,HP:0001250,HP:0001251,HP:0001266,HP:0030195

Run analysis at: https://mseqdr.org/exomiser.php

For demo purpose, the FBXL4 vcf file is not run due to the computation burden on webserver. Pre-computed results are shown as demo.

Save files: AR phenix 1. Original 2. Result: HTML, Genes, Variants, Enhanced Annotation, VCF, log

Save files: AR hiphive 1. Original 2. Result: HTML, Genes, Variants, Enhanced Annotation, VCF, log

This tutorial workshop is the joint effort by: