MSeqDR/Genesis Tutorial at UMDF Mitochondrial Medicine 2016

Presentation: Marni Falk, MD, MSeqDR Organizer; Member, SIMD

                        Lishuang Shen, PhD, MSeqDR Developer

Assistants:      Colleen Clarke Muraresku, MS, LCGC

                        Elizabeth McCormick, MS, LCGC

                        Zolkipli Cunningham, Zarazuela, MBChB

                        Xiaowu Gai, PhD , MSeqDR Co-Organizer

Date:               Saturday, June 18, 2016

Time:               2:30-4:00 pm

Location:         DoubleTree by Hilton, 18740 International Boulevard, Seattle, WA 98188

Welcome! Today we are going to walk you through a hands-on tutorial for using MSeqDR, Genesis/ These databases can be utilized as tools for researchers and clinicians with real time queries, data organization, and more… all for FREE to academic users!  After this tutorial you will be able to login, navigate within the database, submit, explore, and share data. 


Final tutorial

Word , PDF , Web page.


Word (TBA) Web page (TBA)


MSeqDR is described in more details in the publications: 

MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease. Shen L et al Hum Mutat. 2016 Jun;37(6):540-548. Pubmed 26919060

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:

  lecturer  lecturer


Web Links and Demo Accounts

Demo Account 1 (both MSeqDR and its Phenotips server):

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  and

Backup site:  and

MSeqDR Phenotips server:

MSeqDR PhenoTips


MSeqDR PhenoTips Demo1:


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







Phenotype tools and patient input example:

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

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 39th 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)




Subjects 5 and 8 were compound heterozygous carrying both a nonsense mutation together with a missense variant. Subject 5 harbored a c.1067del (p.Gly356Alafs15) 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:

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:

MSeqDR  United Mitochodrial Disease Foundation   Genesis