Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Summary

Here, we present a protocol to access and analyze many human and model organism databases efficiently. This protocol demonstrates the use of MARRVEL to analyze candidate disease-causing variants identified from next-generation sequencing efforts.

Abstract

Through whole-exome/genome sequencing, human geneticists identify rare variants that segregate with disease phenotypes. To assess if a specific variant is pathogenic, one must query many databases to determine whether the gene of interest is linked to a genetic disease, whether the specific variant has been reported before, and what functional data is available in model organism databases that may provide clues about the gene’s function in human. MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration) is a one-stop data collection tool for human genes and variants and their orthologous genes in seven model organisms including in mouse, rat, zebrafish, fruit fly, nematode worm, fission yeast, and budding yeast. In this Protocol, we provide an overview of what MARRVEL can be used for and discuss how different datasets can be used to assess whether a variant of unknown significance (VUS) in a known disease-causing gene or a variant in a gene of uncertain significance (GUS) may be pathogenic. This protocol will guide a user through searching multiple human databases simultaneously starting with a human gene with or without a variant of interest. We also discuss how to utilize data from OMIM, ExAC/gnomAD, ClinVar, Geno₂MP, DGV and DECHIPHER. Moreover, we illustrate how to interpret a list of ortholog candidate genes, expression patterns, and GO terms in model organisms associated with each human gene. Furthermore, we discuss the value protein structural domain annotations provided and explain how to use the multiple species protein alignment feature to assess whether a variant of interest affects an evolutionarily conserved domain or amino acid. Finally, we will discuss three different use-cases of this website. MARRVEL is an easily accessible open access website designed for both clinical and basic researchers and serves as a starting point to design experiments for functional studies.

Introduction

The use of next-generation sequencing technology is expanding in both research and clinical genetic laboratories¹. Whole-exome (WES) and whole-genome sequencing (WGS) analyses reveal numerous rare variants of unknown significance (VUS) in known disease-causing genes as well as variants in genes that are yet to be associated with a Mendelian disease (GUS: genes of uncertain significance). Presented with a list of genes and variants in a clinical sequence report, medical geneticists must manually visit multiple online resources to obtain more information to assess which variant may be responsible for a certain phenotype seen in the patient of int....

Protocol

1. How to begin a search

1. For the human gene and variant-based search, go to steps 1.1.1.-1.1.2. For human gene-based search (no variant input), go to step 1.2. For model organism gene-based search, refer to steps 1.3.1.-1.3.2.
   1. Go to the home page of MARRVEL⁴ at http://marrvel.org/. Start by entering a human gene symbol. Ensure that the candidate gene names are listed below the input box with each character entry. If the search comes back negative, make sure the gene symbol .......

Discussion

Critical steps in this protocol include the initial input (steps 1.1-1.3) and subsequent interpretation of the output. The most common reason why search results are negative is because of the many ways that a gene and/or variant can be described. While MARRVEL is updated on a scheduled basis, these updates may cause disconnects between the different databases that MARRVEL links to. Thus, the first step in troubleshooting is invariably checking to see if alternative names of the gene or variant will lead to a successful s.......

Materials

Name	Company	Catalog Number	Comments
Human Genetics	ClinVar	PMID: 29165669	https://www.ncbi.nlm.nih.gov/clinvar/
Human Genetics	DECIPHER	PMID: 19344873	https://decipher.sanger.ac.uk/
Human Genetics	DGV	PMID: 24174537	http://dgv.tcag.ca/dgv/app/home
Orthology Prediction	DIOPT	PMID: 21880147	https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl
Human Gene/Transcript Nomenclature	Ensembl	PMID: 29155950	https://useast.ensembl.org/
Human Genetics	ExAC	PMID: 27535533	http://exac.broadinstitute.org/
Primary Model Organism Databases	FlyBase (Drosophila)	PMID:26467478	http://flybase.org
Model Organism Database Integration Tools	Gene2Function	PMID: 28663344	http://www.gene2function.org/search/
Human Genetics	Geno2MP	N/A	http://geno2mp.gs.washington.edu/Geno2MP/
Human Genetics	gnomAD	PMID: 27535533	http://gnomad.broadinstitute.org/
Gene Ontology	GO Central	PMID: 10802651, 25428369	http://www.geneontology.org/
Human Gene/Protein Expression	GTEx	PMID: 29019975, 23715323	https://gtexportal.org/home/
Human Gene Nomenclature	HGNC	PMID: 27799471	https://www.genenames.org/
Primary Model Organism Databases	IMPC (mouse)	PMID: 27626380	http://www.mousephenotype.org/
Primary Model Organism Databases	MGI (mouse)	PMID:25348401	http://www.informatics.jax.org/
Model Organism Database Integration Tools	Monarch Initiative	PMID: 27899636	https://monarchinitiative.org/
Human Variant Nomenclature	Mutalyzer	PMID: 18000842	https://mutalyzer.nl/
Human Genetics	OMIM	PMID: 28654725	https://omim.org/
Primary Model Organism Databases	PomBase (fission yeast)	PMID:22039153	https://www.pombase.org/
Literature	PubMed	N/A	https://www.ncbi.nlm.nih.gov/pubmed/
Primary Model Organism Databases	RGD (rat)	PMID:25355511	https://rgd.mcw.edu/
Primary Model Organism Databases	SGD (budding yeast)	PMID: 22110037	https://www.yeastgenome.org/
Human Gene/Protein Expression	The Human Protein Atlas	PMID: 21752111	https://www.proteinatlas.org/
Primary Model Organism Databases	WormBase (C. elegans)	PMID:26578572	http://wormbase.org
Primary Model Organism Databases	ZFIN (zebrafish)	PMID:26097180	https://zfin.org/