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Maroilley T, Rahit KMTH, Chida AR, Cotra F, Rodrigues Alves Barbosa V, Tarailo-Graovac M. Model Organism Modifier (MOM): a user-friendly Galaxy workflow to detect modifiers from genome sequencing data using Caenorhabditis elegans. G3 (BETHESDA, MD.) 2023; 13:jkad184. [PMID: 37585487 PMCID: PMC10627290 DOI: 10.1093/g3journal/jkad184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 04/21/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023]
Abstract
Genetic modifiers are variants modulating phenotypic outcomes of a primary detrimental variant. They contribute to rare diseases phenotypic variability, but their identification is challenging. Genetic screening with model organisms is a widely used method for demystifying genetic modifiers. Forward genetics screening followed by whole genome sequencing allows the detection of variants throughout the genome but typically produces thousands of candidate variants making the interpretation and prioritization process very time-consuming and tedious. Despite whole genome sequencing is more time and cost-efficient, usage of computational pipelines specific to modifier identification remains a challenge for biological-experiment-focused laboratories doing research with model organisms. To facilitate a broader implementation of whole genome sequencing in genetic screens, we have developed Model Organism Modifier or MOM, a pipeline as a user-friendly Galaxy workflow. Model Organism Modifier analyses raw short-read whole genome sequencing data and implements tailored filtering to provide a Candidate Variant List short enough to be further manually curated. We provide a detailed tutorial to run the Galaxy workflow Model Organism Modifier and guidelines to manually curate the Candidate Variant Lists. We have tested Model Organism Modifier on published and validated Caenorhabditis elegans modifiers screening datasets. As whole genome sequencing facilitates high-throughput identification of genetic modifiers in model organisms, Model Organism Modifier provides a user-friendly solution to implement the bioinformatics analysis of the short-read datasets in laboratories without expertise or support in Bioinformatics.
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Affiliation(s)
- Tatiana Maroilley
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - K M Tahsin Hassan Rahit
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Afiya Razia Chida
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Filip Cotra
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Victoria Rodrigues Alves Barbosa
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
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Mew M, Caldwell KA, Caldwell GA. From bugs to bedside: functional annotation of human genetic variation for neurological disorders using invertebrate models. Hum Mol Genet 2022; 31:R37-R46. [PMID: 35994032 PMCID: PMC9585664 DOI: 10.1093/hmg/ddac203] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 02/02/2023] Open
Abstract
The exponential accumulation of DNA sequencing data has opened new avenues for discovering the causative roles of single-nucleotide polymorphisms (SNPs) in neurological diseases. The opportunities emerging from this are staggering, yet only as good as our abilities to glean insights from this surplus of information. Whereas computational biology continues to improve with respect to predictions and molecular modeling, the differences between in silico and in vivo analysis remain substantial. Invertebrate in vivo model systems represent technically advanced, experimentally mature, high-throughput, efficient and cost-effective resources for investigating a disease. With a decades-long track record of enabling investigators to discern function from DNA, fly (Drosophila) and worm (Caenorhabditis elegans) models have never been better poised to serve as living engines of discovery. Both of these animals have already proven useful in the classification of genetic variants as either pathogenic or benign across a range of neurodevelopmental and neurodegenerative disorders-including autism spectrum disorders, ciliopathies, amyotrophic lateral sclerosis, Alzheimer's and Parkinson's disease. Pathogenic SNPs typically display distinctive phenotypes in functional assays when compared with null alleles and frequently lead to protein products with gain-of-function or partial loss-of-function properties that contribute to neurological disease pathogenesis. The utility of invertebrates is logically limited by overt differences in anatomical and physiological characteristics, and also the evolutionary distance in genome structure. Nevertheless, functional annotation of disease-SNPs using invertebrate models can expedite the process of assigning cellular and organismal consequences to mutations, ascertain insights into mechanisms of action, and accelerate therapeutic target discovery and drug development for neurological conditions.
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Affiliation(s)
- Melanie Mew
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kim A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Research Institute on Aging, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Departments of Neurobiology and Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Research in the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Departments of Neurobiology and Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Research in the Basic Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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