scholarly journals The importance of automation in genetic diagnosis: Lessons from analyzing an inherited retinal degeneration cohort with the Mendelian Analysis Toolkit (MATK)

Author(s):  
Erin Zampaglione ◽  
Matthew Maher ◽  
Emily M. Place ◽  
Naomi E. Wagner ◽  
Stephanie DiTroia ◽  
...  
2021 ◽  
Author(s):  
Erin Zampaglione ◽  
Matthew Maher ◽  
Emily M. Place ◽  
Naomi E. Wagner ◽  
Stephanie DiTroia ◽  
...  

Purpose: In Mendelian disease diagnosis, variant analysis is a repetitive, error-prone, and time-consuming process. To address this, we have developed the Mendelian Analysis Toolkit (MATK), a configurable automated variant ranking program. Methods: MATK aggregates variant information from multiple annotation sources and uses expert-designed rules with parameterized weights to produce a ranked list of potentially causal solutions. MATK performance was measured by a comparison of MATK-aided versus human domain-expert analyses of 1060 inherited retinal degeneration (IRD) families investigated with an IRD-specific gene panel (589 families) and exome sequencing (471 families). Results: When comparing MATK-assisted analysis to expert curation, we found that 97.3% (541/556) of potential solutions found by experts were also identified by the MATK-assisted analysis. Furthermore, MATK-assisted analysis identified 114 additional potential solutions. The software also showed utility in data reanalysis after remapping to the GRCh38 genome build. Conclusion: MATK expedites the process of identifying likely solving variants in Mendelian traits and helps to remove variability coming from human error and researcher bias. MATK facilitates data re-analysis to keep up with the constantly improving annotation sources and NGS processing pipelines. The software is open source and available at https://gitlab.partners.org/meei-ogi-bioinformatics/MendelAnalysis


2021 ◽  
Vol 205 ◽  
pp. 108480
Author(s):  
Mansour Rahimi ◽  
Sophie Leahy ◽  
Nathanael Matei ◽  
Norman P. Blair ◽  
Shinwu Jeong ◽  
...  

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1421
Author(s):  
Yu-Chi Sung ◽  
Chang-Hao Yang ◽  
Chung-May Yang ◽  
Chao-Wen Lin ◽  
Ding-Siang Huang ◽  
...  

The ABCA4 gene is one of the most common disease-causing genes of inherited retinal degeneration. In this study, we report different phenotypes of ABCA4-associated retinal dystrophies in the Taiwanese population, its clinical progression, and its relationship with genetic characteristics. Thirty-seven subjects were recruited and all patients underwent serial ophthalmic examinations at a single medical center. Fundus autofluorescence (FAF) images were quantified for clinical evaluation, and panel-based next-generation sequencing testing was performed for genetic diagnosis. Visual preservation, disease progression, and genotype–phenotype correlation were analyzed. In this cohort, ABCA4-associated retinal degeneration presented as Stargardt disease 1 (STGD1, 62.16%), retinitis pigmentosa (32.43%), and cone-rod dystrophy (5.41%). STGD1 could be further divided into central and dispersed types. In each phenotype, the lesion areas quantified by FAF increased with age (p < 0.01) and correlated with poorer visual acuity. However, three patients had the foveal sparing phenotype and had relatively preserved visual acuity. Forty-two ABCA4 variants were identified as disease-causing, with c.1804C>T (p.Arg602Trp) the most frequent (37.84%). Patients with a combination of severe/null variants could have more extensive phenotypes, such as arRP and dispersed STGD1. This is the first cohort study of ABCA4-associated retinal degeneration in Taiwan with wide spectrums of both genotypic and phenotypic characteristics. An extremely high prevalence of c.1804C>T, which has not been reported in East Asia before, was noted. The extensiveness of retinal involvement might be regarded as a spectrum of ABCA4-associated retinal dystrophies. Different types of genetic variations could lead to distinctive phenotypes, according to the coding impact of variants.


1963 ◽  
Vol 3 (7-8) ◽  
pp. 271-280 ◽  
Author(s):  
Vincenzo Bonavita ◽  
Francesco Ponte ◽  
Giuseppe Amore

2018 ◽  
Vol 65 ◽  
pp. 28-49 ◽  
Author(s):  
Erin R. Burnight ◽  
Joseph C. Giacalone ◽  
Jessica A. Cooke ◽  
Jessica R. Thompson ◽  
Laura R. Bohrer ◽  
...  

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Ekaterina S. Lobanova ◽  
Stella Finkelstein ◽  
Jing Li ◽  
Amanda M. Travis ◽  
Ying Hao ◽  
...  

2020 ◽  
Vol 41 (6) ◽  
pp. 533-538
Author(s):  
Sydney Strait ◽  
Rebecca Loman ◽  
Lindsay Erickson ◽  
Meghan DeBenedictis

Cells ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 931 ◽  
Author(s):  
Gayle B. Collin ◽  
Navdeep Gogna ◽  
Bo Chang ◽  
Nattaya Damkham ◽  
Jai Pinkney ◽  
...  

Inherited retinal degeneration (RD) leads to the impairment or loss of vision in millions of individuals worldwide, most frequently due to the loss of photoreceptor (PR) cells. Animal models, particularly the laboratory mouse, have been used to understand the pathogenic mechanisms that underlie PR cell loss and to explore therapies that may prevent, delay, or reverse RD. Here, we reviewed entries in the Mouse Genome Informatics and PubMed databases to compile a comprehensive list of monogenic mouse models in which PR cell loss is demonstrated. The progression of PR cell loss with postnatal age was documented in mutant alleles of genes grouped by biological function. As anticipated, a wide range in the onset and rate of cell loss was observed among the reported models. The analysis underscored relationships between RD genes and ciliary function, transcription-coupled DNA damage repair, and cellular chloride homeostasis. Comparing the mouse gene list to human RD genes identified in the RetNet database revealed that mouse models are available for 40% of the known human diseases, suggesting opportunities for future research. This work may provide insight into the molecular players and pathways through which PR degenerative disease occurs and may be useful for planning translational studies.


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