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MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples

Mutations in ~100 genes cause muscle diseases with complex and often unexplained genotype/phenotype correlations. Next-generation sequencing studies identify a greater-than-expected number of genetic variations in the human genome. This suggests that existing clinical monogenic testing systematicall...

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Autores principales: Savarese, Marco, Di Fruscio, Giuseppina, Mutarelli, Margherita, Torella, Annalaura, Magri, Francesca, Santorelli, Filippo Maria, Comi, Giacomo Pietro, Bruno, Claudio, Nigro, Vincenzo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172906/
https://www.ncbi.nlm.nih.gov/pubmed/25214167
http://dx.doi.org/10.1186/s40478-014-0100-3
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author Savarese, Marco
Di Fruscio, Giuseppina
Mutarelli, Margherita
Torella, Annalaura
Magri, Francesca
Santorelli, Filippo Maria
Comi, Giacomo Pietro
Bruno, Claudio
Nigro, Vincenzo
author_facet Savarese, Marco
Di Fruscio, Giuseppina
Mutarelli, Margherita
Torella, Annalaura
Magri, Francesca
Santorelli, Filippo Maria
Comi, Giacomo Pietro
Bruno, Claudio
Nigro, Vincenzo
author_sort Savarese, Marco
collection PubMed
description Mutations in ~100 genes cause muscle diseases with complex and often unexplained genotype/phenotype correlations. Next-generation sequencing studies identify a greater-than-expected number of genetic variations in the human genome. This suggests that existing clinical monogenic testing systematically miss very relevant information. We have created a core panel of genes that cause all known forms of nonsyndromic muscle disorders (MotorPlex). It comprises 93 loci, among which are the largest and most complex human genes, such as TTN, RYR1, NEB and DMD. MotorPlex captures at least 99.2% of 2,544 exons with a very accurate and uniform coverage. This quality is highlighted by the discovery of 20-30% more variations in comparison with whole exome sequencing. The coverage homogeneity has also made feasible to apply a cost-effective pooled sequencing strategy while maintaining optimal sensitivity and specificity. We studied 177 unresolved cases of myopathies for which the best candidate genes were previously excluded. We have identified known pathogenic variants in 52 patients and potential causative ones in further 56 patients. We have also discovered 23 patients showing multiple true disease-associated variants suggesting complex inheritance. Moreover, we frequently detected other nonsynonymous variants of unknown significance in the largest muscle genes. Cost-effective combinatorial pools of DNA samples were similarly accurate (97-99%). MotorPlex is a very robust platform that overcomes for power, costs, speed, sensitivity and specificity the gene-by-gene strategy. The applicability of pooling makes this tool affordable for the screening of genetic variability of muscle genes also in a larger population. We consider that our strategy can have much broader applications. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40478-014-0100-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-41729062014-09-25 MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples Savarese, Marco Di Fruscio, Giuseppina Mutarelli, Margherita Torella, Annalaura Magri, Francesca Santorelli, Filippo Maria Comi, Giacomo Pietro Bruno, Claudio Nigro, Vincenzo Acta Neuropathol Commun Research Mutations in ~100 genes cause muscle diseases with complex and often unexplained genotype/phenotype correlations. Next-generation sequencing studies identify a greater-than-expected number of genetic variations in the human genome. This suggests that existing clinical monogenic testing systematically miss very relevant information. We have created a core panel of genes that cause all known forms of nonsyndromic muscle disorders (MotorPlex). It comprises 93 loci, among which are the largest and most complex human genes, such as TTN, RYR1, NEB and DMD. MotorPlex captures at least 99.2% of 2,544 exons with a very accurate and uniform coverage. This quality is highlighted by the discovery of 20-30% more variations in comparison with whole exome sequencing. The coverage homogeneity has also made feasible to apply a cost-effective pooled sequencing strategy while maintaining optimal sensitivity and specificity. We studied 177 unresolved cases of myopathies for which the best candidate genes were previously excluded. We have identified known pathogenic variants in 52 patients and potential causative ones in further 56 patients. We have also discovered 23 patients showing multiple true disease-associated variants suggesting complex inheritance. Moreover, we frequently detected other nonsynonymous variants of unknown significance in the largest muscle genes. Cost-effective combinatorial pools of DNA samples were similarly accurate (97-99%). MotorPlex is a very robust platform that overcomes for power, costs, speed, sensitivity and specificity the gene-by-gene strategy. The applicability of pooling makes this tool affordable for the screening of genetic variability of muscle genes also in a larger population. We consider that our strategy can have much broader applications. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40478-014-0100-3) contains supplementary material, which is available to authorized users. BioMed Central 2014-09-11 /pmc/articles/PMC4172906/ /pubmed/25214167 http://dx.doi.org/10.1186/s40478-014-0100-3 Text en © Savarese et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Savarese, Marco
Di Fruscio, Giuseppina
Mutarelli, Margherita
Torella, Annalaura
Magri, Francesca
Santorelli, Filippo Maria
Comi, Giacomo Pietro
Bruno, Claudio
Nigro, Vincenzo
MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples
title MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples
title_full MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples
title_fullStr MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples
title_full_unstemmed MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples
title_short MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples
title_sort motorplex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of dna samples
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172906/
https://www.ncbi.nlm.nih.gov/pubmed/25214167
http://dx.doi.org/10.1186/s40478-014-0100-3
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