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Simultaneous and independent detection of C9ORF72 alleles with low and high number of GGGGCC repeats using an optimised protocol of Southern blot hybridisation
BACKGROUND: Sizing of GGGGCC hexanucleotide repeat expansions within the C9ORF72 locus, which account for approximately 10% of all amyotrophic lateral sclerosis (ALS) cases, is urgently required to answer fundamental questions about mechanisms of pathogenesis in this important genetic variant. Curre...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626718/ https://www.ncbi.nlm.nih.gov/pubmed/23566336 http://dx.doi.org/10.1186/1750-1326-8-12 |
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author | Buchman, Vladimir L Cooper-Knock, Johnathan Connor-Robson, Natalie Higginbottom, Adrian Kirby, Janine Razinskaya, Olga D Ninkina, Natalia Shaw, Pamela J |
author_facet | Buchman, Vladimir L Cooper-Knock, Johnathan Connor-Robson, Natalie Higginbottom, Adrian Kirby, Janine Razinskaya, Olga D Ninkina, Natalia Shaw, Pamela J |
author_sort | Buchman, Vladimir L |
collection | PubMed |
description | BACKGROUND: Sizing of GGGGCC hexanucleotide repeat expansions within the C9ORF72 locus, which account for approximately 10% of all amyotrophic lateral sclerosis (ALS) cases, is urgently required to answer fundamental questions about mechanisms of pathogenesis in this important genetic variant. Currently employed PCR protocols are limited to discrimination between the presence and absence of a modified allele with more than 30 copies of the repeat, while Southern hybridisation-based methods are confounded by the somatic heterogeneity commonly present in blood samples, which might cause false-negative or ambiguous results. RESULTS: We describe an optimised Southern hybridisation-based protocol that allows confident detection of the presence of a C9ORF72 repeat expansion alongside independent assessment of its heterogeneity and the number of repeat units. The protocol can be used with either a radiolabeled or non-radiolabeled probe. Using this method we have successfully sized the C9ORF72 repeat expansion in lymphoblastoid cells, peripheral blood, and post-mortem central nervous system (CNS) tissue from ALS patients. It was also possible to confidently demonstrate the presence of repeat expansion, although of different magnitude, in both C9ORF72 alleles of the genome of one patient. CONCLUSIONS: The suggested protocol has sufficient advantages to warrant adoption as a standard for Southern blot hybridisation analysis of GGGGCC repeat expansions in the C9ORF72 locus. |
format | Online Article Text |
id | pubmed-3626718 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-36267182013-04-16 Simultaneous and independent detection of C9ORF72 alleles with low and high number of GGGGCC repeats using an optimised protocol of Southern blot hybridisation Buchman, Vladimir L Cooper-Knock, Johnathan Connor-Robson, Natalie Higginbottom, Adrian Kirby, Janine Razinskaya, Olga D Ninkina, Natalia Shaw, Pamela J Mol Neurodegener Methodology BACKGROUND: Sizing of GGGGCC hexanucleotide repeat expansions within the C9ORF72 locus, which account for approximately 10% of all amyotrophic lateral sclerosis (ALS) cases, is urgently required to answer fundamental questions about mechanisms of pathogenesis in this important genetic variant. Currently employed PCR protocols are limited to discrimination between the presence and absence of a modified allele with more than 30 copies of the repeat, while Southern hybridisation-based methods are confounded by the somatic heterogeneity commonly present in blood samples, which might cause false-negative or ambiguous results. RESULTS: We describe an optimised Southern hybridisation-based protocol that allows confident detection of the presence of a C9ORF72 repeat expansion alongside independent assessment of its heterogeneity and the number of repeat units. The protocol can be used with either a radiolabeled or non-radiolabeled probe. Using this method we have successfully sized the C9ORF72 repeat expansion in lymphoblastoid cells, peripheral blood, and post-mortem central nervous system (CNS) tissue from ALS patients. It was also possible to confidently demonstrate the presence of repeat expansion, although of different magnitude, in both C9ORF72 alleles of the genome of one patient. CONCLUSIONS: The suggested protocol has sufficient advantages to warrant adoption as a standard for Southern blot hybridisation analysis of GGGGCC repeat expansions in the C9ORF72 locus. BioMed Central 2013-04-08 /pmc/articles/PMC3626718/ /pubmed/23566336 http://dx.doi.org/10.1186/1750-1326-8-12 Text en Copyright © 2013 Buchman et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Buchman, Vladimir L Cooper-Knock, Johnathan Connor-Robson, Natalie Higginbottom, Adrian Kirby, Janine Razinskaya, Olga D Ninkina, Natalia Shaw, Pamela J Simultaneous and independent detection of C9ORF72 alleles with low and high number of GGGGCC repeats using an optimised protocol of Southern blot hybridisation |
title | Simultaneous and independent detection of C9ORF72 alleles with low and high number of GGGGCC repeats using an optimised protocol of Southern blot hybridisation |
title_full | Simultaneous and independent detection of C9ORF72 alleles with low and high number of GGGGCC repeats using an optimised protocol of Southern blot hybridisation |
title_fullStr | Simultaneous and independent detection of C9ORF72 alleles with low and high number of GGGGCC repeats using an optimised protocol of Southern blot hybridisation |
title_full_unstemmed | Simultaneous and independent detection of C9ORF72 alleles with low and high number of GGGGCC repeats using an optimised protocol of Southern blot hybridisation |
title_short | Simultaneous and independent detection of C9ORF72 alleles with low and high number of GGGGCC repeats using an optimised protocol of Southern blot hybridisation |
title_sort | simultaneous and independent detection of c9orf72 alleles with low and high number of ggggcc repeats using an optimised protocol of southern blot hybridisation |
topic | Methodology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626718/ https://www.ncbi.nlm.nih.gov/pubmed/23566336 http://dx.doi.org/10.1186/1750-1326-8-12 |
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