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From the third issue of 2017, Microarrays has changed its name to High-Throughput.

Open AccessFeature PaperArticle
Microarrays 2016, 5(2), 7; doi:10.3390/microarrays5020007

A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations

1
Department of Biology, University of Iowa, Iowa City, IA 52242, USA
2
Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
3
Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
*
Authors to whom correspondence should be addressed.
Academic Editors: Yuriy Alekseyev and Gang Liu
Received: 8 February 2016 / Revised: 21 March 2016 / Accepted: 30 March 2016 / Published: 5 April 2016
(This article belongs to the Special Issue Microarrays in the Era of Next Generation Sequencing)
View Full-Text   |   Download PDF [1582 KB, uploaded 7 April 2016]   |  

Abstract

Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs), point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array)) pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs) as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%. Our technology provides a platform for a variety of applications, including: (1) genotyping known SNPs as well as confirming newly discovered SNPs from whole genome sequencing analyses; (2) identifying novel point mutations and indels in any genomic region from any organism for which genome sequence information is available; and (3) screening panels of genes associated with particular diseases and disorders in patient samples to identify causative mutations. As a proof of principle for using MENA to discover novel mutations, we report identification of a novel allele of the beethoven (btv) gene in Drosophila, which encodes a ciliary cytoplasmic dynein motor protein important for auditory mechanosensation. View Full-Text
Keywords: microarray; mismatch; endonuclease; SNP detection; genetic variation; disease mutation microarray; mismatch; endonuclease; SNP detection; genetic variation; disease mutation
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Comeron, J.M.; Reed, J.; Christie, M.; Jacobs, J.S.; Dierdorff, J.; Eberl, D.F.; Manak, J.R. A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations. Microarrays 2016, 5, 7.

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