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

Josep M Comeron; Jordan Reed; Matthew Christie; Julia S Jacobs; Jason Dierdorff; Daniel F Eberl; J. Robert Manak

doi:10.3390/microarrays5020007

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

Journal article

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

Josep M Comeron, Jordan Reed, Matthew Christie, Julia S Jacobs, Jason Dierdorff, Daniel F Eberl and J. Robert Manak

Microarrays, Vol.5(2), pp.7-7

2016

DOI: 10.3390/microarrays5020007

PMCID: PMC5003483

PMID: 27600073

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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.

endonuclease

genetic variation

microarray

SNP detection

disease mutation

mismatch

Details

Title: Subtitle: A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations
Creators: Josep M Comeron - Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
Jordan Reed - Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
Matthew Christie - Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
Julia S Jacobs - Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
Jason Dierdorff - Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
Daniel F Eberl - Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
J. Robert Manak - Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
Resource Type: Journal article
Publication Details: Microarrays, Vol.5(2), pp.7-7
DOI: 10.3390/microarrays5020007
PMID: 27600073
PMCID: PMC5003483
NLM abbreviation: Microarrays (Basel)
ISSN: 2076-3905
eISSN: 2076-3905
Publisher: MDPI
Grant note: DOI: 10.13039/100000009, name: National Institutes of Health, award: R01 DC04848
Language: English
Date published: 2016
Academic Unit: Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Biology; Craniofacial Anomalies Research Center; Internal Medicine
Record Identifier: 9983992094802771

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