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Microarrays
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Microarrays in the Era of Next Generation Sequencing
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Microarrays in the Era of Next Generation Sequencing

A special issue of Microarrays (ISSN 2076-3905).

Deadline for manuscript submissions: closed (31 August 2016) | Viewed by 19035

Special Issue Editors

Dr. Yuriy Alekseyev

E-Mail Website
Guest Editor
Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
Interests: microarrays; next generation sequencing; genomics; genomics technologies; gene expression; RNA-seq; translational research
Dr. Gang Liu

E-Mail Website
Guest Editor
Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
Interests: translational research; lung disease; genomics technologies; microarrays; next generation sequencing; RNA-seq; gene expression

Special Issue Information

Dear Colleagues,

Genomics technologies are developing at a very fast pace, especially in the last decade. Microarrays, once the most cutting-edge technology, now have lost their leading position as a discovery tool to a newer and superior technology—Next Generation Sequencing (NGS). Despite some predictions that NGS—due to crucial advantages—would have replaced microarrays completely by this time, their use remains significant. The reasons for continued use of microarrays include their proven track record for almost two decades; lower costs and higher throughput in the case of very large-scale studies; lack of well-established molecular biology solutions for NGS platforms for difficult samples (low input, FFPE, etc.); streamlined bioinformatics; and the necessity to validate NGS results with an alternative high-throughput technology, among others. This Special Issue will focus on examples of successful microarray use that adds value to NGS studies in all research areas with a special emphasis on unique, innovative approaches that create a niche for this technology in the current highly competitive environment.

Dr. Yuriy Alekseyev and Dr. Gang Liu
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microarrays is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 350 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


 

Keywords

  • microarrays
  • next generation sequencing
  • biomarkers
  • validation

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Published Papers (3 papers)

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1582 KiB  
Article
A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations
by Josep M. Comeron, Jordan Reed, Matthew Christie, Julia S. Jacobs, Jason Dierdorff, Daniel F. Eberl and J. Robert Manak
Microarrays 2016, 5(2), 7; https://doi.org/10.3390/microarrays5020007 - 5 Apr 2016
Cited by 2 | Viewed by 6309
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Microarrays in the Era of Next Generation Sequencing)
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6222 KiB  
Article
Quantitative Trait Locus and Brain Expression of HLA-DPA1 Offers Evidence of Shared Immune Alterations in Psychiatric Disorders
by Ling Z. Morgan, Brandi Rollins, Adolfo Sequeira, William Byerley, Lynn E. DeLisi, Alan F. Schatzberg, Jack D. Barchas, Richard M. Myers, Stanley J. Watson, Huda Akil, William E. Bunney and Marquis P. Vawter
Microarrays 2016, 5(1), 6; https://doi.org/10.3390/microarrays5010006 - 7 Mar 2016
Cited by 20 | Viewed by 6499
Abstract
Genome-wide association studies of schizophrenia encompassing the major histocompatibility locus (MHC) were highly significant following genome-wide correction. This broad region implicates many genes including the MHC complex class II. Within this interval we examined the expression of two MHC II genes (HLA-DPA1 and [...] Read more.
Genome-wide association studies of schizophrenia encompassing the major histocompatibility locus (MHC) were highly significant following genome-wide correction. This broad region implicates many genes including the MHC complex class II. Within this interval we examined the expression of two MHC II genes (HLA-DPA1 and HLA-DRB1) in brain from individual subjects with schizophrenia (SZ), bipolar disorder (BD), major depressive disorder (MDD), and controls by differential gene expression methods. A third MHC II mRNA, CD74, was studied outside of the MHC II locus, as it interacts within the same immune complex. Exon microarrays were performed in anterior cingulate cortex (ACC) in BD compared to controls, and both HLA-DPA1 and CD74 were decreased in expression in BD. The expression of HLA-DPA1 and CD74 were both reduced in hippocampus, amygdala, and dorsolateral prefrontal cortex regions in SZ and BD compared to controls by specific qPCR assay. We found several novel HLA-DPA1 mRNA variants spanning HLA-DPA1 exons 2-3-4 as suggested by exon microarrays. The intronic rs9277341 SNP was a significant cis expression quantitative trait locus (eQTL) that was associated with the total expression of HLA-DPA1 in five brain regions. A biomarker study of MHC II mRNAs was conducted in SZ, BD, MDD, and control lymphoblastic cell lines (LCL) by qPCR assay of 87 subjects. There was significantly decreased expression of HLA-DPA1 and CD74 in BD, and trends for reductions in SZ in LCLs. The discovery of multiple splicing variants in brain for HLA-DPA1 is important as the HLA-DPA1 gene is highly conserved, there are no reported splicing variants, and the functions in brain are unknown. Future work on the function and localization of MHC Class II proteins in brain will help to understand the role of alterations in neuropsychiatric disorders. The HLA-DPA1 eQTL is located within a large linkage disequilibrium block that has an irrefutable association with schizophrenia. Future tests in a larger cohort are needed to determine the significance of this eQTL association with schizophrenia. Our findings support the long-held hypothesis that alterations in immune function are associated with the pathophysiology of psychiatric disorders. Full article
(This article belongs to the Special Issue Microarrays in the Era of Next Generation Sequencing)
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Review

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217 KiB  
Review
Advantages of Array-Based Technologies for Pre-Emptive Pharmacogenomics Testing
by Al Shahandeh, Daniel M. Johnstone, Joshua R. Atkins, Jean-Marie Sontag, Moones Heidari, Nilofar Daneshi, Elvis Freeman-Acquah and Elizabeth A. Milward
Microarrays 2016, 5(2), 12; https://doi.org/10.3390/microarrays5020012 - 28 May 2016
Cited by 6 | Viewed by 5683
Abstract
As recognised by the National Institutes of Health (NIH) Precision Medicine Initiative (PMI), microarray technology currently provides a rapid, inexpensive means of identifying large numbers of known genomic variants or gene transcripts in experimental and clinical settings. However new generation sequencing techniques are [...] Read more.
As recognised by the National Institutes of Health (NIH) Precision Medicine Initiative (PMI), microarray technology currently provides a rapid, inexpensive means of identifying large numbers of known genomic variants or gene transcripts in experimental and clinical settings. However new generation sequencing techniques are now being introduced in many clinical genetic contexts, particularly where novel mutations are involved. While these methods can be valuable for screening a restricted set of genes for known or novel mutations, implementation of whole genome sequencing in clinical practice continues to present challenges. Even very accurate high-throughput methods with small error rates can generate large numbers of false negative or false positive errors due to the high numbers of simultaneous readings. Additional validation is likely to be required for safe use of any such methods in clinical settings. Custom-designed arrays can offer advantages for screening for common, known mutations and, in this context, may currently be better suited for accredited, quality-controlled clinical genetic screening services, as illustrated by their successful application in several large-scale pre-emptive pharmacogenomics programs now underway. Excessive, inappropriate use of next-generation sequencing may waste scarce research funds and other resources. Microarrays presently remain the technology of choice in applications that require fast, cost-effective genome-wide screening of variants of known importance, particularly for large sample sizes. This commentary considers some of the applications where microarrays continue to offer advantages over next-generation sequencing technologies. Full article
(This article belongs to the Special Issue Microarrays in the Era of Next Generation Sequencing)
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