Special Issue "Copy-Number-Variation Microarrays in Basic Research and Clinical Applications"

Guest Editor
Dr. Tobias Heckel
Department of Molecular Toxicology, F.Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
Website: http://www.roche.com
E-Mail: tobias.heckel@roche.com
Interests: genetic polymorphisms; CNV Arrays; SNP genotyping; molecular karyotyping; transcriptomics; genome structure and expression; integrative genomics; genotype-phenotype correlations

Over the last years microarray technology has greatly improved the fields of structural genetic research and chromosomal disorders. Established cytogenetic and molecular techniques suffer of low resolution, limited to 5–10 megabases, like Giemsa-banded chromosome analysis, or are restricted in detecting only a few specific DNA regions like fluorescence in situ hybridization. Oligonucleotide microarrays containing millions of probes enabled the detection of sub-microscopic structural genetic variations, genome-wide, at ultra-high resolution down to a few hundred till thousand bases. Although high coverage next generation DNA sequencing can detect structural genetic variations, microarray screening is expected to be the main approach for several years due to its user-friendly workflow, lower cost and straightforward data interpretation.
This special issue invites contributions to the application and evaluation of microarrays for the discovery and diagnosis of structural genetic variations with a focus on Copy Number Variations (CNVs). These variations account for a substantial proportion of genetic variability in human and animal populations and range from seemingly neutral polymorphisms over polymorphisms correlating with phenotypic differences to pathological variations predisposing or causing disease.
It will be interesting to the reader of this special issue to increase the understanding of how microarray technology helped revealing the biological meaning of CNVs but also to learn about recent advances in CNV calling, database aided classification, and CNV phenotype correlations.

Dr. Tobias Heckel
Guest Editor

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

• array Comparative Genomic Hybridization
• SNP genotyping arrays
• clinical cytogenetics
• chromosomal disorders
• CNV calling algorithms
• neurobehavioral phenotypes
• genomic instability
• genotype-phenotype correlations

Type of Paper: Review
Title: Comparing Array-Based Studies of Copy Number Variation in the Cattle Genome
Authors: George E. Liu, et al.
Affiliation: USDA-ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, MD 20705, USA; E-Mail: George.Liu@ars.usda.gov
Abstract: Copy number variations (CNVs) are gains and losses of genomic sequence greater than 50 bp between two individuals of a species. Substantial progress has been made in understanding CNVs in humans and rodents. Since year 2008, at least 10 genome-wide cattle CNV studies have been published based on microarray technologies. In this review, we have systematically compared these bovine CNV results. The striking differences among different platforms and calling algorithms highlight the needs for standardizing array data collection, quality assessment and experimental validation. On the other hand, integration of CNV results with SNP and other datasets began to reveal impacts of CNVs on cattle domestication, health and production traits.