Many are aware that Nexus Copy Number software has robust analytical tools and rich visualization for interrogation of copy number and allelic events. The software is multifaceted and handles different types on data (from microarrays to NGS and even integrates gene expression results). Most people who know the software work on human samples but there is less awareness of the software’s versatility in handling other organisms. BioDiscovery customers have used the software for analysis of microorganisms, plants and other animals; here are a few publications showcasing its versatility.
_(5780783616).jpg "Rhesus Macaque (Macaca mulatta) (5780783616)")
A group in Japan looked at the neurogenetics of autistic behavior in monkeys (1). Nexus Copy Number was used to identify a deletion in ABCA13, a gene implicated in human psychiatric disorders. The authors also performed exome sequencing and identified a loss-of function mutation in HTR2C, another gene implicated in neuropsychiatric disorders including ASD (Autism Spectrum Disorders). The current version of Nexus Copy Number allows for copy number estimation from sequencing data. In fact, we have a webinar coming up on Dec. 15 that will introduce a new algorithm for estimating copy number from NGS in the upcoming release of the software. This new algorithm was designed to provide quality results from shallow and targeted sequencing data but it also works very well on normal coverage WGS and WES data. Learn more about this algorithm by attending the webinar.
Goode et. al. used Nexus Copy Number to create a copy number profile of canine lymphoid tumor cell lines (2).
A corresponding author on the paper, Dr. Matthew Breen, NCSU, presented his work on comparative cytogenomics at a past webinar. He also recently filed a patent for canine cancer diagnosis. Read the blog post about his patent work where Nexus Copy Number is used.
And finally, food – so important! The agricultural community has used advances in genetics 
and genomics to create hardier and disease resistant varieties to improve crop yields and feed the world’s growing population.
In this recent Plant Biotechnology Journal article, the authors have used Nexus Copy Number to identify regions of CNVs in bread wheat using a custom Affymetrix Axiom® array they designed for wheat (3). The Axiom® arrays, though a SNP genotyping array, can also be easily loaded into Nexus Copy Number to derive copy number. View a past webinar on how Nexus Copy Number is used for analysis and visualization of copy number and AOH from Axiom arrays.
References
1. Yoshida K, Go Y, Kushima I, Toyoda A, Fujiyama A, Imai H, Saito N, Iriki A, Ozaki N, Isoda M. Single-neuronand genetic correlates of autistic behavior in macaque. Sci Adv. 2016 Sep 21;2(9)
2. Roode SC, Rotroff D, Richards KL, Moore P, Motsinger-Reif A, Okamura Y, Mizuno T, Tsujimoto H, Suter SE, Breen M. Comprehensivegenomic characterization of five canine lymphoid tumor cell lines. BMC Vet Res. 2016 Sep 17;12:207.
3. Allen AM, Winfield MO, Burridge AJ, Downie RC, Benbow HR, Barker GL, Wilkinson PA, Coghill J, Waterfall C, Davassi A, Scopes G, Pirani A, Webster T, Brew F, Bloor C, Griffiths S, Bentley AR, Alda M, Jack P, Phillips AL, Edwards KJ. Characterizationof a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). Plant Biotechnol J. 2016 Sep 14.
