DNA sequencing Analysis Kits now available from Maverix Biomics.
(C)2014 M2 COMMUNICATIONS
20 October 2014 - US next-generation sequencing (NGS) genomic data analysis software developer Maverix Biomics announced over the weekend the availability of Analysis Kits for analysing variants in whole genome, exome, and targeted resequencing data produced by high throughput next generation sequencing systems.
The new DNA sequencing Analysis Kits, together with initial scientific results from researchers who have used the Maverix Analytic Platform for variant analysis, were presented at the 64th Annual Meeting of the American Society for Human Genetics in San Diego, California.
The kits allow customers to identify and annotate genetic variants in their sample data as compared to reference genomes for a great variety of species, and visualise genotypes of these samples in the UCSC Genome Browser and through other filtering and interpretation tools. Equipped with these kits, researchers will be able to easily identify mutations or genetic markers that are part of the gene pathways related to a specific disease or condition, or can be used as unique signatures for diagnostic and testing applications.
John Battles, senior manager of Bioinformatics and Study Management at Beckman Coulter Genomics, said the company had run hundreds of samples through the Maverix Analytic Platform for DNA sequencing variant analysis and that he was really pleased with the data files, visualizations, and reports received from Maverix.
Following the Maverix tradition, the new DNA sequencing Analysis Kits are based on popular peer-reviewed open source tools, such as FastQC for sequencing quality checking, BWA for read mapping, and SnpEff for variant effect prediction. These tools have been assembled into complete end-to-end Analysis Kits which have been tested and validated with public reference data sets to make sure they are able to produce scientifically valid results. Maverix continues to offer researchers a choice of alternative tools, including GATK version 2.3 or FreeBayes for variant detection. Investigators can compare and select the analysis tools that best satisfy their needs based on several factors, such as speed, cost, and accuracy.
Since the Maverix Analytic Platform is highly scalable, customers can manage and analyse extremely large data sets numbering up to thousands of samples, with typical time to completion of data analysis of 72 hours or less.
A unique "sample sheet" input feature enables customers to easily classify hundreds or thousands of samples with unique labels and identifiers, including adding phenotypic or non-genomic information to each sample for use in their analyses. Response to therapy, disease state, or demographic information are some examples of non-genomic information which can be added, among numerous other possibilities.
Besides viewing variant data in an integrated private, secure UCSC Genome Browser, researchers can also use an interactive tabular data visualisation tool to sort and filter variants based on numerous parameters. Those include variant types, sample phenotypes, location within regions of the genome or in a specific gene, and prevalence in public databases such as 1000 Genomes, among other characteristics. The non-genomic data which was entered on the "sample sheet" can also be correlated with variants that are found in the genome.
Results data files, such as VCF files or BAM files, can be easily downloaded from the Maverix Analytic Platform as desired. Users can also generate PDF summary reports, which can be customised as necessary.
The new analysis kits also provide access to the other capabilities of the platform, including secure and compliant management of human patient identifiable information and data in accordance with aspects of the Security Final Rule as established by the Department of Health and Human Services under the Health Insurance Portability and Accountability Act of 1996. An independent HIPAA Security Assessment of controls put in place by Maverix (as a potential business associate of entities required to comply under the omnibus final rules) has been successfully completed.
Brad Lyons, IT Audit Manager of 360 Advanced, PA, a full-service audit and consulting firm specialising in integrated compliance solutions, including HIPAA security assessments, said the completion of the HIPAA Security Compliance Assessment serves as testament to Maverix Biomics' commitment to create and maintain the controls needed to ensure the quality and security of services provided to their customers.
Researchers using the DNA sequencing Analysis Kits on the Maverix Analytic Platform can also use complementary Maverix Analysis Kits, including those for mRNA-seq, small RNA-seq and Exosome RNA-seq. Other platform features are also available, such as sharing and collaboration, or access to public or community data sets to put customers' data in context.
Maverix Biomics' president, CEO and co-founder, Dave Mandelkern, said that by offering multiple types of analyses in a single secure, highly scalable environment with significant value-added functionality beyond that offered by the basic open source algorithms, the company allows researchers to quickly and easily go from exploration of raw data to meaningful insight and discovery for large, challenging biological issues.
The Maverix Analytic Platform is a cloud-based solution designed for use directly by life sciences researchers who may not have software or bioinformatics expertise. The platform uses proven open-source algorithms and applications developed at academic and research centres. After loading sequence data from any organism - human, animal, plant, or microbe, researchers can immediately perform analyses with reliable, scientifically vetted configurations, as cited in peer-reviewed journal publications.
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|Date:||Oct 20, 2014|
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