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Product Focus: SNP Analysis Technology
Product Focus: SNP Analysis Technology
Up Close and Personal The latest approaches to SNP Analysis A single nucleotide polymorphism (SNP) is the most common type of genetic variation between human beings and it’s critical to correlating genotype with disease. SNP arrays detect polymorphisms allowing researchers to map disorders to a specific gene location and may enable prediction of an individual’s disease susceptibility or the effectiveness of a pharmaceutical therapy. Drugs can then be personally designed to selectively act on a group of individuals who share a common allele. As diagnostic and pharmaceutical companies focus more of their research and development efforts on personalized medicine, SNP analysis technology is proving to be a critical step. The latest SNP analysis tools analyze new levels of complexity allowing biologists to gain a deeper understanding of their findings. Integrating SNP data with today’s leading sequencing platforms and bioinformatic pipelines assists researchers in making efficient use of their time and budgets. SNP detection is a critical capability supporting scientists’ in-depth understanding of gene function, disease and many other factors within biological organisms. DNASTAR’s next-generation SeqMan NGen® 3.0 whole genome assembly software
uses a patent-pending algorithm that assembles a whole human genome in less than 24 hours on a desktop computer. The program analyzes data from Sanger, next-generation and third generation sequencing platforms. DNASTAR’s SeqMan NGen 3.0 companion, SeqMan Pro, allows scientists to view SNPs by frequency and distance to areas of interest. They can then align these SNPs to known SNPs using Bayesian statistics, dbSNP or BLAST. Identified SNPs can also be aligned to human, rat and mouse genomes. “SeqMan Pro has proven to be invaluable to our lab for assembling and editing sequencing projects using capillary sequence data from the ABI 3130 and 3730 sequencing platform,” says Kevin Kunstman, lab manager of the Northwestern University Feinberg School of Medicine. “This is one of those applications that just works like it should.” Identifying expressed SNPs provides another layer of SNP analysis. The latest software analysis tool from SoftGenetics® aligns RNA-Seq data to a reference genome allowing detection of alternative splice sites, gene fusions, skipped exons, novel exons and retained introns. As part of SoftGenetics’ comprehensive NextGENe® software package,
the RNA-Seq analysis tool allows users to highlight sequence data of interest, including amino acid changes, INDEL’s and other structural variants through a graphical interface. Additional modules within the package also analyze whole genome alignment; ChIPSeq; miRNA and quantification; and SAGE, enabling and speeding an individual biologists’ research. The Windows®-based software program is compatible with multiple second generation sequencing platforms, including the Illumina® GAII/HiSeq, Roche’s Genome Sequencer FLX, the Applied Biosystems™ SOLiD™ System as well as systems from Pacific Biosciences™ and Ion Torrent. “The new NextGENe tool has an option for specialized analysis of both paired end reads as well as single-strand RNA-Seq data,” says John McGuigan, development biologist at SoftGenetics. Sequencing platforms and microarrays aid researchers in their SNP genotyping efforts, however sorting and analyzing key SNPs of interest can prove cumbersome. Sophisticated software solutions can increase the efficiency of this process, reducing the time and costs of traditional analysis practices. Golden Helix’s SNP & Variation Suite 7 is an integrated desktop software analysis program that allows users to analyze SNP data as well as copy number variation (CNV) and next-generation sequencing (NGS) data. With applications for candidate gene analysis, genome-wide association studies, copy number research and next-generation
Material compiled by Chempetitive Group
whole genome and exome sequencing studies, Golden Helix provides the tools needed to analyze large-scale, complex genomic data for easy, fast, and interactive comparisons. The new tertiary sequence analysis module gives scientists greater control over SNP data analysis. The SNP & Variation Suite allows scientists to selectively choose variants that are important to their study, statistically analyze genomic regions with high frequencies of variants and use functional prediction to understand the role of rare variants. According to Christophe Lambert, founder and CEO of Golden Helix, “Most efforts in the DNA space have focused on aligning or assembling raw reads and generating variant calls. Beyond single purpose tools, there simply haven’t been comprehensive, integrated solutions created for tertiary analysis, the ‘sense making’ part of the process. Our new module leverages the easy-to-use, comprehensive aspects of our existing tools, empowering a broader community of researchers to capitalize on all that next-generation sequencing has to offer.” The SNP & Variation Suite enables scientists to interact with their SNP data using dynamic visuals that allow them to analyze several graphs side by side. The program accommodates large amounts of genomic data, including data generated from common SNP microarrays or sequencing machines. In the past, IT and bioinformatics professionals were responsible for SNP analysis. Now, new software is empowering biologists to produce such results on their own. Strand Scientific Intelligence, Inc.’s Avadis® NGS 1.1 is a platform-independent computer program for downstream analysis of nextgeneration sequencing data. It allows scientists to identify high quality data for SNP discovery and analysis of their effects, enabling them to visualize SNPs and corresponding downstream changes from their desktop computer. “Avadis NGS is an application for the discovery and annotation of SNPs, INDELs and large structural variations using NGS
SoftGenetics’ NextGENe Transcriptome Analysis Module
sequence data, thus shifting the power of analysis from IT and informatics experts to the biologists,” says Thon de Boer, Director of Product Management, Software for Strand Scientific Intelligence. Avadis NGS is compatible with pre-aligned sequence data from Illumina, Life Technologies™ and Roche (454) sequencing technologies. It also allows users to access the commonly used RefSeq and dbSNP databases from within the application. In addition, the program also features transcription and transcription regulation analysis through its RNA-SEQ and ChIP-SEQ applications. The analysis that is needed to locate possible SNPs in the hundreds of primers used by laboratories is impractical without a bioinformatic pipeline. To provide researchers with the most
Companies mentioned in this Product Focus
www.chempetitive.com Golden Helix’s SNP & Variation Suite 7
DNASTAR SoftGenetics Golden Helix Strand Scientific Intelligence, Inc. National Genetics Reference Laboratory Manchester
www.dnastar.com www.softgenetics.com www.goldenhelix.com www.strandsi.com www.ngrl.org.uk
current human genome SNP information, the National Genetics Reference Laboratory Manchester (NGRL) launched their enhanced online bioinformatics program, SNPCheck. Identifying SNPs is essential in primer design. The presence of unmatched base pairs impacts primers annealing to target DNA, resulting in allelic dropout and potential genotyping failure. The SNPCheck program utilizes BLAST and dbSNP to allow scientists to detect and align human SNPs within primer pairs. It also allows scientists to test very large batches of primers at a time. Gaining enhanced access to dbSNP’s extensive knowledge base in a format specifically designed for primer checking has led many genetic research scientists to include SNPCheck as part of their standard laboratory protocol.
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