SoftGenetics - Software PowerTools for Genetic Analysis

 

 

 

 

 

Structural Variation Detection using NextGENe software

Over 68,000 structural variants (SVs) have been reported in the human genome, including deletions, duplications/insertions, and translocations such as gene fusions (1). Alone, there are more than 2,200 catalogued gene fusions (2) making genomic disorders an important area of research (3).

There are several techniques available for detecting SVs. Microarrays, for one, can be useful for
detecting copy number variation but are limited to detecting events relative to specific design probes (4). Next Generation Sequencing can produce higher resolution results and enable the identification of novel events as well as the simultaneous detection of SNPs and small indels.

 

Figure 1: NextGENe Viewer’s Structural Variation Report is an interactive tool for displaying both breakpoints of each detected SVs.

 

NextGENe software can align reads simultaneously to genomic and transcriptomic references. Reads from RNA samples can align across exon junctions more easily, enabling higher sensitivity for the detection of breakpoints. Next generation sequencing reads from instrument manufactures such as Illumina® can be analyzed by NextGENe software for the detection of SVs. Reads with a high level of mismatch at an end are split into two reads and remapped to the DNA/RNA reference. These Link Reads identify the breakpoints of structural variations including gene fusions.

NextGENe software includes templates to easily analyze gene fusion samples, streamlining the analysis of many SVs.

The Seraseq Fusion RNA Mix v2 from SeraCare Life Sciences, Inc. includes many gene fusions, like TPM3-NTRK1, LMNA-NTRK1, SLC45A3-BRAF, EML4-ALK, PAX8-PPARG, FGFR3-TACC3, FGFR3-BAIAP2L1, SLC34A2-ROS1, CD74-ROS1, KIF5B-RET, NCOA4-RET, and ETV6-NTRK3.

 

A sample was run on an Illumina MiSeq instrument and produced about 255K 2x150bps reads. Trimming of adapters yielded reads averaging 112bp. After utilizing the Overlap Merger tool, 90.5% of the pairs were merged into single reads with an average length of 140bp, extending the average length by about 30bp, (see Figure 4).

NextGENe software was run on a standard Windows Desktop computer. 223K (96.4%) of these reads are aligned to the DNA/RNA reference genome in 3 minutes and Structural Variation detection is completed in 8 additional minutes by NextGENe software. Reports in TXT, VCF and PDF formats are automatically generated.

 

The final project can be opened in the NextGENe Viewer software, which offers an interactive tool for viewing the SVs and producing additional reports (see Figure 1). Reads that are split and mapped across breakpoints are called Link Reads, and about 2K of these reads are mapping to all 12 expected fusion events in the SeraCare fusion controls.

 

For further information please review or download the following Application Note:
Structural Variant Detection Application Note

Pricing & Trial Version:
Request 30-day trial/Price Quote

 

Reference Material:
Download/View NextGENe® Brochure
NextGENe User Manual
Annotated Reference Genomes

 

Trademarks property of their respective owners

SoftGenetics - Software PowerTools for Genetic Analysis

 

SoftGenetics - Software PowerTools for Genetic Analysis

 

 

SOFTWARE


Review all of our software products

 

 

 

 

 

 

 

 

 

SoftGenetics - Software PowerTools for Genetic Analysis

 

 

 

SoftGenetics Software PowerTools for Genetic Analysis provides current up-to-date information and pricing on all products.
All requests are secure.

 

SoftGenetics - Software PowerTools for Genetic Analysis

 

 

EXPERTISE


Request trial versions of our software and tap into our knowledge base

 

 

Trial Software

All of our software products are available for review and trial periods. Please use link to request a trial version.

 

Request Trial >>

 

Online Training

Our software professionals are available to you for online training of any of our products. Please contact an expert now.

 

Request Training >>

 

Webinars

SoftGenetics provides online webinars to assist you in the growing knowledge of our products. Visit our Analysis Corner.

 

View Webinars >>

 

SoftGenetics - Software PowerTools for Genetic Analysis

 

 

SEND US A MESSAGE


Representatives are always ready to assist you


Name *
Email *
Phone

###
-
###
-
####
Message *

 

SoftGenetics - Software PowerTools for Genetic Analysis

100 Oakwood Avenue | Suite 350 | State College, PA 16803 | USA
Phone: 814-237-9340 or 888-791-1270
Email: info@softgenetics.com

 

© 2020 SoftGenetics, LLC. All rights reserved

Trademarks are property of their respective owners

Research use only (RUO)

 

Web design by Lovett Creations