Interpret NGS Analysis Software
Interpret is a powerful and easy-to-use next generation sequencing analysis solution. Optimised for use with OGT's CytoSure™ and SureSeq™ NGS panels for confident annotation and reporting of low frequency variants.
Interpret is OGT’s powerful and easy-to-use next-generation sequencing analysis solution, facilitating analysis and visualisation of a wide range of variants and structural aberrations. Coupled with a comprehensive and powerful filtering framework, the software delivers accurate calling of SNVs and indels, as well as structural aberrations, including ITDs, PTDs, CNVs, LOH and translocations. Interpret is designed to work seamlessly with all CytoSure™ and SureSeq™ NGS panels and offers flexible accessibility for data analysis; whether through a stand-alone computer†, laboratory server or another web-enabled device. With a wide range of customisation options and links to various mutation databases, Interpret provides effortless translation of all your NGS data into meaningful results.
- Detection of a wide range of aberrations—reliably call variants ranging from low-frequency SNVs and indels to large structural deletions including CNVs and translocations
- Extensive customisation options—easily customise variant and batch reports and database links to meet the exact needs of your laboratory
- Comprehensive range of filtering options—standardise your analysis workflow and overlay bespoke variant filtering to meet your analytical criteria
- Security and control—log and track user activity and standardise analysis protocols through multiple access permission levels
- Powerful and complimentary with OGT’s NGS panels—optimised for use with SureSeq and CytoSure NGS panels to detect all aberrations covered by your panel
The software provided quick and reliable alignment and variant analysis to interpret results from our core MPN sequencing. Joshua Landreth, Molecular Laboratory Supervisor, Genetic Associates Inc.
Accurate detection of a wide range of aberrations
Used in conjunction with CytoSure and SureSeq NGS panels, Interpret facilitates the analysis and visualisation of a wide range of mutation types and structural variants. Complementing the expert panel design and hybridisation-based approach of our NGS panels to deliver unparalleled coverage uniformity, Interpret is integral in facilitating the detection of low-frequency variants consistently and with confidence. Whether your input DNA is high-quality or formalin-compromised, or your research focuses on oncology or rare diseases, Interpret delivers fast and accurate detection of all aberrations covered by your panel (Figures 1-9).
Figure 1: Following analysis, all variants are displayed in a table, below which is an Integrative Genomics Viewer (IGV)‡ window allowing a more detailed review of the data and additional verification. In this example a low-frequency JAK2 V617F SNV has been selected and the user is able to view the aligned reads generated by the pipeline.
Figure 2: CytoSure Constitutional NGS panel analysed using Interpret, with a 30 Mb deletion on chromosome 5 and LOH across the deletion. [A] Details of the samples and mutations are displayed in a table format. [B] he CNV data is displayed in a log2 ratio plot and [C] a b-allele plot shows the LOH present within the sample.
Figure 3: Detection of FLT3-ITDs of various sizes, including regions containing multiple ITDs. ITD sizes are [A] 174 bp, [B] 225 bp, [C] 195 bp with an additional 6 bp, [D] 120 bp and [E] 168 bp with an additional 69 bp. Note how Interpret can confidently identify even ITDs much longer than the sequencing read length of 150 bp.
Figure 4: Detection of a KMT2A-PTD spanning exons 2-8. In conjunction with OGT’s expert panel design, Interpret offers robust detection of all sizes of PTDs in KMT2A.
Figure 5: Small 231 Kb deletion detected on chromosome 19 using Interpret with CytoSure Constitutional NGS.
Figure 6: Interpret is able to call duplications with the same precision as microarrays, in this example a 1.59 Mb duplication on chromosome 7 is detected using the CytoSure Constitutional NGS Panel.
Figure 7: Detection of trisomy 12 using the SureSeq CLL + CNV Panel, showing a reliable gain call across the whole chromosome. Interpret enables CNV detection ranging from loss of a single exon to full chromosomal arms and trisomies.
Figure 8: Detection of a 7 Mb deletion on a >50% mosaic sample using CytoSure Constitutional NGS.
Figure 9: BCR-ABL translocation. Split-reads covering both BCR (left panel) and ABL1 (right panel) are detected, indicative of the BCR-ABL gene fusion. Interpret agnostically detects split-reads across the genome, enabling detection of both known and unknown translocation partners.
Extensive customisation options
OGT has extensive experience in providing individualised options through its established plug-in infrastructure. This enables the software to be tailored to your laboratory’s specific requirements, whether it be report formats, user controls or variant annotation. Additional outputs from the pipeline include a range of publicly available data resources for annotation of variants detected, including:
Additional licence-based sources, such as HGMD, can be incorporated on provision of suitable credentials.
In Interpret, samples are rapidly processed through customisable protocols and optimised settings in order to generate the variant lists. Your laboratory has the option to use the protocols provided with the software or develop your own through the intuitive user interface. Personal modifications are available for:
- Hardware settings
- Quality metrics
- Variant calling parameters
- Variant filtering parameters
Following analysis, results can be viewed in the user-friendly variant browser showing a tabular display of the calls and an IGV window, which can be maximised in a separate window for greater visibility.
Report generation is implemented through a templating system, prepared by OGT following discussion with your laboratory. Our report templates are highly customisable and designed to be modified to individual requirements. For example, one template could simply provide an overview of user activity in the sequencing analysis while another could provide detailed sample or batch analysis results (Table 1).
Figure 10: An example batch analysis report. Let OGT customise your report to meet your exact requirements.
Comprehensive range of filtering options
An extensive range of dynamic filtering options are available, which allow you to filter your data to meet your exact analytical criteria (Table 2)
Table 1: Overview of the wide range of filtering options available in Interpret.
Interpret provides a sophisticated user interface which facilitates, through the comprehensive range of filtering options available, the standardisation of your laboratory workflow. These filters can be incorporated into any analysis protocol and are automatically deployed when a particular protocol is selected. This facilitates the building of more complex filter sets to optimise the search and identification of your variants to your exact requirements (Figures 11 and 12).
Figure 11: An example of the type of filters that can be easily generated for use within Interpret.
Figure 12: Filtering exists on two levels, firstly within the protocol selected for the analysis and secondly, users are able to filter results dynamically within the variants page.
Security and control
A relational database stores all activities conducted using the software, from the loading of the samples to the variant calls made in those samples. This facilitates the logging and tracking of individual user activity for consistent data processing and laboratory monitoring.
The database enables implementation of security protocols through multiple access permission levels, allowing users with administrator rights to control all functions of the software and the actions of users based on their roles within the laboratory. Additionally, data stored within the relational database can be easily backed up or ported.
Powerful and easy-to-use NGS analysis software.
Complimentary with all CytoSure and SureSeq NGS panels.
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|Product||Contents||Cat. No.||View Product|
|CytoSure Constitutional NGS Solution||Enrichment baits; Interpret Software||various||Find out more|
|SureSeq myPanel NGS Custom Cancer Panels||Enrichment baits; Interpret Software||various||Find out more|
|SureSeq myPanel NGS Custom AML Panel||Enrichment baits; Interpret Software||Various||Find out more|
|SureSeq myPanel NGS Custom Breast Cancer Panel||Enrichment baits; Interpret Software
||various||Find out more|
|CytoSure NGS Custom FH panel||Enrichment baits; Interpret Software||various||Find out more|
|SureSeq NGS Library Preparation Kit||Containing adaptors, PCR primers and enzymes||various||Find out more|
† Computer specification: RAM: min 16Gb, suggested 24Gb; HDD: min 500Gb, suggested 2TB; CPU: 8+ logical cores at 2+ GHz; OS: Windows (7 or newer; Virtualization (VT-x) needs to be enabled in the BIOS) or Unix (any flavour supporting Docker CE).
‡ Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics 14, 178-192 (2013).
CytoSure and SureSeq: For research use only; not for use in diagnostic procedures.
Interpret Quick-Start Guide
Download OGT's Interpret NGS analysis software quick-start guide, for use with SureSeq™ and CytoSure™ NGS panels.
SureSeq™ Quick Reference Guide – Good Quality DNA
Assessment of SureSeq™ Interpret software on low-frequency variants using reference standards
Presented at AMP 2019, this poster demonstrates how OGT’s SureSeq Interpret software shows robust and reproducible results in the detection of low-frequency variants using reference standards.
Interpret NGS Analysis Software – Seamless transition from microarray to NGS in constitutional cytogenetics
At OGT we understand that making the change from microarrays to NGS is a daunting prospect, particularly when it comes to data analysis. This technical note outlines some of the key features we’ve incorporated to help make the change from arrays to NGS as