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 SureSeq Interpret, samples are rapidly processed through customisable protocols and optimised settings in order to generate the variants lists. Users have the option to use the protocols provided with the software or develop their own through the 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. Divided into two parts: a tabular display of the calls and Integrative Genomics Viewer (IGV)^‡ window (figure1).

Figure 1. Following analysis, all variants are displayed in a table, below which is an 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.

Report generation is implemented through a templating system. The report template, or templates, are prepared by OGT following discussion with the user. 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. An example of a batch analysis report is shown below (figure 2) but these are highly customisable and designed to be modified to individual requirements.

Figure 2. 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 can be broad or very specific allowing you to view specific details of the aberration detected:

SureSeq 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 (figure 3 and 4).

Figure 3. An example of the type of filters that can be easily generated for use within SureSeq Interpret.

.Figure 4. 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 analysis capability

Used in conjunction with SureSeq NGS panels, SureSeq Interpret facilitates the analysis and visualisation of a wide range of mutation types and structural variants. Complimenting the expert panel design and hybridisation-based approach of SureSeq to deliver unparalleled coverage uniformity, SureSeq Interpret is integral in facilitating the detection of low-frequency variants consistently and with confidence (figure 5 a – e).

Figure 5a: Detection of a germline SNV in CEBPA, often problematic due to the high GC content of the gene, using a SureSeq myPanel Custom AML panel.

Figure 5b: Detection of low frequency somatic variants, as (A) 1% and (B) 9% JAK2 V617F mutations using a SureSeq Myeloid Panel.

Figure 5c: Detection of FLT3 ITDs of difference sizes, (A) 33 bp, (B) 69 bp, (C) 201 bp, using a SureSeq myPanel Custom AML Panel. Note how OGT’s innovative panel design in conjunction with SureSeq Interpret is able to identify and call ITDs much longer than the sequencing read length of 150 bp.

Figure 5d: Detection of a variety of indels of different sizes. An FFPE type II epithelial ovarian cancer sample was found to have an 18 bp deletion in TP53 (A) at 24% VAF and a 5 bp deletion of in BRCA1 (B) at 28% VAF (using a SureSeq Ovarian Panel). Figure (C) illustrates the detection of a 54 bp deletion in exon 9 of CALR at 47% VAF, using a SureSeq Myeloid Panel.

Figure 5e: Detection of a gain of exons 9-14 of the LDLR gene, confirmed by MLPA, using a SureSeq myPanel custom Familial Hypercholesterolemia (FH) panel.