Interpret is a powerful and easy-to-use next-generation sequencing (NGS) 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 single nucleotide variations (SNVs) and indels, as well as structural aberrations, including internal and partial tandem duplications (ITDs, PTDs), copy-number variations (CNVs), loss-of-heterozygosity (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.

Complementing the expert panel design and hybridisation-based approach of NGS panels to deliver unparalleled coverage uniformity, Interpret is integral in facilitating the detection of low-frequency variants consistently and with confidence. With a wide range of customisation options and links to various mutation databases, Interpret provides effortless translation of NGS data into meaningful results. Additional outputs from the pipeline include a range of publicly available data resources for annotation of variants detected, including ClinVar, COSMIC, dbSNP, Ensembl, gnomAD, PolyPhen, SIFT. Additional licence-based sources, such as HGMD, can be incorporated on provision of suitable credentials.

Using Interpret, samples are rapidly processed through customisable protocols and optimised settings 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 and, 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. Interpret report templates are highly customisable and can be designed to individual requirements.

More details

SNVs

Following analysis, all variants are displayed in a table, below which is an Integrative Genomics Viewer (IGV)¹ window allowing a more detailed review of the data and additional verification.

Figure 1: 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.

ITDs

Detection of FLT3-ITDs of various sizes, including regions containing multiple ITDs. Note how Interpret can confidently identify even ITDs much longer than the sequencing read length of 150 bp.

Figure 2: 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.

PTDs

In conjunction with SureSeq™’s expert panel design, Interpret offers robust detection of all sizes of PTDs in KMT2A.

Figure 3: Detection of a KMT2A-PTD spanning exons 2-8.

Translocation

Interpret agnostically detects split-reads across the genome, enabling detection of both known and unknown translocation partners.

Figure 4: BCR-ABL translocation. Split-reads covering both BCR (left panel) and ABL1 (right panel) are detected, indicative of the BCR-ABL gene fusion.

CNVs

Interpret enables CNV detection ranging from loss of a single exon to full chromosomal arms and trisomies.

Figure 5: Detection of trisomy 12 using the SureSeq™ CLL + CNV V3 Panel, showing a reliable gain call across the whole chromosome.

LOH

CytoSure^® Constitutional NGS panel analysed using Interpret.

Figure 6: 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) The CNV data is displayed in a log2 ratio plot and (C) a b-allele plot shows the LOH present within the sample.

Basic Variant Attributes	Variant Call Attributes	Consequence/ Severity Predictions	Population Frequencies	Classification/ Pathogenicity	Genes, Exons and Proteins	Region/ Variant Lists
Chromosome	Total Depth	Most Severe Consequence	rsID	ClinVar Significance	Gene ID	Region Lists
Start	Ref / Alt Depth	Impact	Minor Allele / Freq		Gene Symbol	Variant Lists
End	Allele Frequency	Terms	American Minor Allele / Freq		Transcript ID
Genome Build	Quality Score	PolyPhen Prediction	European Minor Allele / Freq		Protein ID
Ref	Ref / Alt Quality	PolyPhen Score	African Minor Allele / Freq		Exon ID
Alt	Log Ratio	SIFT Prediction	South Asian Minor Allele / Freq		Exon Number
Genotype	Ref Reads (+) / (-)	SIFT Score	East Asian Minor Allele / Freq
	Alt Reads (+) / (-)
	Ref Strand Bias
	Reads Placed Left / Right

Table 1: Overview of the wide range of filtering options available in Interpret.

References:

1. Helga Thorvaldsdóttir, James T. Robinson and Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics 14(2), 178-192 (2013).

Disclaimer:

SureSeq™ and CytoSure^®: For Research Use Only, not for use in diagnostic procedures. Product availability may vary from country to country. Contact your local representatives for availability.

Manufacturer and Trademarks: SureSeq™ and CytoSure^® (Oxford Gene Technology IP Limited)

Technical specifications

Requirement	Minimum	Recommended
Memory (RAM)	16 GB	32 GB (64 GB for MRD)
CPU cores	8+ logical cores at 2+ GHz	16 CPUs (36 CPUs for MRD)
Storage (disk space)	500 GB	2 TB
Operating system	Windows 10 Pro or newer (+ Virtual Machine) Any Unix supporting Docker CE (no VM)
No requirements for graphic cards
Virtualisation (VT-x) to be enabled in the BIOS