Get the Latest Clinical Insights for Tumor Exome Profiling

Agilent Integrated Whole-Exome Sequencing Solutions Whole-exome sequencing (WES) is increasingly being adopted in oncology testing and research to comprehensively profile tumor samples. WES is the gold standard for determining tumor mutation burden (TMB), which is used to guide treatment selection as TMB is an emerging predictive biomarker for response to immune checkpoint inhibitors. In the field of recurrence monitoring, WES is used to identify mutations in tumor samples in order to create individualized next-generation sequencing (NGS) assays for monitoring minimal residual disease (MRD). WES is also used to identify neoantigens in tumor immunotherapy research. Agilent now provides a WES solution for cancer research labs that includes exome enrichment reagents and software for variant analysis and interpretation. This sequencing solution enables simultaneous detection of somatic single nucleotide variants (SNVs), insertions/deletions (indels), and copy number variations (CNVs), delivering a streamlined workflow with increased sensitivity to detect diseasecausing mutations. The Agilent SureSelect Human All Exon V8 panel provides comprehensive coverage of protein coding regions from RefSeq, CCDS, and GENCODE, as well as the TERT promoter region. The exome panel, powered by machine learning-based probe design and a new production process, delivers excellent enrichment performance, as well as efficient and cost-effective exome sequencing. The exome panel can be easily augmented to include customized content for specific applications. The exome enrichment workflow is natively automated on the Agilent Magnis NGS prep and Bravo Automated Liquid Handling systems for enhanced productivity in the laboratory. Users can readily examine sequencing data using the Agilent Alissa Clinical Informatics platform, an end-to-end exome sequencing solution for seamless and efficient variant analysis, interpretation, and reporting. Raw data can be analyzed with the Agilent Alissa Reporter software, an intuitive and streamlined cloud-based NGS software-as-a-service (SaaS) solution that simultaneously detects SNVs, indels, and CNVs. Users can easily navigate data with integrated genome browsing, a builtin quality control (QC) dashboard, and a seamless connection to the Agilent Alissa Interpret software for variant interpretation and reporting. Exome Enrichment Using Agilent SureSelect Human All Exon V8 Panel for Tumor Profiling Using Agilent Alissa Clinical Informatics Platform Data Sheet Genomics Key benefits – Powerful performance with SureSelect exome enrichment for germline and somatic samples – SureSelect Human All Exon V8 panel provides excellent uniformity of coverage for CNV detection – Alissa Reporter is an integrated and optimized software for somatic exome data analysis – Alissa Interpret enables variant prioritization, interpretation and reporting 2 SureSelect Exome Enrichment System SureSelect Human All Exon V8 SureSelect Library Prep and Enrichment Magnis NGS Prep System Bravo NGS Workstation Exome Library Preparation Sequencing Alissa Clinical Informatics Platform Variant Analysis, Interpretation and Reporting Figure 1. Agilent whole-exome sequencing solutions. The SureSelect human all exon V8 panel can be paired with the Agilent Bravo NGS workstation, Magnis NGS prep system, and the Alissa Clinical Informatics platform to achieve operational efficiency. The exome is readily automated on the Bravo NGS workstation for high-throughput applications. The Magnis human all exon V8 kit is pre-aliquoted for use on the Magnis NGS prep system, which requires only 10 minutes of initial setup time and delivers eight exome-enriched libraries in less than nine hours without further operator intervention. The Alissa Clinical Informatics platform allows clinical workflows to be streamlined from variant analysis to variant annotation, enabling genetics and molecular medicine labs to efficiently triage, curate, and report genomic variants. Figure 2. Alissa Reporter detects SNVs, indels, and CNVs from exome sequencing. The Alissa Reporter CNV detection module detects both CNV amplifications and deletions, down to the gene level. CNVs are visualized in a sortable and filterable table. A link to the detailed view is available from within the overview table, in which CNVs can visually be inspected using an integrated genome browser (CNV viewer). A CNV amplification in gene ANKRD36C is shown. Alissa Reporter for High-Performance Variant Detection From a single genomic sample, researchers can get more valuable information than ever before. Alissa Reporter supports parallel variant detection from somatic DNA specimens. With Alissa Reporter’s secondary analysis capabilities, you can detect SNVs, indels, and CNVs (Figure 2). As a fully transparent solution, Alissa Reporter includes confidence scores next to CNV calls. 3 Built-In QC Dashboard for Operational Excellence Alissa Reporter helps users quickly verify that an NGS assay is performing as planned. With the built-in QC dashboard (Figure 3), users can immediately assess whether key QC metrics of individual samples (or the entire run) are within the anticipated range. Alissa Reporter flags problematic samples and shows users where the QC metric has deviated from recommended values. Alissa Reporter can track and display QC metrics longitudinally. By analyzing quality control data across runs, users can easily identify trends and deviations from expected performance parameters over time. Figure 4. The virtual gene panel option enables users to filter based on genes and/or regions of interest. Figure 3. The Alissa Reporter QC dashboard helps you quickly find the metrics that matter most. Virtual Gene and/or Regions Panels If users are only interested in analyzing a subset of genes or regions, the Alissa Reporter in silico filter (Figure 4) enables the creation of virtual gene panels. Create targeted gene panels in advance based on your subpanels of interest or edit your selected panel when needed. It is easy to manage in silico filters with Alissa Reporter’s intuitive filtering functions. Simply select or upload the gene(s) and/or region(s) to be included, and Alissa Reporter will automatically filter the dataset based on this selection. 4 Figure 5. Comprehensive analysis results of the mitochondrial genome displayed in the SNV/indel table and read pileup view available in Alissa Reporter. Somatic Variant Detection on the Mitochondrial Genome The mitochondrial genome poses several challenges to the identification and understanding of somatic variants. Alissa Reporter’s optimized SureSelect human all exon V8 and SureSelect custom panel pipelines come with a dedicated mitochondrial DNA analysis option (Figure 5). The workflow enables labs to explore the state of mitochondria by enabling the detection of mitochondrial variants (that is, SNVs) to identify heteroplasmy. Alissa Reporter delivers mitochondrial variant detection with high sensitivity, helping labs to confidently identify biomarkers in metabolic disease research. 5 Figure 7. Alissa Interpret integrates with industry standard and best-in-class annotation sources. Advanced decision tree-based filtration system Automate your lab's variant assessment workflow in configurable, versioned pipelines. Sort the data and quickly organize it in levels of detail to identify your variants of interest for further manual review. Store and version your pipelines to support increasing volumes and scale your sample throughput with ease (Figure 6). Figure 6. Flexible classification trees for rapid, transparent variant filtration. Alissa Interpret, a Genomic Data Interpretation and Reporting Solution Alissa Interpret enables molecular pathology labs to efficiently triage, curate, and report genomic variants. Alissa Interpret combines single nucleotide polymorphisms (SNPs), indels, CNVs, fusions, and biomarkers such as TMB and microsatellite instability (MSI) in a single integrated workflow. Direct access to up-to-date clinical findings Collaboratively curate your internal knowledgebase while also accessing an expansive array of up-to-date databases, including variant adaptations and effect annotations, frequency databases, clinically relevant peer-reviewed findings, and expertly curated content from the Jackson Clinical Knowledgebase (JAX-CKB) (Figures 7 and 8). 6 Figure 8. Additional information on the variant impact and clinical significance is available using JAX-CKB information in Alissa Interpret. * * Somatic gene variant annotations and related content have been powered by JAX-CKB. Comprehensive report templates With Alissa Interpret, reports can be fully configured towards lab needs, in both in content and layout. For comprehensive report templates, users can include information on samples, findings, public information, databases, and literature annotations. Additionally, easy-to-read overviews of variants are provided with their various characteristics, such as read depth, Human Genome Variation Society (HGVS) nomenclature, gene definitions, and classification. Automatically generated text can be included in a context-sensitive way. LIMS and EMR integration Alissa Interpret reduces turnaround time and increases productivity with minimal impact on budget, staffing, and IT infrastructure. Increase your lab’s operational efficiency and eliminate genomic data analysis bottlenecks through laboratory information management system (LIMS) and electronic medical records (EMR) integration. 7 An End-to-End Automated NGS Software Workflow Alissa Reporter turns raw NGS FASTQ files into key variant call format (VCF) files for Agilent SureSelect human all exon V7 and V8 somatic and custom somatic applications. As part of the Agilent Alissa Clinical Informatics platform, Alissa Reporter seamlessly transfers data to the Alissa Interpret analysis solution for a fully integrated end-to-end NGS software workflow. After the variant of interest has been identified in Alissa Interpret, users can easily link back to Alissa Reporter to visualize read pileups in Alissa Reporter’s highly responsive, integrated genome browser. Figure 9. Fully optimized and integrated software solution. Users can send data directly from Alissa Reporter to Alissa Interpret for a streamlined NGS data analysis experience. Data is linked back to Alissa Reporter, allowing users to view read pileups for the variant of interest. Send data directly to Alissa Interpret software from Alissa Reporter Link back to Alissa Reporter's integrated genome browser directly from Alissa Interpret to view read pileups www.agilent.com/genomics For Research Use Only. Not for use in diagnostic procedures. Alissa Interpret is a Class I Exempt Medical Device in the US, a CEIVD in the EU and a Class I IVD in Canada and Australia. PR7001-1277 This information is subject to change without notice. © Agilent Technologies, Inc. 2023 Published in the USA, July 17, 2023 5994-6577EN Ordering Information Product Description 16 Rxns 96 Rxns 96 Rxns Auto SureSelect XT HS Human All Exon V8 5191-6873 5191-6874 5191-6875 SureSelect XT HS Human All Exon V8+UTR 5191-7401 5191-7402 5191-7403 SureSelect XT HS Human All Exon V8+NCV 5191-7407 5191-7408 5191-7409 Product Description 2 Hybs 12 Hybs 12 Hybs Auto SureSelect XT HS PreCap Human All Exon V8 5191-6876 5191-6877 5191-6878 SureSelect XT HS PreCap Human All Exon V8+UTR 5191-7404 5191-7405 5191-7406 SureSelect XT HS PreCap Human All Exon V8+NCV 5191-7410 5191-7411 5191-7412 Compatible with Fast Hybridization Product Description 16 Rxns 96 Rxns 96 Rxns Auto SureSelect XT Human All Exon V8 5191-6879 5191-6891 5191-6892 SureSelect XT Human All Exon V8+UTR Contact Sales SureSelect XT Human All Exon V8+NCV Contact Sales Product Description 2 Hybs 12 Hybs 12 Hybs Auto SureSelect XT PreCap Human All Exon V8 5280-0032 5280-0033 5280-0034 SureSelect XT PreCap Human All Exon V8+UTR Contact Sales SureSelect XT PreCap Human All Exon V8+NCV Contact Sales Compatible with Overnight Hybridization Product Description 32 Rxns 96 Rxns Magnis SSEL XT HS Human All Exon V8, Rev B G9772C G9772D Magnis SSEL XT HS2 Human All Exon V8, Rev B G9774A G9774B Magnis SSEL XT HS2 Human All Exon V8+UTR G9779A G9779B Magnis SSEL XT HS2 Human All Exon V8+NCV G9778A G9778B Compatible with Magnis NGS Prep System Product Description SureSelect Human All Exon V8+Pan-Cancer Contact Sales SureSelect Human All Exon V8+Mitochondrial Genome Contact Sales SureSelect Human All Exon V8+OneSeq CNV Backbone Contact Sales Other Configurations Product Description Magnis NGS Prep System Contact Sales Bravo NGS (Option A) Contact Sales Bravo NGS Workstation (Option B) Contact Sales Alissa Reporter Contact Sales Alissa Interpret Contact Sales Automation and Software