Get the Latest Clinical Insights for Tumor Exome Profiling
Whole-exome sequencing (WES) has been increasingly adopted into oncology testing and research to profile tumor samples. It can be used to guide treatment selection, identify emerging biomarkers and predict patient responses to immune checkpoint inhibitors.
Exome enrichment supports deeper coverage, cost effectiveness and improved variant calling. However, the complexity of sequencing data can present challenges for the analysis and interpretation of relevant clinical insights. This whitepaper explores the latest reagents and software available to enhance tumor exome profiling for the generation of accurate, actionable clinical insights. Download this whitepaper to discover: High-performance workflows for somatic mutation detection and SNP variant calling Genomic data reporting, interpretation and quality control solutions An expertly curated internal knowledge base full of up-to-date clinical findings
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
– 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
SureSelect Exome Enrichment System
SureSelect Human All Exon V8
SureSelect Library Prep
Magnis NGS Prep System
Bravo NGS Workstation
Exome Library Preparation
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.
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.
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.
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).
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.
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
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.
This information is subject to change without notice.
© Agilent Technologies, Inc. 2023
Published in the USA, July 17, 2023
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
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
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
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