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CANCER GENETICS SOLUTIONS PUSHING THE BOUNDARIES IN CANCER GENETICS Cancer is a formidable foe that presents significant challenges. The complexity of this disease can be daunting due to the number of mechanisms that can trigger carcinogenesis, including the influence of environmental factors. However, each new discovery can reveal new understanding that can get us one step closer to unraveling this complexity. Innovation drives discovery Leaders in cancer genetics research drive innovations to address complexity and provide a better understanding of targets that may show promise for conquering this disease. At Agilent we continually develop innovative, multi-omic solutions to help you overcome the hurdles of cancer genetics research. Accelerating the pace Providing complementary, advanced molecular solutions for cancer genetic analysis is a core mission of Agilent. Our unparalleled leadership in the development and customization of technologies enables you to focus on the most important targets, increase the pace of discovery, and accelerate breakthroughs. The Range of Genetic Aberrations Detected by Precision Genetic Technologies TECHNOLOGY POINT MUTATION INDEL GENE COPY NUMBER CHANGE BALANCED TRANSLOCATION DNA Seq Target Enrichment √ √ √ √ √ √ √ RNA-Seq STRUCTURAL VARIANT LOH GENE REGULATION √ √ √ Methyl-Seq √ Gene Expression Microarrays √ CGH+SNP Microarrays √ FISH √ qPCR √ √ √ √ √ √ √ ANALYSIS OF STRUCTURAL & SINGLE BASE CHANGES Translocations, loss of heterozygosity (LOH) and copy number variations (CNVs) can all influence susceptibility to cancer1, and single nucleotide polymorphisms (SNPs) are useful biomarkers to identify genomic regions associated with cancer. SureSelect Target Enrichment products for next-generation sequencing (NGS) provide the best tools for sensitive, accurate and comprehensive identification of these somatic variants in both solid tumors and hematological samples. Catalog and custom options provide superior performance with either exome captures or targeted panels. Design your own custom SureSelect DNA panels using intuitive SureDesign software, and your own custom SureSelect RNA panels using intuitive eArray software. • Detect LOH, CNVs, and mutations associated with SNPs using low input DNA amounts • Obtain high genome-wide NGS coverage and uniformity • Choose from catalog and custom target enrichment probes • Complete your target enrichment step in as little as one day Deep Coverage with FFPE Tumor Samples 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% % On Target +/- 100bp 10X Coverage 20X Coverage 50X Coverage % Dups DIN 4.9 FFPE_Breast Tumor DIN 8.6 FF_Breast Tumor DIN 5.4 FFPE_Lung Tumor DIN 9.0 FF_Lung Tumor Figure 1. Sequencing performance of SureSelectXT libraries from FFPE and fresh-frozen (FF) breast and lung tumor samples enriched using the ClearSeq Comprehensive Cancer research panel (240 Mb sequencing/sample). The level of DNA degradation is indicated by the DNA Integrity Number (DIN) provided by the 2200 TapeStation System, where DINs of 10 and 1 indicate gDNA and completely degraded DNA, respectively. SureSelect Catalog Designs Optimized for Cancer Research Product Features SureSelect Human All Exon V6+COSMIC Comprehensive exome-wide analysis, including COSMIC targets SureSelect Human All Exon V6 +UTR Comprehensive transcriptome (RNA) and exome (DNA) analysis ClearSeq Comprehensive Cancer Enables analysis of 151 key genes associated with a wide range of cancers ClearSeq DNA and RNA Kinome Analysis of the kinome, including UTRs 2 DETECTION OF RARE GENETIC VARIANTS Cancer can be caused by rare, low-penetrance genetic variants ranging from allele frequencies of 0.1% or less up to almost 5%2, and extraordinary genetic heterogeneity occurs in both solid and hematologic cancers3. Agilent HaloPlexHS Target Enrichment products enable sensitive and accurate detection of rare variants in cancer samples. HaloPlexHS is a combination of amplicon-based and target enrichment sequencing that delivers accurate results across many genes and from very low DNA inputs. Molecular barcodes enable identification and elimination of sequencer and PCR errors in high coverage NGS data. “The HaloPlexHS technology using molecular barcodes gave us the highest ratio of accuracy and sensitivity to identify low frequency mutations in all the samples.” Ioannis Ragoussis, Ph.D. McGill University • Confidently detect mutations below 1% allele frequency in genetically heterogeneous samples • Differentiate true variants from PCR or FFPE artifacts by targeting both DNA strands • Get high on-target specificity and deep coverage of target bases so key variants are not missed • Perform target enrichment in <6 hours from only 50 ng of gDNA Detection Down to 0.5% Allele Frequency 8.0% 6.0% 5.0% 5% 2.5% 1% 0.5% 4.0% 3.0% 2.0% 92244422 534242 chr7 chr7 chr7 chr7 chr11 chr12 chr12 chr12 chr16 chr21 36165041 55242609 chr7 68863314 55240461 chr6 69233716 55238268 chr4 69233215 55229255 chr3 56494991 1521129077 0.0% 55152040 1.0% 178917005 Expected allele frequency 7.0% Figure 2. HapMap cell lines, NA18507 and NA10831, were mixed to generate allelic fractions ranging from 0.5%-5%. The close agreement between expected and observed frequency at various chromosomal positions demonstrates the high sensitivity of HaloPlexHS for low frequency variant detection. Data shown is representative of replicates (sequencing depth=2000x-4000x) 3 GENE EXPRESSION AND GENE REGULATION IN CANCER RNA splicing disruption is common during cancer genesis4, resulting in significant variations in gene expression. Gene expression changes can lead to unregulated cell division and cancer. SurePrint G3 Gene Expression Microarrays provide 5-log The SureSelect Strand Specific RNA Library Preparation Kit is the ideal discovery tool to find novel splice variants, non-coding elements, antisense transcripts and gene fusions by NGS, with the highest sensitivity for preparing libraries for mRNA or targeted RNA-Seq. dynamic range and produce data that correlates better to RNA-Seq experiments than competitor arrays. • Generate more efficient captures of the top 1,000 expressed genes with RNA-Seq • Use the lowest 5’ and 3’ bias target enrichment chemistry in the industry • Employ a strand-specific RNA-Seq approach to find and confirm antisense transcripts5 • Target difficult fusions, like BCR-ABL, where shorter baits may fail to hybridize to the full transcript Low Duplication Rate 35% % Duplication 40% 20% 0% 17% 18% SSEL-UHRR 1µg SSEL-UHRR-0.2µg Competitor 1 - 1µg 34% Competitor 1 0.2µg Figure 3. SSEL Strand Specific Library Prep for RNA had a duplication rate below 20% whereas the competitive platform had a duplication rate above 30% under the same conditions. In this experiment, all reads were normalized to 20 million/library (2X100bp sequencing) for comparison. Universal Human Reference RNA was the input sample for both platforms to provide equivalence. Each platform was tested with 1µg and 200ng. Before library prep, Poly A purification was performed for all samples. 4 COPY NUMBER VARIATION IS A KEY DRIVER IN CANCER GENESIS A larger percentage of the genome in cancers is affected by somatic cell copy number variants (CNVs) than any other kind of somatic genetic alteration6. The quality of Agilent CGH technology allows faster and They play important roles by inactivating tumor suppressors and activating oncogenes, and the study of CNVs has driven substantial advances in cancer diagnostics and therapeutics. Analysis and characterization of CNVs in hematological cancers have improved significantly through the use of array comparative genomic hybridization (aCGH)7. Agilent catalog and custom CGH microarrays provide exceptional sensitivity and flexibility with the most challenging sample types. more efficient association of disease research phenotypes with genotypes. • Detect aberrations even in heterogeneous samples due to high signal-to-noise ratios, and report clonal fraction The GenetiSure Cancer Research CGH+SNP • Process samples faster than other microarray methods Array combines exon-level • Select from a comprehensive menu of products, including labeling solutions for fresh, frozen and FFPE samples resolution with the detection of copy number and copy- • Design genome-wide custom arrays free of charge with no minimum order neutral changes. Accurately Detect Low Level Deletions CN Illumina SNP SNP Vendor Softwre Agilent CGH+SNP Figure 4. DNA CN and SNP profile of chromosome 13 of a Multiple Myeloma sample hybridized on Agilent SurePrint G3 CGH+SNP 2×400K microarrays and Illumina SNP microarrays analyzed with the respective vendor software. Results indicated that the deletions present in approximately 25% of the cells could be detected on Agilent’s platform in both the CN and SNP data, but was only detectable as an aberration in the Illumina SNP data. 5 THE IMPORTANCE OF SAMPLE QUALITY Many factors can impact quality and/or quantity of the DNA and RNA extracted from samples, including cold ischemia, fixation (FFPE) and processing. An accurate understanding of starting sample quality is absolutely required, as it can significantly affect the quality of genomic and transcriptomic profiling. The Agilent 4200 TapeStation and 2100 Bioanalyzer systems provide automated electrophoresis for DNA and RNA sample quality analysis for any NGS, microarray, or quantitative PCR workflow. Automation frees up researcher time and reduces errors, while providing both DNA (DIN) and RNA (RIN) integrity numbers. • Get fully automated sample processing for up to 96 samples with the 4200 TapeStation System • Maximize assay flexibility with on-chip electrophoresis of DNA or RNA or proteins with the Agilent 2100 Bioanalyzer System Fluorescence 45 40 35 30 25 20 15 10 5 0 [bp] A1 (L) B1 C1 D1 E1 F1 G1 DIN 9.8 DIN 8.2 DIN 8.0 DIN 6.8 DIN 5.5 DIN 4.4 18S 28S Intact RNA: RIN 10 8 7 6 5 4 3 2 1 0 48500 15000 7000 4000 3000 2500 2000 1500 1200 900 Partially degraded RNA: RIN 5 600 28S 18S Fluorescence Fluorescence • Run the NGS FFPE QC Kit on the AriaMx fully integrated quantitative PCR system to enable assessment of the integrity of DNA as well as accurate quantitation of amplifiable template 400 3.0 2.5 2.0 1.5 1.0 0.5 0.0 250 Strongly degraded RNA: RIN 3 19 24 29 34 39 44 49 54 59 64 100 69 Time (seconds) Figure 5. 2100 Bioanalyzer system: The established RNA Integrity Number (RIN) provides quality assessment of total RNA. Figure 6. 4200 TapeStation System: Genomic DNA samples at different degradation stages with DNA Integrity number (DIN). 6 References 1. Bente et al. Genetic variation and its role in malignancy. Int J Biomed Sci. (2011) 7:158-171. 2. Bodmer W. and Tomlinson J. Rare genetic variants and the risk of cancer. Curr Opin Genet Dev (2010) 3:262-267. 3. Spencer et al. Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next- generation sequence data. J Mol Diagn. (2014) 16:75-88. 4. Sveen et al. Transcriptome instability as a molecular pan-cancer characteristic of carcinomas. BMC Genomics (2014) 1471- 2164-15-672. 5. Levin et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nature Methods (2010) 7: 709–715. 6. Zack et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet. (2013) 45: 1134-1140. 7. Hartmann et al. Detection of clonal evolution in hematopoietic malignancies by combining comparative genomic hybridization and single nucleotide polymorphism arrays. Clin Chem (2014) 60: 1558-1568. LEARN MORE AT: www.agilent.com/genomics Find an Agilent customer center in your country: www.agilent.com/genomics/contactus Trusted Answers. Together. U.S. and Canada 1-800-227-9770 [email protected] Europe [email protected] PR7000-0292 © Agilent Technologies, Inc. 2016 Printed in USA, October 28, 2016 5991-7565EN Asia Pacific [email protected] For Research Use Only. Not for use in diagnostic procedures.