QIAGEN s NGS Solutions for Biomarkers NGS & Bioinformatics team QIAGEN (Suzhou) Translational Medicine Co.,Ltd 1
Our current NGS & Bioinformatics Platform 2
Our NGS workflow and applications 3
QIAGEN s solution for targeted DNA sequencing QIAGEN can provide solution for targeted DNA sequencing from DNA isolation to data interpretation 4
GeneRead DNAseq Targeted panels (V2) Benefits of GeneRead DNAseq Targeted Panels (V2): Single panel for all NGS platforms Well-suited for FFPE samples Use as little as 10 ng starting DNA per PCR pool Rapid turn-around time (3 hours) Clinically and biologically relevant content: GeneRead DNAseq Targeted Panels focus on specific mutations, exons, and genes that are most relevant to a particular disease. The content of these panels was selected from the College of American Pathologists(CAP) guidelines, NCCN guidelines, late-stage clinical trials, The Cancer Genome Atlas (TCGA), and Ingenuity Knowledge Base. GeneRead DNAseq Targeted Panels workflow 5
GeneRead DNAseq Targeted panels (V2) The GeneRead DNAseq Targeted Panels(V2) enable enrichment of the coding regions and exon/intron junctions of genes frequently mutated in a particular disease. Using a high-dimension multiplex PCR targeted enrichment approach, DNAseq targeted panels increase the efficiency of sequencing efforts by focusing on the genes most relevant to a specific disease or research area. Multiplex PCR-based targeted enrichment scheme 6
GeneRead DNAseq Targeted panels (V2) Type Product name No. of total primer pairs Size (kb) No. of Target Gene Specifi city Uniformity (0.2x mean) Experim ental coverage Solid Tumor Hematologic malignancies Clinically Relevant Tumor Panel 602 40 24 95.3% 90% 90% Tumor Actionable Mutations Panel 118 7.1 8 98.2% 91% 91% Human Myeloid Neoplasms Panel 2536 236 50 97.4% 94% 94% Human Breast Cancer Panel 2915 269 44 96.8% 91% 91% Human Colorectal Cancer Panel 1954 183 38 98.3% 95% 95% Human Liver Cancer Panel 2052 191 33 96.4% 96% 96% Tissue Specific Human Lung Cancer Panel 3586 333 45 98.1% 90% 90% Human Ovarian Cancer Panel 2021 189 32 96.6% 96% 96% Human Prostate Cancer Panel 1837 167 32 97.3% 94% 94% Human Gastric Cancer Panel 2377 222 29 98.5% 93% 93% Human Cardiomyopathy Panel 2657 250 59 96.7% 87% 87% Comprehensive Human Cancer Predisposition Panel Human Comprehensive Cancer Panel 6582 620 143 96.8% 93% 93% 7951 745 160 97.7% 92% 92% Human Carrier Testing Panel 6943 665 157 97.9% 91% 91% 7
QIAseq Targeted DNAseq panels (V3) Digital DNA sequencing to confidently detect low-frequency variants: Digital sequencing enabled by molecular barcodes to remove PCR duplicates Complete solution streamlines the workflow Compatibility with low-quality DNA enables efficient sequencing of FFPE and cfdna samples Minimal DNA input to preserve precious samples (20 ng input DNA) Optimized buffers and conditions to achieve high coverage of GC-rich regions Applications: SNVs Small indels CNVs Workflow 8
QIAseq Targeted DNAseq panels (V3) Molecular barcode is a tag (barcode) to identify unique DNA or RNA molecules Principle of molecular barcodes 9
QIAseq Targeted DNAseq panels (V3) Catalog no. Product name No. of genes No. of total primers* DHS-001Z Human Breast Cancer Panel 93 4831 1 DHS-002Z Human Colorectal Cancer Panel 71 2929 1 DHS-003Z Human Myeloid Neoplasms Panel 141 5887 1 DHS-005Z Human Lung Cancer Panel 72 4149 1 DHS-104Z Human Pharmacogenomics Panel 31 146 3 DHS-3011Z Human Inherited Disease Panel 298 11579 1 DHS-3501Z Human Comprehensive Cancer Panel 275 11311 1 DHS-101Z Human Actionable Solid Tumor Panel 23 651 2 DHS-102Z Human BRCA1 and BRCA2 Panel 2 223 1 DHS-103Z Human BRCA1 and BRCA2 Plus Panel 6 348 1 DHS-105Z Human Mitochondria Panel Chromosome M 222 4 Type of Coverage * * Types of coverage: 1. Exonic regions of genes plus 10 bases to cover intron/exon junctions 2. Mix of type of coverage 1 (for tumor suppressor genes) and HotSpots for Oncogenes 3. SNPs 4. Full chromosome 10
QIAGEN s solution for RNA-seq QIAseq Targeted RNA Panels and QIAseq targeted RNAscan panels have been developed as a solution for quantitative gene expression and gene fusion profiling using RNA-seq. 11
QIAseq Targeted RNA Panels and RNAscan Panels Panels QIAseq Targeted RNA Panels QIAseq Targeted RNAscan Panels Descriptions Digital RNAseq for gene expression profiling Ability to examine hundreds of genes in hundreds of samples simultaneously Requires only 25 ng of total RNA Go from sample to library in one day Accurate and digital gene expression profiling using molecular barcodes Applying digital RNA sequencing to scan for known and novel fusion genes Accurate quantification of a large number of fusion genes Identify new fusion gene partners, no prior knowledge of breakpoint needed Works with low-quality RNA, including RNA from FFPE and liquid biopsy Requires low RNA input, as low as 15 ng of un-enriched RNA Automation-friendly Title, Location, Date 12
QIAseq Targeted RNA Panels Applications: Gene expression profiling Biomarker research Confirmation of whole transcriptome sequencing data Confirmation of microarray data 13
QIAseq Targeted RNA Panels Digital sequencing(molecular barcodes) principle Different platforms comparison 14
Current QIAseq Targeted RNA Panels (Human) Product name No. of genes Human Angiogenesis & Endothelial Cell Biology 340 Human Apoptosis & Cell Death 264 Human Cancer Transcriptome 395 QIAseq Targeted RNA Panels Human Extracellular Matrix & Cell Adhesion Molecules 421 Human Inflammation & Immunity Transcriptome 475 Human Molecular Toxicology Transcriptome 370 Human Signal Transduction PathwayFinder 405 Human Stem Cell & Differentiation Markers 293 QIAseq Targeted RNA Extended Panels QIAseq Targeted RNA Custom Panel QIAseq Targeted RNA Extended Panel QIAseq Targeted RNA Custom Panels Customized Customized 15
QIAseq Targeted RNAscan Panels Applications: Detection of known gene fusions based on well-characterized breakpoints Discovery of novel gene fusions using exon- or gene-based primer designs Workflow 16
QIAseq Targeted RNAscan Panels Technical advantage Principle of molecular barcodes The unique combination of our proprietary primer design algorithm and rigorous testing of every primer assay guarantees high specificity and accurate results 17
Current QIAseq Targeted RNAscan Panels Panel Product Name No.total primers No.total gene Human Leukemia Panel 156 24 QIAseq Targeted RNAscan Panels Human Solid Tumor Panel 101 11 Human Lung Cancer Panel 137 23 Human Oncology Panel 950 223 Custom Panel QIAseq Targeted RNAscan Custom Panels Customized Customized 18
QIAGEN s solution for Single Cell Sequencing QIAGEN can provide solution for single cell sequencing from single-cell isolation to data interpretation 19
Single Cell Genomics by QIAGEN QIAscout For accessible, affordable and efficient isolation and recovery of single cells. REPLI-g Cell WGA & WTA Kit For parallel whole genome and whole transcriptome amplification from cells and limited samples. REPLI-g Single Cell Kit For highly uniform whole genome amplification (WGA) from single cells or limited sample material. REPLI-g WTA Single Cell Kit For whole transcriptome amplification of total RNA or mrna from single cells. REPLI-g Single Cell DNA Library Kit For DNA library construction from single cells for Illumina sequencing applications. REPLI-g Single Cell RNA Library Kit For RNA library construction from single cells for Illumina sequencing applications. 20
The QIAseq FX Single Cell DNA/RNA Library Kit QIAseq FX Single Cell DNA Library Kit QIAseq FX Single Cell RNA Library Kit Single-cell whole genome libraries with comprehensive coverage and high sequence fidelity. The kit provides a complete solution for whole genome sequencing from isolated single animal or bacterial cells or low amounts of genomic DNA. The kit includes all reagents required for cell lysis, whole genome amplification, enzymatic DNA fragmentation and PCR-free NGS library preparation. Single cell RNA-seq libraries that provide a deeper view of the transcriptome. The QIAseq FX Single Cell RNA Library kit is an end-to-end library preparation solution for RNAseq from single cells or low amounts of RNA. The kit includes all reagents required for cell lysis, reverse transcription, cdna amplification and PCR-free NGS library preparation. 21
The Multiple Displacement Amplification (MDA) technology REPLI-g and QIAseq FX uses isothermal genome amplification, termed MDA, which involves the binding of random hexamers to denatured DNA followed by strand displacement synthesis at a constant temperature using the enzyme Phi 29 polymerase. REPLI-g MDA technology delivers long read lengths with isothermal amplification Unbiased amplification with Phi29 polymerase 22
Our powerful Data Analysis and Visualization-Bioinformatics From sample to insight with QIAGEN Bioinformatics End-to-end NGS data analysis solution and from data to biological insights; With our workflows, it enables easy and accurate discovery, verification, and validation of novel disease in cancer and hereditary disease NGS data. 23
Tumor Mutation Burden (TMB) - Assay Flowchart (1) 24
Tumor Mutation Burden (TMB) - Assay Flowchart (2) 25
Product development based on NGS-TMB detection 26
Our IP of NGS Computer software copyright registration certificate PubMed mass document format conversion system based on MEDLINE format; High - throughput sequencing data analysis software; Data analysis software based on VCF format for gene variation; RNA-seq analysis software based on PDX model; Gene expression profiling data mining analysis software; 27
Contact US Nick Zhang, Ph.D. CEO Email: Nick.zhang@transmedchina.com Address: Suite 901, B5 Building, 218 Xinghu St. Suzhou Industrial Park, China ZIP: 215123 http://www.transmedchina.com Business Contact Wei Zhang (Wesley), Ph.D., Director of Business Development Email: wesley.zhang@transmedchina.com Phone: 0512-86868600-8006 Mobile: 18612485600 Technical Contact Congmao Wang, Ph.D., Manager of NGS & Bioinformatics Email: congmao.wang@transmedchina.com 28