© 2017 Illumina, Inc. All rights reserved. COMPANY CONFIDENTIAL – FOR INTERNAL USE ONLY Illumina各测序系统介绍与 应用比较 任岩 Product Marketing Manager Illumina Greater China September 7, 2017 2 Decreasing price per GB Increasing system output Understand the Equipment Options Sequencing Power for Every Scale HiSeq 2500 1000 Gb | 4B 2x125 NextSeq® 120 Gb | 400M 2x150 MiSeq® 15 Gb | 25M 2x300 HiSeq 3000 750 Gb | 2.5B 2x150 HiSeq 4000 1500 Gb | 5B 2x150 MiniSeq™ 7.5 Gb | 25M 2x150 167-2000 Gb | 1.6-6.6B 2x150 NovaSeq 5000 167-6000 Gb | 1.6-20B 2x150 NovaSeq 6000 HiSeq X 1800 Gb | 6B 2x150 3 Understand the Equipment Options 测序平台需要考虑的因素测序平台需要考虑的因素 我最常用的 应用？ 哪些测序平台 最适合我的应用？ 仪器之外的cost? 所选NGS平台 将如何影响 工作流及进程？ 如何确保数据， 仪器及工作流 的质量？ 数据如何分析？ 后续支持服务怎样？ 4 MiSeq NovaSeq SERIOUS PRODUCTION SCALE! NextSeq 500 Understand the Equipment Options MiniSeq NextSeq 500 PRODUCTION SCALE MANY SAMPLES| RUN HIGH THROUGHPUT WGS | WES | T-OME LOW THROUGHPUT TGRS | WGS (MICROBES) PERSONAL SCALE FEW SAMPLES| RUN NovaSeq HiSeq HiSeq X 5 201 4 $1,000 1st$1,000 genome 201 0 $10,000 1stsub-10K genome 200 8 $200,000 1st30x genome 200 7 $2,000,000 1stNGS Genome 200 6 $20,000,000 1stindividual genome 2003 $3,000,000,000 Human Genome Project Cost Per Human Genome $100 some day in the future… 6 Human Genomes Sequenced on HiSeq X? 0 50 100 150 200 250 300 350 1Q 142Q 143Q 144Q 141Q 152Q 153Q 154Q 151Q 162Q 16 201420152016 Cumulative HiSeq X Genomes Hundreds More Than All Other Platforms Combined! 7 Rapid run capabilities Customer Feedback Ability to sequence larger cohorts Confidence that the platform I invest in will be competitive in the future Better price per sample Lower price per sample X pricing for all applications Power and price to sequence more samples at greater depth Economics that enable deep T/N profiling Rapid WGS of trios Single system with power both novel and known Coding variants Non- coding variants Large SVsBalanced translocati on Uniparent al disomy PanelYesNoKnownsKnownsNo ExomeYesNoPartialNoPartial GenomeYesYesYesYesYes 28 DNA测序策略：优劣对比测序策略：优劣对比 策略策略Approach优势优势Advantages不足不足/Disadvantage 全基因组测序 Whole-Genome •Comprehensive view of whole genome •Can detect all types of mutations •Standardized processing and analysis for all patients •No enrichment bias •More expensive •Large dataset difficult to interpret •Findings may not be actionable •Lower coverage than exome / targeted •IT issues 全外显子组测序 Whole-Exome •Only 1 to 1.5% of the genome is sequenced •About half the cost of whole-genome sequencing •Can detect indels and SNPs •Small data set, easier to interpret •Very deep coverage across majority of exome •Will miss some fusion genes •Findings may not be actionable •Potential enrichment bias 靶向基因重测序 Targeted Gene/Region Resequencing •Cost-effective •Results are easy to interpret •Can restrict to actionable findings •Able to get extremely deep coverage (increased coverage = increased confidence) •Will miss many mutations •Requires a prior knowledge of the genes of interest •Will benefit a sub-set of patients •Difficulties with capture step 29 •Large scale NGS data combined with longitudinal health records •WES & extraction of ANGPTL4 sequence •42,390 samples, 10,552 CADs & 29,223 controls •E40K mutation in ANGPTL4 lower level of triglycerides and a lower risk of CAD than non carriers •Mice and monkeys also result correspondingly •Further publications & insights 30 •Rapid genomic diagnosis of infants with high mortality rate genetic disease •STAT Seq, 26-hour system of WGS, HiSeq 2500, 2*101 rapid mode, 90Gb per sample •Studied 35 NICU/PICU patients (4 months) & family trios •57% of cases had confirmed diagnosis with WGS (100% confirmation with Sanger sequencing) •9% of cases had confirmed diagnosis with standard genetic testing •94 tests of standard genetic testing 31 Application: Whole Transcriptome Deep transcriptome analysis and genome annotation Application: Gene Expression Profiling Alternative transcription Fusion gene Application: Gene Expression Profiling Gene detection Differential Expression Illumina Sequencing Solutions From Single Genes to Whole Transcriptome Application: Targeted RNA Panel 32 ●Accurate targeting of virtually the entire transcriptome for Human, Mouse and Rat - Assay specific gene families including alternative isoforms ▪Individual exons and splice junctions ▪cSNP detection for allele specific expression - Non-coding RNA transcripts ●Add custom content to Fixed Panels TruSeq Targeted RNA Expression Content Create custom panels, select pre-validated fixed, or add-on custom Pre-Validated Fixed Panels Immune ResponseCardiotox Lung CancerApoptosis Breast CancerNeuro Panel Stem Cell Prostate Cancer P53 PathwayWnt Pathway Cytochrome P450 Cell Cycle NFκB PathwayHedgehog Design Studio: Custom Panel Creation 33 Target NGS vs. qPCR and Sanger Sequencing 34 ●Digital counts vs analog intensities ●Increased dynamic range and sensitivity ●No probes or primers – no a priori genome content knowledge required ●Analyze gene ex。