NGS-based innovations within the Leiden Network
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1 NGS-based innovations within the Leiden Network A strong bridge between two partners Dr. Mark de Jong
2 Design accurate and robust NGS tests and generate data sets essential for Diagnostics & Personalized Treatment
3 The foundation of GenomeScan
4
5 /
6 USD/Gb Sequencing costs Jan-10 Apr-10 Jul-10 Oct-10 Jan-11 Apr-11 Jul-11 Oct-11 Jan-12 Apr-12 Jul-12 Oct-12 Jan-13 Apr-13 Jul-13 Oct-13 Jan-14 Apr-14 Jul-14 Oct-14 USD/Genome Jan-15 Apr-15 Jul-15 Oct-15 Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP) Available at: Accessed [ ].
7 Balanced sequencer portfolio to accommodate all research needs HiSeq 4000 NextSeq 500 PacBio Sequel / RSII Read length (max) 150 bp 150 bp kb Total run time day Up to 1 day 1 2 days Output / run ~2000 Gb ~120 Gb ~5 Gb Exomes per run Up to 192 ~12 ~1 Major applications Production scale sequencer for all applications Targeted panel sequencing Fast diagnostics Long read seq de novo seq Pseudogenes
8 Genetic Testing and Diagnostics Research Services Drug Development Services NGS Consultancy
9 Route towards state of the art diagnostics within the Leiden network Sample prepping Sequencing Dataanalysis Data-analysis & interpretation Diagnosis Report to patient Entry QC Patient sample Data storage & retrieval Return to data in case of new clinical insights Provide instrumentation, expertise & infrastructure to the clinic in order to fast track the route towards personalized treatment
10 Our service portfolio www.
11 Phases of genetic test development Phase 1 Phase 2 Kickoff meeting Design Proof of Principle study Data-analysis Pilot study evaluation Research question? Possible solutions Reach consensus on: experimental setup data analysis report format Pilot experiment Performance of total workflow Assess data quality and quantity Optional: adaptations to procedure to fit required results
12 Phases of genetic test development Phase 3 Phase 4 Sample Isolation Sample Preparation Sequencing Data-Analysis Reporting and evaluation Sample shipment DNA purification Sample QC Sample processing according to SOPs Paired end Sequencing on HiSeq 4000 or NextSeq 500 Read Alignment on reference Detection of mutations Reporting Project evaluation
13 Genetic Testing & Diagnostics Accurate and fast workflow, tailored to medical specialists Whole Exome Sequencing, including Priority WES Targeted gene panels (Inherited disease, cardio, custom, ) NIPT HLA typing, microbiome, etc.
14 Identify genetic variations such as SNPs, InDels and CNVs WES / WGS Determine biomarkers for disease and/or resistance (Custom) design of targeted gene panels Analyze tumor DNA leading to altered drug responses (EGFR, KRAS, BRAF, ) Markers for disease predisposition (BRCA, GBA1, ) Pharmacogenetic analysis altered drug metabolism HLA typing Microbial DNA
15 Total RNA analysis: RNA analysis on the whole transcriptome mrna / microrna / lncrna / fusions / rearrangements / isoforms / spice variants Low quality and quantity samples Currently: validation as a tool for patient stratification Tumor RNA isolated from coupes Treatment is dependent on tumor classification Targeted RNAseq: High throughput for genes of interest
16 What we provide Expertise in designing a clinical grade workflow: high accuracy, specificity, reliability All instrumentation & (LUMC compatible) infrastructure required for optimal test development Guidance in the wealth of genetic applications and instruments available: from pilot design to fully validated service Bio informatics pipelines for comprehensive data analysis Speed: fastest TAT in the field All according to ISO17025 / ISO15189 / G(C)LP quality standards
17 www.
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