Leading Genomics. Diagnostic. Discove. Collab. harma. Shanghai Cambridge, MA Reykjavik

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1 Leading Genomics Diagnostic harma Discove Collab Shanghai Cambridge, MA Reykjavik

2 Global leadership for using the genome to create better medicine WuXi NextCODE provides a uniquely proven and integrated system for using the full power of sequence data to understand, prevent, diagnose and treat disease. We offer a full range of CLIA sequencing; unrivalled, seamless capabilities in clinical diagnostics and populationscale research; expertise in every facet of drug development; and the first global network for using and sharing raw NGS data online, in real time. At the heart of WuXi NextCODE is the world s leading sequence analysis system. It was designed to assemble and query the largest collection of sequence data anywhere, comprising whole-genome data on more than 350,000 people. End-to-end capabilities, from CLIA sequencing to data mining, management and clinical reporting An unrivalled proprietary knowledge base of genomic and phenotypic data Proven power for identifying novel variants, with dynamic visualization interfaces for clinicians and research The new standard in data architecture, for efficiently generating, storing and querying genomic big data Total scalability, from single cases to population studies Integrated best practices to help public and private institutions bring genomics into everyday medical practice OUTPUT EXAMPLES Diagnostics and Drug Targets Companion Diagnostics Clinical Sequence Analyzer Sequence Miner & SDL Tumor Mutation Analyzer development Population Databases healthcare delivery and discovery Proprietary Products Tests, Exchange and Cloud WuXi NextCODE offers seamless solutions for diagnostics and discovery. 2 WuXi NextCODE Genomics

3 Setting the industry standard for wholegenome sequence analysis and interpretation Cutting-edge technology, proven at scale Built over sixteen years at decode genetics, our platform has handled, analyzed, and stored whole genome data from 350,000 people and validated more than 40 million variants. That s orders of magnitude more than any other system to date, uniquely positioning us to enable the clinical research community to take full advantage of the vast amount of sequence data that will be generated in the very near future. Our platform has already met and solved those data storage and query challenges at scale, powering more than 350 original publications in gene discovery, diagnostics and other medical applications. An Unrivalled Knowledge Base Integrated solutions, built on best practices WuXi NextCODE offers clinicalgrade sequencing; calibrated data analysis; effective genome interpretation; and proprietary bioinformatics and IT systems to enable the streamlined management of hundreds of thousands of patients from samples to mutation detection and confirmation. These solutions represent best practices derived from successful and pioneering discoveries using linkage, genomewide association, and nextgeneration sequencing. 40 million validated variants annotated from >350,000 whole genomes 1.5 million indels and 6,600 loss-of-function mutations over 4,800 genes Variants with low allelic frequencies down to 0.01% Complements public databases, such as 1,000 Genomes or the NHLBI exome project, backed by more samples and greater breadth and depth of sequence coverage. Key Benefits Fewer false positives. We start from raw data, not VCF files, and run them using our analysis pipeline calibrated with data from thousands of whole genomes. This approach minimizes common alignment errors generated by sub-optimized pipelines and yields a significant reduction in false positive results. Clinical insight on difficult, undiagnosed cases. With 40 million validated variants to add to those in the public domain, we have unrivalled resources for identifying high-impact variants. Rapid Confirmation. Our Genomic Ordered Relational (GOR) architecture facilitates instantaneous viewing of any candidate mutation at the sequence read level, increasing confidence via on-the-fly visual confirmation. Large-scale data storage and management. Raw data, analyzed data, and associated annotations can be stored in the GOR database tied to our Clinical Sequence Analyzer (CSA). No expensive hardware is required. Pay-as-you-go pricing. Our pricing models allow you to affordably analyze, interpret, store, and manage genomics data, without the need to invest in internal IT infrastructure. Our knowledge base enables users to quickly confirm rare mutations and filter out common variants that are unlikely to be high-impact disease variants. 3

4 Comprehensive Products & Services Upstream: Sequencing We provide a full range of both clinical and research-grade sequencing through the first and only CLIA-certified sequencing laboratory in China. From whole-genome to whole-exome, targeted, transcriptome, epigenetic and microarray, we harness the benefits of every major platform to get you the data you need quickly and ready to use. Mid-stream: Analysis We also accept legacy data from our clients. We use raw sequence read files for alignment and variant calling, which are calibrated for optimal results using the large cohorts our platform has already sequenced. Problematic calls are flagged or filtered leveraging our extensive knowledge of the unstable regions of the human genome. Benefits: Provides maximum yield of real variants by reducing both false positives and false negatives. Optimally-calibrated indel caller provides higher sensitivity and specificity. Tags or filters regions that are unstable to help users prioritize validation efforts. Enables instantaneous visualization of raw sequence data for confirmation of variants. Downstream: Genome Interpretation The Clinical Sequence Analyzer (CSA) system enables users to quickly analyze their data through a clinically intuitive interface. The system operates on a petabyte scale using our GOR architecture, providing massively parallel ad hoc query and data analysis capabilities. Features: Custom candidate gene lists can be generated by users with phenotype-gene tools to complement the standard gene lists already included. Variant annotations can be stratified according to frequency, VEP class, predicted functional effects of missense variants, inheritance patterns, and effects on phenotypes, mortality, or expression. 4 WuXi NextCODE Genomics

5 Potential pathogenic mutations are rapidly confirmed by an instant visualization of aligned sequence reads and cross-checked with a continually updated, curated variation knowledge base made up of public domain and NextCODE data. Our CSA collaborative analysis features allow simultaneous access to patient sequence data by multiple users in real time, enabling sharing of analytical results, comments, and annotations. These features greatly facilitate collaborative genome interpretation where multiple users can create studies, and edit and share results and clinical reports within their institution or with collaborators around the world. User-friendly physician interfaces designed by clinicians enable users to manage their patient data, generate final reports, and annotate diagnoses all within the same system, supporting the entire clinical team. Seamlessly integrated with our Sequence Miner, users can leverage diagnostic data for discovery and vice-versa, maximizing the medical and scientific value of your genomic medicine program. Benefits: A clinically intuitive workflow enables users to rapidly analyze genomes, exomes, or transcriptomes, leading to de novo and rare mutation detection and discovery. Instantaneous visualization of raw sequence reads. This example shows that by hitting the Father BAM button, the WuXi NextCODE Genome Browser instantaneously loads BAM sequences enabling users to check the assembly and variant calls between the affected patient and the father. This detailed display of raw reads provides rapid visual confirmation that the father is a heterozygous carrier of the mutant C and his affected child is homozygous for the mutation. Similar analysis can be done for other members of the family and even for large cohorts. 5

6 Bigger Data Solutions Coupled with our web-based CSA system, this solution enables individual investigators and institutions to meet the challenge of managing big data without developing substantial IT infrastructure. Accelerating In-House Development: Rapid Integrations Meeting the Big Data Challenge: The Genomic Ordered Relational (GOR) Database Architecture Unlike other sequence analysis solutions, the WuXi NextCODE informatics systems have already been successfully used to manage sequence variation data for hundreds of thousands of individuals. Central to this capability is the unique design of the GOR architecture and database. Instead of creating multiple data silos, the GOR architecture greatly simplifies the comparisons of variation data across large sets of patients with similar signs and symptoms, thereby leveraging the diagnostic power in the future avalanche of variation data generated by next-gen sequencing technologies. Equally important, the GOR database enables clients to dynamically retrieve, edit, and annotate their sequencing data on-the-fly without the common issues of substantial time-lag in retrieving and storing of data. Plus, user annotations on sequence variants from any given patient can be leveraged in the analysis of subsequent patients. WuXi NextCODE provides an informatics infrastructure that allows medical centers to leverage their institutional experience and expertise in clinical genetics. It is our goal to enable in-house bioinformatics and IT efforts to take advantage of our advanced informatics platform. For example, experienced users and bioinformaticians can create their own data mining and analysis scripts, and deploy them to their own end users via our Sequence Miner tool. Also, the GOR database and data security design can be integrated to manage in-house data. Benefits: With the GOR database, clients can store and manage large amounts of raw and analyzed data at very affordable levels without the need to develop extensive IT infrastructure. WuXi NextCODE components and capabilities can easily be integrated into existing systems to enable internal development of best practices adopted at each institution. NextCODE s professional services team will provide consultations upon request. 6 WuXi NextCODE Genomics

7 Global Collaboration with A global community using the full power of the whole genome in real time The sequencing revolution is providing the raw data required to identify the genetic variants underlying rare diseases and complex traits alike. The WuXi NextCODE Exchange meets the next challenge: it gives you the world s most proven sequence analysis platform and enables you to seamlessly collaborate and validate your findings with clinical and scientific colleagues and institutions around the world securely sharing data to crack more difficult cases and accelerate discovery. Data analysis for the wholegenome era The Exchange is powered by our GOR database system. Optimized on whole-genome data from 350,000 people, it standardizes, manages and queries massive sequence data with unrivalled computational efficiency. You can instantly visualize aligned raw sequence from collaborators and share data in full compliance with your rules and consents, without transferring big files, straight from your browser. The Power of the Exchange k d p World-leading analysis, raw data visualization, scaleable GOR database Sign up, format your VCFs in GOR, upload 15 trios for free Real-time collaboration, user controlled sharing Validate novel variants, accelerate discovery Harmonized public data, constantly updated 7

8 There s big data, and then there s bigger data We combine state-of-the-art sequencing and analytics with integrated, world-leading capabilities in clinical diagnostics, populationscale discovery and clinical development. To learn more contact WuXi NextCODE Genomics 101 Main Street, 14 th Floor Cambridge, MA The NextCODE Clinical Sequence Analyzer, NextCODE Genome Browser, NextCODE Sequence Miner, NextCODE GOR Architecture, NextCODE GOR Database and NextCODE Exchange are registered trademarks of NextCODE Health and WuXi NextCODE Genomics.

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