Automated Lab Management for Illumina SeqLab

Automated Lab Management for Illumina SeqLab

INTRODUCTION Whole genome sequencing holds the promise of understanding genetic variation and disease better than ever before. In response, Illumina developed the HiSeq X instruments, which provide dramatic improvements in the throughput and cost associated with sequencing human genomes. To help labs scale to new levels of throughput generated by the HiSeq X instruments, Illumina partnered with GenoLogics and Hamilton to develop an optimized solution Illumina SeqLab. Illumina SeqLab consists of Illumina Automated Workflow Manager, Clarity LIMS X, and Hamilton Automation. Illumina SeqLab provides positive sample tracking, maximizes quality and throughput, and improves turnaround time for high throughput sequencing and population-level genomics. ILLUMINA SEQLAB SOLUTION As part of Illumina SeqLab, Clarity LIMS X empowers labs to scale to the increased throughput provided by the HiSeq X instruments while maintaining a strict focus on quality and accuracy. Instrument integration and automated, preconfigured workflows continually move samples through the pipeline with minimal need for human interaction to reduce errors. Clarity LIMS X enables labs to: Scale and accelerate deployment with an out-of-the-box solution Reduce costs per sample with positive sample tracking and fewer production errors Improve turnaround time with optimized, preconfigured HiSeq X series workflows Ease user adoption with intuitive interfaces designed specifically for next generation sequencing Support regulated environments such as ISO, CLIA, CAP and 21 CFR Part 11 Figure 1 IMPLEMENTATION Customized consulting to support large scale sequencing implementation LAB WORKFLOW Integrated automation from sample accession to sequencing DATA ANALYSIS Full breadth of variants from a single fast & accurate WGS analysis Solution PERSONALIZED PRACTICES Illumina SeqLab Consulting Service POSITIVE SAMPLE TRACKING Illumina Automated Workflow CLARITY LIMS X EDITION Hamiliton Automation ONE COMPLETE SOFTWARE HiSeq Analysis Software v2.0 Figure 1 Clarity LIMS X is an integral part of Illumina SeqLab. Page 1 2016 GenoLogics Life Sciences Software, Inc., an Illumina company

SCALABILITY Scale to increased throughput With Illumina s HiSeq X systems, labs can sequence more quickly than ever before. However, they must find a way to scale to the increased throughput, while maintaining a rigorous focus on accuracy. Clarity LIMS X enables labs to scale AND maintain accuracy. Two automated, preconfigured workflows TruSeq DNA PCR-Free and TruSeq Nano DNA contain business logic to manage the progression of samples through the pipeline. Minimal human interaction is needed, and the samples are validated throughout the process. The workflows include business logic for each of the key protocols in the sequencing process, below: Preparation Library preparation Cluster generation Sequencing CLARITY LIMS X EMPOWERS LABS TO SCALE TO THE INCREASED THROUGHPUT PROVIDED BY THE HISEQ X INSTRUMENTS WHILE MAINTAINING A STRICT FOCUS ON QUALITY AND ACCURACY. Figure 2 Figure 2 The Prep protocol of the TruSeq Nano workflow in Clarity LIMS X.

EFFICIENCY AND ACCURACY Avoid the 1% problem and reduce costs per sample In his work to establish the high throughput genomics lab at Garvan Medical Institute, Dr. Warren Kaplan refers to something he calls the 1% problem. What is it? One HiSeq X instrument can sequence 150 whole human genomes every three days, so running at capacity, this equates to roughly 18,000 genomes a year. At the cost of approximately $1,000 per genome, this is equal to $18,000,000 a year. Even with a low error rate of 1% labs can lose $180,000 a year in sample kits and reagents. According to Kaplan, A systemic problem across an X 10 fleet not identified early can be devastating. Clarity LIMS solves the 1% problem before it happens with automation and business logic built into each workflow. The business logic built into the HiSeq X Series workflows validates samples and reagents at every step, ensuring you use the appropriate amount never more or less. Repeats and failures are minimized, thus reducing the cost per sample and the resulting turnaround time. Figure 3 Figure 3 Perform key project management tasks from a single dashboard The same automation and business logic also ensures accuracy and positive sample tracking. The integration between Clarity LIMS X and Hamilton Microlab STAR tracks the sample s location in the tube and on the plate, ensuring the highest level of sample tracking and accuracy. USABILITY Ramp up quickly and get visibility and control of samples Designed with the genomics lab in mind, the Clarity LIMS X interface and workflows reflect how lab scientists do their work. Consequently, users adopt Clarity LIMS X quickly so that the full power of Illumina SeqLab is put to work in the lab. An enhanced project management dashboard enables users to understand what is happening in the pipeline at a glance. Page 3 2016 GenoLogics Life Sciences Software, Inc., an Illumina company

CLINICAL Meet and maintain regulatory compliance Clarity LIMS X can aid organizations in meeting compliance standards for regulations such as CLIA, HIPAA, 21 CFR Part 11 & 493, ISO9000, 14155,17025, GLP and GCP. Features that support a regulatory environment include: E-signatures electronic signatures can be set up within a workflow if necessary to prevent progression if special interaction is needed Audit trails human readable reports can be produced for any sample quickly and easily Role-based interfaces restrict access based on user roles and security clearance to keep patient data protected Precision monitoring access detailed information about instrument performance to ensure that systems are performing to specification Further, users can perform all of the following tasks, directly from the dashboard: A SYSTEMIC PROBLEM ACROSS AN X 10 FLEET NOT IDENTIFIED EARLY CAN BE DEVASTATING. Dr. Warren Kaplan, Garvan Institute Re-queue samples Cancel re-queued samples Archive a library to ensure the library is no longer available for use throughout the lab Request for more lanes to increase sample yield Change the workflow Receive a notification of flowcell/lane status failures Rehybridize samples

SYSTEM REQUIREMENTS Meet these requirements to get the most out of Clarity LIMS X Clarity LIMS X supports Illumina s HiSeq X series workflows, By adopting the RA, users receive: Best practices in the HiSeq X series workflows Full automation with minimal hands-on time Highest level of support from Illumina, GenoLogics and Hamilton TruSeq Nano DNA and TruSeq PCR-Free, with business logic and automation. To fully access the business logic and automation, Clarity LIMS X is integrated with six different instruments. These instruments are part of Illumina s Reference Architecture (RA) used for Illumina SeqLab. LAB WORKFLOW ILLUMINA SEQLAB SOLUTION Lab Workflow for Illumina SeqLab Solution Hamilton MICROLAB STAR Automated tracking of library preparation with Hamilton STAR Illumina HiSeq X10/ X5 Accessioning Quant Prep Clustering Sequencing CLARITY LIMS X EDITION Spectro max for dsdna quantitation LabChip GX for insert size detection LightCycler 480 for quantitation cbot for Cluster Generation HiSeq Analysis Software Figure 4 Figure 4 Reference architecture of Illumina SeqLab. By adopting the reference architecture, users receive the fullest level of automation and support. Page 5 2016 GenoLogics Life Sciences Software, Inc., an Illumina company

Instrument Requirements FUNCTION INSTRUMENT VENDOR RECOMMENDED QUANTITY MINIMUM QUANTITY Liquid Handling Workstation MICROLAB STAR Hamiliton 4 2 DNA Quantitation Spectramax Plus 384 microplate reader Molecular Devices 2 1 DNA Shearing for Library Preparation LE220 Focused - ultasonicator Covaris 2 1 Library Quantitation LightCycler 480 Real-time PCR System Roche 2 1 Library Insert Size QC LabChip GX Perkin Elmer 2 1 Cluster Generation cbot 2 Illumina 4 2 DNA Sequencing HiSeqX Illumina 5 5 Table 1 List of instruments required for Illumina s Reference Architecture. FOR MORE INFORMATION Clarity LIMS X is one edition of Clarity LIMS. Other editions include Clarity LIMS Silver and Clarity LIMS Gold. All of the Clarity editions contain preconfigured workflows for common lab instrumentation, enabling rapid scaling for a wide variety of genomics technologies and applications. Further, the application programming interface (API) available in Clarity Gold and Clarity LIMS X editions provides even greater levels of extensibility and customization. For more information about Clarity LIMS X or any of the Clarity editions, visit our website at www.genologics.com. Clarity LIMS X Edition (Full Integration with Illumina SeqLab Solution) Clarity LIMS Silver Clarity LIMS Gold Clarity Run Manager Submission Extraction & QC Prep & Validation Reagent Adding (Adapters) Pooling Instrument Prep & Loading Instrument Run Monitoring Data Analysis Pipelines Custom Reports Results Sharing

For more information visit: genologics.com/clarity-lims-x Canada Office Suite 2302-4464 Markham Street, Victoria, B.C., Canada, V8Z 7X8 Toll free: 1-866-457-5467 Main: 1-250-483-7011 Fax: 1-250-483-7777 US Office 800 Saginaw Dr, Redwood City, CA 94063 Main: 650-632-1680 info@genologics.com genologics.com 2016 GenoLogics Life Sciences Software, Inc., an Illumina company. All Rights Reserved. The information contained in this document is proprietary to GenoLogics Life Sciences Software, Inc. This document is subject to change without notice, and GenoLogics does not warrant that the material contained in this document is free of errors. Clarity LIMS is a trademark of GenoLogics. All other registered trademarks are the property of their respective owners. Any forward looking statements regarding future product direction are for information purposes only and GenoLogics makes no express or implied commitments or representations concerning the timing / content of any future functionality or releases. 1-01012016