Introduction. High Clinical Accuracy. Prep are Lib rary Seq uence Analyze Data. Highlights
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1 VeriSeq NIPT Solution Revolutionizing NIPT, the VeriSeq NIPT Solution is a comprehensive, ready-to-use, wholegenome sequencing assay that generates accurate results for up to 96 samples in ~ 1 day. Highlights High Clinical Accuracy Automated NIPT solution validated in a clinical accuracy study of 3107 samples with known clinical outcomes Fastest Turnaround Simple workflow; sample to analyzed results in ~ 1 day Accessible Solution Comprehensive method includes reagents, instruments, installation, software, and training Introduction Noninvasive prenatal testing (NIPT) provides accurate information about fetal chromosome status as early as 10 weeks gestation using a single tube of maternal blood. NIPT performed with next-generation sequencing (NGS) offers a reliable screen for specific chromosomal abnormalities. 1,2 In a survey of published studies, 99.7% of NIPT samples sequenced using NGS were run on Illumina systems using Illumina NGS technology.* The VeriSeq NIPT Solution takes advantage of powerful Illumina NGS to generate highly sensitive and specific NIPT results with low test failure rates, minimizing the need for invasive testing procedures. 2 The VeriSeq NIPT Solution incorporates workflow, instrument, and software innovations that make NGS-based NIPT accessible to any lab performing clinical prenatal aneuploidy screening. Providing reagents, instruments, workflow and assay software, installation, and training, VeriSeq NIPT is an automated, reliable solution for in-house NIPT (Figure 1, Table 1). Table 1: VeriSeq NIPT Solution, At a Glance Parameter Method Library Preparation Chemistry No. Samples Time to Report No. Technicians 1 Specimen Analysis Offered Description Whole-genome sequencing PCR-free Paired-end sequencing 48 or 96 per batch ~ 26 hours High Clinical Accuracy 7-10 ml of a single tube of maternal blood Status of chromosomes 21, 18, 13, X, and Y in the fetus VeriSeq NIPT Solution has undergone extensive testing to determine clinical accuracy and reliability. The study screened 3107 maternal samples with known outcomes for trisomy 21, trisomy 18, trisomy 13, and certain sex chromosome aneuploidies (SCA) using the VeriSeq NIPT Solution and compared the results to clinical reference data. Results demonstrated exceptionally high sensitivity and specificity for the target aneuploidies (Tables 2 and 3). In this study, VeriSeq NIPT Solution showed an overall sample failure rate of 0.68%, 3 one of the lowest demonstrated failure rates among all NIPT assays. Figure 1: Comprehensive NIPT Workflow The VeriSeq NIPT Solution provides everything needed for NIPT using NGS, including reagents for DNA extraction, library preparation, and sequencing; instrumentation for automated library preparation and sequencing with workflow manager software; an onsite server for secure data storage and analysis; and data analysis software capable of generating clinical reports. *Based on a PubMed search for cell-free, DNA, prenatal, noninvasive prenatal testing, and noninvasive prenatal screening performed on July 25, All validation and clinical studies using unique samples were included, where a current clinical NIPT provider performed sample analysis. Case studies and studies published in a language other than English were excluded. Data from a 2015 ESHG conference abstract was also included. A total of 45 published studies were surveyed. Data calculations on file. Illumina, Inc Data calculations on file. Illumina, Inc
2 Table 2: Sensitivity and Specificity of the VeriSeq NIPT Solution for Detecting Trisomies 21, 18, and 13 Trisomy 21 Trisomy 18 Trisomy 13 Sensitivity 98.9% (90/91) 90.0% (18/20) (8/8) 2-sided 95% Cl a (94.0%, 99.8%) (69.9%, 97.2%) (67.6%, ) Specificity > (2965/2966) (3034/3037) (3045/3049) 2-sided 95% Cl a (99.8%, ) (99.7%, ) (99.7%, ) a. Cl based on Wilson's score method Proven Technology More than 90% of the world s sequencing data are generated using Illumina NGS technology. Combining this proven technology with CE-IVD validation generates a trusted partnership that produces accurate NIPT results. Minimize Test Failure Rates with Whole-Genome Sequencing Test failures, where no call for disomy or aneuploidy can be made, are an important factor in the reliability and clinical utility of NIPT. NIPT test failure rates vary significantly based on the test used. Tests that use a targeted approach demonstrate higher rates of test failure than tests that sequence the whole genome in both validation and clinical experience studies. 4 These no call results can lead to invasive procedures that may have been avoided with a more reliable test. This difference in test failure rates may be due to inherent biases in test design. Targeted sequencing and array-based methods tend to have longer laboratory protocols and employ more rounds of PCR than WGS methods, introducing potential sources of error and increasing bias. In addition, these targeted approaches focus on specific regions of the genome, but the design itself may not provide sufficient coverage to capture all variations. This lack of coverage may be further exacerbated when working with more challenging samples, such as those with a low percent of fetal fraction. In these cases, the information is not distinct enough for the test to provide a reliable result one way or the other (aneuploidy or disomy). Results are deemed uninterpretable and the test is noted as failing. The VeriSeq NIPT Solution uses a PCR-free WGS assay to provide a comprehensive view of genomic material. This provides ample data across the entire genome, effectively removing any biases introduced by common molecular techniques, such as PCR. Having coverage data available across the entire diploid genome produces an analytical reference that current analytical techniques can use to reduce assay- and sample-specific biases. These normalization steps enable calls to be made on samples with low fetal fractions. Correct aneuploidy calls can be made in the range of fetal fractions that typically requires QC rejection when using targeted approaches. 5 Increase Efficiency with Paired-End Sequencing The VeriSeq NIPT Solution uses paired-end sequencing to perform WGS analysis. Paired-end sequencing analyzes both ends of a DNA fragment. Using a 2 36 bp paired-end strategy, the VeriSeq NIPT Solution achieves the high level of accuracy required for NIPT, using as little as one-third the read depth of other sequencing assays. This saves time and resources compared to single-read protocols, producing NIPT results quickly and cost-effectively. Paired-end sequencing distinguishes cell-free DNA (cfdna) fragment size within a single sample. Previous studies have shown that a maternal blood sample contains different lengths of cfdna; longer lengths tend to be maternal while shorter lengths have stronger fetal correlation (Figure 2). 6 Using data from a paired-end read, the algorithm in the VeriSeq NIPT Assay Software is able to enrich for fetal signal, increasing the signal-to-noise ratio of the assay. Figure 2: Size Comparison of Maternal and Fetal cfdna Fragments Paired-end sequencing is able to differentiate cfdna fragments based on size. Studies have shown that longer fragments tend to be maternal in origin while shorter fragments are fetal. Table 3: Concordance of VeriSeq NIPT Solution Results for Fetal Sex Classification with Clinical Reference Standard Outcome VeriSeq NIPT Solution Results Percent Concordant Newborn Physical Exam Outcome (No Cytogenetic Results) Clinical Reference Standard Outcome Cytogenetic Results Female Male XX XY XO XXX XXY XYY Other a (1371/1373) (1420/1422) 97.4% (147/151) (118/118) (6/6) a. 1 sample was 49, XXXXY classified by the VeriSeq NIPT Solution as "sex chromosome not reportable." N/A: Not applicable Data calculations on file. Illumina, Inc For more information on NGS technology, visit % (4/5) 80.0% (4/5) (1/1) N/A
3 Fastest Results The VeriSeq NIPT Solution offers a fast 6-step workflow for NIPT that generates accurate results just over 1 day (Table 4). Following the simple, automated workflow, 1 technician can analyze samples in a single run.** Table 4: VeriSeq NIPT Complete in ~ 1 Day Step Hands-On Time Total Time Sample Preparation (plasma isolation, DNA, extraction, library preparation) Sequencing (library loading and run set up) ~ 2 hours ~ 8 hours ~ 15 min ~ 14 hours Data Analysis and Report Generation a N/A ~ 4 hours Total Time ~ 2.25 hours ~ 26 hours a. Actual time depends on individual lab processes and may vary from site to site. N/A: not applicable Automated Library Preparation The VeriSeq NIPT Solution provides an automated process, minimizing technician time and the potential for error. The workflow starts with 7-10 ml of maternal peripheral whole blood. The VeriSeq NIPT Workflow Manager controls all aspects of sample preparation, including plasma isolation, cfdna extraction, and library preparation. This software provides a user-friendly control interface and sample tracking. Library preparation reagents are optimized for ease of use straight out of the box. Plasma isolation, cfdna extraction, and PCR-free library preparation are automated on the VeriSeq NIPT Microlab STAR, a Hamilton Microlab STAR system custom configured and optimized for use in the VeriSeq NIPT workflow. The automated protocol includes creation of quantification plates, library quantification, and library pooling. The PCR-free protocol decreases the risks of error associated with amplification procedures, reduces the time required for sample preparation, and greatly simplifies the workflow. A single operator can prepare samples in < 8 hours with minimal handson time. Sequencing Optimal WGS performance requires a fast, flexible NGS system that delivers the power of high-throughput sequencing with the simplicity of a desktop sequencer (Table 5). Users will benefit from systems that offer an intuitive user interface and load-and-go operation for rapid sequencing and time-critical analyses. An instrument that has a small footprint will allow it to fit easily into any laboratory environment. Table 5: NGS Instrument Performance Requirements Parameter Read Length Sequencing File Type Sequencing Output Run Time Multiplexing Onsite Analysis Specification 2 36 bp.bcl file 400M reads ~ 14 hours 48 samples per run Data analysis is performed on a dedicated VeriSeq Onsite Server with the CE-IVD marked VeriSeq NIPT Assay Software. The server automatically processes sequencing data. Multiple sample batches can be queued for analysis on a single server. There s no need to send out data for analysis, saving time and protecting sample identity. VeriSeq NIPT Assay Software VeriSeq NIPT Assay Software filters and aligns the reads to a reference genome. An advanced algorithm counts the reads per chromosome. Scores reflect normalized coverage of the test chromosome and aid in the detection and differentiation of aneuploid samples. The software also generates and reports a fetal fraction estimate for each sample. Fetal fraction data are used in combination with coverage and other statistical inputs generated during sequencing to assess aneuploidy status. To maintain low test failure rates, VeriSeq NIPT Assay Software includes the individualized fetal aneuploidy confidence test (ifact) sample quality scoring metric. ifact indicates whether the sequencing system has generated sufficient sequencing coverage and data quality, given the fetal fraction estimate for each sample, to enable a call of aneuploidy or disomy, even for samples with low fetal fraction. 7-9 This dynamic cutoff enables VeriSeq NIPT Assay Software to report on low fetal fraction samples, resulting in lower test failures compared to other NIPT technologies Report Generation After data analysis, the VeriSeq NIPT Assay Software generates an Aneuploidy Detected or No Aneuploidy Detected call for chromosome tested in each sample. Information is output in a.csv file that can be integrated with an existing LIMS. Data can be used to create a custom clinical report according to laboratory needs (Figure 3). **Actual sample number depends on sample preparation kit used.
4 Fully Supported Implementation For seamless laboratory integration, the VeriSeq NIPT Solution includes complete system installation by a skilled Illumina Field Service Engineer and hands-on training. Knowledgeable Illumina scientists lead laboratory personnel step by step through sample extraction, library preparation, sequencing, and analysis (Table 7). When laboratories are up and running, continued support is provided by the Illumina Technical Support team. Figure 3: Example of a Report Generated Using VeriSeq NIPT Assay Software Customers can use data from the VeriSeq NIPT Assay Software and generate a custom clinical report branded for their specific test and laboratory. Accessible Solution The integrated VeriSeq NIPT Solution provides everything needed to run the assay (Table 6). With this automated, easy-to-follow workflow, 1 technician can analyze samples in ~ 1 day. Table 6: Complete NIPT Solution Component VeriSeq NIPT Sample Prep Kits VeriSeq OnSite Server VeriSeq NIPT Solution Enablement Description CE-IVD sample prep kit includes reagents and consumables for the extraction, library preparation, and quantification of cell-free DNA fragments isolated from 48 or 96 maternal whole blood samples. Onsite server includes CE-IVD marked VeriSeq NIPT Assay Software. The assay software provides calls for the detection of fetal trisomy 21, 18, 13, and sex chromosome aneuploidies based on data generated via the VeriSeq NIPT Solution. Activities and materials required to implement the VeriSeq NIPT Solution, including installation and IQ/OQ of both the VeriSeq NIPT Workflow Manager and VeriSeq Onsite Server, full system performance qualification (PQ), hands-on training and workflow instruction, and reagents and samples required to complete training and competency testing. Table 7: VeriSeq NIPT Solution Training Topic Introduction to the VeriSeq NIPT Solution Instrument Operation Training Site Inspection Onsite Training Onsite Competency Testing Onsite Customer Clinical Validation Summary Details Seminar Overview of workflow and analysis Ancillary equipment guide Consumables guide Blood draw protocol Plasma isolation protocol Onsite training Requires installed instrument Onsite confirmation Ancillary equipment installation Needed reagents Connectivity of system components Assay performed by Illumina scientist Pretested plasma samples with known performance characteristics (provided by Illumina) Walkthrough of assay workflow from plasma isolation to instrument operation and data analysis Data analysis training Assay performed by customer Pretested plasma samples with known performance characteristics (provided by Illumina) Assay and analysis performed by customer Samples provided by customer The VeriSeq NIPT Solution is revolutionizing the accessibility and reliability of NIPT. Now any laboratory can harness the power of NGS for fast, reliable NIPT. Following the optimized VeriSeq NIPT workflow, a single technician can generate accurate NIPT results for up to 96 samples in ~ 1 day. As indicated in a clinical validation study of 3107 samples, results are highly accurate with extremely low failure rates. The comprehensive solution includes everything needed to perform the assay and extensive training and support. Learn More To learn more about the VeriSeq NIPT Solution, visit Non-invasive prenatal testing (NIPT) based on cell-free DNA analysis from maternal blood is a screening test; it is not diagnostic. Test results must not be used as the sole basis for diagnosis. Further confirmatory testing is necessary prior to making any irreversible pregnancy decision.
5 Ordering Information Product Catalog No. VeriSeq NIPT Solution Enablement RH VeriSeq Onsite Server RH VeriSeq NIPT Sample Prep Kit (48 samples) RH VeriSeq NIPT Sample Prep Kit (96 samples) RH Intended Use Statement The VeriSeq NIPT Solution is an in vitro diagnostic test intended for use as a sequencing based screening test for the detection of fetal aneuploidies from maternal peripheral whole blood samples in pregnant women of at least 10 weeks gestation. VeriSeq NIPT provides information regarding aneuploidy status for chromosomes: 21, 18, 13, X, and Y. This product must not be used as the sole basis for diagnosis or other pregnancy management decisions. References 1. Bianchi DW, Platt LD, Goldberg JD, Abuhamad AZ, Sehnert AJ, Rava RP. Genome-wide fetal aneuploidy detection by maternal plasma DNA sequencing. Obstet Gynecol. 2012;119(5): Bianchi DW, Parker RL, Wentworth J, et al. CARE Study Group: DNA sequencing versus standard prenatal aneuploidy screening. N Engl J Med. 2014;370: Illumina. VeriSeq NIPT Solution Package Insert. 2017;p Illumina. Don't settle for failure. mkt.illumina.com/rs/600-xex- 927/images/dont-settle-for-failure.pdf. Accessed March 15, Rava RP, Srinivasan A, Sehnert AJ, Bianchi DW. Circulating fetal cell-free DNA fractions differ in autosomal aneuploidies and monosomy X. Clin Chem. 2014;60(1): Lo YM, Chan KC, Sun H, et al. Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med. 2010;2(61):61ra Duenwald S, Chen G, Barbacioru C, et al. Development of a Novel Paired- End Sequencing-Based Noninvasive Prenatal Test. Poster presented at the Society for Maternal-Fetal Medicine 36th Annual Pregnancy Meeting; February 1-6, 2016; Atlanta, Georgia. 8. Cirigliano V, Ordoñez E, Rueda L, Syngelaki A, Nicolaides KH. Performance evaluation of the NeoBona test, a new paired-end massive parallel shotgun sequencing approach for cfdna based aneuploidy screening. Ultrasound Obstet Gynecol. 2016; doi: /uog [Epub ahead of print]. 9. Cirigliano V, Ordonez E, Rueda L, et al. Performance evaluation and clinical application of a new paired end MPSS approach for cfdna based prenatal aneuploidy screening. Poster presented at the International Society for Prenatal Diagnosis. July ; Berlin, Germany. 10. Wang E, Batey A, Struble C, Musci T, Song K, Oliphant A. Gestational age and maternal weight effects on fetal cell-free DNA in maternal plasma. Prenat Diagn. 2013; 33: Pergament E, Cuckle H, Zimmermann B, et al. Single-nucleotide polymorphism-based noninvasive prenatal screening in a high-risk and lowrisk cohort. Obstet Gynecol. 2014; 124(2 Pt 1): Illumina, Inc toll-free (US) tel techsupport@illumina.com Illumina, Inc. All rights reserved. Illumina and the pumpkin orange color are trademarks of Illumina, Inc. and/or its affiliate(s) in the U.S. and/or other countries. Document # v00
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