NextSeq™ 550Dx Instrument
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Prep are Lib rary | Seq uence | Analyze Data | Sup p ort NextSeq™ 550Dx Instrument The NextSeq 550Dx instrument delivers an FDA-regulated, CE-marked as an IVD, highthroughput sequencing platform to the clinical research laboratory. Highlights l FDA-Regulated and CE-marked as an IVD Sequencing Instrument High-throughput, Food and Drug Administration (FDA)regulated and Conformité Européene in vitro diagnostic (CEmarked as an IVD) platform with an expanding IVD and laboratory developed test (LDT) pipeline Highly Flexible to Support Clinical and Research Demands Supports a broad range of basic research and clinical applications with tunable read length and multiple output configurations Fast Turnaround Time and User-Friendly Data Analysis Accelerate research studies and rapidly generate data for time-sensitive clinical needs with streamlined informatics performed onboard or in the cloud Illumina Scientific Support IVD partnerships backed by Illumina science and expertise* Introduction The NextSeq 550Dx instrument is an FDA-regulated and CE-marked as an IVD platform that delivers the power of high-throughput nextgeneration sequencing (NGS) with the affordability of a benchtop system (Figure 1). With dual boot functionality, the NextSeq 500Dx platform includes a Diagnostic Mode (Dx Mode) † and a Research Mode, which provides the flexibility to perform IVD testing, LDT development, and clinical research on a single instrument. For large clinical laboratories, the NextSeq 550Dx instrument offers a validated high-throughput platform and provides access to an ever-expanding pipeline of clinical applications in the fields of oncology, reproductive health, and more. While the NextSeq 550Dx instrument can generate more than 90 Gb of data in less than two days, it also delivers the consistency of a regulated platform and includes robustness improvements in software and instrument design. In addition, running in Research Mode supports all currently available NextSeq 550 System research applications including exome sequencing, transcriptome profiling, customer-designed targeted panels, and microarray scanning. With the NextSeq 550Dx instrument, clinical laboratories can run in Figure 1: The NextSeq 550Dx instrument—By leveraging the latest advances in SBS chemistry and user-friendly, regulated workflows, the NextSeq 550Dx instrument delivers high-quality results for both clinical and research applications. regulated Dx Mode for IVD/LDT testing or run in Research Mode to accelerate clinical studies without sacrificing the speed and power of a high-throughput sequencer. Illumina chemistry delivers exceptional accuracy At the core of the NextSeq 550Dx instrument is proven Illumina sequencing by synthesis (SBS) chemistry which generates 90% of the sequencing data in the world.1 This reversible, terminator–based method detects single bases as they are incorporated into growing DNA strands and enables the parallel sequencing of millions of DNA fragments. Illumina SBS chemistry employs natural competition among all four labeled nucleotides, which reduces incorporation bias and allows more robust sequencing of repetitive regions and homopolymers.2 Compared to capillary electrophoresis-based Sanger sequencing, NGS can detect a broader range of DNA variants, including lowfrequency variants and adjacent phased variants, with a faster time to 34 result and fewer hands-on steps. , Furthermore, NextSeq v2 sequencing reagents deliver improved signal intensities and a lower number of false positives and false negatives.5 With NextSeq v2 SBS chemistry, the NextSeq 550Dx instrument provides exceptional accuracy for clinical tests and research applications. *Please contact an Illumina representative for more information about IVD development partnerships. †Runs performed in Dx Mode are processes regulated by US and EU regulatory bodies. For In Vitro Diagnostic Use. Contact an Illumina representative for regional avai

Prep are Lib rary | Seq uence | Analyze Data | Sup p ort Figure 2: Three-step NextSeq 550Dx assay process—The NextSeq 550Dx instrument is part of an integrated, three-step process. Detailed results reports are available with the TruSeq® Custom Amplicon Dx Assay. Table 1: NextSeq 550Dx instrument performance parameters—Dx Modea,b Flow cell configuration High-output flow cell Read length Data qualityc a. Libraries generated with TruSeq Custom Amplicon Kit Dx. Run performed with NextSeq 550Dx High-Output Reagent Kit v2. b. For performance parameters in Research Mode, see the NextSeq 550...

Prep are Lib rary | Seq uence | Analyze Data | Sup p ort Table 2: Variant calling in Dx Mode No. of samples Analysis timea Somatic Variant Caller Germline Variant Caller a. Average onboard analysis times in two 9-run studies. b. Lowest observed positive percent agreement (PPA) for single nucleotide variants (SNVs), insertions (Ins), deletions (Dels), negative percent agreement (NPA), and overall percent agreement (OPA) across each 9-run study that included three reagent lots, three instruments, and three operators. Platinum Genome samples were tested using a representative assay,...

Prep are Lib rary | Seq uence | Analyze Data | Sup p ort Data calculations on file. Illumina, Inc. 2017. Eberle MA, Fritzilas E, Krusche P, et al.A reference data set of 5.4 million Instrument configuration RFID tracking for consumables phased human variants validated by genetic inheritance from sequencing a Processor: Dual Intel® Xeon® E5-2648L v3 three-generation 17-member pedigree. Genome Res. 2017;27:157-164. 1.8 GHz CPU Instrument control computer Memory: 128 GB Hard Drive, Dx Mode: 2 × 2 TB (RAID 1) Hard Drive, Research Mode: 2 × 2 TB (RAID 1) Operating System: Windows 10...