NextSeq 550 System Manufacture Illumina, Inc.
STATEMENT OF WORK (SOW) 1. Contract Title. Benchtop NextSeq 550 Sequencer System 2. Background. The Illumina NextSeq 550 has flexibility and enables the widest range of applications for a benchtop sequencer. It has the capability of performing gene expression profiling, exome sequencing and whole genome sequencing (WGS). The NextSeq 550 sequencing system delivers a high-toughput sequencing combined with microarray scanning reducing the need for multiple laboratory instruments. The turnaround time (TAT) is rapid and allows for sequencing of exomes, transcriptomes and targeted panels in a single run. It also allows the flexibility to switch from a low or high toughput sequencing based on need. The NextSeq 550 sequencer after library preparation is automated and fast and data can be generated in 12 hours for a 75-cycle sequence run and 30 hours for a paired 150-cycle run. This system gives users a broad access to established protocols, workflows, data sets and data analysis tools. The sequencing system performs a wide range of applications and support broad range of samples: 1-12 exomes, 1-16 transcriptomes, 6-96 targeted panels and 12-40 gene expression profiling samples. This sequencer uses 4 fluorescently labeled nucleotides to sequence millions of DNA fragments, detecting singles bases as they are incorporated into DNA strands. 3. Scope. CTVHCS Research Service will purchase the Illumina NextSeq 550 Sequencing System. The NextSeq 550 System offers a simple, integrated sequencing workflow from sample preparation to data analysis. The workflow time varies by experiment and assay type, analysis results include differential expression and identification of alternative transcripts. The intuitive user interface and load-and-go design allows the CTVHCS researchers to perform various sequencing applications with minimal instrument set-up time. Other platforms require for additional, specialized equipment, but the NextSeq 550 System integrates cluster generation and sequencing into a single instrument with a seamless transition for onsite or cloud-based data analysis. Data after sequencing can be generated in as little as 12 hours for a 75-cycle sequencing run and less than 30 hours for a 150- cycle run. This system includes an embedded touchscreen monitor, on-instrument computer, NextSeq Control Software, installation, training and 12 months of warranty to include labor and parts. CTVHCS Research Service will also purchase the NextSeq 550 Silver Support Plan that includes full coverage for parts, labor and travel. Reagent replacement upon hardware failure. One annual Preventative Maintenance (PM). Available will be 5 days a week 18 hours a day Monday tough Friday access with Technical Support either by email or phone. Remote technical support with a 2-business day on-site response target. Hardware and software updates, discounts on advanced training and remote monitoring available. At no time will Contractor have access to any employee or patient Personally Identifiable Information (PII) or Protected Health Information (PHI). No software is to be placed on VA Networks. 4. Specific Tasks. 4.1 Task 1 - Enterprise Management Controls. The sequencing system performs a wide range of applications and support broad range of samples: 1-12 exomes, 1-16 transcriptomes, 6-96 targeted panels and 12-40 gene expression profiling samples. Vendor will train research personnel on the use of the new sequencer system. Deliverables: NextSeq 550 Sequencing System to include 12-month labor and parts warranty. NextSeq 550 Silver Plan warranty. Contract Management Plan: N/A Monthly Status Report: N/A 5. Performance Monitoring: 5.1 Flow cell configuration Read length Output Run time Data quality Required input High-output 2 x 150 bp 100-120 Gb 29 hours >75% >Q30 100 ng 1ug High-output 2 x 75 bp 50-60 Gb 18 hours >80% >Q30 100 ng 1ug High-output 1 x 75 bp 25-30 Gb 11 hours >80% >Q30 100 ng 1ug Mid-output 2 x 150 bp 32-39 Gb 26 hours >75% >Q30 100 ng 1ug Mid-output 2 x 75 bp 16-19 Gb 15 hours >80% >Q30 100 ng 1ug 5. 2 Data Analysis Software includes several data analysis options: Integrated instrument computer performs quality scoring and base calling. Sequencing run data can be analyzed tough a range of open-source or commercial pipelines. Analysis software includes alignment and variant detection, annotation, visualization and interpretation. Includes data analysis for exome, transcriptome, whole-genome and somatic variant calling. 6. Security Requirements. N/A 7. Government-Furnished Equipment (GFE)/Government-Furnished Information (GFI). N/A 8. Other Pertinent Information or Special Considerations. N/A a. Identification of Possible Follow-on Work. b. Identification of Potential Conflicts of Interest (COI). c. Identification of Non-Disclosure Requirements. 9. Risk Control N/A 10. Place of Performance. 1901 Veterans Memorial Dr., Temple, TX, 76504, Research Service. 11. Period of Performance. Vendor is responsible for installing and training personnel on equipment once it is delivered on-site. 36C25719Q0700 Department of Veterans Affairs Veterans Health Administration Veterans Integrated Service Network 17
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