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FBO DAILY - FEDBIZOPPS ISSUE OF JULY 08, 2018 FBO #6071
DOCUMENT

65 -- GENOTYPING SEQUENCER BRAND NAME OR EQUAL - Attachment

Notice Date

7/6/2018
 

Notice Type

Attachment
 

NAICS

334516 — Analytical Laboratory Instrument Manufacturing
 

Contracting Office

Department of Veterans Affairs;NCO22-Gilbert Network Contracting;New Mexico VA Health Care System;1501 San Pedro Drive SE;Albuquerque NM 87108
 

ZIP Code

87108
 

Solicitation Number

36C25818Q9569
 

Response Due

7/13/2018
 

Archive Date

9/11/2018
 

Point of Contact

Bryan S. Rogers2@va.gov
 

E-Mail Address

Bryan S. Rogers2@va.gov
(bryan.rogers2@va.gov)
 

Small Business Set-Aside

Service-Disabled Veteran-Owned Small Business
 

Description

THIS IS A SOURCES SOUGHT NOTICE. This is not a request for proposals. A solicitation will not be issued at this time. The Department of Veterans Affairs, New Mexico VA Health Care System (NMVAHCS) has a requirement for Brand Name or Equal Genotyping Sequencer. The intent of the procurement is to award a firm-fixed price contract. The below specifications define the minimum salient characteristics of the product to be delivered. Required Items Brand Name or Equal: Item Description QTY MiSeq System Illumina MiSeq System 1 Delivery charge Delivery charge 1 In-Service Per statement of work, to include initial installation, testing and standard one day training. 1 Statement of Work: Background. The Research Department has a requirement for ongoing VA studies to enhance the quality and delivery of care to the Veteran population through improved research capabilities and tests through improved technology in detecting mutations, microbiomes and RNA abundancies. Scope. NMVAHCS investigators and our Personalized Medicine eConsult Service requires developmental sequencing capacity that identifies genotypes, rare mutations, microbiomes and RNA abundancies. These results can then be implemented as CLIA certified clinical assessments at VISN 22 Central Genomics Laboratory. This instrument will benefit clinical and translational researchers from Medicine, Neurology, Behavioral health and Pathology, assist New Mexico Veterans in choosing VA, increase local availability of personalized and precision medicine and aid responses to the Secretary s priorities including overdose and suicide. Specific Tasks. This requirement specifically is a benchtop sequencer which allows the processing of samples to data in a relatively brief period of time, depending on the sample and data requirement(s). Task. The instrument designed specifically for the processing and data collection of samples includes the following: Instrument Instrument footprint requires less than two square feet of benchtop space, less then 150lbs Instrument control computer should be integrated in the sequencer no need for an additional computer purchase Quad core CPU with 16 GB of RAM included for instrument control, processing images, and performing alignment and variant calling Operates as a stand alone instrument, does not need to be connected to internet to function Able to have 8 hour total turnaround time from purified DNA to direct variant reporting with less than 30 minutes total hands-on time Hands-free, completely automated, on-instrument paired-end sequencing Supports up to 2 × 300 bp read length Up to 15 Gb of high-quality data passing filter per 2 × 300 bp run Accurate variant detection by Sequencing by Synthesis (SBS) chemistry able to provide highly accurate sequencing even through homopolymeric regions. SBS chemistry is the demonstrated leader in data accuracy. high quality score distributions at every read length [> 90% of bases with Q scores > 30 (1 × 36 bp), 90% of bases with Q scores > 30 (2 × 25 bp), > 85% of bases with Q scores > 30 (2 × 100 bp), > 80% of bases with Q scores > 30 (2 × 150 bp), > 75% of bases with Q scores > 30 (2 × 250 bp), > 70% of bases with Q scores > 30 (2 × 300 bp)] With multiplexing, prepare >147,000 amplicons in a single day (96 samples × 1536 amplicons per sample = 147,456 amplicons total). Call variants in >147,000 amplicons in two days using standard lab equipment Flexible amplicon sizes smaller to enable custom panel support for FFPE, and larger to take advantage of 2 × 300 bp read lengths. Multiplexed amplicon samples, designed for human and non-human genomes, can be loaded directly onto the machine Variable length amplicon sequencing spanning hundreds to thousands of base pairs Greater than 25 million reads per single-end run to enable small RNA sequencing and assay method development. Greater than 15 Gb of output to allow multiplexed sequencing of viral and bacterial genomes in a single run 22-25 million reads per run (e.g. clusters passing filter) 13.2-15 Gb data per 2 × 300 bp run Set-up options include single-read or paired-end runs Set-up options include imaging top, bottom, or both surfaces of flow cell Flow cell options (e.g. original, micro or nano flow cells) can be used to select image area utilization and thus select data output levels Read-length is fully adjustable from 36-300 base pairs Overlapping 2 × 300 bp reads provides ability to generate 550 bp reads on the same fragment Flow cells Single flow cell system Each flow cell is a substrate with a single channel that can be imaged on either the top, bottom, or both surfaces as needed Flow cells are auto-positioned and held in place by a clamping mechanism Flow cells are keyed such that there is only one correct orientation Reagent handling Machine has a reagent chiller compartment with capacity for one reagent cartridge containing reagents for cluster generation, paired-end chemistry, and up to 600 cycles of sequencing Reagents arrive pre-mixed in an integrated, RFID enabled, reagent cartridge Sequencing synthesis chemistry Uses reversible terminators and a highly efficient DNA polymerase Use of a DNA polymerase that provides efficient addition of nucleotides with cleavable fluorescent dyes and reversible terminators Sequencing reactions are performed in a self-contained single channel flow cell environment Fluorescent dyes on the nucleotides are cleaved after imaging Reversible terminators are removed to allow chain extension Sequenced DNA templates are copied to generate complementary strands, enabling paired-end sequencing Forward DNA strands are selectively washed out of the flow cell Genomic DNA sample libraries can be prepared in <  90 minutes by one full-time employee (FTE) with <  15 minutes hands-on time. Sample prep includes both single and short-insert (<  550 bp) paired-end runs. Hardware for fragmenting or shearing template DNA is not required. Ready-to-use kits are available to prepare samples for: DNA sequencing (single-end, paired-end, or mate-pair reads) RNA sequencing (total RNA, mRNA, small RNA and stranded mRNA) Targeted sequencing (human exome, cancer panel, custom) ChIP-sequencing Sample multiplexing Kits enable a unique combination of paired-end insert size ranges from 200 550 bp (short insert paired-end), 2 10 kb (long insert mate pairs). Amplification Solid-phase isothermal amplification to produce clonal single-molecule array clusters is completely automated, requiring no user intervention No need for emulsion PCR or additional equipment amplification is performed directly on the instrument Genomic DNA sample library can be prepared in < 90 minutes by one full-time employee (FTE) for both single and short-insert (< 550 bp) paired-end runs with a sample prep kit Sample prep kits that enables simultaneous preparation of 96 samples in less than six hours A single operator can amplify up to 96 samples or more on a single channel flow cell in one hour Amplification is fully automated, using an integrated reagent cartridge with pre-mixed and pre-filled reagents Automated simultaneous clonal amplification of hundreds of millions of single molecule DNA templates, producing clusters containing approximately 500-1,000 identical copies of each original DNA sequence Sequencing runs times needed: ~ 4.00 hours for a 1 × 36 bp single-read sequencing run ~ 5.50 hours for a 2 × 25 bp paired-read sequencing run ~ 16.5 hours for a 2 × 100 bp paired-read sequencing run ~ 24.0 hours for a 2 × 150 bp paired-read sequencing run ~ 39.0 hours for a 2 × 250 bp paired-read sequencing run ~ 65.0 hours for a 2 × 300 bp paired-read sequencing run Applications Single instrument performs clonal amplification, sequencing, and data analysis (e.g. basecalling, alignment, variant calling, and reporting) Whole-genome resequencing Targeted resequencing including, but not limited to the following methods: custom enrichment custom amplicon sequencing Long-range PCR Molecular inversion probes De novo sequencing Mate-pair sequencing for libraries with 2-5 kb insert sizes ChIP-Seq of sequence-specific DNA binding proteins ChIP-Seq of histone modifications and epigenetic marks Sequencing of bisulfite-treated DNA to study DNA methylation Metagenomics (16S rRNA-sequencing) mRNA sequencing Tag-based gene expression Small RNA sequencing Ribosome profiling HLA sequence-based typing DNAse 1 hypersensitivity site mapping Nucleosome positioning and chromatin structure studies ChIP-Seq: studying sequence specific protein-RNA interactions CNV-Seq: measuring copy number variation with sequencing GRO-Seq: studying RNA polymerase initiation events Sequencing of ancient DNA samples Paired-end mRNA sequencing DNA imprinting and allele specific expression Software Offers a graphical user interface to input relevant sample information, check for formatting and syntax errors prior to input into the system and define bioinformatics analysis options Ability to monitor their instrument run remotely on the internet with a standard web browser Provide Real Time Analysis (RTA) so operator can see real time, on-instrument image processing and basecalling Provide on-instrument data analysis, including alignment and variant calling Provide somatic variant detection possible without tumor normal pairing Provide alignment and variant reporting in as little as two hours after run completion Provide fully optimized analysis solutions for: Resequencing Small genome de novo sequencing Small RNA sequencing 16S metagenomics Library quality control (QC) Transcriptome sequencing of small genomes (< 5 Mb) Provide a built-in web server that will present easy-to-interpret reports using compatible web browsers for Windows platforms Alignment and variant calling uses industry standard BWA/GATK Operator not required to have bioinformatics skills to generate SNPs and indels Produces FASTQ, BAM, VCF, and txt formatted files for maximum compatibility with 3rd party downstream software packages Graphical user interface (no command-line interface) Stand-alone software available for offline data analysis Reports viewable in Windows environment No separate computer hardware needed Capability to remotely monitor your Instrument on the internet in real-time Automatic data analysis (mapping, alignment, variant calling) Scalable data storage and archiving available for system End Statement of Work Delivery FOB: Destination to: New Mexico VA Healthcare System 1501 San Pedro Dr SE, Albuquerque, NM, 87108-5128 The applicable NAICS code is 334516, Anal Lab Inst Mfg. Small Business manufacturers for this NAICS code have a size standard of 1,000 employees.   The delivery term is to be 90 calendar days ARO, with no options included. PLEASE INDICATE IN YOUR RESPONSE YOUR BUSINESS SIZE AND IF YOU ARE A MANUFACTURER OR DISTRIBUTOR. IF THE ITEMS ARE AVAILABLE ON A FSS SCHEDULE PLEASE INCLUDE THE FSS SCHEDULE NUMBER. ALL RESPONDANTS MUST BE MANFACTURERS OR AUTHORZED DISTRIBUTORS. NO REFURBISHED OR GRAY MARKET ITEMS WILL BE ACCEPTED. It is anticipated that a Request for Quotes will be issued on or about July 16, 2018. Award of a firm fixed price contract is contemplated on or about July 27, 2018. This notice is published to conduct market research to determine if there is a sufficient number of certified Service Disabled Veteran Owned Small Businesses (SDVOSB), Veteran Owned Small Businesses (VOSB), capable of performing the requirements to warrant a socio-economic set-aside or full & open competition. It is strongly recommended that interested parties register in the US Department of Veterans Affairs Vet Biz database and the Small Business Administration (SBA) database. Registration may be accomplished at http://www.vip.vetbiz.gov/ and www.sba.gov/, respectively. Prior to any award, a vendor/contractor must be vendorized. Such forms required for vendorization will be included in any solicitation resulting from this sources sought notice. Interested parties responding to this sources sought request shall submit the following information at a minimum: (1) company name and address, point of contact with phone number, and DUNS number; (2) documentation relating to capability of performance; (3) proof of registration in the VA Vet Biz or SBA websites or intention of registration prior to submission of offers to a solicitation; (4) If you are a distributor, a statement from the manufacturer that your company is an authorized distributor; (5) a statement to inform the government if you are a manufacturer or distributor; (8) any information regarding FSS Schedule availability; (6) any other pertinent company documentation. The response date to this Sources Sought notice is July 13th, 2018 at 8:00 pm NM time. This market research is for informational and planning purposes only to determine if a socio-economic set-aside, or full & open competition, or sole-source procurement is appropriate. The Government will not pay any costs for responses submitted. Electronic submissions are acceptable via Bryan.Rogers2@va.gov. NO ADDITIONAL INFORMATION IS AVAILABLE OTHER THAN WHAT IS NOTED HEREIN.
 

Web Link

FBO.gov Permalink
(https://www.fbo.gov/spg/VA/AlVAMC501/AlVAMC501/36C25818Q9569/listing.html)
 

Document(s)

Attachment
 

File Name: 36C25818Q9569 36C25818Q9569.docx (https://www.vendorportal.ecms.va.gov/FBODocumentServer/DocumentServer.aspx?DocumentId=4463249&FileName=36C25818Q9569-000.docx)

Link: https://www.vendorportal.ecms.va.gov/FBODocumentServer/DocumentServer.aspx?DocumentId=4463249&FileName=36C25818Q9569-000.docx

 

Note: If links are broken, refer to Point of Contact above or contact the FBO Help Desk at 877-472-3779.
 

Place of Performance

Address: NMVAHCS;1501 San Pedro Dr SE;Albuquerque, NM;(Place of Delivery)

Zip Code: 87108-5128
 

Record

SN04981829-W 20180708/180706230533-b0e3e8fbb1f3ce07d5bf42d9fb5c8878 (fbodaily.com)
 

Source

FedBizOpps Link to This Notice
(may not be valid after Archive Date)

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