Specifications Digital PCR Final.pdf

SPECIFICATIONS

Digital PCR Instrument

I. BACKGROUND INFORMATION

The Biomolecular Measurement Division performs fundamental and applied research on the measurement of macromolecules such as proteins and nucleic acids, as well as peptides, glycans, metabolites, lipids, and natural products. The Division provides measurement science, reference materials, reference data, and technologies to foster innovation and confidence in measurements needed to advance biotechnology, DNA forensics, biomedical and bioscience research, and health care.

Digital polymerase chain reaction (PCR) is used to determine the accurate and reproducible concentration of DNA samples. NIST requires a Digital PCR Instrument for use in certifying the concentration of Standard Reference Materials (SRM) produced by the Biomolecular Measurement Division. The instrument is required to produce high quality data for accurate measurement of SRM DNA and RNA samples.

A Digital PCR instrument works on the principal that a single DNA or RNA molecule can be partitioned into compartments and then PCR is applied to amplify the single molecules to be detected and counted. The PCR step can be done on a separate thermocycler, (many are already available at NIST) or integrated instrumentation.

Each partition that contains a single DNA molecule that is amplified by the PCR reaction and produces a fluorescent signal. Partitions without DNA do not produce a signal above background fluorescence. Partitions that contain amplified DNA are termed positives and partitions that do not contain a DNA molecule are termed negatives. The total volume of all partitions is an important empirically measured value which can be used to correlate the measurement with the International System of Units (SI). The number of positive partitions divided by the volume of PCR reaction analyzed by the instrument is used to deduce the concentration of DNA in the original sample. Measurement of the partition volume is essential to conferring traceability to the SI, accessibility to measure chamber volume is a necessary characteristic of the system to be procured.

The instrument must have capability to analyze multiple samples simultaneously (or in rapid succession), a reproducible means of dispersing the samples into the partitions and means of detecting positive partitions with fluorescent dyes. Software must be incorporated into the system for data manipulation and calculation of the concentration values.

II. SPECIFICATIONS

The Contractor shall provide one (1) analytical instrument system that meets the following minimum technical requirements. The Contractor shall install the instrument and provide training as described below.

Salient Characteristics:

• The instrument module must fit on a laboratory bench top size (up to 48 inches in depth, 48 inches in width and 48 inches in height)

• The instrument must be capable of providing at least 20,000 partitions with a partition acceptance rate greater than 99.0 %

• Must use a PCR reaction size of 20 microliters or less

• Must allow accurate quantitation of samples that differ in concentration up to 5 orders of magnitude

• The partitions for the PCR must be in the form of consumable plates using microfluidic array partitioning

• At least 95% of the starting sample volume must incorporated into the partitions

• The instrument must be capable of simultaneous detection of at least four fluorescent channels for at least four target sequences using common fluorescent dyes such as FAM, VIC, HEX, EvaGreen, Cy3, Cy5, TAMRA, and TYE

• The instrument capacity must have capability of automated reading for as few as 1 sample and up to 16 samples in a single run

• The instrument must have the post-PCR waste contained within the consumable for disposal

• Partitions must be physically accessible to measurement to establish an SI-traceable volume estimate, to be accomplished by NIST for certification of SRMs

• Shall be capable so that Unused fluidic partitions can continue to be used in subsequent runs

(up to four times)

• The 16 samples must be analyzed by the instrument in less than two hours.

• The sample-to-sample reproducibility shall be within 10% of the calculated concentration values (precision).

• The instrument shall include a data analysis module that can collect, store and process the data for at least 16 samples simultaneously.

• The instrument shall include software that can calculate the concentration of the DNA in each partition for at least four fluorescent dyes by fitting the fraction of negative partition data to a Poisson calculation to determine the copy numbers of the DNA or RNA targets

• The software shall be able to display the fluorescent dye intensity for at least four dyes for each partition.

• The software shall be able to allow the adjustment of the threshold settings for discrimination between positive and negative partitions in individual wells for up to 16 samples.

• The system shall include an operations and maintenance manual covering proper operation, routine maintenance, and troubleshooting for the instrument and controlling software

Installation:

The Contractor shall install the instrument in Building 227, Room B225, at NIST Gaithersburg, MD. Installation shall include, at a minimum, uncrating/unpacking of all equipment, set-up and hook-up of all equipment, start-up, demonstration of specifications, and removal of all trash.

Instrument will operate to manufacturer’s specifications upon installation. Installation will take place during normal business hours, between 8:30 am and 5:00 pm Eastern Time, Monday through Friday except Federal Holidays, and will be coordinated with the NIST Technical Point of Contact (TPOC). Installation is to occur within 90 days of award.

Warranty:

The Contractor shall provide, at a minimum, a one-year warranty for the equipment. The warranty shall cover all parts, labor and travel. The warranty shall commence upon successful completion of delivery, installation, training, and demonstration of all required specifications.

Training:

Training at NIST for up to two NIST personnel covering normal operation, troubleshooting, and routine maintenance shall be included. Training shall be provided during normal business hours, and will be coordinated with the NIST Technical Point of Contact (TPOC) to ensure maximum availability of NIST personnel. Training is to occur within 30 days of installation. The training may be completed on-site at NIST immediately after installation and demonstration of specifications.

Service Agreement Options:

The contractor shall provide four additional one-year option periods for on-site repair and maintenance services for the instrument being purchased. The services shall include unlimited repair inclusive of travel, parts and labor, repair and maintenance of the instrument and all updates to instrument software and firmware. The contractor is not responsible for PC service.

The Government will be responsible to obtain PC service. However, if PC service does occur, reinstallation of the OEM provided software and PC re-configuration is covered by this agreement.

1) Preventive Maintenance

a. Provide one (1) preventive maintenance visit during each one-year term of the service agreement.

b. Scheduling of the visits shall be consistent with the maintenance requirements of the instrument as detailed in the service and use manuals for the equipment.

c. Preventive maintenance visits shall occur during NIST’s regular business hours.

The contractor shall contact the NIST Technical Point of Contact (TPOC) to schedule a mutually acceptable date and time for the preventive maintenance visit.

The scheduled maintenance visit may be made at the same time as an unscheduled visit for corrective or other action if such a visit occurs within one month before a scheduled preventive maintenance visit. All visits must be scheduled, in advance with the NIST TPOC.

2) Service Calls

a. Respond to an unlimited number of requests for service calls in the event of instrument failure which requires immediate repair.

b. Respond to service calls during regular business hours only, within a 48-hour timeline. A service technician will provide on-site service at NIST Gaithersburg, MD within a 48-hour response time after the call is placed. No weekend service visits shall be required.

c. If the Contractor is unable to resolve the problem during the service call, the Contractor shall provide telephone support and on-site support as needed to expedite a solution for NIST.

d. Responsible to obtain all parts and software updates required for all repairs and maintenance. The Contractor shall make a commercially reasonable effort to secure parts and software updates within 72 hours after identifying the need.

e. Replacement parts provided under this agreement must be OEM Certified and may be either new or remanufactured. The Contractor may exchange and/or repair existing components of the instrument.

f. All repairs must result in the equipment meeting manufacturer’s specifications.

g. Any parts or components removed for replacement shall become the property of the Contractor unless otherwise agreed to by the parties. The Contractor shall remove the parts from the NIST campus at the time of the service call, or provide shipping instructions and return shipping information that NIST may return the parts to the Contractor within 3 days after the service visit is completed. The Contractor shall assume all charges and liability for all shipments.

3) Service Conditions

a. All service provided under this agreement must be provided by factory trained and certified personnel who are fluent in the operation of the covered equipment.

b. Service must be rendered on-site at NIST Gaithersburg, MD unless otherwise agreed by the parties.

c. If a part needs to be repaired off-site, the Contractor shall be responsible for all packaging, shipping, and transportation costs as well as liability for the shipment to and from NIST Gaithersburg. The Contractor shall be responsible for providing a “Return Authorization Number” or other information authorizing return of the shipment to their facility prior to the shipment.

d. All parts shall be OEM certified for use with the instrument. The Contractor shall only employ tools, instruments, test apparatus, methodologies, techniques, and practices approved for use with the instrument by the manufacturer. The service protocols and instrument specifications shall be adhered to always.

4) Service Report The Contractor shall submit a service ticket to the designated TPOC for each instrument prior to departure from NIST on any given service call for maintenance and repairs. The service ticket shall include the following for all instrument repairs and maintenance:

a. Model number.

b. Serial number.

c. Date and time of arrival to NIST.

d. Description of service performed.

e. Name and quantity of any parts that were repaired.

f. Name and quantity of any parts that were replaced.

g. Date and time of departure from NIST.

h. Diagnostic test results or narrative summary demonstrating that the instrument is meeting the performance standards.

i. Any additional comments or recommendations.

j. Printed name and signature of service technician. Signature block for NIST personnel accepting the services rendered.

5) Telephone Support

a. Provide telephone support for the covered equipment during regular business hours.

b. Telephone support must include response to questions about operating practices, application use, and service issues that can be diagnosed and resolved over the telephone. All labor, replacement parts and components (excluding consumables) provided by the Contractor are guaranteed for a period of ninety (90) days from the service visit completion date.

III. PERIOD OF PERFORMANCE

• Delivery, installation, and training shall be completed within 90 days after award.

• Warranty: 12 months from the date of acceptance of the instrument

• Optional Service Agreement Period 1: 12 months from the date of warranty expiration

• Optional Service Agreement Period 2: 12 months from the date of Optional Maintenance

Period 1 expiration

• Optional Service Agreement Period 3: 12 months from the date of Optional Maintenance

Period 2 expiration

• Optional Service Agreement Period 4: 12 months from the date of Optional Maintenance

Period 3 expiration

IV. PLACE OF PERFORMANCE

The instrument shall be manufactured at the Contractor’s facility. Installation of the instrument and training shall be accomplished at NIST, 100 Bureau Drive, Gaithersburg, Maryland during normal business hours.

V. DELIVERABLES

Description Quantity Due Date Analytical instrument One (1) 90 days after award of this requirement.

Installation of the analytical instrument

Once 90 days after award of this requirement.

Operations and maintenance manual for the analytical instrument

One (1) 90 days after award of this requirement

Warranty One (1) 12 months from the date of acceptance of the instrument

Training of NIST personnel at NIST, Gaithersburg, MD

Once 30 days after installation.

Service Agreement Option: Year 1 One (1) 12 months from the date of warranty expiration

Service Agreement Option: Year 2 One (1) 12 months from the date of Optional Service Period 1 expiration

Service Agreement Option: Year 3 One (1) 12 months from the date of Optional

Description Quantity Due Date Service Period 2 expiration

Service Agreement Option: Year 4 One (1) 12 months from the date of Optional Service Period 3 expiration

VI. ACCEPTANCE CRITERIA & PAYMNET

After installation at NIST, the Contractor shall demonstrate performance specifications of the instrument are met. NIST personnel will verify equipment operation meets technical standards post installation via visual inspection, and training during acceptance testing.

Acceptance testing shall occur not later than 10 business days from the date of completed installation. Final acceptance by the Government will be given after successful delivery, and demonstration of instrumentation specifications.

VII. GENERAL INFORMATION

Compliance with NIST Rules and Regulations: While on the NIST campus, the Contractor’s representative(s) shall abide by all NIST rules and regulations. The Contractor shall provide all information necessary for the TPOC to authorize entrance to the NIST campus in accordance with NIST Security Policy and Procedures.

Safety: The Contractor employee shall be responsible for knowing and complying with commercial installation safety prevention regulations. Such regulations include, but are not limited to, general safety, fire prevention, and waste disposal.

Security: NIST is a restricted campus. An identification badge is required for access for entry into buildings and is to be shown to the armed Security Police when entering the campus.

Identification Badges: Contractor employees shall comply with NIST identification and access requirements. The Contractor shall provide the name and citizenship information of employees for on-site visits to the NIST Technical Point of Contact (TPOC) prior to arrival. The TPOC will submit the name(s) and citizenship information to the NIST Office of Security in order for a given Contractor employee to enter the NIST campus. The Contractor employee is responsible for absences due to missing or expired identification and access documents. Each Contractor employee shall wear a visible identification badge provided by the NIST Security Office.

Vehicle Registration: All Contractor employees must register their vehicles with the NIST Security Office to gain access to the campus. A valid driver’s license, Government-furnished civilian ID (which in most cases can be a valid driver's license), proof of insurance and current registration must be presented to the NIST Security Office.