SB134118RQ0282-StatementOfWork-FBO_Amendment_2.pdf

SB134118RQ0282 AMENDMENT 0002

STATEMENT OF WORK

NEXT-GENERATION DNA SEQUENCING SERVICES

BACKGROUND

The Joint Initiative for Metrology in Biology (JIMB) is working to develop technology, standards and applications of DNA barcodes and measurement of whole genome nucleic acid measurements using Next Generation Sequencing. JIMB, located at the National Institute of Standards and Technology (NIST) in Gaithersburg, MD and at Stanford University, requires amplicon and whole-genome measurement services to include library construction, sequencing from contractor and/or JIMB prepared libraries and library QC. A Blanket Purchasing Agreement with a single vendor is desired to provide these services.

SCOPE OF WORK

The contractor shall provide Next Generation DNA Sequencing Services for NIST/JIMB as follows:

Amplicon Sequencing Requirements:

1. JIMB will self-prepare a sequencing library and provide samples to the contractor.

Sequencing of a total of 100 HiSeq lanes is anticipated during each year of performance, and these may be submitted one-at-a-time or in batches.

2. The contractor shall perform quality control by testing the effective concentration by real-time PCR.

3. The contractor shall run the library at the appropriate concentration on a full lane of paired-end 150 base-pair Illumina HiSeq 3000, HiSeq 4000, or comparable Illumina system (2 x 150bp).

4. The contractor shall provide to the technical contact the FASTQ files of the resulting data.

5. No PhiX spike-in is required since this will be performed by JIMB. The contractor will coordinate with the JIMB technical contact to determine the appropriate level of PhiX spike-in for proper calibration of the Illumina system.

6. The resulting FASTQ file(s) will be delivered to the requesting JIMB technical contact within 8 weeks from the sample(s) submission date.

Whole-Genome Sequencing Requirements:

1. Contractor shall perform Illumina and/or Chromium 10X library construction from JIMB supplied genomic DNA.

a. Anticipated genomes are human and whale however service for other genomes maybe be required.

b. Quality control shall be performed by the contractor to ensure libraries meet library construction kit specifications.

c. Library construction requirements will vary by call order.

i. Lower limit on library preparations is one and upper limit estimated to be 20-30.

ii. An example of a call order might require two Chromium preparations (high coverage sequencing) and 20 Illumina preparations (low coverage sequencing) for multiplexing.

2. Sequencing of the contractor-constructed libraries will be performed by the contractor to produce paired-end reads up to 150 bp on HiSeq X or comparable Illumina system.

a. Read length will be specified by the JIMB call order. If read length capabilities increase, the contractor shall provide access to sequencing with longer read lengths.

It is in the interest of JIMB to maximize sequencing read length with Illumina technologies.

b. Sequencing coverage requirements for the aforementioned genomes may vary by call order with lower limit expected to be 15x (multiplexed libraries) and upper ≥ 40x. An example of a call order might require sequencing coverage of 40x for Chromium libraries and 15x for Illumina libraries.

c. Service requests for call orders may be in batches over the term of the contract or all-at-once.

d. Sequencing run quality and yield metrics shall meet or exceed Illumina specifications for the instrument.

3. The resulting FASTQ file(s) will be delivered to the requesting JIMB technical contact within 8 weeks from the sample(s) submission date.

Specific Brand of Instrument

There is the potential that future BPA calls may require the use of a specific brand of instrument listed in this SOW. The reasons for such potential restriction include:

1. JIMB self-prepared libraries have already been prepared for Illumina sequencing platforms and contain adapters for Illumina sequencing. It is required that library construction and sequencing remain consistent with past measurements for data comparability.

2. 10X Chromium library construction is required to obtain long-range information from short read sequencing such as the Illumina systems. While other platforms can provide long range information the platforms have higher error rates that an unsuitable for NIST’s whole genome sequencing requirements.

3. 10X Chromium libraries are constructed for Illumina sequencing platforms and contain adapters for Illumina sequencing.

4. BPA calls that require both 10X Chromium library construction and Illumina preparation must be measured on the same system for data comparability. These measurements will be used together in data analysis.

5. BPA calls may request a specific library construction or sequencing platform to be consistent and comparable with prior measurements that may or may not have been performed by the contractor.

PERIOD OF PERFORMANCE

This instrument shall have one base year of performance plus two renewable one- year options. Orders may be placed at any time during each year of performance.

INDIVIDUALS AUTHORIZED TO PLACE ORDERS

Any warranted NIST Contracting Officer is authorized to place orders under this BPA.

EXTENT OF OBLIGATION

The Government is obligated only to the extent of authorized purchases actually made and then only to the extent of those accepted by the Government.

PURCHASE LIMITATION

The dollar limit for each individual order shall be a maximum of $150,000.00