Combined Synopsis Solicitation Genome Sequencing DNA service.pdf

Notice Type:

Combined Synopsis Solicitation #12305B21Q0038

SYNOPSIS:

The United States Department of Agriculture (USDA), Agricultural Research Service, National Center for Cool and Cold- Water Aquaculture (NCCCWA), Kearneysville, WV., requires DNA Sequencing and Genotype Imputation of Rainbow Trout Sample Services.

PURPOSE AND OBJECTIVES:

The primary objective of issuing this Combined Synopsis Solicitation is to seek information from vendors/laboratories with the capability of providing DNA Sequencing and Genotype Imputation of Rainbow Trout Sample Services.

The services will be used to sequence and impute genotypes.

SCOPE OF WORK AND BACKGROUND INFORMATION:

Whole Genome Sequencing and Genotype Imputation of Rainbow Trout Samples:

1) Whole genome sequencing via Illumina technology of rainbow trout samples (Genome size ~2.4Gb).

a) 10X coverage sequencing of 151 reference samples.

b) 1X coverage sequencing of 2022 target samples (including replicated samples for quality control).

2) SNP genotype imputation of the 2022 target samples using the 151 reference samples as a reference panel OR a combined reference panel including other rainbow trout samples (206 samples) with high genome coverage sequences available in NCBI (PRJNA386519, PRJNA402066, PRJNA681179).

*Contractor shall provide all services, supplies, equipment, and facilities necessary to sequence and impute genotypes in accordance with the required performance elements and benchmarks.

Schedule of Line Items:

Line Item 01 151 reference samples Line Item 02 2022 target samples

Samples will be provided by: TBD.

REQUIRED PERFORMANCE ELEMENTS AND BENCHMARKS:

1. DNA quality check of all samples using Qubit or other instruments.

2. Standard Illumina genomic DNA library preparation performed by the vendor (Insert size approximately 400bp-

550bp).

3. Platform and configuration: Illumina technology, PE 150 cycles.

4. Read Length: 2 x 150 nucleotides (paired end).

5. Data Output: A minimum of 24 Gbases output DNA sequence per reference sample from 160M quality-filtered non-duplicate paired-end reads (80M reads in each direction), and a minimum of 2.4 Gbases output DNA sequence per target sample from 16M quality-filtered non-duplicate paired-end reads (8M reads in each direction). The minimum sequence coverage is required for at least 95% of the reference samples and 95% of the target samples. The sequence files are in standard fast format.

6. Vendor must have in place a series of quality control (QC) steps during libraries preparation, genomic DNA sequencing and genotype imputation. The QC procedures must be documented and included in the final project report, including the adaptor sequences used and actual size of DNA inserts.

7. Read mapping: map quality-trimmed sequence reads of all samples to the rainbow trout reference genome USDA_OmykA_1.1 (GCA_013265735.3), and mark duplicated reads.

8. Reference panel: vendor must document the steps and programs used to build the reference panel in the project report.

9. Genotype imputation of the 2022 target samples: vendor must document the steps and programs used for genotype imputation in the project report.

10. A subset of the target samples will be genotyped with the 57K SNP chip. The imputed genotypes (allele dosages) must correlate well (R2 >0.9) with the SNP chip genotypes.

11. One sample is replicated multiple times, and the imputed genotypes must be able to identify the replicated sample correctly.

12. Deliverables will include the DNA sequence files in FASTQ format, read mapping files in BAM format, genotypes of the reference samples and imputed genotypes of the target samples in VCF format, and a Final Project Report describing DNA library preparation, sequencing, read mapping, variant calling of the reference samples and genotype imputation of the target samples.

Sequencing should be completed within 30 days from receipt of samples, and genotype imputation and return of all deliverables are required within 90 days from receipt of samples. The order number shall be included on all documentation and shipments.

(All dates/times are approximate).

*Data Rights USDA will provide samples and pay the service in full at the end of the performance period. USDA will retain the full rights of the use, production, and disclosure of this data. All data must be provided via secure portal download or in external hard drives to the USDA-ARS-NCCCWA.

NAICS: 541380, Testing Laboratories.

PSC: B599, Special Studies/analysis- Other.

NOTE TO OFFERS:

This is a Combined Synopsis Solicitation for Commercial Items prepared in accordance with the format in Far Subpart 12.6, Streamlined Procedures for Evaluation and Solicitation for Commercial Items, as supplemented. Additional information included in this notice is in accordance with procurement procedures of Far 13, Simplified Acquisition Procedures. This announcement constitutes the only solicitation.

If you are an interested vendor, please provide the following information: 1.) Business name and point of contact; 2.)

DUNS number and CAGE code; 3.) Business size; 4.) GSA Schedule number (if any); and 5.) A brief Statement of Capability (no more than three pages), which demonstrates the ability to meet the specialized work requirements above.

In addition, include any past performance information on contracts of similar size and scope. All vendors are required to have an active registration in the System of Award Management (https://sam.gov/SAM/).

Clauses/Provisions Incorporated by reference:

This requirement incorporates one or more clauses by reference with the same force and effect as if they were given in full text. Upon request, the Contracting Officer will make their full text available. The full text of a clauses of the Federal Acquisition Register (FAR) may be accessed at the following address: https://www.acquisition.gov/browse/index/far

52.204-7 - System for Award Management (OCT 2018) 52.204-13 - System for System for Award Management Maintenance (OCT 2018) 52.204-16 - Commercial and Government Entity Code Reporting (AUG 2020) 52.209-2 - Prohibition on Contracting with Inverted Domestic Corporations - Representation (NOV 2015) 52.212-1 - Instructions to Offerors Commercial Items (JUL 2021) 52.212-3 - Offeror Representations and Certifications-Commercial Item (FEB 2021) 52.212-4 - Contract Terms and Conditions-Commercial Items (OCT 2018) 52.212-5 - Contract Terms and Conditions Required to Implement Statutes or Executive Orders-Commercial Items (JUL 2021) 52.223-1 - Bio-Based Product Certification (MAY 2012) 52.232-39 - Unenforceability of Unauthorized Obligations (JUNE 2013) 52.232-40 - Providing Accelerated Payments to Small Business Sub¬ contractors (DEC 2013) https://sam.gov/SAM/ https://www.acquisition.gov/browse/index/far

52.237-2 - Protection of Government Buildings, Equipment and Vegetation (APR 1984)

EVALATION and BAIS FOR AWARD

• Lowest Price Technically Acceptable (LPTA) (Note: Technically Acceptability could outweigh price).

Electronic responses are mandatory. Information provided will not be used as a part of any subsequent solicitation requirement. Interested vendors who submit data are responsible for appropriately marking information if it is proprietary in nature. A determination by the Government not to award this proposed action, based on this notice, is solely within the discretion of the Government.

Responses are due: See main posting page/website. Please email all responses to: Tiffany Pimble, Contract Specialist:

Tiffany.Pimble@usda.gov

Contracting Office:

U.S. Dept of Agriculture Beltsville Agricultural Research Center (BARC) 10300 Baltimore Ave, Beltsville, MD 20705 Wk: (301) 504-3761 tiffany.pimble@usda.gov

Agricultural Research Service, Administrative and Financial Management NEA Area Administrative Office, Acquisitions & Personal Property/Fleet

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