Att 21_Sample TO with Year 1 Contract Prices.pdf

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Sample Task Order: Funding of the NIDA Center for Genetic Studies (NCGS)

PART I. TASK ORDER REQUEST FOR PROPOSAL (TORFP)

A. Estimated Period of Performance: March 14, 2023 – March 13, 2024

B. Task Description:

This Sample Task Order covers any work in the Statement of Work related to Lines 1-65 & 68 in the Schedule of Contract Prices (see attached Schedule of Contract Prices) for the Period of Performance described above.

Contractor must perform TO in accordance with contract terms, and especially in accordance with the Statement of Work (SOW) and deliverable requirements of the contract. In addition, Contractor must perform TO in accordance with its Technical Proposal.

Regarding the “NCGS Administrative, IT, and Database Work” for the NIDA Center for Genetic Studies (NCGS) (see Line 43 in the attached Schedule of Contract Prices), Contractor will invoice a fixed amount on a monthly basis. In order to be reimbursed for Line 43, Contractor must submit along with its monthly invoice an “NCGS Monthly Progress Report” summarizing the “NCGS Administrative, IT, and Database Work” performed during that month.

Regarding its regular monthly technical reports (i.e., the three reports Contractor/RUCDR emails NIDA each month) and as directed by the NIDA COR, Contractor shall include the NCGS data in these reports, but in a way that allows NIDA to view the NCGS data summed together on both a monthly basis as well as a cumulative basis. Please contact the NIDA COR for additional information on how to include the requested data in these reports.

Furthermore, as part of the monthly deliverable Contractor shall update and maintain a Gantt chart to track the progress of work when genotyping or sequencing samples. The Gantt chart shall report:

a. The receipt of approval by COR for samples to be genotyped,

b. The date of receipt of sample manifest,

c. The date of receipt of biological samples,

d. The date for beginning and completion of genotyping or sequencing Quality Control

(QC) for the samples,

e. The date for beginning and completion of genotyping,

f. The date of receipt of data and receipt of data dictionary,

g. The date when data cleaning began and when data cleaning was completed,

h. The date of submission of genotype and phenotypic data to dbGaP,

i. The date of query from dbGAP requesting clarification or amending the submission to dbGaP, 2 | P a g e

j. The date when dbGAP accepts of genotype and phenotypic data,

k. The date when dbGAP publishes the study.

See paragraph “H. Invoice Instructions” below for additional information on invoices for TO.

C. Task Leader: NIDA Contracting Officer’s Representative (COR)

D. Deliverables: See the Statement of Work and Section C.2., Reporting Requirements.

Regarding the “Administrative, IT, and Database Work” for the NCGS (Line 43) in the Schedule of Contract Prices, see the requirement for two Monthly Progress Reports mentioned in the Task Description above; one report is required for line 43.

E. Task Order Response Due Date: TBD

F. Proposal Instructions: Please confirm Part II, “Contractor’s Response to Task Order Request for Proposal (TORFP)”.

G. Evaluation Factors for Award: The Government will evaluate the Task Order proposal against the requirements of the TORFP. Specifically, the Government will conduct a price evaluation of Contractor’ proposal and ensure the proposed prices are fair and reasonable.

The Government may conduct discussions prior to awarding a Task Order or may award this Task Order without discussions. The Government reserves the right to cancel this TORFP any time prior to task order award.

H. Invoice Instructions: In the contract, see Article G.5, “Invoice Submission,” Contractor shall submit one invoice per month:

• Monthly costs for the NCGS, including the Administrative, IT, and Database Task for the

NCGS (line 43 in the Schedule of Contract Prices).

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PART II. CONTRACTOR’S RESPONSE TO TASK ORDER REQUEST FOR PROPOSAL

A. Description of the approach to be used and of the deliverable(s).

Offeror to provide response in the technical proposal.

B. Effort and Price/Estimated Cost:

NIDA anticipates this task order to be fixed price. In order to complete a price analysis

NIDA needs to see the cost/price elements that make up the overall proposed amount.

1. List T.O. leader, specific individuals to be assigned, labor category, estimated hours, and estimated hourly rates for each.

2. Fringe benefits (if applicable).

3. Other direct costs

4. Travel

5. Subcontracts

6. Consultants

7. Indirect costs

8. Total estimated costs for this Order

9. Fee, if applicable

10. Total estimated costs and fee for this Order

C. Period of Performance:

March 14, 2023, through March 13, 2024

D. APPROVAL TO PROCEED:

The Contractor shall not exceed the estimated TO amount or change the TO leader without the prior written approval of the Contracting Officer Representative and the Contracting Officer.

l. For the Contractor: (Signature)

Name and Title:

_______________________ Date: ______________

2. For the Government: __

(COR)

Date: ______________

Name and Title: _______________________ Date: _______________ (Contracting Officer)

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PART III. CONTRACTOR'S REPORT OF TASK ORDER PERFORMANCE

(Contractor may attach additional sheets to this form to present the requested data.)

A. Price: $

B. Report of Deliverables:

REVIEW AND APPROVAL OF SATISFACTORY PERFORMANCE

The signatures below indicate that the services/products required have been delivered, received and satisfactorily meet the requirements of this Task Order.

l. For the Contractor: (Signature)

Name and Title:

_______________________ Date: ______________

2. For the Government: __

(COR)

Date: ______________

(Contracting Officer)

Date: _______________

Item NoDescription of Service Price Per Unit Number of Units Estimated Cost 1 Receive Blood Shipment -$ 2 DNA Extraction from Whole Blood -$ 3 DNA Extraction from Blood Spot Cards -$ 4 DNA Extraction from Saliva -$ 5 DNA Extraction from LCL -$ 6 RNA Extraction -$ 7 Transform Lymphocytes -$ 8 Plasma Isolation and Aliquoting -$ 9 Metabolic Assays for Total Cholesterol, HDL, and HbA1C -$

10 Cryopreserve PBMCs -$ 11 Transform PBMCs -$ 12 Regrow LCLs -$ 13 Whole Genome Amplification -$ 14 Whole Genome Amplification Blood Spot Cards -$ 15 Whole Genome Amplification Serum -$ 16 DNA Distribution Preparation -$ 17 DNA Distribution in 96-well plates -$ 18 DNA Shipment -$ 19 LCL Distribution Preparation -$ 20 Cell Line Shipment -$ 21 RNA or WGA DNA Distribution 22 RNA Shipment 23 WGA DNA Shipment 24 Plasma Distribution 25 Plasma Shipment

Receipt Externally Producted LCLs (Culture, QC, mycoplasma test and verification)

27 Pedigree Relationships 28 External Mycoplasma Test 29 Storage of Plasma* 30 Storage of Cryopreserved PBMC** 31 Storage of LCL** 32 Storage of LCL (Old NIDA)** 33 Storage - DNA (Mechanical/Cuft)*

34 Storage - Mechanical/per tube/year - DNA WB, DNA- LCL, Plasma -$

35 Storage - LN2/per ampule/year - LCL and Cryopreserved PBMC -$ 36 Microarray - UK BioBanking - Budget based on 1000 37 Microarray - Exome Array 38 Illumina Microarray(s) all platforms -$

Microarray and Genotyping - processing, licensing, and data management for Smokescreen****

Microarray - SmokeScreen (chip / array)****

Genotyping - processing, licensing, and data management for Smokescreen****

42 Receive Blood Shipment - Only Bioinformatic and Inventory

43 Administrative, IT, and Database (Monthly Charge)*** 44 RNA Sequencing

RNA Sequencing (50M single end reads) @ 2x100bp RNA Sequencing (80M single end reads) @ 2x100bp

45 Whole Genome Sequencing 30x******* 46 Whole Genome Sequencing 50x 47 Genomic Data Analysis

PACBio Library prep (15-20Kb) SMRT PacBio Seq all variant detection SMRT PacBio Seq Structural Variant detection SMRT whole transcriptome characterizing splicing with full length transcripts

20X Oxford Nanopore Whole Genome Sequencing with library prep Hi-C or Micro-seq per library Cut and Run ChipSeq Whole Genome Bisulfate Sequencing

48 cDNA Synthesis and Storage 49 cDNA Distribution Preparation 50 cDNA Shipment 51 RNA/cDNA archival iPSC Derivation-Reprogramming of Primary Lymphocytes: Sendai (NO QC): external source cells

EP-iPSC Processing: per subclone-Receipt, expansion, and cryopreservation of one subclone from an iPSC line derived outside the RUCDR (20 ampules)

IPSC-Quality Control and Characterization - Sendai persistence assay: QPCR assay to demonstrate loss of Sendai gene products

IPSC-Quality Control and Characterization -RUID SNP (DNA extraction and SNP profiling): identity validation and tracking

IPSC-Quality Control and Characterization - Basic iPSC characterization: Alkaline Phosphatase + Immunocytochemistry

IPSC -Quality Control and Characterization - iPSC characterization by FACS: Oct-4 and Tra-1-60 pluripotency markers (others available upon request)

IPSC - Quality Control and Characterization - Expression Array (Illumina HT12) analysis: includes RNA extraction, QC, and cDNA synthesis

IPSC -Quality Control and Characterization - Embryoid body formation and characterization

IPSC -Quality Control and Characterization - Karyotyping (G-banding)

IPSC - Quality Control and Characterization - CNV analysis (Illumina OmniExpress arrays)

IPSC - Quality Control and Characterization - Teratoma formation service: pricing available upon request

63 Storage of iPS Cells 64 Shipment of iPS Cells - Shipment of Cryopreserved

Generation of Neural Stem Cells - Details available upon request

66 ABCD Study Travel and Training***** 67 Administrative, IT, and Database (Monthly Charge)*** -$ 68 DNA Extraction from Buffy Coat

* Storage price is included by aliquot in #33 Storage- Mechnical Storage.

** Storage price is included by aliquot in #34 Storage - LN2 Storage.

*** Monthly charge for NCGS Administrative, IT, and Database Work for the NIDA Center for Genetic Studies.

**** These prices are available with minimum order of 10,000 microarrays for ultimate genotyping over the life of the contract.

****** Monthly Charge for Administrative Work for the ABCD Stud

Schedule of Contract Prices

ABCD Study: Adolescent Brain and Cognitive Development Study.

Estimated Priced for the New Contract FY2023, Contract Year 1 Prices