Attachment_4_-_Statement_of_Work.pdf

Attachment 4 – Statement of Work

STATEMENT OF WORK

TITLE: Whole Genome Sequencing and Omics Projects for NHLBI TOPMed Program

BACKGROUND

The Whole Genome Sequencing (WGS) project is part of NHLBI's Trans-Omics for Precision Medicine (TOPMed) program and serves as an initial step for the larger initiative. In recent years, genetic research of complex diseases using Genome-Wide Association Study (GWAS) and Exome-sequencing approaches has resulted in an unprecedented explosion of genetic discovery. However, a large portion of heritability in complex diseases remains elusive. Whole Genome Sequencing (WGS) will provide a comprehensive view of the genome, an opportunity to further understand the genetic architecture (rare and common genetic variants) relevant to heart, lung, blood and sleep disorders (HLBS), and an unprecedented resource to the scientific community.

In addition, the program hopes to couple WGS with additional phenotype data using Trans-Omic approaches by generating and incorporating DNA methylation, RNA expression patterns and metabolic profiling with other extant phenotype and clinical outcome data from studies focused on HLBS disorders.

Thus the program seeks to discover factors that influence disease risk, identify subtypes of disease, and develop more targeted and personalized treatments. In addition to providing a comprehensive view of the genetic architecture, an unprecedented rich and multilayered data resource will be available to the scientific community stimulating innovative approaches to examine novel questions and generate cutting-edge methodologies to address HLBS disorders.

SUMMARY OBJECTIVES

The NHLBI has a requirement for large scale Whole Genome Sequencing (WGS) and three (3) smaller Omic projects. The Statement of Work includes separate TOPIC AREAS for each requirement as follows: Topic Area 1: Large Scale WGS; Topic Area 2: DNA Methylation; Topic Area 3: RNA Sequencing; Topic Area 4:

Metabolic Profiling.

NOTE #1 TO OFFERORS:

Offerors are encouraged to submit proposals for one or more Topic Areas as their capability permits.

All awards will be evaluated independently and awarded independently of one another.

NOTE #2 TO OFFERORS:

In response to this solicitation offerors shall provide a separate technical proposal and a separate detailed budget for each Topic Area.

NOTE #3 TO OFFERORS:

The Government reserves the right, but is not required to award any/all of the below areas, including for reasons but not limited to sample quality and/or availability.

NOTE #4 TO OFFERORS:

For each topic area the offeror is requested to provide, as part of their proposal, a schedule with a process timeline for the completion of work in each Topic Area for the 12 month period of performance.

Statement of Work

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Topic Area 1: Whole Genome Sequencing

1) Sample receipt and handling with coordination with NHLBI designated Data Coordinating Center (DCC) and NHLBI selected studies;

2) Provide large-scale >30X mappable average sequence coverage (i.e. Standard Coverage) WGS using Illumina HiSeq X Ten platform including quality control measures during production to identify sequencing errors and sample mix-ups on a minimum of 5,000 and in additional increments of 1,000 sequences, up to maximum capacity that can be completed within one year by offeror;

NOTE #5 TO OFFERORS: All proposals shall provide best pricing overall and shall include best pricing at each 1,000 sequences increment.

3) Data cleaning, including but not limited to checks for Hardy-Weinberg equilibrium, Mendelian inconsistencies, visualization of base quality scores and nucleotide distributions, trimming of reads and read filtering based on base quality score and sequence properties such as primer contaminations, N content and GC bias;

4) WGS assembly consisting of raw data QC; preprocessing, mapping, post-alignment processing, variant calling, annotation, and prioritization;

5) Secure transfer of each of the completed and cleaned data sets to the NHLBI designate Informatics Resource Center (IRC) or dbGaP using protocols agreed to with NHLBI and/or NCBI; and

6) Participate in NHLBI TOPMed designated in person-meetings and conference calls dealing with data integration, formats, QC/QA and others as designated by the NHLBI Program Office.

Topic Area 2: DNA Methylation Profiles

1) Sample receipt and handling with coordination with NHLBI designated DCC and NHLBI selected studies;

2) Provide genome-wide DNA methylation profiles that include transcriptional start sites for a minimum of 500, but not to exceed 2000 designated NHLBI samples (in increments of 100) within 12 months of award;

3) Provide genome-wide DNA hydroxymethylation profiles for a minimum of 500, but not to exceed 2000 designated NHLBI samples (in increments of 100) within 12 months of award;

4) Include negative, sample-independent, sample-dependent controls and other appropriate controls as necessary; provide robust quantitative measurement accuracy;

5) Data cleaning and secure transfer of each of the completed and cleaned data sets to the NHLBI designate IRC or dbGaP using protocols agreed to with NHLBI and/or National Center for Biotechnology Information (NCBI); and

6) Participate in NHLBI TOPMed designated in person-meetings and conference calls dealing with data

Topic Area 3: RNA Sequence Profiles

1) Sample receipt and handling with coordination with NHLBI designated Data Coordinating Center (DCC) and NHLBI selected studies;

2) Provide state-of-the art RNA sequence profiles for a minimum of 500, but not to exceed 2000 designated NHLBI samples (in increments of 100) within 12 months of award;

3) Perform paired-end sequencing to increase mapping accuracy and enhance detection of spliced transcripts;

4) Provide read lengths of at least 150 bp to minimize error reads and enable more complete transcriptome assembly;

5) Incorporate quality measures to minimize false discovery rates;

6) Utilize libraries that enable both small and long RNA species detection;

7) Data cleaning and secure transfer of each of the completed and cleaned data sets to the NHLBI designate IRC or dbGaP using protocols agreed to with NHLBI and/or NCBI. For the RNA sequence profiles; and,

8) Participate in NHLBI TOPMed designated in person-meetings and conference calls dealing with data

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Topic Area 4: Metabolite Profiles

1) Sample receipt and handling with coordination with NHLBI designated DCC and NHLBI selected studies;

2) Provide targeted and non-targeted metabolite profiling for a minimum of 500, but not to exceed 2000 designated NHLBI samples (in increments of 100) within 12 months of award;

3) Provide robust metabolite identification;

4) Provide broad coverage of the metabolome including key metabolic pathways;

5) Provide broad coverage of the metabolome include authentic standards for the targeted approach;

6) Utilize state –of-the art computational tools and algorithms for metabolite identification, quantitation and analysis; and

7) Data cleaning and secure transfer of each of the completed and cleaned data sets to the NHLBI designate IRC or dbGaP using protocols agreed to with NHLBI and/or NCBI; and,

8) Participate in NHLBI TOPMed designated in person-meetings and conference calls dealing with data integration, formats, QC/QA and others as designated by the NHLBI Program Office

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DETAILED DESCRIPTION OF THE TECHNICAL REQUIREMENTS:

The successful Contractor shall:

Topic Area 1: Large Scale Whole Genome Sequencing

1) Provide at a minimum whole genome sequencing (WGS) using Illumina HiSeq X Ten platform with mean mappable coverage >30x with the following baseline criteria:

a. Read groups that identify project sample identifiers, libraries, sequencing center and sequencing lane,

b. 90% of genome covered at 20x, 95% at 10x, with a contamination rate of <1%,

c. Minimum of 86 x 10^9 mapped, aligned bases with Q20 or higher,

d. Minimum read length of 100 bp, paired end,

e. No filtering of low quality, unmapped, or duplicate reads [reads with too few Q20 and large fraction of N bases may be filtered],

f. Data delivered in CRAM format (optimally) or BAM files with binned 8-bit qualities and no optional quality tags (avoid OQ, BD, BI), NOTE #6 TO OFFERORS:

Offerors are requested to propose additional pricing for samples requiring PCR amplification on a per sample bases if not included in the baseline.

NOTE #7 TO OFFERORS: Offerors are requested to provide a separate optional line price for CRAM format and/or BAM squeeze (if it is not already included as part of the base price)

g. Provide sequential Just In Time secured/encrypted transfer of sequence data to the NHLBI designated repository(ies).

NOTE #8 TO OFFERORS:

Provide a separate optional line price for WGS (if not already included as part of the base price) with additional post-sequencing processing beyond that designated as “baseline criteria”:

h. Data mapped to hs37d5 decoy reference using BWA-MEM (version 0.7.12) or newer,

i. Incorporate dbSNP build 142 for recalibration and indel realignment,

j. VCF or gVCF, and

k. Provide correct and complete .xml meta data for submission to the NCBI Sequence Read

Archive

2) Provide personnel with expertise and experience in high throughput large-scale WGS, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities).

3) Provide personnel with expertise and experience in DNA preparation, aliquotting, labeling, whole genome amplification, shipping, and minimum acceptable standards for DNA quantity and quality for samples submitted for whole genome sequencing.

4) Provide personnel with expertise and experience in sample receipt, tracking, handling and storage, including the use of an in-house Laboratory Information Management System (LIMS); develop and implement procedures for these activities.

5) Provide personnel with expertise and experience in genetic analyses and bioinformatics for data cleaning.

6) Provide personnel with expertise and experience in the secure physical and electronic transfer of large-

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7) Provide raw data and final WGS data to the Project Office or its designee on request in a complete and timely manner.

8) Provide a Final Manual of Operations within 30 days of contract initiation. Details in Reporting Requirements.

9) Provide weekly Status Reports to the NHLBI Project Office and designated committees. The weekly Status Report shall summarize the status of the sequencing, the weekly QC data, the weekly production, completeness, and quality metrics. Details are given in the Reporting Requirements.

10) Communicate with NHLBI’s designated Data Coordinating Center (DCC), and the respective NHLBI designated studies to coordinate DNA and sample delivery and de-identified sample study information (e.g. Study Participant ID, Study Sample ID, and Gender).

11) Communicate with NHLBI’s designated Informatics Research Center (IRC) and/or NCBI to coordinate WGS data delivery to dbGaP.

12) Provide materials and information promptly and communicate with the Program Office, NHLBI designated studies, DCC, and IRC frequently and regularly.

13) Maintain the confidentiality of the data received, produced, and distributed and to adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to the sequence data.

14) Maintain security guidelines that meet or exceed the current dbGaP Security Best Practices, including its detailed description of requirements for security and encryption http://www.ncbi.nlm.nih.gov/projects/gap/pdf/dbgap_2b_security_procedures.pdf.

In addition, this includes, but is not limited to:

a. all approved users have completed all required institutional computer security training, e.g.

http://irtsectraining.nih.gov/, or the equivalent;

b. the data will always be physically secured (e.g. through camera surveillance, locks on doors/computers, security guard);

c. servers must not be accessible directly from the internet (i.e. must be behind a firewall or not connected to a larger network), and unnecessary services disabled;

d. use of portable media, e.g., on a CD, flash drive or laptop, is discouraged; if necessary then they must be encrypted;

e. updated anti-virus/anti-spyware/anti-malware software;

f. security auditing/intrusion detection software, detection and regular scans of potential data intrusions;

g. strong password for file access and never share it; and,

h. All copies of the dataset must be destroyed whenever NHLBI requests destruction of the dataset.

15) Provide secure backup of all data essential to the project, including but not limited to all sequencing data generated (including raw data), study data received, sample tracking and storage information, and QC information.

16) Provide shipping and handling of DNA and related samples to and from the NHLBI designated DNA repositories. Bar-coded DNA sample arrays will be provided without charge. Offeror will provide best practices for sample concentration and plating and will initiate pilot QC testing of study DNA within 7 days of contract initiation.

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17) Receive and process data and samples from NHLBI designated studies, including:

a. Verify and obtain records of Institutional Review Board approval(s) for the study prior to accepting samples for sequencing; and,

b. Receive, track, and store DNA and other samples and accompanying data from NHLBI designated studies in preparation for sequencing.

18) Pilot QC of representative study DNA samples within 7 days of the start of the contract period.

19) Initiate and deliver sequencing data of the initial 150 NHLBI designated samples received and an additional 14 controls as designated by NHLBI within the first 10 weeks (30 days for sample receipt, 6 weeks for sequencing completion and delivery to NHLBI and designees) of contract award for review by NHLBI and designees.

NOTE #9 TO OFFERORS:

Offerors should deliver and price sequencing data to include the additional 14 controls as a part of the overall proposal.

20) Following review and authorization of initial samples by NHLBI and designees, complete a minimum overall capacity of 150 genomes per week during production and provide a schedule for completion

21) Complete sequencing and electronic delivery of appropriately cleaned and formatted data from all samples received (including quality control measures during production to identify sequencing errors and sample mix-ups) by end of contract period (12 months). Quality control methods should include both positive and negative controls. See technical acceptability criteria in item 1 above.

NOTE #10 TO OFFERORS:

Offerors are asked to include recommendations on suggested controls during production and the impact on project costs should be clarified in the initial response and during the contracted production period.

22) Perform appropriate QC for quantification, post library prep, on-instrument sequencing and post genome build.

23) Transfer sample identifiers including electronic and genetic barcodes; a complete, cleaned data set including intensity data; and work products for failed genotypes to NCBI and NHLBI within six months of sequencing initiation pending Contracting Officer Representative (COR) approval.

24) Participate in NHLBI TOPMed designated in person-meetings (1 or 2 during performance period expected to be in Bethesda, MD) and conference calls dealing with data integration, formats, QC/QA, data deposition into dbGaP and others as designated by the NHLBI Program Office.

25) While the samples to be sequenced have been de-identified, the organization’s Institutional Review Board (IRB) or equivalent must approve the Contractor for handling human DNA. Contract employees in contact with human DNA or data derived from these human subjects must provide Certification of Human Subjects Training prior to a contract award.

26) Provide a Draft Final and Final Report according to the details in the Reporting Requirements.

NOTE #11 TO OFFERORS:

Offerors are asked to provide an optional line item for data storage options for both 6 months and 12 months post project.

The anticipated period of performance is 12 months from the date of the award.

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Topic Area 2: DNA Methylation Profiles

1. Provide personnel with expertise and experience genome-wide DNA methylation, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities)

2. Provide personnel with expertise and experience in preparing samples for genome-wide methylation assays

3. Provide personnel with expertise and experience in sample receipt, tracking, handling and storage, implement procedures for these activities

4. Provide personnel with expertise and experience in genetic analyses, genome-wide DNA methylation, and bioinformatics for data cleaning

5. Provide personnel with expertise and experience in the secure physical and electronic transfer of large-quantities of genetic, DNA methylation data as well as securing in-house data

6. Provide raw data and final sequencing data to the NHLBI Project Office or its designee on request in a complete and timely manner

7. Provide encrypted raw and transformed data as well as the final transformed data for DNA methylation patterns

8. Provide a Final Manual of Operations within 30 days of contract initiation. Details in Reporting Requirements

9. Provide biweekly Status Reports to the Project Office and designated committees. The biweekly Status Report shall summarize the status of the DNA methylation, the biweekly QC data, the weekly production, completeness, and quality metrics. Details are given in the Reporting Requirements

10. Communicate with NHLBI’s designated Data Coordinating Center (DCC), and the respective NHLBI designated studies to coordinate DNA and sample delivery and de-identified sample study information (e.g. Study Participant ID, Study Sample ID, and Gender)

11. Communicate with NHLBI’s designated Informatics Research Center (IRC) and/or NCBI to coordinate DNA methylation data delivery to dbGaP

12. Provide materials and information promptly and communicate with the Program Office, NHLBI designated studies, DCC, and IRC frequently and regularly

13. Maintain the confidentiality of the data received, produced, and distributed and to adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to the DNA methylation data

14. Maintain security guidelines that meet or exceed the current dbGaP Security Best Practices, including http://www.ncbi.nlm.nih.gov/projects/gap/pdf/dbgap_2b_security_procedures.pdf. In addition, this includes, but is not limited to:

b. the data will always be physically secured (e.g. through camera surveillance, locks on doors/computers, security guard);

c. servers must not be accessible directly from the internet (i.e. must be behind a firewall or not

Whole Genome Sequencing and Omics Projects for NHLBI TOPMed Program Page 9 of 13 connected to a larger network), and unnecessary services disabled;

d. use of portable media, e.g., on a CD, flash drive or laptop, is discouraged; if necessary then they must be encrypted;

e. updated anti-virus/anti-spyware/anti-malware software;

f. security auditing/intrusion detection software, detection and regular scans of potential data intrusions;

g. strong password for file access and never share it; and, dataset

15. Provide secure backup of all data essential to the project, including but not limited to all methylation data generated (including raw data), study data received, sample tracking and storage information, and QC information

16. Provide shipping and handling of samples to and from the NHLBI designated repositories. Offeror will provide best practices for sample processing and will initiate pilot QC testing of study samples within 30 days of contract initiation

17. Receive and process data and samples from NHLBI designated studies, including:

a. Verify and obtain records of Institutional Review Board approval(s) for the study prior to accepting samples for DNA methylation; and,

b. Receive, track, and store samples and accompanying data from NHLBI designated studies in preparation for sequencing

18. Pilot QC of representative study samples within 30 days of the start of the contract period

19. Genome-wide methylation data must begin to flow to the Government (NHLBI designated IRC and/or NCBI’s dbGaP within 60 days after receipt of samples

20. Demonstrate support for completing genome-wide methylation at 90 days, 6 months, 9 months and 1 year.

21. Complete genome-wide DNA methylation and electronic delivery of appropriately cleaned and transformed data from all received (including QC/QA analysis) by end of the contract period (12 months). Quality control methods should include negative controls, sample-independent and sample-dependent controls

22. Participate in NHLBI TOPMed designated in person-meetings (1 or 2 during performance person data deposition into dbGaP and others as designated by the NHLBI Program Office

23. The organization’s Institutional Review Board (IRB) or equivalent must approve the Contractor for handling human samples. Contract employees in contact with samples or data derived from these human subjects must provide Certification of Human Subjects Training prior to a contract award

24. Provide a Final Report prior to end of contract according to the details in the Reporting Requirements

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Topic Area 3: RNA Sequence Profiles

1. Provide personnel with expertise and experience in RNA sequencing, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities)

2. Provide personnel with expertise and experience in preparing samples for RNA sequencing

3. Provide personnel with expertise and experience in sample receipt, tracking, handling and storage,

4. Provide personnel with expertise and experience in RNA sequence and bioinformatics for data cleaning

5. Provide personnel with expertise and experience in the secure physical and electronic transfer of large-quantities of RNA sequence data as well as securing in-house data

6. Provide raw data and final sequencing data to the Project Office or its designee on request in a

7. Provide encrypted raw and transformed data as well as the final transformed data

9. Provide biweekly Status Reports to the Project Office and designated committees. The biweekly Status Report shall summarize the status of the RNA sequencing, the biweekly QC data, the weekly production, completeness, and quality metrics. Details are given in the Reporting Requirements designated studies to coordinate sample delivery and de-identified sample study information (e.g. Study Participant ID, Study Sample ID, and Gender).

RNA sequence delivery to dbGaP

13. Maintain the confidentiality of the data received, produced, and distributed and to adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to the transcriptomic data

14. Maintain security guidelines that meet or exceed the current dbGaP Security Best Practices, including

b. the data will always be physically secured (e.g. through camera surveillance, locks on doors/computers, security guard);

c. servers must not be accessible directly from the internet (i.e. must be behind a firewall or not connected to a larger network), and unnecessary services disabled;

d. use of portable media, e.g., on a CD, flash drive or laptop, is discouraged; if necessary then they must be encrypted;

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e. updated anti-virus/anti-spyware/anti-malware software;

f. security auditing/intrusion detection software, detection and regular scans of potential data intrusions;

g. strong password for file access and never share it; and, dataset.

15. Provide secure backup of all data essential to the project, including but not limited to all sequencing data generated (including raw data), study data received, sample tracking and storage information, and QC information

16. Provide shipping and handling of samples to and from the NHLBI designated repositories. Offeror will provide best practices for sample processing and will initiate pilot QC testing of study samples within 30 accepting samples for RNA sequencing; and, preparation for sequencing

18. Pilot QC of representative study samples within 30 days of the start of the contract period.

19. RNA sequencing data must begin to flow to the Government (NHLBI designated IRC and/or NCBI’s dbGaP within 60 days after receipt of samples

20. Complete RNA sequencing and electronic delivery of appropriately cleaned and transformed data from all received (including QC/QA analysis) by end of the contract period (12 months). Quality control methods should include negative controls, sample-independent and sample-dependent controls.

21. Demonstrate support for completing RNA sequencing data at 90 days, 6 months, 9 months and 1 year

22. Participate in NHLBI TOPMed designated in person-meetings (1 or 2 during performance person

23. The organization’s Institutional Review Board (IRB) or equivalent must approve the Contractor for handling human samples. Contract employees in contact with samples or data derived from these human subjects must provide Certification of Human Subjects Training prior to a contract award.

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Topic Area 4: Metabolite Profiles

1. Provide personnel with expertise and experience in metabolite profiling, general laboratory management, and quality control (QC) (used here and throughout encompassing quality assurance and quality control activities)

2. Provide personnel with expertise and experience in preparing samples for metabolite profiling

3. Provide personnel with expertise and experience in sample receipt, tracking, handling and storage,

4. Provide personnel with expertise and experience in metabolomic analyses and bioinformatics for data cleaning

5. Provide personnel with expertise and experience in the secure physical and electronic transfer of large-quantities of metabolomic data as well as securing in-house data

6. Provide raw data and final sequencing data to the Project Office or its designee on request in a

7. Provide encrypted raw and transformed data as well as the final transformed data

9. Provide bi-weekly Status Reports to the Project Office and designated committees. The bi-weekly Status Report shall summarize the status of the metabolite profiling, the bi-weekly QC data, the weekly production, completeness, and quality metrics. Details are given in the Reporting Requirements.

designated studies to coordinate sample delivery and de-identified sample study information (e.g. Study Participant ID, Study Sample ID, and Gender).

metabolite data delivery to dbGaP

13. Maintain the confidentiality of the data received, produced, and distributed and to adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to the metabolomic data

14. Maintain security guidelines that meet or exceed the current dbGaP Security Best Practices, including

b. the data will always be physically secured (e.g. through camera surveillance, locks on doors/computers, security guard);

c. servers must not be accessible directly from the internet (i.e. must be behind a firewall or not connected to a larger network), and unnecessary services disabled;

d. use of portable media, e.g., on a CD, flash drive or laptop, is discouraged; if necessary then

Whole Genome Sequencing and Omics Projects for NHLBI TOPMed Program Page 13 of 13 they must be encrypted;

e. updated anti-virus/anti-spyware/anti-malware software;

f. security auditing/intrusion detection software, detection and regular scans of potential data intrusions;

g. strong password for file access and never share it; and, dataset

15. Provide secure backup of all data essential to the project, including but not limited to all data generated (including raw data), study data received, sample tracking and storage information, and QC information

16. Provide shipping and handling of samples to and from the NHLBI designated repositories. Offeror will provide best practices for sample processing and will initiate pilot QC testing of study samples within 30 accepting samples for metabolite profiling; and, preparation for metabolite profiling

18. Pilot QC of representative study samples within 30 days of the start of the contract period

19. Metabolite profiling data must begin to flow to the Government (NHLBI designated IRC and/or NCBI’s dbGaP within 60 days after receipt of samples

21. Complete metabolite profiling and electronic delivery of appropriately cleaned and transformed data from all received (including QC/QA analysis) by end of the contract period (12 months). Quality control methods should include negative controls, sample-independent and sample-dependent controls

22. Participate in NHLBI TOP Med designated in person-meetings (1 or 2 during performance person

23. The organization’s Institutional Review Board (IRB) or equivalent must approve the Contractor for handling human samples. Contract employees in contact with samples derived from these human subjects must provide Certification of Human Subjects Training prior to a contract award

24. Provide a Final Report prior to end of contract according to the details in the Reporting Requirements