Attachment_6_-_Technical_Evaluation_Criteria.pdf

Attachment 6 – Technical Evaluation Criteria

TOPIC AREA 1: Large Scale Whole Genome Sequencing

Technical Evaluation Criteria (100 points)

1) Documented Experience (20 pts.)

• Documented WG and Exome Sequencing experience with similar large-scale project requirements in which the organization and proposed personnel have participated (provide list of projects for the past three years; Letters of support for previous WGS may be included in the Appendix).

• Demonstrated established in-house Laboratory Information Management System (LIMS), including number of projects completed and samples processed on LIMS for the past three years.

2) Expertise and experience of key personnel (25 pts.)

• Expertise and experience of proposed personnel and organization in large-scale sequencing and data management.

• Commitment and capability of offerors to:

Provide cost effective WGS in quantity and quality required with adequate plans for QC/QA for quantification, post library prep, on-instrument sequencing and post genome build.

3) Whole genome sequencing methodology and throughput (30 pts.)

• Demonstration of appropriate understanding of use and problems associated with the methods and materials proposed, including reproducibility, accuracy, efficiency, capacity and success rate.

• Adequacy of the proposed approach for providing a capable pipeline for the workflow needed for WGS analysis: e.g. raw data QC, preprocessing, mapping, post-alignment processing, variant calling, annotation, and prioritization. Provide a flow-chart, operational criteria, and versioning for listed tools or reference builds and standards. Adequacy of proposed schedule to complete WG sequencing and data transmission within 12 months of award.

• Demonstrated ability to complete WG sequencing on 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

• Demonstrated ability to complete a minimum overall capacity of 150 genomes per week during production and provide a schedule for completion

• Demonstrated ability to meet "NIH Security Best Practices for Controlled-Access Data Subject to the NIH Genomic Data Sharing (GDS) Policy" http://www.ncbi.nlm.nih.gov/projects/gap/pdf/dbgap_2b_security_procedures.pdf

4) Feasibility of the proposed informatics management plan (15 pts.)

• Feasibility of the proposed informatics management plan for organizing and integrating WGS into a secure database (see SOW for criteria). Document efficiency and security of the existing database system to be used or modified including data tracking, data synchronization, data transfer and interoperability, and backup of electronically based information. The ability to provide push and or pull capability for the generated WGS data to the NHLBI designated recipient. Hardware media solutions for data transmission should issues arise in network access rates.

5) Equipment and Facilities (10 pts.)

• Availability and adequacy of facilities and equipment including but not limited to genotyping equipment, computing facilities, sample storage facilities and backup plans, the physical security of data, samples, communications, and equipment. Plans for replacing, maintaining, and repairing equipment.

TOPIC AREA 2 – Genome-Wide Methylation Profiles

1) Documented Experience (20 pts.)

• Documented genome-wide methylation experience with similar scale project requirements in which the organization and proposed personnel have participated (provide list of projects for the past three years;

letters of support for previous genome-wide methylation may be included in the Appendix).

2) Expertise and experience of key personnel (25 pts.)

• Expertise and experience of proposed personnel and organization in similar scale genome-wide methylation and data management.

• Commitment and capability of offerors to: Provide cost effective genome-wide methylation in quantity and quality required and adequate plans for QC/QA for quantification, and minimizing false discovery rates.

3) Genome-wide methylation methodology and throughput (30 pts.)

materials proposed, including reproducibility, accuracy, efficiency, capacity and success rate.

• Adequacy of the proposed approach to provide the workflow needed for genome-wide methylation analysis: e.g. raw data QC, preprocessing, peak feature mapping, post-alignment processing, annotation, and prioritization. Provide a flow-chart, operational criteria, and versioning for listed tools or reference builds and standards.

4) Feasibility of the proposed informatics management plan (15 pts.)

• Feasibility of the proposed informatics management plan for organizing and integrating genome-wide methylation into a secure database (see SOW for criteria). Documented efficiency and security of the existing database system to be used or modified including data tracking, data synchronization, data transfer and interoperability, and backup of electronically based information. The ability to provide push and or pull capability for the generated genome-wide methylation data to the NHLBI designated recipient. Hardware media solutions for data transmission should issues arise in network access rates.

5) Equipment and Facilities (10 pts.)

• Availability and adequacy of facilities and equipment including but not limited to genome-wide methylation equipment, computing facilities, sample storage facilities and backup plans, the physical security of data, samples, communications, and equipment. Plans for replacing, maintaining, and repairing equipment

TOPIC AREA 3 - RNA Sequence Profiles

6) Documented Experience (20 pts.)

• Documented RNA-seq profiling experience with similar scale project requirements in which the organization and proposed personnel have participated (provide list of projects for the past three years;

Letters of support for previous RNA-seq may be included in the Appendix).

7) Expertise and experience of key personnel (25 pts.)

• Expertise and experience of proposed personnel and organization in similar scale RNA-seq and data management.

• Commitment and capability of offerors to:

Provide cost effective RNA-seq in quantity and quality required and adequate plans for QC/QA for quantification, and minimizing false discovery rates.

8) RNA-seq methodology and throughput (30 pts.)

• Demonstrated appropriate understanding of use and problems associated with the methods and materials proposed, including reproducibility, accuracy, efficiency, capacity and success rate.

• Adequacy of the proposed approach to provide the workflow needed for RNA-seq analysis: e.g. raw data QC, preprocessing, peak feature mapping, post-alignment processing, annotation, and prioritization. Provide a flow-chart, operational criteria, and versioning for listed tools or reference builds and standards.

9) Feasibility of the proposed informatics management plan (15 pts.)

• Feasibility of the proposed informatics management plan for organizing and integrating RNA-seq into a secure database (see SOW for criteria). Documented efficiency and security of the existing database system to be used or modified including data tracking, data synchronization, data transfer and interoperability, and backup of electronically based information. The ability to provide push and or pull capability for the generated RNA-seq data to the NHLBI designated recipient. Hardware media solutions for data transmission should issues arise in network access rates.

10) Equipment and Facilities (10 pts.)

• Availability and adequacy of facilities and equipment including but not limited to RNA-seq equipment, computing facilities, sample storage facilities and backup plans, the physical security of data, samples, communications, and equipment. Plans for replacing, maintaining, and repairing equipment.

TOPIC AREA 4 - Metabolic Profiles

11) Documented Experience (20 pts.)

• Documented metabolite profiling experience with similar scale project requirements in which the organization and proposed personnel have participated (provide list of projects for the past three years; letters of support for previous metabolite profiling may be included in the Appendix).

• Demonstrated an established in-house Laboratory Information Management System (LIMS), including number of projects completed and samples processed on LIMS for the past three years.

12) Expertise and experience of key personnel (25 pts.)

• Expertise and experience of proposed personnel and organization for similar scale metabolite profiling and data management

• Commitment and capability of offerors to:

Provide cost effective metabolite profiling in quantity and quality required and adequate plans for QC/QA for quantification, and minimizing false discovery rates

13) Metabolite profiling methodology and throughput (30 pts.)

materials proposed, including reproducibility, accuracy, efficiency, capacity and success rate

• Adequacy of the proposed approach to provide the workflow needed for metabolite profiling analysis:

e.g. raw data QC, preprocessing, peak feature mapping, post-alignment processing, annotation, and prioritization. Provide a flow-chart, operational criteria, and versioning for listed tools or reference builds and standards

• Adequacy of proposed schedule to complete metabolite profiling on 500 NHLBI samples within 12 months of award

• Demonstrated ability to meet "NIH Security Best Practices for Controlled-Access Data Subject to the NIH Genomic Data Sharing (GDS) Policy" http://www.ncbi.nlm.nih.gov/projects/gap/pdf/dbgap_2b_security_procedures.pdf

• Demonstrated ability to generate metabolite profiling data within 60 calendar days after receipt of samples by the Government, or designee

• Adequacy of plan to complete metabolite profiling data at 90 days, 6 months, 9 months and 1 year

14) Feasibility of the proposed informatics management plan (15 pts.)

• Feasibility of the proposed informatics management plan for organizing and integrating metabolite profiling into a secure database (see SOW for criteria). Documented efficiency and security of the existing database system to be used or modified including data tracking, data synchronization, data transfer and interoperability, and backup of electronically based information. The ability to provide push and or pull capability for the generated metabolite profiling data to the NHLBI designated recipient.

Hardware media solutions for data transmission should issues arise in network access rates

15) Equipment and Facilities (10 pts.)

• Availability and adequacy of facilities and equipment including but not limited to metabolite profiling equipment, computing facilities, sample storage facilities and backup plans, the physical security of data, samples, communications, and equipment. Plans for replacing, maintaining, and repairing equipment