Attachment_23_Information_for_Offerors.pdf

PDF 849 KB Posted Nov 22, 2016

Attached to: Biospecimen Core Resource
Solicitation number: N02CN65002-45
Issued by: Department of Health and Human Services National Institutes of Health

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File	Type	Posted
Amendment_1_RFP_N02CN65002-45.pdf	PDF	Dec 9, 2016
Attachment_7_Business_Proposal_Instructions.pdf	PDF	Nov 22, 2016
Attachment_11_Additional_Technical_Proposal_Instructions.pdf	PDF	Nov 22, 2016
Attachment_3_General_SOW.pdf	PDF	Nov 22, 2016
Attachment_2_Proposal_Intent_Response_Sheet.pdf	PDF	Nov 22, 2016
Attachment_5_Government_Property_Schedule.pdf	PDF	Nov 22, 2016
toc.pdf	PDF	Nov 22, 2016
Attachment_6_SectionK_Representations_Certifications_Other_Statements_of_Offerors.pdf	PDF	Nov 22, 2016
Attachment_1_packaging_and_delivery_of_proposals_via_ecps_002.pdf	PDF	Nov 22, 2016
Attachment_4_Sample_TaskOrder_SOW.pdf	PDF	Nov 22, 2016

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Attachment 23 Information for Offerors

1. Task Areas A and B: Biospecimen Processing Center (BPC) and the Center for Cancer Genomics (CCG) Biorepository and Archive (CBA) Services

Lessons Learned from The Cancer Genome Atlas (TCGA) Biospecimen Core Resource (BCR)

Per objectives of any project, many lessons were learned from the TCGA project about how a BCR should operate to support a cancer genomics investigation, and are included in the Statement of Work (SOW). A summary of those lessons included:

a. The BCR was the primary day-to-day interface with tissue source sites, and as such was in the position to work with the National Cancer Institute (NCI) to understand the number of potential cases and samples available, the degree of difficulty the Tissue Source Site (TSS) would have to access those cases, and, as sample receipt began, the rate at which samples from those cases passed the quality control metrics. Therefore, the BCR was the major source of this data to TCGA project management and investigators performing genomic characterization and data analysis.

TCGA BCR systems (including informatics) required enhancement to capture and report such data in coordination with the NCI COR.

b. The number of TSSs required to meet biospecimen needs was larger than expected and the administrative requirements for TSSs participating in TCGA were atypical compared to other requirements that sites had experienced working with other programs. The BCR expended considerable effort and resources to establish the documentation prerequisite to receiving tissue and data. Such documentation included execution of Material Transfer Agreement ( MTAs) in which are embodied project policies on intellectual property, redistribution of biospecimen derivatives, and ability to receive and redistribute data that may be regulated under the Health Insurance Portability and Accountability Act (HIPAA). Additionally, the BCR receipt of specimens and data was dependent upon the independent establishment of funding for the TSS, so the BCR had to be familiar with this need and maintain constant, constructive communication with the NCI to ensure expectations were appropriately tracked in real time. This factor also required the BCR to support more resources for logistics (e.g., shipping) and for logistics training at the TSS.

c. Standard Operating Procedures (SOPs) required frequent development, review and improvement. SOPs were required to cover all processes and included results capture and other metrics to enable process improvement and to discover where processes failed in that event.

The BCR required continual process management improvements to cover all aspects of workflow.

d. Workflow informatics (e.g., Laboratory Information Management Systems or LIMS) to guide processes, and capture status and results, were required. Workflow informatics required constant technical development and improvement to support capture and reporting of developed or modified experimental protocols. Development of a BCR required capital investment in commercial LIMS and subsequent information technology (IT) support to meet the experimental protocol support, data capture and reporting requirements of the TCGA Project (the LIMS system used by the current BCR Contractor is LabVantage®). Workflow informatics was also required to be linked to production equipment with automated upload of data to the LIMS.

Bar coding of samples was essential.

e. Reporting needs for management and operations during TCGA required collecting operational and processing metrics. The BCR was required to work alongside TCGA Program Management to modify pathology and laboratory processes (and supporting informatics) in order to collect these data appropriately as program needs and metrics changed.

Attachment 23

f. New cancers being studied by TCGA necessitated development of processing customization to capture histopathological Quality Control (QC) metrics, and to most efficiently yield deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Further, variable composition and cellularity of tissues and variable rates of processing success meant that the mass of tissue per case required from a TSS could change as experience was gained. Additionally, changes over time in clinical practice have varied the size of tissue specimens being available for research use.

The BCR needed to balance the need for standardized protocols to support comparison of data across tumor types with the need for cancer-specific tissue processing protocols and their optimization. Such projects included, for example, the development of extraction protocols for highly pigmented tissues, where miRNA isolation may be compromised.

g. Characterization technologies have evolved over the course of the project. The BCR had to be able to adopt new analyte extraction and handling protocols, for example, to isolate different types (e.g., whole RNA for miRNA expression analysis) of nucleic acids for new types of characterization (e.g., sequencing for expression). The quantity of nucleic acid required also continued to change.

h. Portioning of samples increased the number of samples resulting in a higher pass rate through pathology QC. Macrodissection techniques have proven less successful, only providing a small number of additional samples into the pipeline. These techniques also slowed down production and increased costs and therefore the BCR would be encouraged to use these technologies only if appropriate but they are not likely to be broadly implemented in the future.

Additional Intellectual Property Considerations

CCG-supported genomics studies shall follow the intellectual properties considerations of the TCGA program. TCGA complies with all current National Institutes of Health (NIH) requirements including an IP policy specific to The Cancer Genome Atlas (TCGA) Intellectual Property Policy.

The goal of the TCGA Intellectual Property policy is to maximize the benefits of all work funded as part of CCG programs for the improvement of public health through discoveries of the scientific community.

TCGA Data Sharing and Data Release policies provide for a broad freedom-to-operate for all users of CCG data by rapidly placing all data in the public domain. The TCGA Intellectual Property policy ensures that this data is unencumbered by intellectual property claims. In addition to data, any algorithm produced specifically to analyze CCG data, software source code or other resource made possible under the auspices of CCG will be made available to the public domain without intellectual property restrictions.

It is expected that any data produced for CCG will be available, without requirement for licensing, for applications such as, but not necessarily limited to, the use of markers in developing assays or targets for therapeutics and diagnostics. CCG encourages broad use of this data coupled with a responsible approach to management of intellectual property derived from downstream discoveries that are consistent both with the recommendations cited in NIH’s Best Practices for the Licensing of Genomic Inventions and the NIH Research Tools Policy.

Task Area A: BPC Services List of Biospecimen Core Resource Standard Operating Procedures

1. Administrative:

A001 Chain of Custody for TCGA Samples.doc

A002 Assigning Specimen Identification.doc

A003 Patient Withdrawal.docx

A004 Preparation, Numbering, Approval, and Review of Standard Operating Procedures.docx

A005 LabVantage User Manual.docx

A007 Principal Investigator (Director) Qualifications, Responsibilities, and Delegation.doc

A008 Continuing Education.doc

A009 Training and Competency Evaluation.doc

A011 Confidentiality.doc

A013 Incidents, Feedback and Event Reporting.doc

A014 Compliance with Laws, Contractual Obligations, and Terms of Accreditation.doc

A015 Brady Labeler Cleaning .docx

A016 Tracking Capital and Sensitive Equipment.docx

A017 Notifications from Vendors.doc

A018 Relabeling TCGA Samples.docx

A019 Ordering, Receiving, and Stocking Suplies.docx

2. Histology:

H001 Hematoxylin and Eosin Frozen Section Stainer.doc

H002 Cryostat Cleaning and Decontamination.doc

H004 HE_Stainer_Cleaning_and_Decontamination.docx

H005 Automated WG Stain of Leukemia Slides.doc

H006 Sectioning Frozen Tissue Sample in Histology.docx

H007 Microtome and Razor Blades Disposal.doc

H008 Monitoring Laboratory + Equipment Temperatures.doc

H009 Reagent Tracking in the BCR Histology Lab.doc

H010 Receiving Tissue in Histology from Logistics.doc

H013 Preparation of Paraffin Slides and Scrolls.docx

a. Information Systems:

I001 Informatics - Custom IT System.docx

I002 IT System Integrity Security and Inventory Validation.docx

I003 IT System Testing and Tracking Changes mg.docx

I005 Access Data Input ID Interface Result Integrity.docx

I006 Clinical Data XML Submission.pdf

I007 Biospecimen Data XML Submission.doc

I010 Application Access and Application User Audits.docx

I011Creating and Administering User IDs and Passwords in OpenClinica.docx

I013Creation of Upload Spreadsheets for OpenClinica Data Import.doc

I014 - Contingency Planning.docx

b. Other:

C003 Quality Control of Incoming BCR Shipments by Clinical Outreach.docx

C006 Disqualification of TCGA Cases Prior to BCR Processing.doc

C009 Confirmation of Diagnosis of Frozen Section.docx

C028 Qualification Reporting and Quality Control.doc

C032 Quality Control of Case Qualification Metrics for Analyte Shipment.docx

c. Logistics:

L001 Using the Mettler Scale.doc

L003 Cryocart Filling and Cleaning.doc

L005 Document Archiving.doc

L006 Proof of Sample Disposal.doc

L007 Creating a Shipment.docx

L010 Shipping Specimens on Dry Ice.docx

L012 Receiving WGA Plates from Qiagen.doc

L013 Top and Diagnostic Slides.doc

L014 Naughty List and Annotations Database.doc

L015 Histology Internal Transfer Logs.docx

L016 Preparing Frozen Tissue for Molecular Analysis.doc

L017 Preparation of Tissue Samples for Proteome Characterization Centers (PCC).docx

L019 Returning Specimens to a Tissue Source Site (TSS).docx

L020 Sectioning and Portioning Frozen Tissue Samples in Logistics.doc

L021 Accessioning of FFPE Blocks.doc

L022 Shipping and Receiving Cryoports.docx

L023 Unstained Slides Submitted.docx

d. Molecular Processing:

M001 DNA_RNA AllPrep and mirVana two Column Isolation.doc

M002 RNA Nano Assay.doc

M003 Gel Electrophoresis With the E-GEL System.doc

M006 Normalization of Whole Genome Amplification Samples.doc

M010 Tissue Matching by SNP Analysis.doc

M011 Pooling of Molecular Analytes from Different Tissue Portions.doc

M014 DNA Extraction from Blood with QIAamp MIDI Kit.doc

M015 DNA Extraction with QIAamp MINI Kit.doc

M016 Culturing and Harvesting Cell Lines.docx

M017 PicoGreen DNA Quantification (Manual).doc

M018 Shipping Analytes to Downstream Centers.doc

M019 DNA_RNA Extraction with AllPrep (DNA) and mirVana (Total RNA with small RNA) 3 Column- Modified Melanoma Protocol.doc

M020 Nine Marker Microsatellite Instability (MSI) Analysis by Polymerase Chain Reaction.doc

M021 Molecular Identity Investigations.doc

M022 DNA_RNA Extraction with AllPrep (DNA) and mirVana (Total RNA with small RNA) Modified AML Protocol.doc

M024 Scinomix Tube Labeler.doc

M025 Case Metrics Review.doc

M026 Monitoring Molecular Lab Quality Indicators.doc

M027 FFPE RNA-DNA Co-Isolation.doc

M028 Confirming Specimen Identity using the Identifiler SSTR Multiplex Assay.docx

e. Pathology Verification:

P001 Data Entry of Pathology Review Forms.doc

P002 Quality Control of Pathology Paper Forms.doc

P003 Virtual Imaging for Pathology Education Research (VIPER) Quality Control.doc

P005 Daily Case Creation List in Virtual Microscopy (VM).docx

P006 Pathology Review Invoicing Payments.docx

P007 Receiving Whole Slide Images.doc

f. Safety:

SAF-001 Responsibility and Overview of Biospecimen Core Resource (BCR) Safety.docx

SAF-002 Chemical Hazards and Safety.docx

SAF-003 Chemical Hygiene Plan.docx

SAF-004 Compressed Gases Hazards and Safety.docx

SAF-005 Electrical Hazards and Safety.docx

SAF-006 Ergonomics.docx

SAF-007 Fire Prevention and Control.docx

SAF-008 General Requirements for Personal and Lab Safety.doc

SAF-009 Hazardous Waste Disposal.docx

SAF-010 Laboratory Exposure Plan.docx

SAF-011 Microbiological Hazards and Safety.docx

SAF-013 Biohazard and Chemical Waste Disposal.docx

SAF-014 Warning Signs and Labels.docx

SAF-015 Disaster and Evacuation Plan.docx

SAF-016 Electrical Power Outage.docx

SAF-018 Biohazard and Chemical Spill Clean-up.docx

- Sample forms

- Sample alternate data form: CCLE CSV

B. Task Area B: CBA Services List of Biospecimen Core Resource Standard Operating Procedures