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FRED HUTCHINSON CANCER CENTER
SEATTLE, WA, 98109
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Prime contracting experience
12 records from government sources. Past participation is not evidence of current teaming interest.
| Role | Agency | Description | Vehicle | Obligated | Action date | Period |
|---|---|---|---|---|---|---|
| Prime | Department of Veterans Affairs Department of Veterans Affairs | CELL STORAGE OF CRYOPRESERVED CELLS | — | $524,798 | Oct 16, 2026 | Jul 1, 2024 – Jun 30, 2026 |
| Prime | Department of Health and Human Services National Institutes of Health | IGF::OT::IGF CORE INFRASTRUCTURE SUPPORT FOR SURVEILLANCE, EPIDEMIOLOGY, AND END RESULTS (SEER) | 75N91018D00004USAspending | $39,002,751 | Aug 31, 2026 | May 1, 2018 – Apr 30, 2027 |
| Prime | Department of Health and Human Services National Institutes of Health | THE NATIONAL CANCER INSTITUTE'S (NCI) CANCER INFORMATION SERVICE (CIS) IS AN EXISTING AND ESTABLISHED CRITICAL COMPONENT OF HEALTHCARE DELIVERY, PARTICULARLY IN FACILITATING PUBLIC ACCESS TO CLINICAL TRIALS. ESTABLISHED UNDER THE NATIONAL CANCER | — | $14,298,742 | Aug 17, 2026 | May 1, 2025 – Apr 30, 2027 |
| Prime | Department of Health and Human Services National Institutes of Health | SEER*EDUCATE BASE AWARD | 75N91018D00004USAspending | $1,399,684 | Aug 11, 2026 | Sep 17, 2024 – Aug 16, 2027 |
| Prime | Department of Health and Human Services National Institutes of Health | WOMEN'S HEALTH INITIATIVE (WHI) - CLINICAL COORDINATING CENTER (CCC) - TASK AREA A | 75N92021D00001USAspending | $47,182,207 | Jul 21, 2026 | Feb 1, 2021 – Jan 31, 2026 |
| Prime | Department of Health and Human Services National Institutes of Health | WOMEN'S HEALTH INITIATIVE (WHI) CLINICAL COORDINATING CENTER - TASK AREA A AND A2 | 75N92021D00001USAspending | $10,225,386 | Jun 11, 2026 | Feb 1, 2026 – Jan 31, 2027 |
| Prime | Department of Health and Human Services National Institutes of Health | TASK AREA_A.3 - WHI BIOREPOSITORY REDUCTION AND CONSOLIDATION - WOMEN'S HEALTH INITIATIVE (WHI) - CLINICAL COORDINATING CENTER (CCC) | 75N92021D00001USAspending | $745,423 | Jun 5, 2025 | Sep 29, 2021 – Mar 31, 2023 |
| Prime | Department of Health and Human Services National Institutes of Health | NATIONAL CANCER INSTITUTE'S CONTACT CENTER | — | $36,974,020 | May 16, 2025 | May 1, 2020 – Apr 30, 2025 |
| Prime | Department of Health and Human Services National Institutes of Health | IGF::OT::IGF - TARGETED CLINICAL RESEARCH TO ADDRESS SELECT VIRAL INFECTIONS | — | $5,635,565 | Dec 10, 2024 | Jul 1, 2016 – Dec 31, 2025 |
| Prime | Department of Health and Human Services Centers for Disease Control and Prevention | CONSULTATION AND CANCER RESEARCH SERVICES | — | $377,278 | Nov 1, 2024 | Aug 11, 2022 – Aug 31, 2023 |
| Prime | Department of Health and Human Services National Institutes of Health | SEER*EDUCATE | 75N91018D00004USAspending | $2,475,522 | Aug 15, 2024 | Sep 13, 2019 – Sep 16, 2024 |
| Prime | Department of Health and Human Services National Institutes of Health | WOMEN'S HEALTH INITIATIVE - CLINICAL COORDINATING CENTER: TASK AREA B - LONG LIFE STUDY VISIT 2 LIMITED HOME VISIT | 75N92021D00001USAspending | $4,291,793 | May 30, 2024 | Mar 4, 2022 – Sep 30, 2024 |
Contract vehicles are shown only when present in the source record. Linked award numbers and vehicles open the authoritative record on USAspending.gov.
Subcontracting experience
25 records from government sources. Past participation is not evidence of current teaming interest.
| Role | Agency | Description | Vehicle | Obligated | Action date | Period |
|---|---|---|---|---|---|---|
| Subcontractor | Department of Health and Human Services | BLOOM LAB
THE BLOOM LAB WILL PERFORM EXPERIMENTAL AND COMPUTATIONAL WORK TO CHARACTERIZE INFLUENZA VIRUS
EVOLUTION. IN PROJECT 3, THEY WILL USE MUTATIONAL ANTIGENIC PROFILING TO EXPERIMENTALLY MAP THE
EFFECTS OF VIRAL MUTATIONS ON IMMUNE RECOGNITION.
BEDFORD LAB
THE BEDFORD LAB AT THE FRED HUTCH WILL BE RESPONSIBLE FOR IMPLEMENTATION OF PROJECT 3, AIM 2
(PREDICT AND VISUALIZE WHICH CIRCULATING CLADES OF INFLUENZA WILL DOMINATE USING PHYLOGENETIC
ANALYSES, AGE-STRUCTURED SEROLOGY, MUTATIONAL ANTIGENIC PROFILING, AND VACCINATION COVERAGE). FOR
THIS, THE BEDFORD LAB WILL DEVELOP AND IMPLEMENT A PREDICTIVE MODEL THAT INCORPORATES DATA
GENERATED BY THE BLOOM LAB FOR PROJECT 3, AIM 1 AS WELL AS OTHER SEROLOGICAL DATA GENERATED BY
THE CENTER. THE BEDFORD LAB WILL INTEGRATE THIS SEROLOGICAL DATA WITH PUBLICLY AVAILABLE INFLUENZA
GENETIC SEQUENCE DATA. THIS MODEL WILL ESTIMATE THE EVOLUTIONARY TRAJECTORY OF THE INFLUENZA VIRUS
POPULATION. 504429 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: PA Parent award description: AWARD OF THE BASE TO UPENN FOR CEIRR CONTRACT 75N93021C00015. THIS CONTRACT WILL SUPPORT THE NIAID CENTERS OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (CEIRR) View parent award on USAspending | — | $590,411 | May 20, 2026 | — – — |
| Subcontractor | Department of Health and Human Services | 4.4.1 FRED HUTCH COMPREHENSIVE IMMUNOLOGICAL PROFILES OF INFLUENZA INFECTION SUSCEPTIBILITY (THOMAS) (MOD 29) GR-0011277-PO259843 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: TN Parent award description: AWARD OF THE BASE TO ST. JUDE FOR CEIRR CONTRACT 75N93021C00016. THIS CONTRACT WILL SUPPORT NIAID CENTERS OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (CEIRR). View parent award on USAspending | — | $334,369 | May 1, 2026 | — – — |
| Subcontractor | Department of Health and Human Services | OPTION 16D: CURATING THE COVID CODEX FOR CORRELATES (THOMAS) (MOD 21) GR-0011132-PO243611 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: TN Parent award description: AWARD OF THE BASE TO ST. JUDE FOR CEIRR CONTRACT 75N93021C00016. THIS CONTRACT WILL SUPPORT NIAID CENTERS OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (CEIRR). View parent award on USAspending | — | $254,583 | Mar 27, 2026 | — – — |
| Subcontractor | Department of Health and Human Services | 4.4.1 COMPREHENSIVE IMMUNOLOGICAL PROFILES OF INFLUENZA INFECTION SUSCEPTIBILITY (THOMAS) GR-0011134-PO243614 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: TN Parent award description: AWARD OF THE BASE TO ST. JUDE FOR CEIRR CONTRACT 75N93021C00016. THIS CONTRACT WILL SUPPORT NIAID CENTERS OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (CEIRR). View parent award on USAspending | — | $202,263 | Mar 17, 2026 | — – — |
| Subcontractor | Department of Health and Human Services | 3. STATEMENT OF WORK
1. SCOPE: THE UNIVERSITY OF PENNSYLVANIA CENTER OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE
(PENN-CEIRR) BRINGS TOGETHER RENOWNED RESEARCHERS AND CUTTING-EDGE TECHNOLOGIES TO DISCOVER NEW
INFORMATION AND TOOLS NEEDED TO DECREASE THE MORTALITY AND MORBIDITY ASSOCIATED WITH INFLUENZA
VIRUSES AND OTHER PATHOGENS.
2. TECHNICAL REQUIREMENTS. INDEPENDENTLY, AND NOT AS AN AGENT OF THE GOVERNMENT, THE CONTRACTOR
SHALL FURNISH ALL NECESSARY SERVICES, QUALIFIED PROFESSIONAL, TECHNICAL, AND ADMINISTRATIVE
PERSONNEL, MATERIAL, EQUIPMENT AND FACILITIES, NOT OTHERWISE PROVIDED BY THE GOVERNMENT UNDER THE
TERMS OF THIS CONTRACT, AS NEEDED TO PERFORM THE TASKS SET FORTH BELOW. SPECIFICALLY, THE CONTRACTOR SHALL: 503816 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: PA Parent award description: AWARD OF THE BASE TO UPENN FOR CEIRR CONTRACT 75N93021C00015. THIS CONTRACT WILL SUPPORT THE NIAID CENTERS OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (CEIRR) View parent award on USAspending | — | $231,180 | Jan 16, 2026 | — – — |
| Subcontractor | Department of Health and Human Services | THE CISNET COLORECTAL CANCER WORKING GROUP SHALL CONDUCT A DECISION ANALYSIS USING A COLLABORATIVE MODELING APPROACH TO SUPPORT THE USPSTF SCREENING FOR COLORECTAL CANCER RECOMMENDATION STATEMENT. AS PART OF THIS WORK, A RESEARCH PLAN, DECISION ANALYSIS REPORT, AND MANUSCRIPT WILL BE PRODUCED. CHR0000850-FREDHUTCH Parent award context Parent award agency: Department of Health and Human Services · Office of the Assistant Secretary for Financial Resources Parent award NAICS: 541715 Parent award performance state: OR Parent award description: SYSTEMATIC EVIDENCE REVIEWS TO SUPPORT THE U.S. PREVENTIVE SERVICES TASK FORCE (USPSTF) View parent award on USAspending | 75Q80125D00004USAspending | $220,002 | Jan 16, 2026 | — – — |
| Subcontractor | Department of Health and Human Services | 3. STATEMENT OF WORK
1. SCOPE: THE UNIVERSITY OF PENNSYLVANIA CENTER OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (PENN-CEIRR) BRINGS TOGETHER RENOWNED RESEARCHERS AND CUTTING-EDGE TECHNOLOGIES TO DISCOVER NEW INFORMATION AND TOOLS NEEDED TO DECREASE THE MORTALITY AND MORBIDITY ASSOCIATED WITH INFLUENZA VIRUSES AND OTHER PATHOGENS.
2. TECHNICAL REQUIREMENTS. INDEPENDENTLY, AND NOT AS AN AGENT OF THE GOVERNMENT, THE CONTRACTOR SHALL FURNISH ALL NECESSARY SERVICES, QUALIFIED PROFESSIONAL, TECHNICAL, AND ADMINISTRATIVE PERSONNEL, MATERIAL, EQUIPMENT AND FACILITIES, NOT OTHERWISE PROVIDED BY THE GOVERNMENT UNDER THE TERMS OF THIS CONTRACT, AS NEEDED TO PERFORM THE TASKS SET FORTH BELOW. SPECIFICALLY, THE CONTRACTOR SHALL: 503779 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: PA Parent award description: AWARD OF THE BASE TO UPENN FOR CEIRR CONTRACT 75N93021C00015. THIS CONTRACT WILL SUPPORT THE NIAID CENTERS OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (CEIRR) View parent award on USAspending | — | $121,274 | Jan 15, 2026 | — – — |
| Subcontractor | Department of Health and Human Services | IMPLEMENT, OPERATIONALIZE, AND MAINTAIN INFRASTRUCTURE TO SUPPORT MDNET MYELOMATCH ASSAYS AND ANALYSES; CYTOGENETIC ANALYSIS OF MDNET MYELOMATCH SPECIMENS; AND NCI MYELOID ASSAY (GENEXUS MYELOID NGS) ANALYSIS OF MDNET MYELOMATCH SPECIMENS. 20X088F3 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: MD Parent award description: MD NET View parent award on USAspending | 75N91019D00024USAspending | $10,500,418 | Dec 1, 2025 | — – — |
| Subcontractor | Department of Health and Human Services | IN YEAR 7, THE EDLEFSEN GROUP AT FRED HUTCHINSON CANCER CENTER (FRED HUTCH) WILL PROVIDE DATA QUALITY ASSURANCE PROCESSES AND ENSURE THE TIMELINESS AND ACCURACY OF STATISTICAL ANALYSES AND THE EFFECTIVE COMMUNICATION OF RESULTS. FRED HUTCH WILL DEVELOP REPRODUCIBLE RESEARCH ANALYSIS SOFTWARE AND NOVEL ANALYTICAL METHODS. IN ADDITION, FRED HUTCH WILL CONTRIBUTE TO THE DESIGN AND PROPER STATISTICAL CONDUCT OF ALL AIMS, AND ASSOCIATED DATA. DR. EDLEFSEN WILL COLLABORATE WITH AN INDEPENDENT CONTRACTOR BASED IN GDANSK, POLAND, TO PROVIDE BIOINFORMATICS EXPERTISE ON THE PROJECT. FRED HUTCH IS CONDUCTING THESE ACTIVITIES ON AN ONGOING BASIS AND CONDUCTING ACTIVITIES MEETING THESE DESCRIPTIONS IN ALL YEARS OF THE CONTRACT. SUB00002530 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541714 Parent award performance state: WA Parent award description: IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB) View parent award on USAspending | — | $230,009 | Nov 14, 2025 | — – — |
| Subcontractor | Department of Health and Human Services | IMPLEMENT, OPERATIONALIZE, AND MAINTAIN INFRASTRUCTURE TO SUPPORT MDNET MYELOMATCH ASSAYS AND ANALYSES; CYTOGENETIC ANALYSIS OF MDNET MYELOMATCH SPECIMENS; AND NCI MYELOID ASSAY (GENEXUS MYELOID NGS) ANALYSIS OF MDNET MYELOMATCH SPECIMENS. 20X088F3 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: MD Parent award description: MD NET View parent award on USAspending | 75N91019D00024USAspending | $306,961 | Oct 31, 2025 | — – — |
| Subcontractor | Department of Health and Human Services | THIS STATEMENT OF WORK (SOW) OUTLINES THE ACTIVITIES THAT FRED HUTCHINSON CANCER CENTER (FHCC EDLEFSEN) WILL BE PERFORMING. NOTE THAT THE TASK NUMBERS BELOW REFLECT THE NUMBERING OF THE OVERALL ACTIVITIES IN THE PRIME CONTRACT.
ALTHOUGH THIS SOW DETAILS THE COMPLETE SUITE OF PROPOSED WORK, THE TASKS ASSOCIATED WITH THIS CONTRACT ITERATION ARE LIMITED TO THE SPECIFIC ACTIVITIES OUTLINED BELOW, DELIVERABLES FOR THIS CONTRACT PERIOD ARE HIGHLIGHTED.
YEAR 6 (BASE) €€Œ EDLEFSEN
IN YEAR 6, THE EDLEFSEN GROUP AT FRED HUTCHINSON CANCER CENTER (FRED HUTCH) WILL PROVIDE DATA QUALITY ASSURANCE PROCESSES AND ENSURE THE TIMELINESS AND ACCURACY OF STATISTICAL ANALYSES AND THE EFFECTIVE COMMUNICATION OF RESULTS. FRED HUTCH WILL DEVELOP REPRODUCIBLE RESEARCH ANALYSIS SOFTWARE AND NOVEL ANALYTICAL METHODS. IN ADDITION, FRED HUTCH WILL CONTRIBUTE TO THE DESIGN AND PROPER STATISTICAL CONDUCT OF ALL AIMS, AND ASSOCIATED DATA. DR. EDLEFSEN WILL COLLABORATE WITH AN INDEPENDENT CONTRACTOR BASED IN GDANSK, POLAND, TO PROVIDE BIOINFORMATICS EXPERTISE ON THE PROJECT. FRED HUTCH IS CONDUCTING THESE ACTIVITIES ON AN ONGOING BASIS AND CONDUCTING ACTIVITIES MEETING THESE DESCRIPTIONS IN ALL YEARS OF THE CONTRACT. 13487SUB Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541714 Parent award performance state: WA Parent award description: IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB) View parent award on USAspending | — | $281,067 | Oct 17, 2025 | — – — |
| Subcontractor | Department of Health and Human Services | THIS STATEMENT OF WORK (SOW) OUTLINES THE ACTIVITIES THAT FRED HUTCHINSON CANCER CENTER (FHCC) WILL BE PERFORMING. NOTE THAT THE TASK NUMBERS BELOW REFLECT THE NUMBERING OF THE OVERALL ACTIVITIES IN THE PRIME CONTRACT.
ALTHOUGH THIS SOW DETAILS THE COMPLETE SUITE OF PROPOSED WORK, THE TASKS ASSOCIATED WITH THIS CONTRACT ITERATION ARE LIMITED TO THE SPECIFIC ACTIVITIES OUTLINED BELOW, DELIVERABLES FOR THIS CONTRACT PERIOD ARE HIGHLIGHTED.
THROUGH THE EXECUTION OF THIS CONTRACT, WE WILL EXAMINE BASIC INDUCTION OF INNATE AND ADAPTIVE IMMUNITY FROM VACCINATION, INCLUDING STUDIES THAT ADDRESS NONTUBERCULOUS MYCOBACTERIA (NTM) INTERFERENCE, RNA VACCINE DELIVERY, PRIME-BOOST REGIMENS (INCLUDING BCG PRE-EXPOSURE), TRANSCRIPTOMIC HOST SIGNATURES, SYSTEMS BIOLOGY AND DURABLE IMMUNE MEMORY FOR THE FURTHER ADVANCEMENT OF THE EFFORT TO DESIGN AND EVALUATE AN EFFICACIOUS VACCINE AGAINST MYCOBACTERIUM TUBERCULOSIS (M.TB)
THE WORK UNDER THIS CONTRACT MAY INCLUDE THE POSSIBLE DISTRIBUTION OF DE-IDENTIFIED HUMAN SUBJECT PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMC), SERUM, AND OTHER CLINICAL SAMPLES TO SCRI AND THE PHOENIX PARTNERS. NHP SAMPLES AND/OR DOWNSTREAM DATA MAY BE SHARED WITH THE PARTNERS ON THIS CONTRACT.
OPTION 3 ACTIVITIES: EVALUATE OPTIMIZED M.TB VACCINE CANDIDATES FOR SAFETY, IMMUNOGENICITY AND EFFICACY IN THE NHP MODEL OF TB
TASK 3.5 TRANSCRIPTOMIC ANALYSIS OF NHP SAMPLES.
FHCC WILL EXECUTE GENE EXPRESSION PROFILING WITH RNASEQ/NANOSTRING ASSAYS ON NHP SAMPLES GENERATED IN OPTION 3 AT UKHSA. TRANSCRIPTOMIC ANALYSIS WILL BE FOCUSED ON IDENTIFYING A PERIPHERAL BLOOD SURROGATE ENDPOINT FOR THE M.TB ERDMAN ULDA CHALLENGE OUTCOMES. THE INITIAL UNBIASED RNA SEQUENCING APPROACH WILL USE WHOLE-BLOOD SAMPLES FROM PRE- AND POST-CHALLENGE TIME POINTS. SPECIFICALLY, WE WILL LOOK FOR TRANSCRIPTS THAT ARE CORRELATED WITH M.TB COLONY FORMING UNITS (CFU) AND M.TB QPCR ASSAYS FROM BRONCHOALVEOLAR LAVAGE (BAL), THE PRIMARY CHALLENGE OUTCOMES. IN ADDITION TO ABSOLUTE ABUNDANCE AT POST-CHALLENGE TIME POINTS, WE WILL ALSO LOOK FOR CHANGES IN TRANSCRIPT ABUNDANCE RELATIVE TO THE DAY OF CHALLENGE AS A POTENTIAL CORRELATE OF CHALLENGE OUTCOME. AS WE BUILD A MODEL TO PREDICT CHALLENGE OUTCOME FROM THESE GENE EXPRESSION MEASURES WE WILL SPECIFICALLY CONSIDER TRANSCRIPTS THAT HAVE PREVIOUSLY BEEN IDENTIFIED AS PREDICTORS OF PROGRESSION TO TB DISEASE, SUCH AS TYPE I IFN-RELATED GENES WHOSE EXPRESSION INCREASES DURING DISEASE PROGRESSION. THE HUMAN EXPRESSION SIGNATURES WILL BE EVALUATED IN NHPS AND VICE VERSA; ADDITIONALLY, A JOINT MODEL WILL BE DEVELOPED, ALLOWING FOR DIFFERENCES IN NHP AND HUMAN ASSOCIATIONS, WHILE IDENTIFYING A COMMON GENE SIGNATURE. ONCE TRANSCRIPTS OR GENES HAVE BEEN IDENTIFIED, A TARGETED CROSS-SPECIES NANOSTRING PANEL WILL BE DEVELOPED FOR EVALUATION IN THE SMALL ANIMAL MODELS AS WELL AS IN FUTURE NHP AND CLINICAL TRIALS. WE PLAN TO DEVELOP A NANOSTRING NCOUNTER GENE PANEL WHICH CAN ACCOMMODATE UP TO 800 GENES AND WOULD BE SIGNIFICANTLY MORE COST EFFECTIVE THAN RNA SEQUENCING. ALTERNATIVELY, DEPENDING ON THE COMPLEXITY OF THE GENE PANEL, IT COULD BE DEVELOPED AS A 96 TRANSCRIPT/GENE (INCLUDING HOUSEKEEPING GENES) QPCR BIOMARK FLUIDIGM ASSAY.
TASK 3.7 COMPARE IMMUNE PROFILES IN NHP, SMALL ANIMAL MODELS AND HUMANS TO IDENTIFY CORRELATES OF PROTECTION.
SUBTASK 3.7.4 INTEGRATED ANALYSIS AND DYNAMICAL SYSTEMS MODELING OF EXPERIMENTAL IMMUNOLOGY DATA ACROSS ALL SPECIES
EXPERIMENTAL DATA WILL BE TRANSFERRED TO THE STATISTICAL CENTER AND A FORMAL INTER-SITE AND INTER-SPECIES VARIABILITY ASSESSMENT WILL BE PERFORMED. VARIABILITY WILL BE DETERMINED USING COEFFICIENTS OF VARIATION (CV), MEAN AND STANDARD DEVIATION OF RESPONSES. DESIRED CUT-OFFS FOR ACCEPTABLE CVS WILL BE PRE-SPECIFIED FOR EACH ASSAY. EFFORT IN THE BASE PERIOD WILL HAVE BEEN MADE TO STANDARDIZE THE ASSAYS AND HARMONIZATION ASSESSMENTS WILL HAVE BEEN REPEATED IF CVS DID NOT MEET THE CUT OFF.
IMMUNOGENICITY AND SYSTEMS BIOLOGY: INNATE AND ADAPTIVE IMMUNITY, INCLUDING EX-V SUB00002493 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: WA Parent award description: IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB) View parent award on USAspending | — | $456,623 | Sep 10, 2025 | — – — |
| Subcontractor | Department of Health and Human Services | THE SCOPE OF THIS WORK IS TO ADAPT THE IO-MASTER (IO-1, IO-2, AND IO-3) AND IO-4 ASSAYS FOR PARALLEL REACTION MONITORING. THE WORK SHALL INCLUDE CELL LINE AND PEPTIDE TESTING, DESIGN AND PRELIMINARY OPTIMIZATION OF PRM ASSAYS FOR CELL LINES, CLINICAL SAMPLE PREPARATION, OPTIMIZATION OF PRM ASSAYS FOR CLINICAL SAMPLES, AND VALIDATING THE PRM ASSAYS. UPDATES WILL BE PROVIDED TO THE LEIDOS BIOMEDICAL RESEARCH, INC. (LEIDOS BIOMED) TECHNICAL PROJECT MANAGER (TPM) AT MONTHLY TELECONFERENCES TO ENSURE THE WORK IS ON SCHEDULE AND MEETS CPTAC QUALITY STANDARDS. SEE CPTAC DCC WEBSITE FOR CPTAC STANDARD DETAILS: HTTPS://CPTAC-DATA-PORTAL.GEORGETOWN.EDU/CPTAC/STUDY/DISCLAIMER. 25X069F Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: MD Parent award description: N/A View parent award on USAspending | 75N91019D00024USAspending | $445,362 | May 5, 2025 | — – — |
| Subcontractor | Department of Health and Human Services | STATEMENT OF WORK – FRED HUTCHINSON CANCER RESEARCH CENTER
BLOOM LAB
THE BLOOM LAB WILL PERFORM EXPERIMENTAL AND COMPUTATIONAL WORK TO CHARACTERIZE INFLUENZA VIRUS
EVOLUTION. IN PROJECT 3, THEY WILL USE MUTATIONAL ANTIGENIC PROFILING TO EXPERIMENTALLY MAP THE
EFFECTS OF VIRAL MUTATIONS ON IMMUNE RECOGNITION. IN THE COMPUTATIONAL CORE, THEY WILL DEVELOP
TOOL TO ANALYZE AND VISUALIZE THE EFFECTS OF VIRAL MUTATIONS.
BEDFORD LAB
THE BEDFORD LAB AT THE FRED HUTCH WILL BE RESPONSIBLE FOR IMPLEMENTATION OF PROJECT 3, AIM 2
(PREDICT AND VISUALIZE WHICH CIRCULATING CLADES OF INFLUENZA WILL DOMINATE USING PHYLOGENETIC
ANALYSES, AGE-STRUCTURED SEROLOGY, MUTATIONAL ANTIGENIC PROFILING, AND VACCINATION COVERAGE). FOR
THIS, THE BEDFORD LAB WILL DEVELOP AND IMPLEMENT A PREDICTIVE MODEL THAT INCORPORATES DATA
GENERATED BY THE BLOOM LAB FOR PROJECT 3, AIM 1 AS WELL AS OTHER SEROLOGICAL DATA GENERATED BY
THE CENTER. THE BEDFORD LAB WILL INTEGRATE THIS SEROLOGICAL DATA WITH PUBLICLY AVAILABLE INFLUENZA
GENETIC SEQUENCE DATA. THIS MODEL WILL ESTIMATE THE EVOLUTIONARY TRAJECTORY OF THE INFLUENZA VIRUS
POPULATION.
THE BEDFORD LAB WILL ALSO BE RESPONSIBLE FOR CONTRIBUTING KEY COMPONENTS TO THE MODELING AND
COMPUTATIONAL CORE. THIS PRIMARILY CONSISTS OF USING THE EXISTING NEXTSTRAIN FRAMEWORK TO
SUPPORT ANALYSIS AND SHARING OF DATA GENERATED BY THE CENTER. THE BEDFORD LAB ALREADY WORKS
CLOSELY WITH WHO COLLABORATING CENTERS TO INTEGRATE AND ANALYZE INFLUENZA SEROLOGICAL AND
SEQUENCE DATA. THE INTERACTION WITH THE CENTER SHOULD BE SIMILAR.
THE BEDFORD LAB WILL DEVELOP A COMPUTATIONAL PREDICTIVE MODEL TO (1) ESTIMATE THE HUMAN
POPULATION IMMUNE LANDSCAPE AGAINST DIFFERENT STRAINS OF SEASONAL INFLUENZA AND (2) PREDICT
UPCOMING STRAIN DYNAMICS FOR THE INFLUENZA VIRUS POPULATION. DATA TO INFORM (1) WILL BE INTEGRATED
FROM THE DEEP MUTATIONAL SCANNING (DMS) EXPERIMENTS CONDUCTED BY THE BLOOM LAB ALONGSIDE
OTHER SEROLOGICAL DATA GENERATED BY OTHER STUDIES IN THE CENTER. WITH AN ESTIMATE OF POPULATION
IMMUNITY IN HAND, WE WILL INFER FITNESS VALUES FOR CIRCULATING VIRUSES AND USE THESE FITNESS VALUES
TO PREDICT WHETHER STRAINS INCREASE IN FREQUENCY OR DECLINE. THIS MODEL WILL BE IMPLEMENTED IN AN
OPEN SOURCE PYTHON FRAMEWORK FOLLOWING OUR EXISTING STRAIN FORECASTING CODEBASE. THE PRIMARY
ADDITIONS FOR THE CURRENT PROJECT ARE TO: (1) INTEGRATE HUMAN POPULATION IMMUNITY THROUGH DMS
AND SEROLOGICAL DATA AND (2) INCORPORATE A GEOGRAPHICALLY STRUCTURED VIRUS POPULATION. THIS
MODEL WILL BE RUN CONTINUALLY AS NEW DATA BECOMES AVAILABLE AND UP-TO-DATE FORECASTS PROVIDED
FROM THE NEXTSTRAIN.ORG WEBSITE.
THE BEDFORD LAB WILL EXTEND THE NEXTSTRAIN PLATFORM TO INTEGRATE AND SHARE DATA GENERATED BY
THE CENTER. THE BEDFORD LAB WILL CREATE A NEW CEIRR NEXTSTRAIN GROUP THAT WILL HOUSE ALL THE
CEIRR ANALYSES. THIS GROUP ALLOWS FOR BOTH PUBLIC DATASETS AND FOR PRIVATE DATASETS, BOTH OF
WHICH SHOULD BE USEFUL FOR THESE PURPOSES. THE BEDFORD LAB WILL ALSO HOUSE A DATABASE OF
SEROLOGICAL AND SEQUENCE DATA FOR CENTER PROJECTS CORRESPONDING TO THE WAY THE BEDFORD LAB
CURRENTLY HOUSES WHO COLLABORATING CENTER DATA. 502355 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: PA Parent award description: AWARD OF THE BASE TO UPENN FOR CEIRR CONTRACT 75N93021C00015. THIS CONTRACT WILL SUPPORT THE NIAID CENTERS OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (CEIRR) View parent award on USAspending | — | $571,602 | Apr 11, 2025 | — – — |
| Subcontractor | Department of Health and Human Services | SCOPE OF WORK FOR BLOOM LAB (FRED HUTCH CANCER CENTER) FOR SAVE OPTION “DEEP
MUTATIONAL SCANNING OF HOW MUTATIONS TO THE SARS-COV-2 SPIKE AƯECT ACE2 BINDING”
SARS-COV-2’S EVOLUTION OVER THE LAST 4.5 YEARS HAS INVOLVED THE REPEATED EMERGENCE OF
NEW VARIANTS WITH AMINO-ACID MUTATIONS IN THE SPIKE, ESPECIALLY IN THE RECEPTOR-BINDING
DOMAIN (RBD) AND N-TERMINAL DOMAIN (NTD). THIS EVOLUTION IS DRIVEN IN SUBSTANTIAL PART BY
TWO FORCES: PRESSURE FOR ANTIGENIC MUTATIONS THAT ESCAPE ANTIBODY NEUTRALIZATION AND
THEREBY ENABLE THE VIRUS TO REINFECT INDIVIDUALS WITH IMMUNITY FROM PRIOR
INFECTIONS/VACCINATIONS, AND PRESSURE FOR THE SPIKE TO MAINTAIN THE BINDING TO ACE2
RECEPTOR THAT IS CRUCIAL FOR VIRAL CELL ENTRY.
THE WORK IN THE BLOOM LAB WILL USE A FULL-SPIKE PSEUDOVIRUS DEEP MUTATIONAL SCANNING
SYSTEM TO MEASURE HOW ALL MUTATIONS TO THE SPIKE OF RECENT SARS-COV-2 VARIANTS AƯECT
ACE2 BINDING (FOR DETAILS ON THE APPROACH THAT WILL BE USED, SEE DADONAITE ET AL, NATURE,
631:617-626, 2024). BRIEFLY, WE WILL CHOOSE THE DOMINANT SARS-COV-2 VARIANT, CONSTRUCT A
LIBRARY CONTAINING ALL TOLERATED AMINO-ACID MUTATIONS THAT VARIANT’S SPIKE, GENERATE
PSEUDOVIRUSES CARRYING THOSE MUTANTS, AND ASSAY THEM TO DETERMINE HOW THE MUTATIONS
AƯECT ACE2 BINDING. WE WILL THEN ANALYZE THE DATA TO CREATE INTERACTIVE MAPS OF THE
MUTATIONAL EƯECTS ON ACE2 BINDING, AND SHARE THESE DATA PUBLICLY ALONG WITH PUBLISHING
THEM.
INITIAL WORK WILL BEGIN WITH THE SPIKE OF THE KP.3.1.1 VARIANT, WHICH IS CURRENTLY THE GLOBALLY
DOMINANT VARIANT. WE ALSO ANTICIPATE STUDYING A SECOND VARIANT THAT IS DOMINANT IN THE
SUMMER OF 2025.
SO OVERALL MILESTONES ARE:
- CREATE PSEUDOVIRUS MUTANT LIBRARY WITH KP.3.1.1 SPIKE (LAST QUARTER OF 2024)
- MEASURE HOW ALL MUTATIONS TO KP.3.1.1 SPIKE AƯECT ACE2 BINDING, ANALYZE DATA, AND
PUBLISH RESULTS ALONGSIDE INTERACTIVE VISUALIZATIONS OF DATA (FIRST HALF OF 2025).
- CHOOSE A SECOND SARS-COV-2 VARIANT THAT IS DOMINANT IN THE SPRING OF 2025 AND
REPEAT THE ABOVE PROCESS 501314 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: PA Parent award description: AWARD OF THE BASE TO UPENN FOR CEIRR CONTRACT 75N93021C00015. THIS CONTRACT WILL SUPPORT THE NIAID CENTERS OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (CEIRR) View parent award on USAspending | — | $200,363 | Apr 7, 2025 | — – — |
| Subcontractor | Department of Health and Human Services | THIS STATEMENT OF WORK (SOW) OUTLINES THE ACTIVITIES THAT FRED HUTCHINSON CANCER CENTER (FHCC) WILL BE PERFORMING. NOTE THAT THE TASK NUMBERS BELOW REFLECT THE NUMBERING OF THE OVERALL ACTIVITIES IN THE PRIME CONTRACT.
ALTHOUGH THIS SOW DETAILS THE COMPLETE SUITE OF PROPOSED WORK, THE TASKS ASSOCIATED WITH THIS CONTRACT ITERATION ARE LIMITED TO THE SPECIFIC ACTIVITIES OUTLINED BELOW, DELIVERABLES FOR THIS CONTRACT PERIOD ARE HIGHLIGHTED.
THROUGH THE EXECUTION OF THIS CONTRACT, WE WILL EXAMINE BASIC INDUCTION OF INNATE AND ADAPTIVE IMMUNITY FROM VACCINATION, INCLUDING STUDIES THAT ADDRESS NONTUBERCULOUS MYCOBACTERIA (NTM) INTERFERENCE, RNA VACCINE DELIVERY, PRIME-BOOST REGIMENS (INCLUDING BCG PRE-EXPOSURE), TRANSCRIPTOMIC HOST SIGNATURES, SYSTEMS BIOLOGY AND DURABLE IMMUNE MEMORY FOR THE FURTHER ADVANCEMENT OF THE EFFORT TO DESIGN AND EVALUATE AN EFFICACIOUS VACCINE AGAINST MYCOBACTERIUM TUBERCULOSIS (M.TB)
THE WORK UNDER THIS CONTRACT MAY INCLUDE THE POSSIBLE DISTRIBUTION OF DE-IDENTIFIED HUMAN SUBJECT PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMC), SERUM, AND OTHER CLINICAL SAMPLES TO SCRI AND THE PHOENIX PARTNERS. NHP SAMPLES AND/OR DOWNSTREAM DATA MAY BE SHARED WITH THE PARTNERS ON THIS CONTRACT.
OPTION 3 ACTIVITIES: EVALUATE OPTIMIZED M.TB VACCINE CANDIDATES FOR SAFETY, IMMUNOGENICITY AND EFFICACY IN THE NHP MODEL OF TB
TASK 3.5 TRANSCRIPTOMIC ANALYSIS OF NHP SAMPLES.
FHCC WILL EXECUTE GENE EXPRESSION PROFILING WITH RNASEQ/NANOSTRING ASSAYS ON NHP SAMPLES GENERATED IN OPTION 3 AT UKHSA. TRANSCRIPTOMIC ANALYSIS WILL BE FOCUSED ON IDENTIFYING A PERIPHERAL BLOOD SURROGATE ENDPOINT FOR THE M.TB ERDMAN ULDA CHALLENGE OUTCOMES. THE INITIAL UNBIASED RNA SEQUENCING APPROACH WILL USE WHOLE-BLOOD SAMPLES FROM PRE- AND POST-CHALLENGE TIME POINTS. SPECIFICALLY, WE WILL LOOK FOR TRANSCRIPTS THAT ARE CORRELATED WITH M.TB COLONY FORMING UNITS (CFU) AND M.TB QPCR ASSAYS FROM BRONCHOALVEOLAR LAVAGE (BAL), THE PRIMARY CHALLENGE OUTCOMES. IN ADDITION TO ABSOLUTE ABUNDANCE AT POST-CHALLENGE TIME POINTS, WE WILL ALSO LOOK FOR CHANGES IN TRANSCRIPT ABUNDANCE RELATIVE TO THE DAY OF CHALLENGE AS A POTENTIAL CORRELATE OF CHALLENGE OUTCOME. AS WE BUILD A MODEL TO PREDICT CHALLENGE OUTCOME FROM THESE GENE EXPRESSION MEASURES WE WILL SPECIFICALLY CONSIDER TRANSCRIPTS THAT HAVE PREVIOUSLY BEEN IDENTIFIED AS PREDICTORS OF PROGRESSION TO TB DISEASE, SUCH AS TYPE I IFN-RELATED GENES WHOSE EXPRESSION INCREASES DURING DISEASE PROGRESSION. THE HUMAN EXPRESSION SIGNATURES WILL BE EVALUATED IN NHPS AND VICE VERSA; ADDITIONALLY, A JOINT MODEL WILL BE DEVELOPED, ALLOWING FOR DIFFERENCES IN NHP AND HUMAN ASSOCIATIONS, WHILE IDENTIFYING A COMMON GENE SIGNATURE. ONCE TRANSCRIPTS OR GENES HAVE BEEN IDENTIFIED, A TARGETED CROSS-SPECIES NANOSTRING PANEL WILL BE DEVELOPED FOR EVALUATION IN THE SMALL ANIMAL MODELS AS WELL AS IN FUTURE NHP AND CLINICAL TRIALS. WE PLAN TO DEVELOP A NANOSTRING NCOUNTER GENE PANEL WHICH CAN ACCOMMODATE UP TO 800 GENES AND WOULD BE SIGNIFICANTLY MORE COST EFFECTIVE THAN RNA SEQUENCING. ALTERNATIVELY, DEPENDING ON THE COMPLEXITY OF THE GENE PANEL, IT COULD BE DEVELOPED AS A 96 TRANSCRIPT/GENE (INCLUDING HOUSEKEEPING GENES) QPCR BIOMARK FLUIDIGM ASSAY.
TASK 3.7 COMPARE IMMUNE PROFILES IN NHP, SMALL ANIMAL MODELS AND HUMANS TO IDENTIFY CORRELATES OF PROTECTION.
SUBTASK 3.7.4 INTEGRATED ANALYSIS AND DYNAMICAL SYSTEMS MODELING OF EXPERIMENTAL IMMUNOLOGY DATA ACROSS ALL SPECIES
EXPERIMENTAL DATA WILL BE TRANSFERRED TO THE STATISTICAL CENTER AND A FORMAL INTER-SITE AND INTER-SPECIES VARIABILITY ASSESSMENT WILL BE PERFORMED. VARIABILITY WILL BE DETERMINED USING COEFFICIENTS OF VARIATION (CV), MEAN AND STANDARD DEVIATION OF RESPONSES. DESIRED CUT-OFFS FOR ACCEPTABLE CVS WILL BE PRE-SPECIFIED FOR EACH ASSAY. EFFORT IN THE BASE PERIOD WILL HAVE BEEN MADE TO STANDARDIZE THE ASSAYS AND HARMONIZATION ASSESSMENTS WILL HAVE BEEN REPEATED IF CVS DID NOT MEET THE CUT OFF.
IMMUNOGENICITY AND SYSTEMS BIOLOGY: INNATE AND ADAPTIVE IMMUNITY, INCLUDING EX-V 13476SUB Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: WA Parent award description: IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB) View parent award on USAspending | — | $237,088 | Nov 30, 2024 | — – — |
| Subcontractor | Department of Health and Human Services | HISPANIC COMMUNITY HEALTH STUDY - STUDY OF LATINOS RESEARCH SUPPLEMENTS TO PROMOTE
DIVERSITY IN HEALTH RELATED RESEARCH-DR. MARIO TREJO 312455 · Prime awardUSAspending | 75N92019D00011USAspending | $137,834 | Jan 9, 2024 | — – — |
| Subcontractor | Department of Health and Human Services | IN YEAR 5, THE EDLEFSEN GROUP AT FRED HUTCH CANCER CENTER (FRED HUTCH) WILL PROVIDE DATA QUALITY ASSURANCE PROCESSES AND ENSURE THE TIMELINESS AND ACCURACY OF STATISTICAL ANALYSES AND THE EFFECTIVE COMMUNICATION OF RESULTS. FRED HUTCH WILL DEVELOP REPRODUCIBLE RESEARCH ANALYSIS SOFTWARE AND NOVEL ANALYTICAL METHODS. IN ADDITION, FRED HUTCH WILL CONTRIBUTE TO THE DESIGN AND PROPER STATISTICAL CONDUCT OF ALL AIMS, AND ASSOCIATED DATA. DR. EDLEFSEN WILL COLLABORATE WITH TWO INDEPENDENT CONTRACTORS, ONE BASED IN GDANSK, POLAND AND ONE BASED IN HANGZHOU, CHINA, TO PROVIDE BIOINFORMATICS EXPERTISE ON THE PROJECT. FRED HUTCH IS CONDUCTING THESE ACTIVITIES ON AN ONGOING BASIS AND CONDUCTING ACTIVITIES MEETING THESE DESCRIPTIONS IN ALL YEARS OF THE CONTRACT. 13207SUB Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541714 Parent award performance state: WA Parent award description: IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB) View parent award on USAspending | — | $273,484 | Nov 30, 2023 | — – — |
| Subcontractor | Department of Health and Human Services | FRED HUTCH INVESTIGATORS WILL CONTRIBUTE TO ALL ASPECTS OF THE PROPOSAL. THIS INCLUDES SUPPORTING THE SOIL MICROBIOME RESEARCH FROM SAMPLE COLLECTION THROUGH ANALYSIS AND PUBLICATION. FRED HUTCH WILL ALSO CONTRIBUTE TO THE ORGANIZATION AND OPERATION OF THE GENOMIC DATA SCIENCE COMMUNITY NETWORK, ESPECIALLY TO SUPPORT FACULTY AND STUDENTS AT DIVERSE INSTITUTIONS. 2006132034 Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541990 Parent award performance state: MD Parent award description: EXPANDING THE GENOMIC DATA SCIENCE COMMUNITY NETWORK FOR NHGRI. View parent award on USAspending | — | $160,843 | Nov 20, 2023 | — – — |
| Subcontractor | Department of Health and Human Services | HISPANIC COMMUNITY HEALTH STUDY - STUDY OF LATINOS RESEARCH SUPPLEMENTS TO PROMOTE DIVERSITY IN HEALTH RELATED RESEARCH 312305 · Prime awardUSAspending | 75N92019D00011USAspending | $102,353 | Apr 21, 2023 | — – — |
| Subcontractor | Department of Health and Human Services | IN YEAR 4, THE EDLEFSEN LABORATORY AT FRED HUTCH CANCER CENTER (FRED HUTCH) WILL PROVIDE DATA QUALITY ASSURANCE PROCESSES AND ENSURE THE TIMELINESS AND ACCURACY OF STATISTICAL ANALYSES AND THE EFFECTIVE COMMUNICATION OF RESULTS. FRED HUTCH WILL DEVELOP REPRODUCIBLE RESEARCH ANALYSIS SOFTWARE AND NOVEL ANALYTICAL METHODS. IN ADDITION, FRED HUTCH WILL CONTRIBUTE TO THE DESIGN AND PROPER STATISTICAL CONDUCT OF ALL AIMS, AND ASSOCIATED DATA. DR. EDLEFSEN WILL SUPERVISE THE BIOINFORMATICS ANALYST. FRED HUTCH IS CONDUCTING THESE ACTIVITIES ON AN ONGOING BASIS AND CONDUCTING ACTIVITIES MEETING THESE DESCRIPTIONS IN ALL YEARS OF THE CONTRACT. 12931SUB Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541714 Parent award performance state: WA Parent award description: IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB) View parent award on USAspending | — | $267,724 | Mar 31, 2023 | — – — |
| Subcontractor | Department of Health and Human Services | THROUGH THE EXECUTION OF THIS CONTRACT, WE WILL EXAMINE BASIC INDUCTION OF INNATE AND ADAPTIVE IMMUNITY FROM VACCINATION, INCLUDING STUDIES THAT ADDRESS NTM INTERFERENCE, RNA DELIVERY, PRIME-BOOST REGIMENS (INCLUDING BCG PRE-EXPOSURE), TRANSCRIPTOMIC HOST SIGNATURES, PROTEOMICS, SYSTEMS BIOLOGY AND DURABLE IMMUNE MEMORY FOR THE FURTHER ADVANCEMENT OF THE EFFORT TO DESIGN AND EVALUATE AN EFFICACIOUS VACCINE AGAINST MYCOBACTERIUM TUBERCULOSIS.
OPTION 3 ACTIVITIES: EVALUATE OPTIMIZED M.TB VACCINE CANDIDATES FOR SAFETY, IMMUNOGENICITY AND EFFICACY IN THE NHP MODEL OF TB
TASK 3.5 TRANSCRIPTOMIC ANALYSIS OF NHP SAMPLES.
FHCC WILL EXECUTE GENE EXPRESSION PROFILING WITH RNASEQ/NANOSTRING ASSAYS ON NHP SAMPLES GENERATED IN OPTION 3 AT UKHSA. TRANSCRIPTOMIC ANALYSIS WILL BE FOCUSED ON IDENTIFYING A PERIPHERAL BLOOD SURROGATE ENDPOINT FOR THE M.TB ERDMAN ULDA CHALLENGE OUTCOMES. THE INITIAL UNBIASED RNA SEQUENCING APPROACH WILL USE WHOLE-BLOOD SAMPLES FROM PRE AND POST-CHALLENGE TIME POINTS. SPECIFICALLY, WE WILL LOOK FOR TRANSCRIPTS THAT ARE CORRELATED WITH M.TB CFU AND M.TB QPCR ASSAYS FROM BAL, THE PRIMARY CHALLENGE OUTCOMES. IN ADDITION TO ABSOLUTE ABUNDANCE AT POST-CHALLENGE TIME POINTS, WE WILL ALSO LOOK FOR CHANGES IN TRANSCRIPT ABUNDANCE RELATIVE TO THE DAY OF CHALLENGE AS A POTENTIAL CORRELATE OF CHALLENGE OUTCOME. AS WE BUILD A MODEL TO PREDICT CHALLENGE OUTCOME FROM THESE GENE EXPRESSION MEASURES WE WILL SPECIFICALLY CONSIDER TRANSCRIPTS THAT HAVE PREVIOUSLY BEEN IDENTIFIED AS PREDICTORS OF PROGRESSION TO TB DISEASE, SUCH AS TYPE I IFN-RELATED GENES WHOSE EXPRESSION INCREASES DURING DISEASE PROGRESSION. THE HUMAN EXPRESSION SIGNATURES WILL BE EVALUATED IN NHPS AND VICE VERSA; ADDITIONALLY, A JOINT MODEL WILL BE DEVELOPED, ALLOWING FOR DIFFERENCES IN NHP AND HUMAN ASSOCIATIONS, WHILE IDENTIFYING A COMMON GENE SIGNATURE. ONCE TRANSCRIPTS OR GENES HAVE BEEN IDENTIFIED, A TARGETED CROSS-SPECIES NANOSTRING PANEL WILL BE DEVELOPED FOR EVALUATION IN THE SMALL ANIMAL MODELS AS WELL AS IN FUTURE NHP AND CLINICAL TRIALS. WE PLAN TO DEVELOP A NANOSTRING NCOUNTER GENE PANEL WHICH CAN ACCOMMODATE UP TO 800 GENES AND WOULD BE SIGNIFICANTLY MORE COST EFFECTIVE THAN RNA SEQUENCING. ALTERNATIVELY, DEPENDING ON THE COMPLEXITY OF THE GENE PANEL, IT COULD BE DEVELOPED AS A 96 TRANSCRIPT/GENE (INCLUDING HOUSEKEEPING GENES) QPCR BIOMARK FLUIDIGM ASSAY.
TASK 3.7 COMPARE IMMUNE PROFILES IN NHP, SMALL ANIMAL MODELS AND HUMANS TO IDENTIFY CORRELATES OF PROTECTION.
SUBTASK 3.7.4 INTEGRATED ANALYSIS AND DYNAMICAL SYSTEMS MODELING OF EXPERIMENTAL IMMUNOLOGY DATA ACROSS ALL SPECIES
EXPERIMENTAL DATA WILL BE TRANSFERRED TO THE STATISTICAL CENTER AND A FORMAL INTER-SITE AND INTER-SPECIES VARIABILITY ASSESSMENT WILL BE PERFORMED. VARIABILITY WILL BE DETERMINED USING COEFFICIENTS OF VARIATION (CV), MEAN AND STANDARD DEVIATION OF RESPONSES. DESIRED CUT-OFFS FOR ACCEPTABLE CVS WILL BE PRE-SPECIFIED FOR EACH ASSAY. EFFORT IN THE BASE PERIOD WILL HAVE BEEN MADE TO STANDARDIZE THE ASSAYS AND HARMONIZATION ASSESSMENTS WILL HAVE BEEN REPEATED IF CV€„¢S DID NOT MEET THE CUT OFF.
IMMUNOGENICITY AND SYSTEMS BIOLOGY: INNATE AND ADAPTIVE IMMUNITY, INCLUDING EX-VIVO ELISPOT, ELISAS AND RNA SEQUENCE ANALYSIS AND INTRACELLULAR CYTOKINE STAINING OF BLOOD WILL BE PERFORMED BY SCHARP AND COLLABORATORS. THIS WILL INCLUDE STATE OF THE ART CELLULAR AND HUMORAL IMMUNO-MONITORING IN ORDER TO COMPREHENSIVELY DEFINE THE IMMUNE RESPONSE: EX VIVO ELISPOTS, ELISAS, MULTI-PARAMETER FLOW CYTOMETRY, MULTIPLEX ASSAYS, MGIA AND RNA SEQUENCE ANALYSIS. COMPARISON OF EX-VIVO ELISPOT ASSAY RESPONSES WILL BE COMPLETED USING THE AREA UNDER THE CURVE (AUC) OF EACH ANIMAL'S RESPONSE CALCULATED USING SIGMAPLOT VERSION 10 AND COMPARED BETWEEN TEST GROUPS USING THE NON-PARAMETRIC MANN€€ŒWHITNEY U TEST. DIFFERENCES IN THE QUALITATIVE PATHOLOGY SCORES WILL BE COMPARED BETWEEN SPECIES AND TEST GROUPS USING THE NON-PARAMETRIC MANN€€ŒWHITNEY U TEST, MINITAB VERSION 15. THE SPEARMAN CORR 12872SUB Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: WA Parent award description: IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB) View parent award on USAspending | — | $31,356 | Dec 31, 2022 | — – — |
| Subcontractor | Department of Health and Human Services | PMBC ANALYSIS 836737N Parent award context Parent award agency: Department of Health and Human Services · Office of Assistant Secretary for Preparedness and Response Parent award NAICS: 541715 Parent award performance state: OH Parent award description: ASSESSING CORRELATES OF PROTECTION IN RHESUS MACAQUES ADMINISTERED VARIOUS VACCINE CANDIDATES DESIGNED TO PROTECT AGAINST SARS-COV-2 INFECTION View parent award on USAspending | — | $332,512 | Aug 22, 2022 | — – — |
| Subcontractor | Department of Health and Human Services | DR. EDLEFSEN WILL COORDINATE RESEARCH ACTIVITY AT FRED HUTCH. IN YEAR 3 HE WILL OVERSEE DATA QUALITY ASSURANCE PROCESSES AND ENSURE THE TIMELINESS AND ACCURACY OF STATISTICAL ANALYSES AND THE EFFECTIVE COMMUNICATION OF RESULTS. HE WILL DEVELOP REPRODUCIBLE RESEARCH ANALYSIS SOFTWARE AND NOVEL ANALYTICAL METHODS. IN ADDITION, HE WILL CONTRIBUTE TO THE DESIGN AND PROPER STATISTICAL CONDUCT OF ALL AIMS, AND ASSOCIATED DATA, AND TO THE SUPERVISION OF THE BIOINFORMATICS ANALYST.
DR. EDLEFSEN IS CONDUCTING THESE ACTIVITIES ON AN ONGOING BASIS AND IS CONDUCTING ACTIVITIES MEETING THESE DESCRIPTIONS IN ALL YEARS OF THE CONTRACT 12701SUB Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541714 Parent award performance state: WA Parent award description: IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB) View parent award on USAspending | — | $258,776 | May 31, 2022 | — – — |
| Subcontractor | Department of Health and Human Services | BASE ACTIVITIES: DEVELOP IMMUNE RESPONSE ASSAYS AND HARMONIZE PROTOCOLS AND ASSAYS
TASK B.2: IMMUNOLOGICAL ASSAY DEVELOPMENT, HARMONIZATION OF PROTOCOLS AND IN VIVO STUDIES
TASK B.4: HUMAN CLINICAL PROTOCOL DEVELOPMENT
TO ENSURE THAT BIOLOGICAL RESULTS GENERATED IN THE VARIOUS CONSORTIUM LABS ARE COMPARABLE, WE WILL STANDARDIZE THE PRIMARY ASSAYS USED IN IMMUNOGENICITY ASSESSMENTS FOR EACH SPECIES (TABLE 1). IN LINE WITH THE PROJECT GOALS TO DEVELOP A CROSS-SPECIES INTERROGATION PLATFORM, WE WILL HARMONIZE KEY ASSAYS ACROSS MULTIPLE SPECIES AND ENSURE STATISTICAL PLANS FOR CROSS SPECIES ANALYSIS ARE IN PLACE. SCRI WILL APPOINT AN OVERALL TASK LEADER TO COORDINATE AND OVERSEE THE WORK. ALL ASSAY STANDARD OPERATING PROCEDURES (SOP) WILL BE SHARED WITH A PRECLINICAL OR CLINICAL LABORATORY LEAD, DESIGNATED FOR EACH ASSAY, WHO WILL BE RESPONSIBLE FOR HARMONIZING. FINAL SOPS WILL BE SHARED AND LEAD ASSAY LABS WILL CONDUCT SIDE-BY-SIDE TRAINING SESSIONS, AS WELL AS, MAINTAIN AND DISTRIBUTE COMMON REFERENCE STANDARDS AND REAGENTS, SUCH AS IDENTICAL STIMULATION ANTIGENS (BCG, PPD, SEB, 15-MER PEPTIDES, NTM AND M.TB LYSATE AND CULTURE FILTRATE AND UNSTIMULATED) AND BCG VACCINATION STRAIN (BCG AJ/BCG SSI). THIS BASE-PERIOD HARMONIZATION WILL INCLUDE OPTIMIZED MULTICOLOR IMMUNOFLUORESCENCE PANEL (OMIP) DEVELOPMENT. FURTHERMORE, IN THE BASE PERIOD WE WILL AGREE TO A SPECIFIC MONTH IN WHICH EACH TEAM WILL ANNUALLY THAW INFECTION STOCKS AND PLATE FOR BACTERIAL ENUMERATION TO ENSURE VIABILITY AND STOCK CONCENTRATION IS MAINTAINED OVER THE ENTIRE COURSE OF THE CONTRACT. THESE STOCK COUNTS AND VIABILITY MAINTENANCE TESTS WILL BE REPORTED BACK TO SCRI.
FHCRC INDIVIDUALS WILL ENSURE THAT THE ASSAY HARMONIZATION EFFORTS WILL LEAD TO APPROACHES FOR THE PROPOSED EXPERIMENTS THAT ARE STATISTICALLY SOUND AND ADEQUATELY POWERED, INCLUDING EXPERIMENTS INVOLVING PRIMARY AND EXPLORATORY ENDPOINTS IN PRECLINICAL AND CLINICAL STUDIES. DATA FROM HARMONIZATION EXPERIMENTS WILL BE TRANSFERRED TO THE STATISTICAL CENTER AND A FORMAL INTER-SITE AND INTER-SPECIES VARIABILITY ASSESSMENT WILL BE PERFORMED. VARIABILITY WILL BE DETERMINED USING COEFFICIENTS OF VARIATION (CV), MEAN AND STANDARD DEVIATION OF RESPONSES. DESIRED CUT-OFFS FOR ACCEPTABLE CVS WILL BE PRE-SPECIFIED FOR EACH ASSAY. IF CV€„¢S DO NOT MEET THESE CUT-OFFS, FOR EXAMPLE >30%, FURTHER EFFORTS WILL BE MADE TO STANDARDIZE THE ASSAYS AND HARMONIZATION ASSESSMENTS WILL BE REPEATED.
A SUMMARY REPORT OF ALL ACTIVITIES AND STANDARDIZED PROTOCOLS FROM THE BASE PERIOD WILL BE DRAFTED AND SUBMITTED TO NIAID FOR REVIEW AND APPROVAL. FHCRC AND CSU WILL PROVIDE ALL THE NECESSARY DATA AND INPUT REQUIRED FOR THE COMPLETION AND ACCEPTANCE OF THE FINAL REPORT FOR BASE PERIOD ACTIVITIES.
FHCRC WILL ALSO SERVE AS THE LEAD SITE (CLINICAL AND PRECLINICAL) FOR GENE EXPRESSION PROFILING WITH RNASEQ/NANOSTRING ASSAYS. TRANSCRIPTOMIC ANALYSIS WILL BE FOCUSED ON IDENTIFYING A PERIPHERAL BLOOD SURROGATE ENDPOINT FOR THE BCG/MYCOBACTERIUM TUBERCULOSIS (MTB) ERDMAN/MTB HN878 CHALLENGE OUTCOMES. IN THE STATISTICAL LITERATURE THIS IS REFERRED TO A CORRELATE OF RISK (COR) OR CORRELATE OF PROTECTION (COP) ANALYSIS, WITH THE ULTIMATE GOAL OF DEVELOPING A SURROGATE ENDPOINT (A KIND OF COP) FOR FUTURE VACCINE STUDIES. THE STRATEGY WILL BE TO START WITH AN UNBIASED RNA SEQUENCING APPROACH USING WHOLE-BLOOD HUMAN SAMPLES FROM PRE AND POST-CHALLENGE TIME POINTS. SPECIFICALLY, WE WILL LOOK FOR TRANSCRIPTS THAT ARE CORRELATED WITH BCG CFU AND BCG QPCR ASSAYS FROM BAL, THE PRIMARY CHALLENGE OUTCOMES. IN ADDITION TO ABSOLUTE ABUNDANCE AT POST-CHALLENGE TIME POINTS, WE WILL ALSO LOOK FOR CHANGES IN TRANSCRIPT ABUNDANCE RELATIVE TO THE DAY OF CHALLENGE AS A POTENTIAL CORRELATE OF CHALLENGE OUTCOME. 12718SUB Parent award context Parent award agency: Department of Health and Human Services · National Institutes of Health Parent award NAICS: 541715 Parent award performance state: WA Parent award description: IMMUNE MECHANISMS OF PROTECTION AGAINST MYCOBACTERIUM TUBERCULOSIS CENTER (IMPAC-TB) View parent award on USAspending | — | $187,952 | Mar 31, 2022 | — – — |
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Agencies supported
- Department of Veterans AffairsGov-sourced
- Department of Health and Human ServicesGov-sourced
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