AWARD
A -- Determination of Genetic Susceptibility to Lung Cancer in Families from Southern Louisiana - JOFOC
- Notice Date
- 12/16/2016
- Notice Type
- Award Notice
- NAICS
- 541712
— Research and Development in the Physical, Engineering, and Life Sciences (except Biotechnology)
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Heart, Lung and Blood Institute, Rockledge Dr. Bethesda, MD, Office of Acquisitions, 6701 Rockledge Dr RKL2/6100 MSC 7902, Bethesda, Maryland, 20892-7902
- ZIP Code
- 20892-7902
- Solicitation Number
- NHLBI-CSB-HG-2017-09-KC
- Archive Date
- 1/16/2017
- Point of Contact
- Stacy C. Turner,
- E-Mail Address
-
turners@nhlbi.nih.gov
(turners@nhlbi.nih.gov)
- Small Business Set-Aside
- N/A
- Award Number
- HHSN268201700012C
- Award Date
- 12/1/2016
- Awardee
- Louisiana State University Health Sciences Center, 533 Bolivar Street, New Orleans, Louisiana 70112, United States
- Award Amount
- $650,618
- Description
- JOFOC A fixed price, follow-on contract for the following work was awarded to Louisiana State University Health Sciences Center on a sole source basis. The contract has a base period of one year and two option periods of one year each. See the attached Justification for Other than Full and Open Competition. The study of familial lung cancer patients and their families will continue using multiple genetic tools and strategies: 1) linkage studies to help localize genes with rare, high-penetrance susceptibility alleles; 2) a genome-wide association study of cases with a family history compared to controls matched on age, smoking history, ethnicity and region of residence to localize genes with common, lower-penetrance risk alleles; 3) targeted and whole exome/whole genome sequencing of DNA from familial lung cancer patients to identify these risk loci; and 4) characterization of candidate genes such as RGS17. To accomplish these goals, additional families, familial cases and controls are needed for linkage confirmation, fine-mapping association, and sequencing studies so that these susceptibility loci can be identified and characterized. Since the published loci do not appear to account for all highly aggregated lung cancer families, these additional data collection efforts are also critical to enable the identification of additional lung cancer susceptibility loci using linkage, genome-wide association and sequencing studies. Families in Louisiana are particularly appropriate for these studies because of the historic large family sizes, stable population with little migration out of the area, historical high smoking rates and extremely low radon exposures, and the previous studies in this population that have shown increased familial aggregation after adjusting for smoking. The Louisiana families collected under this contract will be combined with families collected by other members of the GELCC (funded by a separate grant from the National Cancer Institute, NIH) to increase power to identify the genetic components of lung cancer. The contribution of Louisiana patients and families funded by this contract will make an important contribution to this effort. These data may also be more broadly shared with other scientists to increase understanding of the genetic contributions to risk of this deadly disease. B. Objectives 1. Ascertain lung cancer patients from the State of Louisiana in a rapid ascertainment network. 2. Collect phenotypic and environmental exposure data and biologic specimens from selected lung cancer patients (selected because they have a family history of lung cancer) and their families. The coded data and biologic specimens shall be delivered to the Government so that the following analyses can be performed: genotyping, genetic linkage analyses, familial-case-control genome-wide and targeted association analyses, genome sequencing analyses and genotype-phenotype correlation analyses. 3. Collect phenotypic and environmental exposure data and biologic specimens on additional matched control (unaffected) individuals (frequency matched on age, smoking status, area of residence, race/ethnicity) who are biologically unrelated to the lung cancer patients for use in the analyses described in B.2 above. 4. Continue follow-up of previously enrolled lung cancer patients and their families to allow updating of new cancer diagnoses within the families. This is a required and critically important objective. C. Description of Work Independently, and not as an agent of the Government, the Contractor shall furnish all necessary services, qualified personnel, materials, facilities, and equipment not otherwise furnished by the Government, as needed to perform the work set forth below: 1. Use the existing rapid-surveillance system to collect data on patients diagnosed with lung cancer between December 1, 2016 and November 30, 2019 in all the participating hospitals diagnosing lung cancer patients within 27 parishes in southern Louisiana. The contract consists of one (1) one-year base period and two (2) one-year option periods which will need to be exercised via contract modifications to extend the period of performance. Hospitals within these 27 parishes shall be contacted on a rotating basis to identify living patients recently diagnosed with cancer of the trachea, bronchus or lung. The contractor shall also identify lung cancer patients for potential enrollment into the study through other mechanisms, including (but not limited to) the following: the Louisiana Tumor Registry, the Hematology-Oncology and Radiation Oncology service of Tulane University Hospital, the Oncology and Radiation Oncology services within the Louisiana State University Health Sciences System including University Hospital, other private Oncology and Urology groups, lung cancer support groups, the Louisiana Cancer Association, church groups, oncology physician waiting rooms, a study web site, articles/advertisements in local newspapers, interviews and publicity through local news media. 2. For all LC patients that are ascertained through the Louisiana Tumor Registry or any hospital or medical records, the LC patient shall be interviewed after verifying with the patient's physician that the patient is aware of the diagnosis of lung cancer and obtaining the physician's consent to contact the patient. The patient shall then be sent an initial contact letter explaining the purpose of the study, inviting the patient to enroll, and providing a post card to be returned if the patient is willing to participate. All such letters shall be followed up in one week with a telephone call from the research associate who shall further explain the study and answer any questions that the patient may have. After obtaining the patient's consent to participate, a brief telephone screening interview will determine if the LC patient has a family history of lung cancer. If so, DNA samples will be collected immediately from the LC patient, the LC patient will be asked to assist with contact of additional family members, and extended family history and environmental risk factor questionnaires shall be administered to the LC patient. Patients who directly contact the study investigators asking to participate in the study will be sent study documents, consented, interviewed and will have biological samples collected without the need for physician consent. Proxy interviews by next-of-kin shall be used if the patient is deceased or too ill to participate but the family desires to participate. 3. Data collected from each patient shall include the following: a. cancer history b. history of any type of cancer in relatives 4. Additional data collected from any LC patient with at least one first or second degree relative affected with lung cancer OR any LC patient with age at diagnosis less than 40 years of age shall include: a. environmental and lifestyle risk-factor information b. detailed family history questionnaire and pedigree drawing c. biological specimens, as available, including but not limited to, blood samples, saliva samples, tumor samples and non-cancerous tissue samples. These coded samples shall be shipped to the COR at NHGRI or to a laboratory designated by the COR, using appropriate packaging and overnight shipping to maintain the usability of the samples for DNA extraction. 5. In families where there are at least three relatives affected with lung cancer in addition to the initial LC patient, the Contractor shall contact all 1st and 2nd degree relatives of the initial LC patient, additional biological relatives as appropriate and appropriate spouses (next of kin if targeted relative or spouse is deceased) to obtain the following: a. cancer history b. verification of cancer via death certificate, pathology report or other medical records c. environmental and lifestyle risk-factor information d. blood samples, saliva samples and/or tissue samples (the latter from affected individuals, particularly deceased affected individuals). These coded samples shall be shipped to the COR at NHGRI or to a laboratory designated by the COR, using appropriate packaging and overnight shipping to maintain the usability of the samples for DNA extraction. 6. Continue follow-up on the familial cases and the set of highly aggregated families (each having at least 3 persons affected with lung cancer) who were ascertained during the previous contracted years of this study, for inclusion in the linkage and association studies. This section refers to almost 300 LC cases plus family members. The highly aggregated families have been ascertained and extended (by collecting phenotype data and DNA samples on all available family members, both living and deceased, and frequently re-contacting the families to update the cancer history of family members) during the past 10 years (funded by NHGRI contract N01-HG-65404) and continue to be monitored for newly diagnosed lung cancer in family members. Cases with at least 1 affected relative who have been enrolled in the association study should also be recontacted (or the next of kin should be recontacted) to determine if new family members have become affected since last recontact. If additional cases are detected, then these families may be converted to "highly-aggregated family" status and family members shall be invited to enroll. Blood and/or saliva samples shall be collected on all living informative members of these families who have not previously been sampled, and tissue samples shall be obtained, if possible, for all deceased family members. These coded samples shall be shipped to the COR at NHGRI or to a laboratory designated by the COR, using appropriate packaging and overnight shipping to maintain the usability of the samples for DNA extraction. This is an essential and critical task and is a definite requirement for this contract. 7. Per year, recruit 10-20 LC patients with a family history of LC (at least 1 other affected relative) for the association study (using procedures in 3 above) and 1-3 new highly aggregated families (initial LC patient has at least 3 other affected relatives AND enough affected individuals plus necessary unaffected relatives participate to make the family informative for linkage analysis) for the linkage study (using the procedures in 4 above) from among the lung cancer patients ascertained during this contract. The data collection in these families shall include collection of all informative risk factor exposure history from all living relatives in the linkage families and from all LC patients with a family history. Proxy interviews shall be conducted with the next-of-kin for all deceased informative individuals (i.e. all deceased relatives affected with cancer and all deceased unaffected relatives who connect affected individuals in the linkage families). As described above, a 20 ml blood sample and/or a saliva sample in appropriate sampling tubes for DNA extraction shall be collected from the LC patients and all available informative relatives and spouses, and attempts will be made to obtain histologic tissue samples from deceased family members who are affected with any type of cancer (not only lung cancer). For all deceased individuals in linkage families, whether normal histologic tissue samples are available or not, the Contractor shall collect phenotype and environmental questionnaire data plus blood and/or saliva samples from their spouses and offspring to provide information on their genotypes at marker loci. The Contractor shall use the same informed consent procedures when collecting data and biologic samples on relatives of the LC patients as are used for collecting data and biologic samples from the LC patients. The current contractor has previously collected over 200 age, smoking, gender and geographically frequency-matched control individuals. The Contractor shall collect an additional 50-100 control individuals over the duration of this contract (10-40 per year) using these same criteria. Blood and/or saliva samples shall be collected from all controls, as well as a detailed personal and family history of cancer and the environmental risk factor questionnaire. The coded biological samples shall be shipped to the COR at NHGRI or to a laboratory designated by the COR, using appropriate packaging and overnight shipping to maintain the usability of the samples for DNA extraction. 8. Provide a Statistical Geneticist to assist NHGRI staff with methodological research, as well as to advise the data collection staff about prioritization of their data collection efforts (to ensure collection of the most powerful families). The Statistical Geneticist shall also assist NHGRI staff with analyses of the data as needed, and perform evaluations of various statistical genetic methods needed to analyze this extremely complex trait. 9. Verify all reported cases of cancer at any site in original patients and in affected relatives by review of hospital charts, pathologist or physician medical records, or death certificates (if appropriate) and information on histologic type whenever available. If the Contractor is unable to review such documents for particular patients or affected relatives, corroboration of primary cancer site by additional family members shall be obtained and provided to the COR, who will decide whether to treat this individual as "known to be affected" with cancer at a specific site in the linkage analyses. Utilize the family history and environmental risk factor questionnaires previously approved for use by the Institutional Review Board at LSUHSC and that have been used in the previous lung cancer linkage data collection. It is imperative that the same questionnaires be used so that the existing data on the lung cancer families can be combined with the new data to be collected. 10. Data Entry and Management The data generated from the study shall comprise family structure data (variables that determine an individual's parents, spouses, offspring, sibs, etc.), trait and covariate data (variables that include cancer status, variables obtained from the tobacco consumption, passive smoking, diet and employment history questionnaires, and other variables obtained during the course of the interview, including age, sex, race, cancer status, etc.), and genotype data (results from the determination of DNA polymorphisms). All questionnaires, medical records and other documents that have personal identifiers on them shall be kept in locked filing cabinets in a secure room with limited access. No data with personal identifiers shall be published or released without the written consent of the individual concerned (or of next of kin if the individual is deceased). Data shall be abstracted from the written records and entered into a computer database by the Contractor. All data generated for each individual shall be coded with an identifying number. A limited access clinical database shall be maintained by the Contractor that shall include both the personal identifier information and the coded identifiers. Access to this password-protected database shall be limited to the Contract P.I. and the Clinical personnel involved in patient contact. All appropriate security measures shall be taken to protect the personally identifiable information on study participants as required by the Institutional Review Board overseeing the study at the Contractor's site. The coded identifying number shall be used on all computer records to be sent to the Government or to any other outside parties. No personal identifiers shall be included in any data released to the Government or any other outside parties. The data in the database shall be used to prepare the data for subsequent statistical and genetic analysis. Summaries of this database information shall be provided to the COR on a monthly basis and the actual phenotype, environmental data and family history data shall be provided to the COR in analyzable form (computer data files) as needed (at least at the time of submission of samples for genotyping and more often if needed by the COR). Coded biological specimens shall be shipped by the contractor to the COR or to a laboratory to be named by the COR for archival and study purposes. 11. Travel Requirement Interviewing staff shall visit or otherwise contact the participating hospitals frequently (at least once every 2 months) and interview staff and/or phlebotomists shall visit the homes of family members to collect blood/saliva samples as needed. The Principal Investigator shall attend two scientific meetings of the GELCC consortium per year.
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