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Gastman B, Agarwal PK, Berger A, Boland G, Broderick S, Butterfield LH, Byrd D, Fecci PE, Ferris RL, Fong Y, Goff SL, Grabowski MM, Ito F, Lim M, Lotze MT, Mahdi H, Malafa M, Morris CD, Murthy P, Neves RI, Odunsi A, Pai SI, Prabhakaran S, Rosenberg SA, Saoud R, Sethuraman J, Skitzki J, Slingluff CL, Sondak VK, Sunwoo JB, Turcotte S, Yeung CC, Kaufman HL. Defining best practices for tissue procurement in immuno-oncology clinical trials: consensus statement from the Society for Immunotherapy of Cancer Surgery Committee. J Immunother Cancer 2020; 8:e001583. [PMID: 33199512 PMCID: PMC7670953 DOI: 10.1136/jitc-2020-001583] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
Immunotherapy is now a cornerstone for cancer treatment, and much attention has been placed on the identification of prognostic and predictive biomarkers. The success of biomarker development is dependent on accurate and timely collection of biospecimens and high-quality processing, storage and shipping. Tumors are also increasingly used as source material for the generation of therapeutic T cells. There have been few guidelines or consensus statements on how to optimally collect and manage biospecimens and source material being used for immunotherapy and related research. The Society for Immunotherapy of Cancer Surgery Committee has brought together surgical experts from multiple subspecialty disciplines to identify best practices and to provide consensus on how best to access and manage specific tissues for immuno-oncology treatments and clinical investigation. In addition, the committee recommends early integration of surgeons and other interventional physicians with expertise in biospecimen collection, especially in clinical trials, to optimize the quality of tissue and the validity of correlative clinical studies in cancer immunotherapy.
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Affiliation(s)
- Brian Gastman
- Department of Plastic Surgery, Cleveland Clinic, Cleveland, Ohio, USA
| | - Piyush K Agarwal
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Adam Berger
- Division of Surgical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Genevieve Boland
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Stephen Broderick
- Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
- Department of Surgery, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Lisa H Butterfield
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
- Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - David Byrd
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Peter E Fecci
- Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Robert L Ferris
- Departments of Otolaryngology, Immunology, and Radiation Oncology, University of Pittsburgh Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Yuman Fong
- Department of Surgery, City of Hope National Medical Center, Duarte, California, USA
| | | | - Matthew M Grabowski
- Department of Neurosurgery, Duke Center for Brain and Spine Metastasis, Durham, North Carolina, USA
| | - Fumito Ito
- Center for Immunotherapy, Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Michael Lim
- Departments of Neurosurgery, Oncology, Radiation Oncology, and Otolaryngology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael T Lotze
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Haider Mahdi
- OBGYN and Women's Health Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Mokenge Malafa
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Carol D Morris
- Division of Orthopaedic Oncology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pranav Murthy
- Department of Surgery, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rogerio I Neves
- Department of Surgery, Penn State Cancer Institute, Hershey, Pennsylvania, USA
| | - Adekunle Odunsi
- Departments of Immunology and Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Sara I Pai
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sangeetha Prabhakaran
- Division of Surgical Oncology, Department of Surgery, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA
| | | | - Ragheed Saoud
- Department of Surgery, University of Chicago Hospitals, Chicago, Illinois, United States
| | | | - Joseph Skitzki
- Departments of Surgical Oncology and Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Craig L Slingluff
- Department of Surgery, Division of Surgical Oncology, Breast and Melanoma Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Vernon K Sondak
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - John B Sunwoo
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, California, USA
| | - Simon Turcotte
- Surgery Department, Centre Hospitalier de l'Universite de Montreal, Montreal, Quebec, Canada
| | - Cecilia Cs Yeung
- Department of Pathology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Howard L Kaufman
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Immuneering Corp, Cambridge, Massachusetts, USA
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Fisher WE, Cruz-Monserrate Z, McElhany AL, Lesinski GB, Hart PA, Ghos R, Van Bure G, Fishman DS, Rinaudo JAS, Serrano J, Srivastava S, Mace T, Topazian M, Feng Z, Yadav D, Pandol SJ, Hughes SJ, Liu RY, Lu E, Orr R, Whitcomb DC, Abouhamze AS, Steen H, Sellers ZM, Troendle DM, Uc A, Lowe ME, Conwell DL. Standard Operating Procedures for Biospecimen Collection, Processing, and Storage: From the Consortium for the Study of Chronic Pancreatitis, Diabetes, and Pancreatic Cancer. Pancreas 2019; 47:1213-1221. [PMID: 30325860 PMCID: PMC6197069 DOI: 10.1097/mpa.0000000000001171] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-quality and well-annotated biorepositories are needed to better understand the pathophysiology and biologic mechanisms of chronic pancreatitis (CP) and its consequences. We report a methodology for the development of a robust standard operating procedure (SOP) for a biorepository based on the experience of the clinical centers within the consortium to study Chronic Pancreatitis, Diabetes and Pancreas Cancer Clinical Centers (CPDPC), supported by the National Cancer Institute and the National Institute for Diabetes and Digestive and Kidney Diseases as a unique multidisciplinary model to study CP, diabetes, and pancreatic cancer in both children and adults. Standard operating procedures from the CPDPC centers were evaluated and consolidated. The literature was reviewed for standard biorepository operating procedures that facilitated downstream molecular analysis. The existing literature on biobanking practices was harmonized with the SOPs from the clinical centers to produce a biorepository for pancreatic research. This article reports the methods and basic principles behind the creation of SOPs to develop a biorepository for the CPDPC. These will serve as a guide for investigators developing biorepositories in pancreas research. Rigorous and meticulous adherence to standardized biospecimen collection will facilitate investigations to better understand the pathophysiology and biologic mechanisms of CP, diabetes, and pancreatic cancer.
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Affiliation(s)
- William E. Fisher
- The Elkins Pancreas Center, Michael E. DeBakey Department of Surgery, and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Zobeida Cruz-Monserrate
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, and Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Amy L. McElhany
- The Elkins Pancreas Center, Michael E. DeBakey Department of Surgery, and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Gregory B. Lesinski
- Winship Cancer Institute, Department of Hematology and Medical Oncology, Emory University, Atlanta, GA
| | - Phil A. Hart
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, and Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Ria Ghos
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - George Van Bure
- The Elkins Pancreas Center, Michael E. DeBakey Department of Surgery, and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | | | - Jo Ann S. Rinaudo
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute (NCI), Rockville, MD
| | - Jose Serrano
- Division of Digestive Diseases and Nutrition, National Institutes of Diabetes and Digestive and Kidney Diseases (NIDDK), Bethesda, MD
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute (NCI), Rockville, MD
| | - Thomas Mace
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, and Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Mark Topazian
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Ziding Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dhiraj Yadav
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Stephen J. Pandol
- Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Steven J. Hughes
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL
| | - Robert Y. Liu
- Clinical Research Support Center, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Emily Lu
- Clinical Research Support Center, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Robert Orr
- Indiana Clinical and Translational Sciences Institute, Specimen Storage Facility, Indianapolis, IN
| | - David C. Whitcomb
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Amer S. Abouhamze
- Clinical and Translational Sciences, University of Florida, Gainesville, FL
| | - Hanno Steen
- Departments of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA
| | - Zachary M. Sellers
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Lucile Packard Children’s Hospital and Stanford University School of Medicine, Stanford, CA
| | - David M. Troendle
- Department of Pediatrics, University of Texas Southwestern Medical School, Dallas, TX
| | - Aliye Uc
- Stead Family Department of Pediatrics, University of Iowa, Stead Family Children’s Hospital, Iowa City, IA
| | - Mark E. Lowe
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Darwin L. Conwell
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, and Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
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Park HS, Cho H, Kim HS. Development of an Integrated Biospecimen Database among the Regional Biobanks in Korea. Healthc Inform Res 2016; 22:129-41. [PMID: 27200223 PMCID: PMC4871843 DOI: 10.4258/hir.2016.22.2.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/19/2016] [Accepted: 04/22/2016] [Indexed: 11/23/2022] Open
Abstract
Objectives This study developed an integrated database for 15 regional biobanks that provides large quantities of high-quality bio-data to researchers to be used for the prevention of disease, for the development of personalized medicines, and in genetics studies. Methods We collected raw data, managed independently by 15 regional biobanks, for database modeling and analyzed and defined the metadata of the items. We also built a three-step (high, middle, and low) classification system for classifying the item concepts based on the metadata. To generate clear meanings of the items, clinical items were defined using the Systematized Nomenclature of Medicine Clinical Terms, and specimen items were defined using the Logical Observation Identifiers Names and Codes. To optimize database performance, we set up a multi-column index based on the classification system and the international standard code. Results As a result of subdividing 7,197,252 raw data items collected, we refined the metadata into 1,796 clinical items and 1,792 specimen items. The classification system consists of 15 high, 163 middle, and 3,588 low class items. International standard codes were linked to 69.9% of the clinical items and 71.7% of the specimen items. The database consists of 18 tables based on a table from MySQL Server 5.6. As a result of the performance evaluation, the multi-column index shortened query time by as much as nine times. Conclusions The database developed was based on an international standard terminology system, providing an infrastructure that can integrate the 7,197,252 raw data items managed by the 15 regional biobanks. In particular, it resolved the inevitable interoperability issues in the exchange of information among the biobanks, and provided a solution to the synonym problem, which arises when the same concept is expressed in a variety of ways.
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Affiliation(s)
- Hyun Sang Park
- Department of Medical Informatics, Kyungpook National University, Daegu, Korea
| | - Hune Cho
- Department of Medical Informatics, Kyungpook National University, Daegu, Korea
| | - Hwa Sun Kim
- Faculty of Medical Industry Convergence, Daegu Haany University, Gyeongsan, Korea
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Rush A, Byrne JA. Quality and reporting practices in an Australian cancer biobank cohort. Clin Biochem 2016; 49:492-497. [DOI: 10.1016/j.clinbiochem.2015.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 12/16/2022]
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Linkage of Data from Diverse Data Sources (LDS): A Data Combination Model Provides Clinical Data of Corresponding Specimens in Biobanking Information System. J Med Syst 2013; 37:9975. [DOI: 10.1007/s10916-013-9975-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/29/2013] [Indexed: 11/26/2022]
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Brunicardi FC, Gibbs RA, Wheeler DA, Nemunaitis J, Fisher W, Goss J, Chen C. Overview of the development of personalized genomic medicine and surgery. World J Surg 2011; 35:1693-9. [PMID: 21424870 PMCID: PMC3281749 DOI: 10.1007/s00268-011-1056-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Personalized genomic medicine and surgery (PGMS) represents a new approach to health care that customizes patients' medical treatment according to their own genetic information. This new approach is the result of increased knowledge of the human genome and ways this information can be applied by physicians in the medical and surgical management of their patients. A patient's genotype can yield important information concerning disease susceptibility and the effectiveness of medications, therefore guiding specific, targeted imaging and treatment therapies. This review summarizes major achievements of human genomic studies and applications of genomics in health care. Five years ago we developed a model for the development of PGMS in which genomic profile guides choice of therapy. In this article we discussed our progress, including an updating of the model, and a future vision of PGMS.
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Affiliation(s)
- F Charles Brunicardi
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, 1709 Dryden Street, Suite 1500, Houston, TX 77030, USA.
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7
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Nguyen NTT, Cotton RT, Harring TR, Guiteau JJ, Gingras MC, Wheeler DA, O'Mahony CA, Gibbs RA, Brunicardi FC, Goss JA. A primer on a hepatocellular carcinoma bioresource bank using the cancer genome atlas guidelines: practical issues and pitfalls. World J Surg 2011; 35:1732-7. [PMID: 21221581 DOI: 10.1007/s00268-010-0953-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Since the advent of the human genome, the era of personalized genomic medicine is indisputably in progress. METHODS In an effort to contribute to the evolving knowledge of genomic medicine, we have aimed directly at building a bioresource bank for hepatocellular carcinoma. This tumor bank is based on the rigorous guidelines set forth by the National Cancer Institute, and it offers analytes to help elucidate the mechanisms of progression from cirrhosis to malignancy, risk factors for recurrence, and applicability of current treatment options to a diverse group of people. CONCLUSIONS Surgeons have a privileged position between patients (and their cancer) and the benches of basic science. Thus, we offer a primer based on our own experiences, from which surgeons may take elements to build their own bioresource bank for use in collaboration with others. We highlight some practicalities and pitfalls that could be overlooked, as well as a discussion of possible solutions.
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Affiliation(s)
- N Thao T Nguyen
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, 1709 Dryden Road, Suite #1500, BCM390, Houston, TX 77030, USA
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Späth MB, Grimson J. Applying the archetype approach to the database of a biobank information management system. Int J Med Inform 2010; 80:205-26. [PMID: 21131230 DOI: 10.1016/j.ijmedinf.2010.11.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 11/17/2022]
Abstract
PURPOSE The purpose of this study is to investigate the feasibility of applying the openEHR archetype approach to modelling the data in the database of an existing proprietary biobank information management system. A biobank information management system stores the clinical/phenotypic data of the sample donor and sample related information. The clinical/phenotypic data is potentially sourced from the donor's electronic health record (EHR). The study evaluates the reuse of openEHR archetypes that have been developed for the creation of an interoperable EHR in the context of biobanking, and proposes a new set of archetypes specifically for biobanks. The ultimate goal of the research is the development of an interoperable electronic biomedical research record (eBMRR) to support biomedical knowledge discovery. METHODS The database of the prostate cancer biobank of the Irish Prostate Cancer Research Consortium (PCRC), which supports the identification of novel biomarkers for prostate cancer, was taken as the basis for the modelling effort. First the database schema of the biobank was analyzed and reorganized into archetype-friendly concepts. Then, archetype repositories were searched for matching archetypes. Some existing archetypes were reused without change, some were modified or specialized, and new archetypes were developed where needed. The fields of the biobank database schema were then mapped to the elements in the archetypes. Finally, the archetypes were arranged into templates specifically to meet the requirements of the PCRC biobank. RESULTS A set of 47 archetypes was found to cover all the concepts used in the biobank. Of these, 29 (62%) were reused without change, 6 were modified and/or extended, 1 was specialized, and 11 were newly defined. These archetypes were arranged into 8 templates specifically required for this biobank. A number of issues were encountered in this research. Some arose from the immaturity of the archetype approach, such as immature modelling support tools, difficulties in defining high-quality archetypes and the problem of overlapping archetypes. In addition, the identification of suitable existing archetypes was time-consuming and many semantic conflicts were encountered during the process of mapping the PCRC BIMS database to existing archetypes. These include differences in the granularity of documentation, in metadata-level versus data-level modelling, in terminologies and vocabularies used, and in the amount of structure imposed on the information to be recorded. Furthermore, the current way of modelling the sample entity was found to be cumbersome in the sample-centric activity of biobanking. CONCLUSIONS The archetype approach is a promising approach to create a shareable eBMRR based on the study participant/donor for biobanks. Many archetypes originally developed for the EHR domain can be reused to model the clinical/phenotypic and sample information in the biobank context, which validates the genericity of these archetypes and their potential for reuse in the context of biomedical research. However, finding suitable archetypes in the repositories and establishing an exact mapping between the fields in the PCRC BIMS database and the elements of existing archetypes that have been designed for clinical practice can be challenging and time-consuming and involves resolving many common system integration conflicts. These may be attributable to differences in the requirements for information documentation between clinical practice and biobanking. This research also recognized the need for better support tools, modelling guidelines and best practice rules and reconfirmed the need for better domain knowledge governance. Furthermore, the authors propose that the establishment of an independent sample record with the sample as record subject should be investigated. The research presented in this paper is limited by the fact that the new archetypes developed during this research are based on a single biobank instance. These new archetypes may not be complete, representing only those subsets of items required by this particular database. Nevertheless, this exercise exposes some of the gaps that exist in the archetype modelling landscape and highlights the concepts that need to be modelled with archetypes to enable the development of an eBMRR.
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Affiliation(s)
- Melanie Bettina Späth
- Centre for Health Informatics, School of Computer Science and Statistics, Trinity College Dublin, Dublin 2, Ireland.
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Cotton RT, Li D, Scherer SE, Muzny DM, Hodges SE, Catania RL, Witkiewicz AK, Brody JR, Kennedy EP, Yeo CJ, Brunicardi FC, Gibbs RA, Gingras MC, Fisher WE. Single nucleotide polymorphism in RECQL and survival in resectable pancreatic adenocarcinoma. HPB (Oxford) 2009; 11:435-44. [PMID: 19768149 PMCID: PMC2742614 DOI: 10.1111/j.1477-2574.2009.00089.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Accepted: 05/07/2009] [Indexed: 12/12/2022]
Abstract
BACKGROUND RECQL is a DNA helicase involved in DNA mismatch repair. The RECQL polymorphism, 3' untranslated region (UTR) A159C, was previously associated with overall survival of patients with resectable pancreatic adenocarcinoma treated with neoadjuvant chemoradiation. In the present study, we examined RECQL for somatic mutations and other polymorphisms and compared these findings with the outcome in patients who received adjuvant or neoadjuvant chemoradiation. We hypothesized that RECQL (i) would be mutated in cancer, (ii) would have polymorphisms linked to the 3'UTR A159C and that either or both events would affect function. We also hypothesized that (iii) these changes would be associated with survival in both cohorts of patients. MATERIAL AND METHODS We sequenced RECQL's 15 exons and surrounding sequences in paired blood and tumour DNA of 39 patients. The 3'UTR A159C genotype was determined in blood DNA samples from 176 patients with resectable pancreatic adenocarcinoma treated with adjuvant (53) or neoadjuvant (123) chemoradiation. Survival was calculated using the Kaplan-Meier method, with log rank comparisons between groups. The relative impact of genotype on time to overall survival was performed using the Cox proportional hazards model. RESULTS Somatic mutations were found in UTRs and intronic regions but not in exonic coding regions of the RECQL gene. Two single nucleotide polymorphisms (SNPs), located in introns 2 and 11, were found to be part of the same haplotype block as the RECQL A159C SNP and showed a similar association with overall survival. No short-term difference in survival between treatment strategies was found. We identified a subgroup of patients responsive to neoadjuvant therapy in which the 159 A allele conferred strikingly improved long-term survival. DISCUSSION The RECQL 3'UTR A159C SNP is not linked with other functional SNPs within RECQL but may function as a site for regulatory molecules. The mechanism of action needs to be clarified further.
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Affiliation(s)
- Ronald T Cotton
- Department of Molecular and Human Genetics, Human Genome Sequencing CenterHouston, TX,Michael DeBakey Department of Surgery and Elkins Pancreas Center, Baylor College of MedicineHouston, TX
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas M.D. Anderson Cancer CenterHouston, TX
| | - Steven E Scherer
- Department of Molecular and Human Genetics, Human Genome Sequencing CenterHouston, TX
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Human Genome Sequencing CenterHouston, TX
| | - Sally E Hodges
- Michael DeBakey Department of Surgery and Elkins Pancreas Center, Baylor College of MedicineHouston, TX
| | - Robbi L Catania
- Department of Molecular and Human Genetics, Human Genome Sequencing CenterHouston, TX,Michael DeBakey Department of Surgery and Elkins Pancreas Center, Baylor College of MedicineHouston, TX
| | - Agnieszka K Witkiewicz
- Department of Surgery, Jefferson Center for Pancreatic, Biliary and Related CancersPhiladelphia, PA, USA,Department of Pathology, Kimmel Cancer Center, Thomas Jefferson UniversityPhiladelphia, PA, USA
| | - Jonathan R Brody
- Department of Surgery, Jefferson Center for Pancreatic, Biliary and Related CancersPhiladelphia, PA, USA
| | - Eugene P Kennedy
- Department of Surgery, Jefferson Center for Pancreatic, Biliary and Related CancersPhiladelphia, PA, USA
| | - Charles J Yeo
- Department of Surgery, Jefferson Center for Pancreatic, Biliary and Related CancersPhiladelphia, PA, USA
| | - F Charles Brunicardi
- Michael DeBakey Department of Surgery and Elkins Pancreas Center, Baylor College of MedicineHouston, TX
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing CenterHouston, TX
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Human Genome Sequencing CenterHouston, TX,Michael DeBakey Department of Surgery and Elkins Pancreas Center, Baylor College of MedicineHouston, TX
| | - William E Fisher
- Michael DeBakey Department of Surgery and Elkins Pancreas Center, Baylor College of MedicineHouston, TX
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