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The purpose of this study is to characterize the breadth of molecular features present in participants receiving care within a large, integrated, community-based healthcare system. Through comprehensive genomic profiling, investigators aim to identify the underlying genomic drivers of premalignant and malignant conditions across a range of disease stages and cancer types.
Comprehensive molecular profiling will include somatic tumor testing (tissue and/or blood) using next-generation sequencing. Selected subsets of samples may undergo whole exome and/or whole transcriptome sequencing for research purposes. Pharmacogenomic testing will also be performed to better understand individual variability in medication response and to identify opportunities for optimizing treatment. In addition, participants may optionally provide microbiome samples.
To maximize the value of the genomic data, participants who consent to this protocol will have their electronic health records-both retrospective and prospective-abstracted, curated, annotated, and linked to the genomic data generated through study testing. Given the long-term value of these data, participants may also voluntarily consent to the storage of their biological samples in a biobank and to the use of their de-identified information for future research.
Data collected from this participant population will support efforts to advance the understanding of cancer biology, as well as the discovery and validation of biomarkers associated with clinical outcomes. Findings may also be shared through collaborative research initiatives to further promote advancements in cancer research.
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| Measure | Description | Time Frame |
|---|---|---|
| Percent of patients participating in comprehensive molecular profiling | 5 years | |
| Percent of patients referred for cascade genetic testing | 5 years | |
| Percent of patients referred for molecularly targeted clinical trials | 5 years |
| Measure | Description | Time Frame |
|---|---|---|
| Percent of patients that had therapy changed due to comprehensive molecular profiling | 5 years | |
| Percent of patients that had therapy changed due to pharmacogenomic testing | 5 years | |
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Inclusion Criteria:
Exclusion Criteria:
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Participants with a premalignant or malignant condition and able/willing to consent/participate in the study.
| Name | Role | Phone | Extension | |
|---|---|---|---|---|
| Rachel Elsey, PharmD | Contact | 605-322-3225 | Rachel.Elsey@avera.org | |
| Avera Precision Research Team | Contact | 888-422-1410 | McK-MBX-PrecisionResearch@avera.org |
| Name | Affiliation | Role |
|---|---|---|
| Rachel Elsey, PharmD | Avera Cancer Institute | Principal Investigator |
| Facility | Status | City | State | ZIP | Country | Contacts |
|---|---|---|---|---|---|---|
| Avera Cancer Institute - Marshall | Recruiting | Marshall | Minnesota | 56258 | United States |
| PubMed Identifier | Type | Citation | Retractions |
|---|---|---|---|
| 29345757 | Background | Nakagawa H, Fujita M. Whole genome sequencing analysis for cancer genomics and precision medicine. Cancer Sci. 2018 Mar;109(3):513-522. doi: 10.1111/cas.13505. Epub 2018 Feb 26. | |
| 30666631 | Background | Yi T, Feng Y, Sundaram R, Tie Y, Zheng H, Qian Y, You D, Yi T, Wang P, Zhao X. Antitumor efficacy of PARP inhibitors in homologous recombination deficient carcinomas. Int J Cancer. 2019 Sep 1;145(5):1209-1220. doi: 10.1002/ijc.32143. Epub 2019 Feb 23. |
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Retention: Samples with DNA/RNA, and protein Description: Tissue, blood, stool, saliva, skin
| Percent of patient participating in microbiome collection and analysis |
| 5 years |
| Avera Cancer Institute - Aberdeen | Recruiting | Aberdeen | South Dakota | 57401 | United States |
|
| Avera Cancer Institute - Mitchell | Recruiting | Mitchell | South Dakota | 57301 | United States |
|
| Avera Cancer Institute - Pierre | Recruiting | Pierre | South Dakota | 57501 | United States |
|
| Avera Cancer Institute | Recruiting | Sioux Falls | South Dakota | 57105 | United States |
|
| Avera Cancer Institute - Yankton | Recruiting | Yankton | South Dakota | 57078 | United States |
|
| 29607586 | Background | Lee B, Tran B, Hsu AL, Taylor GR, Fox SB, Fellowes A, Marquis R, Mooi J, Desai J, Doig K, Ekert P, Gaff C, Herath D, Hamilton A, James P, Roberts A, Snyder R, Waring P, McArthur G. Exploring the feasibility and utility of exome-scale tumour sequencing in a clinical setting. Intern Med J. 2018 Jul;48(7):786-794. doi: 10.1111/imj.13806. |
| 31923800 | Background | Reda M, Richard C, Bertaut A, Niogret J, Collot T, Fumet JD, Blanc J, Truntzer C, Desmoulins I, Ladoire S, Hennequin A, Favier L, Bengrine L, Vincent J, Hervieu A, Dusserre JG, Lepage C, Foucher P, Borg C, Albuisson J, Arnould L, Nambot S, Faivre L, Boidot R, Ghiringhelli F. Implementation and use of whole exome sequencing for metastatic solid cancer. EBioMedicine. 2020 Jan;51:102624. doi: 10.1016/j.ebiom.2019.102624. Epub 2020 Jan 7. |
| 26181256 | Background | Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Pauli C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic V, Emde AK, Oschwald D, Tan AY, Chen Z, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson BD, Nanus DM, Tagawa ST, Xiang JZ, Smogorzewska A, Demichelis F, Rickman DS, Sboner A, Elemento O, Rubin MA. Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response. JAMA Oncol. 2015 Jul;1(4):466-74. doi: 10.1001/jamaoncol.2015.1313. |
| 28398847 | Background | Samimi G, Bernardini MQ, Brody LC, Caga-Anan CF, Campbell IG, Chenevix-Trench G, Couch FJ, Dean M, de Hullu JA, Domchek SM, Drapkin R, Spencer Feigelson H, Friedlander M, Gaudet MM, Harmsen MG, Hurley K, James PA, Kwon JS, Lacbawan F, Lheureux S, Mai PL, Mechanic LE, Minasian LM, Myers ER, Robson ME, Ramus SJ, Rezende LF, Shaw PA, Slavin TP, Swisher EM, Takenaka M, Bowtell DD, Sherman ME. Traceback: A Proposed Framework to Increase Identification and Genetic Counseling of BRCA1 and BRCA2 Mutation Carriers Through Family-Based Outreach. J Clin Oncol. 2017 Jul 10;35(20):2329-2337. doi: 10.1200/JCO.2016.70.3439. Epub 2017 Apr 11. |
| 27799157 | Background | Win AK, Jenkins MA, Dowty JG, Antoniou AC, Lee A, Giles GG, Buchanan DD, Clendenning M, Rosty C, Ahnen DJ, Thibodeau SN, Casey G, Gallinger S, Le Marchand L, Haile RW, Potter JD, Zheng Y, Lindor NM, Newcomb PA, Hopper JL, MacInnis RJ. Prevalence and Penetrance of Major Genes and Polygenes for Colorectal Cancer. Cancer Epidemiol Biomarkers Prev. 2017 Mar;26(3):404-412. doi: 10.1158/1055-9965.EPI-16-0693. Epub 2016 Oct 31. |
| 27551127 | Background | Maxwell KN, Domchek SM, Nathanson KL, Robson ME. Population Frequency of Germline BRCA1/2 Mutations. J Clin Oncol. 2016 Dec;34(34):4183-4185. doi: 10.1200/JCO.2016.67.0554. Epub 2016 Oct 31. No abstract available. |
| 28632866 | Background | Kuchenbaecker KB, Hopper JL, Barnes DR, Phillips KA, Mooij TM, Roos-Blom MJ, Jervis S, van Leeuwen FE, Milne RL, Andrieu N, Goldgar DE, Terry MB, Rookus MA, Easton DF, Antoniou AC; BRCA1 and BRCA2 Cohort Consortium; McGuffog L, Evans DG, Barrowdale D, Frost D, Adlard J, Ong KR, Izatt L, Tischkowitz M, Eeles R, Davidson R, Hodgson S, Ellis S, Nogues C, Lasset C, Stoppa-Lyonnet D, Fricker JP, Faivre L, Berthet P, Hooning MJ, van der Kolk LE, Kets CM, Adank MA, John EM, Chung WK, Andrulis IL, Southey M, Daly MB, Buys SS, Osorio A, Engel C, Kast K, Schmutzler RK, Caldes T, Jakubowska A, Simard J, Friedlander ML, McLachlan SA, Machackova E, Foretova L, Tan YY, Singer CF, Olah E, Gerdes AM, Arver B, Olsson H. Risks of Breast, Ovarian, and Contralateral Breast Cancer for BRCA1 and BRCA2 Mutation Carriers. JAMA. 2017 Jun 20;317(23):2402-2416. doi: 10.1001/jama.2017.7112. |
| 26873718 | Background | Peltomaki P. Update on Lynch syndrome genomics. Fam Cancer. 2016 Jul;15(3):385-93. doi: 10.1007/s10689-016-9882-8. |
| 30964716 | Background | Kurian AW, Ward KC, Howlader N, Deapen D, Hamilton AS, Mariotto A, Miller D, Penberthy LS, Katz SJ. Genetic Testing and Results in a Population-Based Cohort of Breast Cancer Patients and Ovarian Cancer Patients. J Clin Oncol. 2019 May 20;37(15):1305-1315. doi: 10.1200/JCO.18.01854. Epub 2019 Apr 9. |
| 30753636 | Background | Knerr S, Bowles EJA, Leppig KA, Buist DSM, Gao H, Wernli KJ. Trends in BRCA Test Utilization in an Integrated Health System, 2005-2015. J Natl Cancer Inst. 2019 Aug 1;111(8):795-802. doi: 10.1093/jnci/djz008. |
| 19622575 | Background | O'Donnell PH, Dolan ME. Cancer pharmacoethnicity: ethnic differences in susceptibility to the effects of chemotherapy. Clin Cancer Res. 2009 Aug 1;15(15):4806-14. doi: 10.1158/1078-0432.CCR-09-0344. Epub 2009 Jul 21. |
| 24001330 | Background | Shaw DM, Elger BS, Colledge F. What is a biobank? Differing definitions among biobank stakeholders. Clin Genet. 2014 Mar;85(3):223-7. doi: 10.1111/cge.12268. Epub 2013 Oct 16. |
| 30365879 | Background | UK Biobank data on 500,000 people paves way to precision medicine. Nature. 2018 Oct;562(7726):163-164. doi: 10.1038/d41586-018-06950-9. No abstract available. |
| ID | Term |
|---|---|
| D009369 | Neoplasms |
| D001943 | Breast Neoplasms |
| D008175 | Lung Neoplasms |
| D003110 | Colonic Neoplasms |
| D005770 | Gastrointestinal Neoplasms |
| D010051 | Ovarian Neoplasms |
| D016889 | Endometrial Neoplasms |
| D016543 | Central Nervous System Neoplasms |
| D019337 | Hematologic Neoplasms |
| ID | Term |
|---|---|
| D009371 | Neoplasms by Site |
| D001941 | Breast Diseases |
| D012871 | Skin Diseases |
| D017437 | Skin and Connective Tissue Diseases |
| D012142 | Respiratory Tract Neoplasms |
| D013899 | Thoracic Neoplasms |
| D008171 | Lung Diseases |
| D012140 | Respiratory Tract Diseases |
| D015179 | Colorectal Neoplasms |
| D007414 | Intestinal Neoplasms |
| D004067 | Digestive System Neoplasms |
| D004066 | Digestive System Diseases |
| D005767 | Gastrointestinal Diseases |
| D003108 | Colonic Diseases |
| D007410 | Intestinal Diseases |
| D004701 | Endocrine Gland Neoplasms |
| D010049 | Ovarian Diseases |
| D000291 | Adnexal Diseases |
| D005831 | Genital Diseases, Female |
| D052776 | Female Urogenital Diseases |
| D005261 | Female Urogenital Diseases and Pregnancy Complications |
| D000091642 | Urogenital Diseases |
| D005833 | Genital Neoplasms, Female |
| D014565 | Urogenital Neoplasms |
| D000091662 | Genital Diseases |
| D004700 | Endocrine System Diseases |
| D006058 | Gonadal Disorders |
| D014594 | Uterine Neoplasms |
| D014591 | Uterine Diseases |
| D009423 | Nervous System Neoplasms |
| D009422 | Nervous System Diseases |
| D006402 | Hematologic Diseases |
| D006425 | Hemic and Lymphatic Diseases |
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