Principal Investigator

Kord Michael
Kober
Awardee Organization

University Of California, San Francisco
United States

Fiscal Year
2023
Activity Code
R37
Early Stage Investigator Grants (ESI)
Not Applicable
Project End Date

An Evaluation of Cloud Computing for Symptom Science Research: Moving Genomics and Machine Learning Analyses of Cancer Chemotherapy-Related Fatigue to the Cloud

Cancer-related fatigue (CRF) is the most common symptom associated with cancer and its treatments. Moderate to severe CRF has a negative impact on patients’ ability to tolerate treatments as well as on their quality of life. The parent grant addressed two of the major knowledge gaps for CRF: the lack of a risk prediction model and a lack of knowledge of its underlying mechanisms. Given these analyses are data and resource intensive, they are unavailable to many symptom science researchers. In terms of implementation, two of the major gaps for symptom science researchers are the lack of access to the necessary computational resources and a lack of understanding of benefits and costs of a cloud deployment. Symptom science is a prominent research focus for many extramural and intramural nurse scientists. An evaluation of the analytic pipelines of the parent grant would identify resource intensive analyses that could be efficiently deployed to the cloud. Given the potential benefits of cloud services, increased knowledge of the opportunities for using the cloud for symptom science research and an evaluation of the costs and benefits could guide future research planning and an increased adoption of cloud computing in the nursing research community. To address these limitations, we propose to deploy and evaluate the performance of the RNA-seq and machine learning pipelines to the cloud; develop and release a cloud-supported container for performing expression quantitative methylation (eQTM) mapping in the cloud; and provide educational opportunities for the nursing research community describing our experience deploying these analytic pipelines to the cloud and providing guidance to aid in planning omics and machine learning symptom science research projects.

Publications

  • Oppegaard KR, Mayo SJ, Armstrong TS, Dokiparthi V, Melisko M, Levine JD, Olshen AB, Anguera JA, Roy R, Paul S, Cooper B, Conley YP, Hammer MJ, Miaskowski C, Kober KM. Neurodegenerative disease pathways are perturbed in patients with cancer who self-report cognitive changes and anxiety: A pathway impact analysis. Cancer. 2024 Apr 27. Epub 2024 Apr 27. PMID: 38676932
  • Kober KM, Berger L, Roy R, Olshen A. Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units. bioRxiv : the preprint server for biology. 2023 Mar 10. PMID: 36945384
  • Kober KM, Yom SS. Doc, I feel tired… oh really, so how's your mucositis? Cancer. 2021 Sep 15;127(18):3294-3297. Epub 2021 May 24. PMID: 34028000
  • Harris CS, Miaskowski CA, Conley YP, Hammer MJ, Dhruva AA, Levine JD, Olshen AB, Kober KM. Gastrointestinal Symptom Cluster is Associated With Epigenetic Regulation of Lymphotoxin Beta in Oncology Patients Receiving Chemotherapy. Biological research for nursing. 2023 Jan;25(1):51-64. Epub 2022 Aug 5. PMID: 35929442
  • Kober KM, Roy R, Dhruva A, Conley YP, Chan RJ, Cooper B, Olshen A, Miaskowski C. Prediction of evening fatigue severity in outpatients receiving chemotherapy: less may be more. Fatigue : biomedicine, health & behavior. 2021;9(1):14-32. Epub 2021 Feb 16. PMID: 34249477
  • Kober KM, Harris C, Conley YP, Dhruva A, Dokiparthi V, Hammer MJ, Levine JD, Oppegaard K, Paul S, Shin J, Sucher A, Wright F, Yuen B, Olshen AB, Miaskowski C. Perturbations in common and distinct inflammatory pathways associated with morning and evening fatigue in outpatients receiving chemotherapy. Cancer medicine. 2023 Mar;12(6):7369-7380. Epub 2022 Nov 14. PMID: 36373573
  • Harris CS, Miaskowski CA, Dhruva AA, Cataldo J, Kober KM. Multi-Staged Data-Integrated Multi-Omics Analysis for Symptom Science Research. Biological research for nursing. 2021 Oct;23(4):596-607. Epub 2021 Apr 8. PMID: 33827270
  • Harris CS, Miaskowski CA, Conley YP, Hammer MJ, Dunn LB, Dhruva AA, Levine JD, Olshen AB, Kober KM. Epigenetic Regulation of Inflammatory Mechanisms and a Psychological Symptom Cluster in Patients Receiving Chemotherapy. Nursing research. 2023 May-Jun 1;72(3):200-210. Epub 2023 Mar 17. PMID: 36929768
  • Wright F, Cooper BA, Paul SM, Hammer MJ, Conley YP, Levine JD, Miaskowski C, Kober KM. Distinct Profiles of Morning and Evening Fatigue Co-Occurrence in Patients During Chemotherapy. Nursing research. 2023 Jul-Aug 1;72(4):259-271. Epub 2023 Apr 18. PMID: 37084242
  • Mortlock S, Houshdaran S, Kosti I, Rahmioglu N, Nezhat C, Vitonis AF, Andrews SV, Grosjean P, Paranjpe M, Horne AW, Jacoby A, Lager J, Opoku-Anane J, Vo KC, Manvelyan E, Sen S, Ghukasyan Z, Collins F, Santamaria X, Saunders P, Kober K, McRae AF, Terry KL, Vallvé-Juanico J, Becker C, Rogers PAW, Irwin JC, Zondervan K, Montgomery GW, Missmer S, Sirota M, Giudice L. Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function. Communications biology. 2023 Aug 16;6(1):780. PMID: 37587191
  • Harris CS, Pozzar RA, Conley Y, Eicher M, Hammer MJ, Kober KM, Miaskowski C, Colomer-Lahiguera S. Big Data in Oncology Nursing Research: State of the Science. Seminars in oncology nursing. 2023 Jun;39(3):151428. Epub 2023 Apr 19. PMID: 37085404
  • Calvo-Schimmel A, Kober KM, Paul SM, Cooper BA, Harris C, Shin J, Hammer MJ, Conley YP, Dokiparthi V, Olshen A, Levine JD, Miaskowski C. Sleep disturbance is associated with perturbations in immune-inflammatory pathways in oncology outpatients undergoing chemotherapy. Sleep medicine. 2023 Jan;101:305-315. Epub 2022 Nov 21. PMID: 36470166
  • Kober KM, Berger L, Roy R, Olshen A. Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units. BMC bioinformatics. 2024 Feb 14;25(1):71. PMID: 38355413