Pharmacogenomic testing and prescribing patterns for patients with cancer in a large national precision medicine cohort

Precision Medicine Landscape of Genomic Testing for Patients With Cancer in the National Institutes of Health All of Us Database Using Informatics Approaches

JCO Clinical Cancer Informatics ◽

10.1200/cci.21.00152 ◽

2022 ◽

Author(s):

Jay G. Ronquillo ◽

William T. Lester

Keyword(s):

Precision Medicine ◽

Race And Ethnicity ◽

Gene Mutations ◽

National Institutes Of Health ◽

Genomic Testing ◽

Biomedical Data ◽

Data Repositories ◽

Cancer Data ◽

Patients With Cancer ◽

Significant Difference

PURPOSE The rapid growth of biomedical data ecosystems has catalyzed research for oncology and precision medicine. We leverage federal cloud-based precision medicine databases and tools to better understand the current landscape of precision medicine and genomic testing for patients with cancer. METHODS Retrospective observational study of genomic testing for patients with cancer in the National Institutes of Health All of Us Research Program, with the cancer cohort defined as having at least two documented or reported cancer diagnoses. RESULTS There were 5,678 (1.8%) All of Us participants in the cancer cohort, with a significant difference between cancer status by age category, sex, race, and ethnicity ( P < .001 for all). There were 295 (5.2%) patients with cancer who received genomic testing compared with 6,734 (2.2%) of noncancer patients, with 752 genomic tests commonly focused on gene mutations (primarily pharmacogenomics), molecular pathology, or clinical cytogenetic reports. CONCLUSION Although not yet ubiquitous, diverse clinical genomic analyses in oncology can set the stage to grow the practice of precision medicine by integrating research patient data repositories, cancer data ecosystems, and biomedical informatics.

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Assessing the readiness of precision medicine interoperabilty: An exploratory study of the National Institutes of Health genetic testing registry

Journal of Innovation in Health Informatics ◽

10.14236/jhi.v24i4.918 ◽

2017 ◽

Vol 24 (4) ◽

pp. 323 ◽

Cited By ~ 1

Author(s):

Jay G Ronquillo ◽

Chunhua Weng ◽

William T Lester

Keyword(s):

Genetic Testing ◽

Precision Medicine ◽

Healthcare Providers ◽

National Institutes Of Health ◽

Snomed Ct ◽

Genetic Tests ◽

Test Characteristics ◽

Current State ◽

Starting Point ◽

Systematized Nomenclature Of Medicine

Background: Precision medicine involves three major innovations currently taking place in healthcare: electronic health records, genomics, and big data. A major challenge for healthcare providers, however, is understanding the readiness for practical application of initiatives like precision medicine.Objective: To better understand the current state and challenges of precision medicine interoperability using a national genetic testing registry as a starting point, placed in the context of established interoperability formats.Methods: We performed an exploratory analysis of the National Institutes of Health Genetic Testing Registry. Relevant standards included Health Level Seven International Version 3 Implementation Guide for Family History, the Human Genome Organization Gene Nomenclature Committee (HGNC) database, and Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT). We analyzed the distribution of genetic testing laboratories, genetic test characteristics, and standardized genome/clinical code mappings, stratified by laboratory setting.Results: There were a total of 25472 genetic tests from 240 laboratories testing for approximately 3632 distinct genes. Most tests focused on diagnosis, mutation confirmation, and/or risk assessment of germline mutations that could be passed to offspring. Genes were successfully mapped to all HGNC identifiers, but less than half of tests mapped to SNOMED CT codes, highlighting significant gaps when linking genetic tests to standardized clinical codes that explain the medical motivations behind test ordering. Conclusion: While precision medicine could potentially transform healthcare, successful practical and clinical application will first require the comprehensive and responsible adoption of interoperable standards, terminologies, and formats across all aspects of the precision medicine pipeline.

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Status of BRCA1/2 Genetic Testing Practices in Korea (2014)

Laboratory Medicine Online ◽

10.3343/lmo.2018.8.3.107 ◽

2018 ◽

Vol 8 (3) ◽

pp. 107 ◽

Cited By ~ 1

Author(s):

Kyungju Lee ◽

Ja-Hyun Jang ◽

Seung-Tae Lee ◽

Kyong-Ah Yoon ◽

Eun Sook Lee ◽

...

Keyword(s):

Genetic Testing ◽

Testing Practices

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Profil Penyakit Malaria Di Rumah Sakit Islam Siti Rahmah Padang Tahun 2018

Health & Medical Journal ◽

10.33854/heme.v2i2.546 ◽

2020 ◽

Vol 2 (2) ◽

pp. 08-15

Author(s):

Rahma Triyana ◽

Salmi Salmi

Keyword(s):

Observational Study ◽

Frequency Distribution ◽

Cross Section ◽

Laboratory Tests ◽

Age Group ◽

Normal Range ◽

Cross Sectional ◽

West Sumatra ◽

Severity Of The Disease

Malaria is one of the health problems in Indonesia, especially West Sumatra. Determination of the description of Malaria disease in an area is needed to determine the spread and severity of the disease. This study aims to determine the frequency distribution according to age, sex and place of residence, description of the types of Plasmodium causes of Malaria and hematological features in Malaria patients at Siti Rahmah Padang Hospital in 2018. This type of research is a descriptive observational study with an approach or design cross section (cross sectional). The frequency distribution of Malaria sufferers in Siti Rahmah Padang Hospital in 2018 according to the highest age was in the age group 21-30 years as many as 28 cases (36.8%), the highest sex among men was 46 (60.5%) and the highest number of residences was found in Koto Tangah sub-district there were 31 cases (40.8%). The type of Plasmodium found in Malaria cases in Siti Rahmah Padang Hospital in 2018 was P. vivax (73 cases (96.05%)) and P. falciparum (3 cases (3.95%)). The results of laboratory tests on Hb, hematocrit, platelet and leukocyte levels in Malaria positive patients in Siti Rahmah Padang Hospital in 2018 were in the normal range.

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Profil Penyakit Malaria di Rumah Sakit Islam Siti Rahmah Padang Tahun 2018

Health & Medical Journal ◽

10.33854/heme.v2i2.452 ◽

2020 ◽

Vol 2 (2) ◽

pp. 08-15

Author(s):

Rahma Triyana Y ◽

Salmi Salmi

Keyword(s):

Observational Study ◽

Frequency Distribution ◽

Cross Section ◽

Laboratory Tests ◽

Age Group ◽

Normal Range ◽

Cross Sectional ◽

West Sumatra ◽

Severity Of The Disease

Malaria is one of the health problems in Indonesia, especially West Sumatra. Determination of the description of Malaria disease in an area is needed to determine the spread and severity of the disease. This study aims to determine the frequency distribution according to age, sex and place of residence, description of the types of Plasmodium causes of Malaria and hematological features in Malaria patients at Siti Rahmah Padang Hospital in 2018. This type of research is a descriptive observational study with an approach or design cross section (cross sectional). The frequency distribution of Malaria sufferers in Siti Rahmah Padang Hospital in 2018 according to the highest age was in the age group 21-30 years as many as 28 cases (36.8%), the highest sex among men was 46 (60.5%) and the highest number of residences was found in Koto Tangah sub-district there were 31 cases (40.8%). The type of Plasmodium found in Malaria cases in Siti Rahmah Padang Hospital in 2018 was P. vivax (73 cases (96.05%)) and P. falciparum (3 cases (3.95%)). The results of laboratory tests on Hb, hematocrit, platelet and leukocyte levels in Malaria positive patients in Siti Rahmah Padang Hospital in 2018 were in the normal range.

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Exercise Intensity during Olympic-Distance Triathlon in Well-Trained Age-Group Athletes: An Observational Study

Sports ◽

10.3390/sports9020018 ◽

2021 ◽

Vol 9 (2) ◽

pp. 18

Author(s):

Atsushi Aoyagi ◽

Keisuke Ishikura ◽

Yoshiharu Nabekura

Keyword(s):

Heart Rate ◽

Observational Study ◽

Exercise Intensity ◽

Time Range ◽

Age Group ◽

Slow Group ◽

H 41 ◽

The Mean ◽

Aerobic And Anaerobic ◽

Very High

The aim of this study was to examine the exercise intensity during the swimming, cycling, and running legs of nondraft legal, Olympic-distance triathlons in well-trained, age-group triathletes. Seventeen male triathletes completed incremental swimming, cycling, and running tests to exhaustion. Heart rate (HR) and workload corresponding to aerobic and anaerobic thresholds, maximal workloads, and maximal HR (HRmax) in each exercise mode were analyzed. HR and workload were monitored throughout the race. The intensity distributions in three HR zones for each discipline and five workload zones in cycling and running were quantified. The subjects were then assigned to a fast or slow group based on the total race time (range, 2 h 07 min–2 h 41 min). The mean percentages of HRmax in the swimming, cycling, and running legs were 89.8% ± 3.7%, 91.1% ± 4.4%, and 90.7% ± 5.1%, respectively, for all participants. The mean percentage of HRmax and intensity distributions during the swimming and cycling legs were similar between groups. In the running leg, the faster group spent relatively more time above HR at anaerobic threshold (AnT) and between workload at AnT and maximal workload. In conclusion, well-trained male triathletes performed at very high intensity throughout a nondraft legal, Olympic-distance triathlon race, and sustaining higher intensity during running might play a role in the success of these athletes.

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Observational study on effectiveness and safety of multiple regimens of Triclabendazole in Human Fascioliasis after failure to standard of care regimens.

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2021.03.023 ◽

2021 ◽

Author(s):

Angélica Terashima ◽

Marco Canales ◽

Vicente Maco ◽

Luis A. Marcos

Keyword(s):

Observational Study ◽

Standard Of Care ◽

Human Fascioliasis

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A System for Phenotype Harmonization in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program

American Journal of Epidemiology ◽

10.1093/aje/kwab115 ◽

2021 ◽

Author(s):

Adrienne M Stilp ◽

Leslie S Emery ◽

Jai G Broome ◽

Erin J Buth ◽

Alyna T Khan ◽

...

Keyword(s):

Precision Medicine ◽

Association Studies ◽

Controlled Vocabulary ◽

National Institutes Of Health ◽

Design Data ◽

Data Set ◽

Data Repositories ◽

Phenotype Data ◽

National Heart Lung ◽

Centralized System

Abstract Genotype-phenotype association studies often combine phenotype data from multiple studies to increase power. Harmonization of the data usually requires substantial effort due to heterogeneity in phenotype definitions, study design, data collection procedures, and data set organization. Here we describe a centralized system for phenotype harmonization that includes input from phenotype domain and study experts, quality control, documentation, reproducible results, and data sharing mechanisms. This system was developed for the National Heart, Lung and Blood Institute’s Trans-Omics for Precision Medicine program, which is generating genomic and other omics data for >80 studies with extensive phenotype data. To date, 63 phenotypes have been harmonized across thousands of participants from up to 17 studies per phenotype (participants recruited 1948-2012). We discuss challenges in this undertaking and how they were addressed. The harmonized phenotype data and associated documentation have been submitted to National Institutes of Health data repositories for controlled-access by the scientific community. We also provide materials to facilitate future harmonization efforts by the community, which include (1) the code used to generate the 63 harmonized phenotypes, enabling others to reproduce, modify or extend these harmonizations to additional studies; and (2) results of labeling thousands of phenotype variables with controlled vocabulary terms.

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