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

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.

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

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 &gt;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.

scholarly journals Prevalence of anxiety disorder among workers with cancer in Amman, Jordan

2020 ◽  
Author(s):  
Abdel Rahman Aref Ali Abu Shreea ◽  
Lee Khuan ◽  
Sharifah Norkhadijah Syed Ismail ◽  
Nasrudin Subhi ◽  
Sobuh (Moh’d Sobhi) Ahmad Abu-Shanab ◽  
...  
Keyword(s):  
Anxiety Disorder ◽  
Marital Status ◽  
Sampling Technique ◽  
Cross Sectional Study ◽  
Sample Population ◽  
Cross Sectional ◽  
Long Term Conditions ◽  
Cancer Data ◽  
Patients With Cancer ◽  
Significant Difference

AbstractIntroductionCancer is now being recognised as a long term conditions due to advances in treatments that increase the survival rate of patients with cancer to as long as 10 years from the time of the disease. Anxiety is among the commonly discovered psychiatric illness in patients with cancer and is often neglected. Approximately 10% of patients with cancer are affected with anxiety worldwide. Hence, this study was aimed to determine the prevalence of anxiety disorder and its associated factors among workers with cancer in Jordanian population.MethodsA cross-sectional study was conducted at the King Husain Cancer Centre (KHCC) in Amman, Jordan. Proportional sampling technique was used to obtain the sample population of 355 workers with cancer. Data were collected through self-administered Generalized Anxiety Disorder (GAD-7) questionnaire and analyses were carried out using SPSS version 25.ResultsResponse rate of 100% were obtained from the participants. Prevalence of anxiety disorder among workers with cancer was recorded at 20.8% with male (23.1%) having the higher prevalence rate than female (17.3%) workers with cancers. A significant difference in anxiety between marital status (p=0.025), types of cancer (p=0.001), treatment types (p=0.024) were observed. A multiple regression was run to predict anxiety disorder from marital status, type of cancer and treatment types. These variables statistically significantly predicted anxiety disorder [F(3, 351) = 8.117, p < .001, R2 = 0.225].ConclusionThere is high prevalent of anxiety disorder among workers with cancer in Jordan. Predictors of anxiety among workers with cancer were also identified in this report.

scholarly journals A system for phenotype harmonization in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program

2020 ◽  
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

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 (TOPMed) 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 TOPMed studies per phenotype. We discuss the challenges faced 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.

Comparable survival of African-Americans and Caucasian patients with multiple myeloma: A hospital-based study including 117,926 patients.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e18170-e18170
Author(s):  
Ehsan Malek ◽  
Kamal Chamoun ◽  
Paolo Fabrizio Caimi ◽  
Stanton L. Gerson ◽  
Ben Kent Tomlinson ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
African Americans ◽  
Race And Ethnicity ◽  
Cox Model ◽  
National Cancer Data Base ◽  
Rank Test ◽  
Racial Groups ◽  
Cancer Data ◽  
Significant Difference ◽  
The Usa

e18170 Background: Multiple Myeloma (MM) counts the most common hematologic malignance among African-Americans with twice the incidence of whites. The outcomes have greatly improved during the last 15 years, however with changing demographics there is an increasing focus on how various subgroups, based on race and ethnicity may be benefiting from survival improvement in MM. Previous studies showed that if access to care is assured, racial disparity-driven differences in outcome may be mitigated. Here, we conducted a study using the National Cancer Data Base (NCDB), which covers more than 70% of cancer pts in the USA, to evaluate survival patterns by race. Methods: MM patients (pts) diagnosed between years 2005 and 2014 and reported to the NCDB were analyzed (n = 117926). Pts were divided in three groups based on the year (y) of diagnosis (2005-07, 2008-10 and 2011-14). Kaplan-Meier method and log-rank test were used for overall survival analysis (OS). The effect size, hazard ratio (HR), of race on OS was estimated by Cox model adjusted by confounders. Results: Median age at diagnosis was 67 y (19 - 90); 55% were males. Median follow up was 30 months (m) (0 - 145). Median OS for white and black pts was 46 m (95% CI: 45.4 - 46.6) and 50.6 m (95% CI: 49.1 - 52.3), respectively (p < 0.0001). Black had longer OS compared to white pts by univariable analysis in all three study periods, noticeably with a trend toward higher survival benefit in most recent years. After adjusting for a variety of factors there was no statistically significant difference between the two racial groups (Table). Conclusions: This large study confirmed that after adjusting for confounding factors survival is similar for white and black MM pts. [Table: see text]

Endovascular thrombectomy for acute ischemic stroke in patients with cancer: a propensity-matched analysis

2021 ◽  
pp. neurintsurg-2021-018211
Author(s):  
Krishna C Joshi ◽  
Parneet Grewal ◽  
André Beer-Furlan ◽  
Alejandro Vargas ◽  
Nicholas Osteraas ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Acute Ischemic Stroke ◽  
Group Versus ◽  
Hemorrhagic Transformation ◽  
National Institutes Of Health ◽  
Endovascular Thrombectomy ◽  
Patients With Cancer ◽  
Cancer Group ◽  
Significant Difference ◽  
Active Cancer

BackgroundThere is a paucity of data and a belief that endovascular thrombectomy (EVT) has low efficacy for acute ischemic stroke (AIS) in patients with cancer. We aimed to critically compare the clinical outcomes of EVT for AIS in patients with and without cancer.MethodsRecords of all patients undergoing EVT for AIS between January 2015 and 2020 were screened for cancer at the time of EVT. Active cancer was defined as patients who were diagnosed with cancer and were undergoing or refused treatment for that cancer. Baseline modified Rankin Scale (mRS), age and sex were used in a 1:5 propensity score matching ratio. After matching we evaluated for any change in the National Institutes of Health Stroke Scale (NIHSS) from baseline to discharge, hemorrhagic transformation (HT), and 90-day mRS and mortality.ResultsThere were 19 patients with cancer and 95 matched controls. The mean±SD age was 70.89±11.16 years, and 17 (89.47%) were female. The baseline NIHSS was 22±7.5 and baseline mRS was 1 (IQR 1). There was no significant difference in change in baseline to discharge NIHSS, 90-day mRS or mortality; 90-day mRS 0–2 was 45.2% in the non-cancer group versus 46.7% in cancer group (p=0.54). HT was significantly higher in patients with cancer (57.89% vs 6.49%, p<0.001).ConclusionsIn propensity matched analysis of patients undergoing EVT for AIS with and without cancer, 90-day functional outcomes and mortality were similar. However, there was a significantly higher rate of HT in cancer patients.

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

2021 ◽  
pp. jmedgenet-2021-108112
Author(s):  
Jay G Ronquillo ◽  
William T Lester
Keyword(s):  
Genetic Testing ◽  
Observational Study ◽  
Precision Medicine ◽  
Standard Of Care ◽  
National Institutes Of Health ◽  
Prescribing Patterns ◽  
Age Group ◽  
Patients With Cancer ◽  
Testing Practices ◽  
Population Databases

Population databases could help patients with cancer and providers better understand current pharmacogenomic prescribing and testing practices. This retrospective observational study analysed patients with cancer, drugs with pharmacogenomic evidence and related genetic testing in the National Institutes of Health All of Us database. Most patients with cancer (19 633 (88.3%) vs 2590 (11.7%)) received ≥1 drug and 36 (0.2%) received genetic testing, with a significant association between receiving ≥1 drug and age group (p<0.001), but not sex (p=0.612), race (p=0.232) or ethnicity (p=0.971). Drugs with pharmacogenomic evidence—but not genetic testing—were common for patients with cancer, reflecting key gaps preventing precision medicine from becoming standard of care.

scholarly journals Adverse reactions of targeted therapy in cancer patients: a retrospective study of hospital medical data in China

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ruofei Du ◽  
Xin Wang ◽  
Lixia Ma ◽  
Leon M. Larcher ◽  
Han Tang ◽  
...  
Keyword(s):  
Targeted Therapy ◽  
Cancer Patients ◽  
Adverse Reactions ◽  
Cox Regression ◽  
Target Therapy ◽  
Skin Damage ◽  
Data Set ◽  
Patients With Cancer ◽  
Number Of Patients ◽  
Significant Difference

Abstract Background The adverse reactions (ADRs) of targeted therapy were closely associated with treatment response, clinical outcome, quality of life (QoL) of patients with cancer. However, few studies presented the correlation between ADRs of targeted therapy and treatment effects among cancer patients. This study was to explore the characteristics of ADRs with targeted therapy and the prognosis of cancer patients based on the clinical data. Methods A retrospective secondary data analysis was conducted within an ADR data set including 2703 patients with targeted therapy from three Henan medical centers of China between January 2018 and December 2019. The significance was evaluated with chi-square test between groups with or without ADRs. Univariate and multivariate logistic regression with backward stepwise method were applied to assess the difference of pathological characteristics in patients with cancer. Using the univariate Cox regression method, the actuarial probability of overall survival was performed to compare the clinical outcomes between these two groups. Results A total of 485 patients were enrolled in this study. Of all patients, 61.0% (n = 296) occurred ADRs including skin damage, fatigue, mucosal damage, hypertension and gastrointestinal discomfort as the top 5 complications during the target therapy. And 62.1% of ADRs were mild to moderate, more than half of the ADRs occurred within one month, 68.6% ADRs lasted more than one month. Older patients (P = 0.022) and patients with lower education level (P = 0.036), more than 2 comorbidities (P = 0.021), longer medication time (P = 0.022), drug combination (P = 0.033) and intravenous administration (P = 0.019) were more likely to have ADRs. Those with ADRs were more likely to stop taking (P = 0.000), change (P = 0.000), adjust (P = 0.000), or not take the medicine on time (P = 0.000). The number of patients with recurrence (P = 0.000) and metastasis (P = 0.006) were statistically significant difference between ADRs and non-ADRs group. And the patients were significantly poor prognosis in ADRs groups compared with non-ADRs group. Conclusion The high incidence of ADRs would affect the treatment and prognosis of patients with cancer. We should pay more attention to these ADRs and develop effective management strategies.

scholarly journals Khorana Score: Νew Predictor of Early Mortality in Patients With Lung Adenocarcinoma

2018 ◽  
Vol 24 (8) ◽  
pp. 1347-1351 ◽  
Author(s):  
Ioannis Vathiotis ◽  
Evangelos P. Dimakakos ◽  
Paraskevi Boura ◽  
Angeliki Ntineri ◽  
Andiani Charpidou ◽  
...  
Keyword(s):  
Venous Thromboembolism ◽  
Adjuvant Chemotherapy ◽  
Lung Adenocarcinoma ◽  
Treatment Period ◽  
Predictive Value ◽  
First Line ◽  
Thromboembolic Risk ◽  
Patients With Cancer ◽  
Risk Of Death ◽  
Significant Difference

Venous thromboembolism (VTE) is a typical complication in patients with lung cancer. Khorana score is an established tool for thromboembolic risk stratification of ambulatory patients with cancer undergoing outpatient chemotherapy. The aim of this study was to evaluate the predictive value of the Khorana score for VTE and death in patients with lung adenocarcinoma during first-line or adjuvant chemotherapy. Medical records of 130 patients with lung adenocarcinoma receiving first-line or adjuvant chemotherapy were retrospectively studied during the time period June 2013 to May 2015. Venous thromboembolism occurred in 13 (10.0%) patients. Thromboembolic events were significantly correlated with reduced survival during treatment period (hazard ratio [HR]: 3.24; 95% confidence interval [CI]: 1.11-9.49; P = .032). The VTE rates did not present statistically significant difference between different Khorana score groups ( P = .96). In univariate analysis, the risk of death during treatment period (median: 16 weeks) was 3.75 times higher in high-risk versus intermediate-risk patients (HR: 3.75, 95% CI: 1.36-10.36; P = .001) and had 2.25 times higher per point increase in the Khorana score (HR: 2.25, 95% CI: 1.36-3.73; P = .002); the above results were also reproduced in multivariate analysis. Khorana score represents a valuable tool for identifying patients with cancer in low thromboembolic risk but does not preserve its predictive value for higher risk individuals. Khorana score is an independent risk factor for death in patients with lung adenocarcinoma receiving first-line or adjuvant chemotherapy.

scholarly journals Finding useful data across multiple biomedical data repositories using DataMed

2017 ◽  
Vol 49 (6) ◽  
pp. 816-819 ◽  
Author(s):  
Lucila Ohno-Machado ◽  
Susanna-Assunta Sansone ◽  
George Alter ◽  
Ian Fore ◽  
Jeffrey Grethe ◽  
...  
Keyword(s):  
Biomedical Data ◽  
Data Repositories

scholarly journals Common Mediterranean Fever (MEFV) Gene Mutations Associated with Ankylosing Spondylitis in Turkish Population

2012 ◽  
Vol 33 (3) ◽  
pp. 113-118 ◽  
Author(s):  
Serbulent Yigit ◽  
Ahmet Inanir ◽  
Nevin Karakus ◽  
Esra Kesici ◽  
Nihan Bozkurt
Keyword(s):  
Ankylosing Spondylitis ◽  
Mefv Gene ◽  
Gene Mutations ◽  
Turkish Population ◽  
M694v Mutation ◽  
Significant Difference ◽  
Mediterranean Fever ◽  
Genomic Dnas ◽  
Polymerase Chain ◽  
Turkish Patients

Ankylosing spondylitis (AS) is a common inflammatory rheumatic disease. Mediterranean fever (MEFV) gene, which has already been identified as being responsible for familial Mediterranean fever (FMF), is also a suspicious gene for AS because of the clinical association of these two diseases. The aim of this study was to explore the frequency and clinical significance ofMEFVgene mutations (M694V, M680I, V726A, E148Q and P369S) in a cohort of Turkish patients with AS. Genomic DNAs of 103 AS patients and 120 controls were isolated and genotyped using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) methods. There was a statistically significant difference of theMEFVgene mutation carrier rates between AS patients and healthy controls (p= 0.004, OR: 2.5, 95% CI: 1.32–4.76). This association was also observed in allele frequencies (p= 0.005, OR: 2.3, 95% CI: 1.27–4.2). A relatively higher frequency was observed for M694V mutation in AS patients than controls (10.7% versus 4.2% ,p= 0.060). There were no significant differences between MEFV mutation carriers and non-carriers with respect to the clinical and demographic characteristics. The results of this study suggest thatMEFVgene mutations are positively associated with a predisposition to develop AS.

Sign in / Sign up

Export Citation Format

Share Document