Journal of Personalized Medicine

9 pages, 822 KiB

Open AccessReview

The Role of Next-Generation Sequencing in Precision Medicine: A Review of Outcomes in Oncology

by Margaret Morash, Hannah Mitchell, Himisha Beltran, Olivier Elemento and Jyotishman Pathak

J. Pers. Med. 2018, 8(3), 30; https://doi.org/10.3390/jpm8030030 - 17 Sep 2018

Cited by 100 | Viewed by 15734

Precision medicine seeks to use genomic data to help provide the right treatment to the right patient at the right time. Next-generation sequencing technology allows for the rapid and accurate sequencing of many genes at once. This technology is becoming more common in [...] Read more.

Precision medicine seeks to use genomic data to help provide the right treatment to the right patient at the right time. Next-generation sequencing technology allows for the rapid and accurate sequencing of many genes at once. This technology is becoming more common in oncology, though the clinical benefit of incorporating it into precision medicine strategies remains under significant debate. In this manuscript, we discuss the early findings of the impact of next-generation sequencing on cancer patient outcomes. We investigate why not all patients with genomic variants linked to a specific therapy receive that therapy and describe current barriers. Finally, we explore the current state of health insurance coverage for individual genome sequencing and targeted therapies for cancer. Based on our analysis, we recommend increased transparency around the determination of “actionable mutations” and a heightened focus on investigating the variations in health insurance coverage across patients receiving sequencing-matched therapies. Full article

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0 pages, 2309 KiB

Open AccessArticle

Individualized Transcriptional Resolution of Complicated Malaria in a Colombian Study

by Mónica L. Rojas-Peña, Meixue Duan, Dalia Arafat, Lina Rengifo, Socrates Herrera, Myriam Arévalo-Herrera and Greg Gibson

J. Pers. Med. 2018, 8(3), 29; https://doi.org/10.3390/jpm8030029 - 14 Sep 2018

Cited by 4 | Viewed by 5907 | Correction

Abstract

To evaluate whether recovery from complicated malaria follows a common trajectory in terms of immunological mechanism or, rather, is highly individualized for each patient, we performed longitudinal gene expression profiling of whole blood. RNA sequencing (RNAseq) was performed on blood samples obtained from [...] Read more.

To evaluate whether recovery from complicated malaria follows a common trajectory in terms of immunological mechanism or, rather, is highly individualized for each patient, we performed longitudinal gene expression profiling of whole blood. RNA sequencing (RNAseq) was performed on blood samples obtained from eight patients on four consecutive days between hospital admission and discharge. Six patients were infected with Plasmodium falciparum, and two with Plasmodium vivax; one patient was a pregnant woman infected with P. falciparum, who was hospitalized for several weeks. The characterization of blood transcript modules (BTM) and blood informative transcripts (BIT) revealed that patients’ responses showed little commonality, being dominated by the balance of gene activity relating to lymphocyte function, inflammation, and interferon responses specific to each patient. Only weak correlations with specific complicated malaria symptoms such as jaundice, thrombocytopenia, or anemia were observed. The differential expression of individual genes, including transcripts derived from the human leukocyte antigen (HLA) complex, generally reflected differences in the underlying immune processes. Although the results of this pilot study do not point to any single process that might provide a target for complicated malaria treatment or prevention or personalized medical strategies, larger patient series and more extensive blood sampling may allow the classification of patients according to their type of response in order to develop novel therapeutic approaches. Full article

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15 pages, 2009 KiB

Open AccessReview

A Metabolomics Approach to Pharmacotherapy Personalization

by Elena E. Balashova, Dmitry L. Maslov and Petr G. Lokhov

J. Pers. Med. 2018, 8(3), 28; https://doi.org/10.3390/jpm8030028 - 5 Sep 2018

Cited by 59 | Viewed by 12843

Abstract

The optimization of drug therapy according to the personal characteristics of patients is a perspective direction in modern medicine. One of the possible ways to achieve such personalization is through the application of “omics” technologies, including current, promising metabolomics methods. This review demonstrates [...] Read more.

The optimization of drug therapy according to the personal characteristics of patients is a perspective direction in modern medicine. One of the possible ways to achieve such personalization is through the application of “omics” technologies, including current, promising metabolomics methods. This review demonstrates that the analysis of pre-dose metabolite biofluid profiles allows clinicians to predict the effectiveness of a selected drug treatment for a given individual. In the review, it is also shown that the monitoring of post-dose metabolite profiles could allow clinicians to evaluate drug efficiency, the reaction of the host to the treatment, and the outcome of the therapy. A comparative description of pharmacotherapy personalization (pharmacogenomics, pharmacoproteomics, and therapeutic drug monitoring) and personalization based on the analysis of metabolite profiles for biofluids (pharmacometabolomics) is also provided. Full article

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10 pages, 1420 KiB

Open AccessArticle

Design of a Controlled Trial of Cascade Screening for Hypercholesterolemia: The (CASH) Study

by Iftikhar J. Kullo and Kent R. Bailey

J. Pers. Med. 2018, 8(3), 27; https://doi.org/10.3390/jpm8030027 - 23 Aug 2018

Cited by 9 | Viewed by 6223

Abstract

To inform guidelines for screening family members of patients with familial hypercholesterolemia (FH), we designed a clinical trial to compare the yield of cascade screening in FH patients with and without an identifiable pathogenic variant. Participants with hypercholesterolemia (Low-density lipoprotein cholesterol (LDL-C) > [...] Read more.

To inform guidelines for screening family members of patients with familial hypercholesterolemia (FH), we designed a clinical trial to compare the yield of cascade screening in FH patients with and without an identifiable pathogenic variant. Participants with hypercholesterolemia (Low-density lipoprotein cholesterol (LDL-C) > 155 mg/dL) underwent sequencing of LDLR, APOB, and PCSK9 and genotyping of six single nucleotide polymorphisms associated with LDL-C followed by calculation of a polygenic score for LDL-C. We identified 24 patients with definite FH (pathogenic variant in one of the three FH genes), 76 patients with probable FH (Dutch lipid clinic network (DLCN) score ≥ 6, no pathogenic variant), and 262 patients with possible FH (DLCN score 3–5, no pathogenic variant). We will enroll 50 patients with definite FH by recruiting an additional 26 from the FH Clinic at Mayo and 50 patients each with probable and possible FH, matching on age and sex. Family members of patients with definite FH will undergo testing for the relevant pathogenic variant using saliva kits and family members of those with probable/possible FH will have a lipid profile checked. We will assess the number of new cases detected (defined as presence of a pathogenic variant in the family member of definite FH patient or LDL-C > 155 mg/dL (>130 mg/dL in children) in family members of probable/possible FH patients, and the cost of detecting a new case. The proposed clinical trial will compare the yield and cost of cascade screening for FH patients with/without an identifiable pathogenic variant, and thereby inform guidelines for cascade screening for FH. Full article

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18 pages, 1885 KiB

Open AccessArticle

Gene-Metabolite Interaction in the One Carbon Metabolism Pathway: Predictors of Colorectal Cancer in Multi-Ethnic Families

by S. Pamela K. Shiao, James Grayson and Chong Ho Yu

J. Pers. Med. 2018, 8(3), 26; https://doi.org/10.3390/jpm8030026 - 6 Aug 2018

Cited by 6 | Viewed by 6889

Abstract

For personalized healthcare, the purpose of this study was to examine the key genes and metabolites in the one-carbon metabolism (OCM) pathway and their interactions as predictors of colorectal cancer (CRC) in multi-ethnic families. In this proof-of-concept study, we included a total of [...] Read more.

For personalized healthcare, the purpose of this study was to examine the key genes and metabolites in the one-carbon metabolism (OCM) pathway and their interactions as predictors of colorectal cancer (CRC) in multi-ethnic families. In this proof-of-concept study, we included a total of 30 participants, 15 CRC cases and 15 matched family/friends representing major ethnic groups in southern California. Analytics based on supervised machine learning were applied, with the target variable being specified as cancer, including the ensemble method and generalized regression (GR) prediction. Elastic Net with Akaike’s Information Criterion with correction (AICc) and Leave-One-Out cross validation GR methods were used to validate the results for enhanced optimality, prediction, and reproducibility. The results revealed that despite some family members sharing genetic heritage, the CRC group had greater combined gene polymorphism-mutations than the family controls (p < 0.1) for five genes including MTHFR C677T, MTHFR A1298C, MTR A2756G, MTRR A66G, and DHFR 19bp. Blood metabolites including homocysteine (7 µmol/L), methyl-folate (40 nmol/L) with total gene mutations (≥4); age (51 years) and vegetable intake (2 cups), and interactions of gene mutations and methylmalonic acid (MMA) (400 nmol/L) were significant predictors (all p < 0.0001) using the AICc. The results were validated by a 3% misclassification rate, AICc of 26, and >99% area under the receiver operating characteristic curve. These results point to the important roles of blood metabolites as potential markers in the prevention of CRC. Future intervention studies can be designed to target the ways to mitigate the enzyme-metabolite deficiencies in the OCM pathway to prevent cancer. Full article

(This article belongs to the Special Issue Biomarkers in Colorectal Cancer)

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15 pages, 1223 KiB

Open AccessArticle

Early Outcome Data Assessing Utility of a Post-Test Genomic Counseling Framework for the Scalable Delivery of Precision Health

by Amy C. Sturm, Tara Schmidlen, Laura Scheinfeldt, Shelly Hovick, Joseph P. McElroy, Amanda E. Toland, J. Scott Roberts and Kevin Sweet

J. Pers. Med. 2018, 8(3), 25; https://doi.org/10.3390/jpm8030025 - 25 Jul 2018

Cited by 9 | Viewed by 6672

Abstract

Information on patients’ preferences is essential to guide the development of more efficient genomic counseling service delivery models. We examined patient preferences in the context of use of a post-test genomic counseling framework on patients (n = 44) with chronic disease receiving [...] Read more.

Information on patients’ preferences is essential to guide the development of more efficient genomic counseling service delivery models. We examined patient preferences in the context of use of a post-test genomic counseling framework on patients (n = 44) with chronic disease receiving online test reports for eight different diseases and one drug-response result. We also explored patients’ disease risk awareness, recall of test report information, and confidence in knowing what to do with their test results. Prior to the post-test genomic counseling session, all participants viewed at least one test report; 81.6% of available test reports were reviewed in total. Participants requested more phone (36) than in-person counseling sessions (8), and phone sessions were shorter (mean 29.1 min; range 12–75 min) than in-person sessions (mean 52.8 min; range 23–85 min). A total of 182 test reports were discussed over the course of 44 counseling sessions (mean 4.13, range 1–9). Thirty-six (81.8%) participants requested assessment for additional medical/family history concerns. In exploring patient experiences of disease risk awareness and recall, no significant differences were identified in comparison to those of participants (n = 199) that had received in-person post-test genomic counseling in a parent study randomized controlled trial (RCT). In summary, a novel post-test genomic counseling framework allowed for a tailored approach to counseling based on the participants’ predetermined choices. Full article

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13 pages, 238 KiB

Open AccessArticle

Physician-Reported Benefits and Barriers to Clinical Implementation of Genomic Medicine: A Multi-Site IGNITE-Network Survey

by Aniwaa Owusu Obeng, Kezhen Fei, Kenneth D. Levy, Amanda R. Elsey, Toni I. Pollin, Andrea H. Ramirez, Kristin W. Weitzel and Carol R. Horowitz

J. Pers. Med. 2018, 8(3), 24; https://doi.org/10.3390/jpm8030024 - 24 Jul 2018

Cited by 100 | Viewed by 10843

Abstract

Genetic medicine is one of the key components of personalized medicine, but adoption in clinical practice is still limited. To understand potential barriers and provider attitudes, we surveyed 285 physicians from five Implementing GeNomics In pracTicE (IGNITE) sites about their perceptions as to [...] Read more.

Genetic medicine is one of the key components of personalized medicine, but adoption in clinical practice is still limited. To understand potential barriers and provider attitudes, we surveyed 285 physicians from five Implementing GeNomics In pracTicE (IGNITE) sites about their perceptions as to the clinical utility of genetic data as well as their preparedness to integrate it into practice. These responses were also analyzed in comparison to the type of study occurring at the physicians’ institution (pharmacogenetics versus disease genetics). The majority believed that genetic testing is clinically useful; however, only a third believed that they had obtained adequate training to care for genetically “high-risk” patients. Physicians involved in pharmacogenetics initiatives were more favorable towards genetic testing applications; they found it to be clinically useful and felt more prepared and confident in their abilities to adopt it into their practice in comparison to those participating in disease genetics initiatives. These results suggest that investigators should explore which attributes of clinical pharmacogenetics (such as the use of simplified genetics-guided recommendations) can be implemented to improve attitudes and preparedness to implement disease genetics in care. Most physicians felt unprepared to use genetic information in their practice; accordingly, major steps should be taken to develop effective clinical tools and training strategies for physicians. Full article

(This article belongs to the Collection Genomic Medicine and Policy)

2 pages, 358 KiB

Open AccessEditorial

Preface to Special Issue on ‘Cytochrome P450 Variation in Pharmacogenomics’

by Allan E. Rettie and Stephen B. Liggett

J. Pers. Med. 2018, 8(3), 23; https://doi.org/10.3390/jpm8030023 - 4 Jul 2018

Viewed by 6361

Abstract

n/a Full article

(This article belongs to the Special Issue Cytochrome P450 Variation in Pharmacogenomics)

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9 pages, 697 KiB

Open AccessFeature PaperReview

Warfarin: The End or the End of One Size Fits All Therapy?

by Munir Pirmohamed

J. Pers. Med. 2018, 8(3), 22; https://doi.org/10.3390/jpm8030022 - 28 Jun 2018

Cited by 28 | Viewed by 8972

Abstract

Oral anticoagulants are required for both treatment and prophylaxis in many different diseases. Clinicians and patients now have a choice of oral anticoagulants, including the vitamin K antagonists (of which warfarin is the most widely used and is used as the exemplar in [...] Read more.

Oral anticoagulants are required for both treatment and prophylaxis in many different diseases. Clinicians and patients now have a choice of oral anticoagulants, including the vitamin K antagonists (of which warfarin is the most widely used and is used as the exemplar in this paper), and direct oral anticoagulants (DOACs: dabigatran, apixaban, rivaroxaban, and edoxaban). This paper explores the recent advances and controversies in oral anticoagulation. While some commentators may favour a complete switchover to DOACs, this paper argues that warfarin still has a place in therapy, and a stratified approach that enables the correct choice of both drug and dose would improve both patient outcomes and affordability. Full article

(This article belongs to the Special Issue Cytochrome P450 Variation in Pharmacogenomics)

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11 pages, 467 KiB

Open AccessArticle

Willingness to Participate in a National Precision Medicine Cohort: Attitudes of Chronic Kidney Disease Patients at a Cleveland Public Hospital

by Jessica N. Cooke Bailey, Dana C. Crawford, Aaron Goldenberg, Anne Slaven, Julie Pencak, Marleen Schachere, William S. Bush, John R. Sedor and John F. O’Toole

J. Pers. Med. 2018, 8(3), 21; https://doi.org/10.3390/jpm8030021 - 26 Jun 2018

Cited by 9 | Viewed by 6708

Abstract

Multiple ongoing, government-funded national efforts longitudinally collect health data and biospecimens for precision medicine research with ascertainment strategies increasingly emphasizing underrepresented groups in biomedical research. We surveyed chronic kidney disease patients from an academic, public integrated tertiary care system in Cleveland, Ohio, to [...] Read more.

Multiple ongoing, government-funded national efforts longitudinally collect health data and biospecimens for precision medicine research with ascertainment strategies increasingly emphasizing underrepresented groups in biomedical research. We surveyed chronic kidney disease patients from an academic, public integrated tertiary care system in Cleveland, Ohio, to examine local attitudes toward participation in large-scale government-funded studies. Responses (n = 103) indicate the majority (71%) would participate in a hypothetical national precision medicine cohort and were willing to send biospecimens to a national repository and share de-identified data, but <50% of respondents were willing to install a phone app to track personal data. The majority of participants (62%) indicated that return of research results was very important, and the majority (54%) also wanted all of their research-collected health and genetic data returned. Response patterns did not differ by race/ethnicity. Overall, we found high willingness to participate among this Cleveland patient population already participating in a local genetic study. These data suggest that despite common perceptions, subjects from communities traditionally underrepresented in genetic research will participate and agree to store samples and health data in repositories. Furthermore, most participants want return of research results, which will require a plan to provide these data in a secure, accessible, and understandable manner. Full article

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J. Pers. Med., Volume 8, Issue 3 (September 2018) – 10 articles

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