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Daalman WKG, Sweep E, Laan L. A tractable physical model for the yeast polarity predicts epistasis and fitness. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220044. [PMID: 37004720 PMCID: PMC10067261 DOI: 10.1098/rstb.2022.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Accurate phenotype prediction based on genetic information has numerous societal applications, such as crop design or cellular factories. Epistasis, when biological components interact, complicates modelling phenotypes from genotypes. Here we show an approach to mitigate this complication for polarity establishment in budding yeast, where mechanistic information is abundant. We coarse-grain molecular interactions into a so-called mesotype, which we combine with gene expression noise into a physical cell cycle model. First, we show with computer simulations that the mesotype allows validation of the most current biochemical polarity models by quantitatively matching doubling times. Second, the mesotype elucidates epistasis emergence as exemplified by evaluating the predicted mutational effect of key polarity protein Bem1p when combined with known interactors or under different growth conditions. This example also illustrates how unlikely evolutionary trajectories can become more accessible. The tractability of our biophysically justifiable approach inspires a road-map towards bottom-up modelling complementary to statistical inferences. This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
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Affiliation(s)
| | - Els Sweep
- Department of Bionanoscience, TU Delft, 2629 HZ Delft, The Netherlands
| | - Liedewij Laan
- Department of Bionanoscience, TU Delft, 2629 HZ Delft, The Netherlands
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2
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Chang HH, Hsueh YS, Cheng YW, Tseng HH. A Longitudinal Study of the Association between the LEPR Polymorphism and Treatment Response in Patients with Bipolar Disorder. Int J Mol Sci 2022; 23:ijms23179635. [PMID: 36077028 PMCID: PMC9455965 DOI: 10.3390/ijms23179635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Patients with bipolar disorder (BD) exhibit individual variability in the treatment outcome, and genetic background could contribute to BD itself and the treatment outcome. Leptin levels significantly change in BD patients treated with valproate (VPA), but whether LEPR polymorphisms are associated with treatment response is still unknown. This longitudinal study aimed to investigate the associations between LEPR polymorphisms and VPA treatment response in BD patients who were drug naïve at their first diagnosis of BD. The single-nucleotide polymorphisms (SNPs) of LEPR (rs1137101, rs1137100, rs8179183, and rs12145690) were assayed, and the LEPR polymorphism frequencies of alleles and genotypes were not significantly different between the controls (n = 77) and BD patients (n = 130). In addition, after the 12-week course of VPA treatment in BD patients, the LEPR polymorphisms showed significant effects on changes in disease severity. Moreover, considering the effect of the LEPR haplotype, the frequency of the CAGG haplotype in BD patients was higher than that in the controls (9.3 vs. 2.9%, p = 0.016), and the LEPR CAGG haplotype was associated with a better treatment response than the other haplotypes in BD patients receiving VPA treatment. Therefore, LEPR polymorphisms might serve as mediators involved in the therapeutic action of VPA treatment.
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Affiliation(s)
- Hui Hua Chang
- Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- School of Pharmacy, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Department of Pharmacy, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Department of Pharmacy, National Cheng Kung University Hospital, Dou-Liou Branch, Yunlin 640, Taiwan
- Correspondence: ; Tel.: +886-6-2353535 (ext. 5683)
| | - Yuan-Shuo Hsueh
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan 711, Taiwan
| | - Yung Wen Cheng
- Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Huai-Hsuan Tseng
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
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3
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Ormond KE, O'Daniel JM, Kalia SS. Secondary findings: How did we get here, and where are we going? J Genet Couns 2019; 28:326-333. [DOI: 10.1002/jgc4.1098] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/13/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Kelly E. Ormond
- Department of Genetics and Stanford Center for Biomedical Ethics; Stanford University School of Medicine; Stanford California
| | - Julianne M. O'Daniel
- Department of Genetics; University of North Carolina at Chapel Hill; Chapel Hill Carolina
| | - Sarah S. Kalia
- Department of Epidemiology; Harvard T.H. Chan School of Public Health; Boston Massachusetts
- Graduate School of Arts and Sciences; Harvard University; Cambridge Massachusetts
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Larios Delgado N, Usuyama N, Hall AK, Hazen RJ, Ma M, Sahu S, Lundin J. Fast and accurate medication identification. NPJ Digit Med 2019; 2:10. [PMID: 31304359 PMCID: PMC6550183 DOI: 10.1038/s41746-019-0086-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 02/07/2019] [Indexed: 12/31/2022] Open
Abstract
Much of the AI work in healthcare is focused around disease prediction in clinical settings, which is an important application that has yet to deliver in earnest. However, there are other fundamental aspects like helping patients and care teams interact and communicate in efficient and meaningful ways, which could deliver quadruple-aim improvements. After heart disease and cancer, preventable medical errors are the third leading cause of death in the United States. The largest subset of medical errors is medication error. Providing the right treatment plan for patients includes knowledge about their current medications and drug allergies, an often challenging task. The widespread growth of prescribing and consuming medications has increased the need for applications that support medication reconciliation. We show a deep-learning application that can help reduce avoidable errors with their attendant risk, i.e., correctly identifying prescription medication, which is currently a tedious and error-prone task. We demonstrate prescription-pill identification from mobile images in the NIH NLM Pill Image Recognition Challenge dataset. Our application recognizes the correct pill within the top-5 results at 94% accuracy, which compares favorably to the original competition winner at 83.3% for top-5 under comparable, though not identical configurations. The Institute of Medicine claims that better use of information technology can be an important step in reducing medication errors. Therefore, we believe that a more immediate impact of AI in healthcare will occur with a seamless integration of AI into clinical workflows, readily addressing the quadruple aim of healthcare.
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Affiliation(s)
| | - Naoto Usuyama
- Microsoft Research, One Microsoft Way, Redmond, WA 98052 USA
| | - Amanda K. Hall
- Microsoft Research, One Microsoft Way, Redmond, WA 98052 USA
| | | | - Max Ma
- Microsoft Research, One Microsoft Way, Redmond, WA 98052 USA
| | - Siva Sahu
- Microsoft Research, One Microsoft Way, Redmond, WA 98052 USA
| | - Jessica Lundin
- Microsoft Research, One Microsoft Way, Redmond, WA 98052 USA
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5
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Dean DC, Lange N, Travers BG, Prigge MB, Matsunami N, Kellett KA, Freeman A, Kane KL, Adluru N, Tromp DPM, Destiche DJ, Samsin D, Zielinski BA, Fletcher PT, Anderson JS, Froehlich AL, Leppert MF, Bigler ED, Lainhart JE, Alexander AL. Multivariate characterization of white matter heterogeneity in autism spectrum disorder. Neuroimage Clin 2017; 14:54-66. [PMID: 28138427 PMCID: PMC5257193 DOI: 10.1016/j.nicl.2017.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/21/2016] [Accepted: 01/03/2017] [Indexed: 12/20/2022]
Abstract
The complexity and heterogeneity of neuroimaging findings in individuals with autism spectrum disorder has suggested that many of the underlying alterations are subtle and involve many brain regions and networks. The ability to account for multivariate brain features and identify neuroimaging measures that can be used to characterize individual variation have thus become increasingly important for interpreting and understanding the neurobiological mechanisms of autism. In the present study, we utilize the Mahalanobis distance, a multidimensional counterpart of the Euclidean distance, as an informative index to characterize individual brain variation and deviation in autism. Longitudinal diffusion tensor imaging data from 149 participants (92 diagnosed with autism spectrum disorder and 57 typically developing controls) between 3.1 and 36.83 years of age were acquired over a roughly 10-year period and used to construct the Mahalanobis distance from regional measures of white matter microstructure. Mahalanobis distances were significantly greater and more variable in the autistic individuals as compared to control participants, demonstrating increased atypicalities and variation in the group of individuals diagnosed with autism spectrum disorder. Distributions of multivariate measures were also found to provide greater discrimination and more sensitive delineation between autistic and typically developing individuals than conventional univariate measures, while also being significantly associated with observed traits of the autism group. These results help substantiate autism as a truly heterogeneous neurodevelopmental disorder, while also suggesting that collectively considering neuroimaging measures from multiple brain regions provides improved insight into the diversity of brain measures in autism that is not observed when considering the same regions separately. Distinguishing multidimensional brain relationships may thus be informative for identifying neuroimaging-based phenotypes, as well as help elucidate underlying neural mechanisms of brain variation in autism spectrum disorders.
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Affiliation(s)
- D C Dean
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - N Lange
- Department of Psychiatry, Harvard School of Medicine, Boston, MA, USA; Child and Adolescent Psychiatry, McLean Hospital, Belmont, MA, USA
| | - B G Travers
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA; Occupational Therapy Program, Department of Kinesiology, University of Wisconsin-Madison, Madison, WI, USA
| | - M B Prigge
- Department of Radiology, University of Utah, Salt Lake City, UT, USA; Department of Pediatrics, University of Utah and Primary Children's Medical Center, Salt Lake City, UT, USA
| | - N Matsunami
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - K A Kellett
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA; Department of Psychology, University of Wisconsin-Madison, Madison, WI, USA
| | - A Freeman
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - K L Kane
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - N Adluru
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - D P M Tromp
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA; Department of Psychiatry, University of Wisconsin-Madison, Madison, WI, USA
| | - D J Destiche
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - D Samsin
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - B A Zielinski
- Department of Pediatrics, University of Utah and Primary Children's Medical Center, Salt Lake City, UT, USA; Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - P T Fletcher
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA; School of Computing, University of Utah, Salt Lake City, UT, USA
| | - J S Anderson
- Department of Radiology, University of Utah, Salt Lake City, UT, USA; Interdepartmental Program in Neuroscience, University of Utah, Salt Lake City, UT, USA
| | - A L Froehlich
- School of Computing, University of Utah, Salt Lake City, UT, USA
| | - M F Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - E D Bigler
- Department of Psychology, Brigham Young University, Provo, UT, USA; Neuroscience Center, Brigham Young University, Provo, UT 84602, USA
| | - J E Lainhart
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA; Department of Psychiatry, University of Wisconsin-Madison, Madison, WI, USA
| | - A L Alexander
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA; Department of Psychiatry, University of Wisconsin-Madison, Madison, WI, USA; Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
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6
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Middleton B, Sittig DF, Wright A. Clinical Decision Support: a 25 Year Retrospective and a 25 Year Vision. Yearb Med Inform 2016; Suppl 1:S103-16. [PMID: 27488402 DOI: 10.15265/iys-2016-s034] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE The objective of this review is to summarize the state of the art of clinical decision support (CDS) circa 1990, review progress in the 25 year interval from that time, and provide a vision of what CDS might look like 25 years hence, or circa 2040. METHOD Informal review of the medical literature with iterative review and discussion among the authors to arrive at six axes (data, knowledge, inference, architecture and technology, implementation and integration, and users) to frame the review and discussion of selected barriers and facilitators to the effective use of CDS. RESULT In each of the six axes, significant progress has been made. Key advances in structuring and encoding standardized data with an increased availability of data, development of knowledge bases for CDS, and improvement of capabilities to share knowledge artifacts, explosion of methods analyzing and inferring from clinical data, evolution of information technologies and architectures to facilitate the broad application of CDS, improvement of methods to implement CDS and integrate CDS into the clinical workflow, and increasing sophistication of the end-user, all have played a role in improving the effective use of CDS in healthcare delivery. CONCLUSION CDS has evolved dramatically over the past 25 years and will likely evolve just as dramatically or more so over the next 25 years. Increasingly, the clinical encounter between a clinician and a patient will be supported by a wide variety of cognitive aides to support diagnosis, treatment, care-coordination, surveillance and prevention, and health maintenance or wellness.
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Affiliation(s)
- B Middleton
- Blackford Middleton, Cell: +1 617 335 7098, E-Mail:
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7
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Challenges of Personalized Medicine: Socio-Legal Disputes and Possible Solutions. Per Med 2016. [DOI: 10.1007/978-3-319-39349-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Nicholls SG, Wilson BJ, Castle D, Etchegary H, Carroll JC. Personalized medicine and genome-based treatments: Why personalized medicine ≠ individualized treatments. ACTA ACUST UNITED AC 2014. [DOI: 10.1177/1477750914558556] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The sequencing of the human genome and decreasing costs of sequencing technology have led to the notion of ‘personalized medicine’. This has been taken by some authors to indicate that personalized medicine will provide individualized treatments solely based on one’s DNA sequence. We argue this is overly optimistic and misconstrues the notion of personalization. Such interpretations fail to account for economic, policy and structural constraints on the delivery of healthcare. Furthermore, notions of individualization based on genomic data potentially take us down the road of genetic reductionism obscuring the role of environmental factors in disease and ill health. We propose that one should see personalized medicine as a way of using personal genomic information to stratify individuals into subpopulations and suggest that personalized medicine be seen within a broader idea of personalized healthcare, reflecting healthcare that integrates personal genomic data into cultural, environmental and personal contexts.
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Affiliation(s)
| | | | | | | | - JC Carroll
- Mount Sinai Hospital, University of Toronto, Canada
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9
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Nicholls SG, Wilson BJ, Etchegary H, Brehaut JC, Potter BK, Hayeems R, Chakraborty P, Milburn J, Pullman D, Turner L, Carroll JC. Benefits and burdens of newborn screening: public understanding and decision-making. Per Med 2014; 11:593-607. [PMID: 29758802 DOI: 10.2217/pme.14.46] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this article we review the literature regarding the public understanding of the potential benefits and burdens of expanded newborn bloodspot screening. We draw attention to broadened notions of benefit that go beyond early identification of asymptomatic individuals and interventions to reduce morbidity or mortality, and include benefits gained by families through knowledge that may facilitate life choices, as well as gains generated by avoiding diagnostic delays. We also reflect on burdens such as increasing false-positive results and parental anxiety, together with risks of overdiagnosis when the natural history of a condition is poorly understood. We conclude that expanded notions of benefit and burden bring with them implications for parental consent and confidentiality and the secondary use of bloodspots.
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Affiliation(s)
- Stuart G Nicholls
- Department of Epidemiology & Community Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Brenda J Wilson
- Department of Epidemiology & Community Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Holly Etchegary
- Clinical Epidemiology, Memorial University, St John's, Newfoundland and Labrador, Canada
| | - Jamie C Brehaut
- Department of Epidemiology & Community Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Centre for Practice Changing Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Beth K Potter
- Department of Epidemiology & Community Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Robin Hayeems
- Hospital for Sick Children Research Institute, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada.,Institute of Health Policy Management & Evaluation, University of Toronto, Canada
| | - Pranesh Chakraborty
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario (CHEO), Ottawa, Ontario, Canada
| | - Jennifer Milburn
- Better Outcomes Registry & Network (BORN), Children's Hospital of Eastern Ontario (CHEO), Ottawa, Ontario, Canada
| | - Daryl Pullman
- Faculty of Medicine, Memorial University, St Johns, Newfoundland & Labrador, Canada
| | - Lesley Turner
- Eastern Health, St John's, Newfoundland & Labrador, Canada
| | - June C Carroll
- Department of Family & Community Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Canada
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10
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Comparison of commercial genetic-testing services in Korea with 23andMe service. BIOMED RESEARCH INTERNATIONAL 2014; 2014:539151. [PMID: 25057494 PMCID: PMC4095651 DOI: 10.1155/2014/539151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/04/2014] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Genetic testing services for disease prediction, drug responses, and traits are commercially available by several companies in Korea. However, there has been no evaluation study for the accuracy and usefulness of these services. We aimed to compare two genetic testing services popular in Korea with 23andMe service in the United States. MATERIALS AND METHODS We compared the results of two persons (one man and one woman) serviced by Hellogene Platinum (Theragen Bio Institute), DNAGPS Optimus (DNAlink), and 23andMe service. RESULTS Among 3 services, there were differences in the estimation of relative risks for the same disease. For lung cancer, the range of relative risk was from 0.9 to 2.09. These differences were thought to be due to the differences of applied single nucleotide polymorphisms (SNPs) in each service for the calculation of risk. Also, the algorithm and population database would have influence on the estimation of relative disease risks. The concordance rate of SNP calls between DNAGPS Optimus and 23andMe services was 100% (30/30). conclusions: Our study showed differences in disease risk estimations among three services, although they gave good concordance rate for SNP calls. We realized that the genetic services need further evaluation and standardization, especially in disease risk estimation algorithm.
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11
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Petersen KE, Prows CA, Martin LJ, Maglo KN. Personalized medicine, availability, and group disparity: an inquiry into how physicians perceive and rate the elements and barriers of personalized medicine. Public Health Genomics 2014; 17:209-20. [PMID: 24852571 DOI: 10.1159/000362359] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/20/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The success of personalized medicine depends on factors influencing the availability and implementation of its new tools to individualize clinical care. However, little is known about physicians' views of the availability of personalized medicine across racial/ethnic groups and the relationship between perceived availability and clinical implementation. This study examines physicians' perceptions of key elements/tools and potential barriers to personalized medicine in connection with their perceptions of the availability of the latter across subpopulations. METHODS Study subjects consisted of physicians recruited from Cincinnati Children's Hospital Medical Center and UC Health. An electronic survey conducted from September 2012 to November 2012 recruited 104 physicians. Wilcoxon rank sum analysis compared groups. RESULTS Physicians were divided about whether personalized medicine contributes to health equality, as 37.4% of them believe that personalized medicine is currently available only for some subpopulations. They also rated the importance of racial/ethnic background almost as high as the importance of genetic information in the delivery of personalized medicine. Actual elements of personalized medicine rated highest include family history, drug-drug interaction alerts in medical records, and biomarker measurements to guide therapy. Costs of gene-based therapies and genetic testing were rated the most significant barriers. The ratings of several elements and barriers were associated with perceived availability of personalized medicine across subpopulations. CONCLUSION While physicians hold differing views about the availability and implementation of personalized medicine, they likewise establish complex relationships between race/ethnicity and personalized medicine that may carry serious implications for its clinical success.
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Affiliation(s)
- Katelin E Petersen
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
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12
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Brierley KL, Bonadies DC, Moyer A, Matloff ET. "Would you test your children without their consent?" and other sticky dilemmas in the field of cancer genetic testing. Fam Cancer 2014; 13:345-50. [PMID: 24804937 DOI: 10.1007/s10689-014-9723-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cancer genetic testing is surrounded by myriad ethical, legal, and psychosocial implications which are being revisited as testing expands into an everyday practice and into more complicated areas like whole exome and direct-to-consumer testing. We chose to survey cancer genetic counselors and physicians from a wide range of non-genetics specialties to determine what they would do if faced with the complex decisions associated with cancer genetic testing, how their views compare, and how they align with current guidelines and data. Genetic counselors were significantly more likely than non-genetics physicians to bill their insurance for testing (94.9 vs. 86.8 %; p = 0.001) and purchase life insurance before testing (86.6 vs. 68.6 %; p = 0.000) and were less likely to use an alias (3.2 vs. 13.2 %; p = 0.000) or order testing on their own DNA (15.3 vs. 24.2 %; p = 0.004). They were also less likely to test their minor children (0.9 vs. 33.1 %; p = 0.000) or test their children without their knowledge and consent/assent (1.4 vs.11.5 %; p = 0.000). The results of our study indicate that there is wide variation regarding what clinicians predict they would do in the areas of ethical, legal and psychosocial issues in cancer genetic testing. Cancer genetic counselors' choices are more aligned with professional guidelines, likely due to their experience in the field and awareness of current guidelines. These data are a starting point for a broader discussion of who should offer cancer genetic counseling and testing to patients, particularly as the complexity of the available testing options and associated issues increase with whole exome sequencing.
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Affiliation(s)
- Karina L Brierley
- Cancer Genetic Counseling, Yale Cancer Center, Yale School of Medicine, 55 Church Street, Suite 402, New Haven, CT, 06510, USA
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13
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Skirton H, Jackson L, Goldsmith L, O'Connor A. Are health professionals ready for direct-to-consumer genetic and genomic testing? Per Med 2013; 10:673-682. [PMID: 29768754 DOI: 10.2217/pme.13.71] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Direct-to-consumer genetic and genomic tests have been offered for over a decade. With the reduction in the cost of sequencing, the options for consumers will increase, with subsequent pressure on health services to interpret data and integrate the results into healthcare management. However, indications are that health professionals are grossly unprepared to deal with requests for support from those who have undertaken direct-to-consumer genetic or genomic tests. While benefits may be derived from patient-driven investigations, distinction needs to be made between the mostly uncertain clinical utility of susceptibility testing and the potential benefits of a reliably interpreted sequencing result. It is essential that we develop strategies, including enhanced professional education, to cope with the potential impact on the health services, rather than ignoring these developments. There may also be implications for the future of genetic counseling, with potential changes in the current paradigm.
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Affiliation(s)
- Heather Skirton
- Applied Health Genetics Research Group, Faculty of Health, Education & Society, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK.
| | - Leigh Jackson
- Applied Health Genetics Research Group, Faculty of Health, Education & Society, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
| | - Lesley Goldsmith
- Applied Health Genetics Research Group, Faculty of Health, Education & Society, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
| | - Anita O'Connor
- Applied Health Genetics Research Group, Faculty of Health, Education & Society, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK
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14
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Kim N, Branch CA, Kim M, Lipton ML. Whole brain approaches for identification of microstructural abnormalities in individual patients: comparison of techniques applied to mild traumatic brain injury. PLoS One 2013; 8:e59382. [PMID: 23555665 PMCID: PMC3608654 DOI: 10.1371/journal.pone.0059382] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/14/2013] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Group-wise analyses of DTI in mTBI have demonstrated evidence of traumatic axonal injury (TAI), associated with adverse clinical outcomes. Although mTBI is likely to have a unique spatial pattern in each patient, group analyses implicitly assume that location of injury will be the same across patients. The purpose of this study was to optimize and validate a procedure for analysis of DTI images acquired in individual patients, which could detect inter-individual differences and be applied in the clinical setting, where patients must be assessed as individuals. MATERIALS AND METHODS After informed consent and in compliance with HIPAA, 34 mTBI patients and 42 normal subjects underwent 3.0 Tesla DTI. Four voxelwise assessment methods (standard Z-score, "one vs. many" t-test, Family-Wise Error Rate control using pseudo t-distribution, EZ-MAP) for use in individual patients, were applied to each patient's fractional anisotropy (FA) maps and tested for its ability to discriminate patients from controls. Receiver Operating Characteristic (ROC) analyses were used to define optimal thresholds (voxel-level significance and spatial extent) for reliable and robust detection of mTBI pathology. RESULTS ROC analyses showed EZ-MAP (specificity 71%, sensitivity 71%), "one vs. many" t-test and standard Z-score (sensitivity 65%, specificity 76% for both methods) resulted in a significant area under the curve (AUC) score for discriminating mTBI patients from controls in terms of the total number of abnormal white matter voxels detected while the FWER test was not significant. EZ-MAP is demonstrated to be robust to assumptions of Gaussian behavior and may serve as an alternative to methods that require strict Gaussian assumptions. CONCLUSION EZ-MAP provides a robust approach for delineation of regional abnormal anisotropy in individual mTBI patients.
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Affiliation(s)
- Namhee Kim
- The Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- Department of Radiology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Craig A. Branch
- The Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- Department of Radiology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Mimi Kim
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Michael L. Lipton
- The Gruss Magnetic Resonance Research Center, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- Department of Radiology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- The Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- Department of Radiology, Montefiore Medical Center, Bronx, New York, United States of America
- * E-mail:
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Goldsmith L, Jackson L, O'Connor A, Skirton H. Direct-to-consumer genomic testing from the perspective of the health professional: a systematic review of the literature. J Community Genet 2013; 4:169-80. [PMID: 23322235 DOI: 10.1007/s12687-012-0135-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 12/26/2012] [Indexed: 01/21/2023] Open
Abstract
Since the 1990s, there has been a rapid expansion in the number and type of genetic tests available via health professionals; the last 10 years, however, have seen certain types of genetic and genomic tests available direct-to-consumer. The aim of this systematic review was to explore the topic of direct-to-consumer genetic testing from the health professional perspective. Search terms used to identify studies were 'direct-to-consumer', personal genom*, health* professional*, physician* 'genomic, genetic' in five bibliographic databases, together with citation searching. Eight quantitative papers were reviewed. Findings indicate a low level of awareness and experience of direct-to-consumer testing in health professionals. Inconsistent levels of knowledge and understanding were also found with two studies showing significant effects for gender and age. Concerns about clinical utility and lack of counselling were identified. Health professionals specialising in genetics were most likely to express concerns. There was also evidence of perceived increased workload for health professionals post-testing. However, some health professionals rated such tests clinically useful and cited benefits such as the increased opportunity for early screening. Despite limited awareness, knowledge and experience of actual cases, we concluded that the concerns and potential benefits expressed may be warranted. It may be useful to explore the attitudes and experiences of health professionals in more depth using a qualitative approach. Finally, it is essential that health professionals receive sufficient education and guidelines to equip them to help patients presenting with the results of these tests.
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Affiliation(s)
- Lesley Goldsmith
- Faculty of Health, Education and Society, School of Nursing and Midwifery, Plymouth University, Room 300, Hepworth House, Drake Circus, Plymouth, PL4 8AA, UK,
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Groisman IJ, Mathieu G, Godard B. Use of next generation sequencing technologies in research and beyond: are participants with mental health disorders fully protected? BMC Med Ethics 2012; 13:36. [PMID: 23256847 PMCID: PMC3537639 DOI: 10.1186/1472-6939-13-36] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 12/10/2012] [Indexed: 11/10/2022] Open
Abstract
Background Next Generation Sequencing (NGS) is expected to help find the elusive, causative genetic defects associated with Bipolar Disorder (BD). This article identifies the importance of NGS and further analyses the social and ethical implications of this approach when used in research projects studying BD, as well as other psychiatric ailments, with a view to ensuring the protection of research participants. Methods We performed a systematic review of studies through PubMed, followed by a manual search through the titles and abstracts of original articles, including the reviews, commentaries and letters published in the last five years and dealing with the ethical and social issues raised by NGS technologies and genomics studies of mental disorders, especially BD. A total of 217 studies contributed to identify the themes discussed herein. Results The amount of information generated by NGS renders individuals suffering from BD particularly vulnerable, and increases the need for educational support throughout the consent process, and, subsequently, of genetic counselling, when communicating individual research results and incidental findings to them. Our results highlight the importance and difficulty of respecting participants’ autonomy while avoiding any therapeutic misconception. We also analysed the need for specific regulations on the use and communication of incidental findings, as well as the increasing influence of NGS in health care. Conclusions Shared efforts on the part of researchers and their institutions, Research Ethics Boards as well as participants’ representatives are needed to delineate a tailored consent process so as to better protect research participants. However, health care professionals involved in BD care and treatment need to first determine the scientific validity and clinical utility of NGS-generated findings, and thereafter their prevention and treatment significance.
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Affiliation(s)
- Iris Jaitovich Groisman
- Groupe de recherche Omics-Ethics, Programmes de bioéthique, Faculté de médecine, Université de Montréal, C.P. 6128, succ. Centre-ville, Montreal, H3C 3J7, Canada
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Emerging real-time technologies in molecular medicine and the evolution of integrated ‘pharmacomics’ approaches to personalized medicine and drug discovery. Pharmacol Ther 2012; 136:295-304. [DOI: 10.1016/j.pharmthera.2012.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 08/07/2012] [Indexed: 01/05/2023]
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18
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Crockett DK, Ridge PG, Wilson AR, Lyon E, Williams MS, Narus SP, Facelli JC, Mitchell JA. Consensus: a framework for evaluation of uncertain gene variants in laboratory test reporting. Genome Med 2012; 4:48. [PMID: 22640420 PMCID: PMC3506914 DOI: 10.1186/gm347] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 04/05/2012] [Accepted: 05/28/2012] [Indexed: 12/15/2022] Open
Abstract
Accurate interpretation of gene testing is a key component in customizing patient therapy. Where confirming evidence for a gene variant is lacking, computational prediction may be employed. A standardized framework, however, does not yet exist for quantitative evaluation of disease association for uncertain or novel gene variants in an objective manner. Here, complementary predictors for missense gene variants were incorporated into a weighted Consensus framework that includes calculated reference intervals from known disease outcomes. Data visualization for clinical reporting is also discussed.
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Affiliation(s)
- David K Crockett
- University of Utah School of Medicine, Biomedical Informatics, 26 South 2000 East, Salt Lake City, UT 84112, USA.
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Baudhuin LM, Donato LJ, Uphoff TS. How novel molecular diagnostic technologies and biomarkers are revolutionizing genetic testing and patient care. Expert Rev Mol Diagn 2012; 12:25-37. [PMID: 22133117 DOI: 10.1586/erm.11.85] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Technological applications and novel biomarkers in the field of molecular diagnostics have never been evolving at a more rapid pace. These novel applications have the promise to change the face of clinical care as we move into the era of personalized medicine. While some of these technologies and biomarkers have been adopted by some clinical laboratories, most laboratories face a steep learning curve in bringing these dramatically new and different molecular diagnostic applications on board. Furthermore, interpreting the vast amounts and new types of data produced by these novel applications brings forth challenges for laboratorians and clinicians alike. In this article, we discuss how some of these emerging novel molecular diagnostic technologies and analytes, such as next-generation sequencing, chromosomal microarray, microRNAs and circulating fetal nucleic acids are revolutionizing patient care and personalized medicine.
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Affiliation(s)
- Linnea M Baudhuin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.
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Crockett DK, Lyon E, Williams MS, Narus SP, Facelli JC, Mitchell JA. Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants. J Am Med Inform Assoc 2011; 19:207-11. [PMID: 22037892 DOI: 10.1136/amiajnl-2011-000309] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The rapid advance of gene sequencing technologies has produced an unprecedented rate of discovery of genome variation in humans. A growing number of authoritative clinical repositories archive gene variants and disease phenotypes, yet there are currently many more gene variants that lack clear annotation or disease association. To date, there has been very limited coverage of gene-specific predictors in the literature. Here the evaluation is presented of "gene-specific" predictor models based on a naïve Bayesian classifier for 20 gene-disease datasets, containing 3986 variants with clinically characterized patient conditions. The utility of gene-specific prediction is then compared with "all-gene" generalized prediction and also with existing popular predictors. Gene-specific computational prediction models derived from clinically curated gene variant disease datasets often outperform established generalized algorithms for novel and uncertain gene variants.
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Affiliation(s)
- David K Crockett
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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Abstract
BACKGROUND Genetic testing in inherited disease has traditionally relied upon recognition of the presenting clinical syndrome and targeted analysis of genes known to be linked to that syndrome. Consequently, many patients with genetic syndromes remain without a specific diagnosis. AREAS OF AGREEMENT New 'next-generation' sequencing (NGS) techniques permit simultaneous sequencing of enormous amounts of DNA. A slew of research publications have recently demonstrated the tremendous power of these technologies in increasing understanding of human genetic disease. AREAS OF CONTROVERSY These approaches are likely to be increasingly employed in routine diagnostic practice, but the scale of the genetic information yielded about individuals means that caution must be exercised to avoid net harm in this setting. AREAS TIMELY FOR DEVELOPING RESEARCH Use of NGS in a research setting will increasingly have a major but indirect beneficial impact on clinical practice. However, important technical, ethical and social challenges need to be addressed through informed professional and public dialogue before it finds its mature niche as a direct tool in the clinical diagnostic armoury.
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Affiliation(s)
- Eleanor Raffan
- Metabolic Research Laboratories, Institute of Metabolic Science, University of Cambridge, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
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