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J. Pers. Med., Volume 6, Issue 1 (March 2016) – 13 articles

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1078 KiB  
Article
Infrastructure for Personalized Medicine at Partners HealthCare
by Scott T. Weiss and Meini Sumbada Shin
J. Pers. Med. 2016, 6(1), 13; https://doi.org/10.3390/jpm6010013 - 27 Feb 2016
Cited by 15 | Viewed by 10663
Abstract
Partners HealthCare Personalized Medicine (PPM) is a center within the Partners HealthCare system (founded by Massachusetts General Hospital and Brigham and Women’s Hospital) whose mission is to utilize genetics and genomics to improve the care of patients in a cost effective manner. PPM [...] Read more.
Partners HealthCare Personalized Medicine (PPM) is a center within the Partners HealthCare system (founded by Massachusetts General Hospital and Brigham and Women’s Hospital) whose mission is to utilize genetics and genomics to improve the care of patients in a cost effective manner. PPM consists of five interconnected components: (1) Laboratory for Molecular Medicine (LMM), a CLIA laboratory performing genetic testing for patients world-wide; (2) Translational Genomics Core (TGC), a core laboratory providing genomic platforms for Partners investigators; (3) Partners Biobank, a biobank of samples (DNA, plasma and serum) for 50,000 Consented Partners patients; (4) Biobank Portal, an IT infrastructure and viewer to bring together genotypes, samples, phenotypes (validated diagnoses, radiology, and clinical chemistry) from the electronic medical record to Partners investigators. These components are united by (5) a common IT system that brings researchers, clinicians, and patients together for optimal research and patient care. Full article
(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)
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Article
Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine
by Ellen A. Tsai, Rimma Shakbatyan, Jason Evans, Peter Rossetti, Chet Graham, Himanshu Sharma, Chiao-Feng Lin and Matthew S. Lebo
J. Pers. Med. 2016, 6(1), 12; https://doi.org/10.3390/jpm6010012 - 27 Feb 2016
Cited by 23 | Viewed by 10882
Abstract
Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient’s genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence information of a complete genome for each [...] Read more.
Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient’s genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence information of a complete genome for each individual. At Partners HealthCare Personalized Medicine, we have developed a clinical process for whole genome sequencing (WGS) with application in both healthy individuals and those with disease. In this manuscript, we will describe our bioinformatics strategy to efficiently process and deliver genomic data to geneticists for clinical interpretation. We describe the handling of data from FASTQ to the final variant list for clinical review for the final report. We will also discuss our methodology for validating this workflow and the cost implications of running WGS. Full article
(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)
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Article
The Biobank Portal for Partners Personalized Medicine: A Query Tool for Working with Consented Biobank Samples, Genotypes, and Phenotypes Using i2b2
by Vivian S. Gainer, Andrew Cagan, Victor M. Castro, Stacey Duey, Bhaswati Ghosh, Alyssa P. Goodson, Sergey Goryachev, Reeta Metta, Taowei David Wang, Nich Wattanasin and Shawn N. Murphy
J. Pers. Med. 2016, 6(1), 11; https://doi.org/10.3390/jpm6010011 - 26 Feb 2016
Cited by 44 | Viewed by 10543
Abstract
We have designed a Biobank Portal that lets researchers request Biobank samples and genotypic data, query associated electronic health records, and design and download datasets containing de-identified attributes about consented Biobank subjects. This do-it-yourself functionality puts a wide variety and volume of data [...] Read more.
We have designed a Biobank Portal that lets researchers request Biobank samples and genotypic data, query associated electronic health records, and design and download datasets containing de-identified attributes about consented Biobank subjects. This do-it-yourself functionality puts a wide variety and volume of data at the fingertips of investigators, allowing them to create custom datasets for their clinical and genomic research from complex phenotypic data and quickly obtain corresponding samples and genomic data. The Biobank Portal is built upon the i2b2 infrastructure [1] and uses an open-source web client that is available to faculty members and other investigators behind an institutional firewall. Built-in privacy measures [2] ensure that the data in the Portal are utilized only according to the processes to which the patients have given consent. Full article
(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)
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Article
The Translational Genomics Core at Partners Personalized Medicine: Facilitating the Transition of Research towards Personalized Medicine
by Ashley Blau, Alison Brown, Lisa Mahanta and Sami S. Amr
J. Pers. Med. 2016, 6(1), 10; https://doi.org/10.3390/jpm6010010 - 26 Feb 2016
Cited by 8 | Viewed by 7887
Abstract
The Translational Genomics Core (TGC) at Partners Personalized Medicine (PPM) serves as a fee-for-service core laboratory for Partners Healthcare researchers, providing access to technology platforms and analysis pipelines for genomic, transcriptomic, and epigenomic research projects. The interaction of the TGC with various components [...] Read more.
The Translational Genomics Core (TGC) at Partners Personalized Medicine (PPM) serves as a fee-for-service core laboratory for Partners Healthcare researchers, providing access to technology platforms and analysis pipelines for genomic, transcriptomic, and epigenomic research projects. The interaction of the TGC with various components of PPM provides it with a unique infrastructure that allows for greater IT and bioinformatics opportunities, such as sample tracking and data analysis. The following article describes some of the unique opportunities available to an academic research core operating within PPM, such the ability to develop analysis pipelines with a dedicated bioinformatics team and maintain a flexible Laboratory Information Management System (LIMS) with the support of an internal IT team, as well as the operational challenges encountered to respond to emerging technologies, diverse investigator needs, and high staff turnover. In addition, the implementation and operational role of the TGC in the Partners Biobank genotyping project of over 25,000 samples is presented as an example of core activities working with other components of PPM. Full article
(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)
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Article
Serotonin 2A Receptor SNP rs7330461 Association with Treatment Response to Pomaglumetad Methionil in Patients with Schizophrenia
by Laura K. Nisenbaum, AnnCatherine M. Downing, Fangyi Zhao, Brian A. Millen, Leanne Munsie, Bruce J. Kinon, David H. Adams, Juan Carlos Gomez and Michelle Ann Penny
J. Pers. Med. 2016, 6(1), 9; https://doi.org/10.3390/jpm6010009 - 5 Feb 2016
Cited by 19 | Viewed by 8035
Abstract
This study aims to confirm the initial pharmacogenetic finding observed within the clinical proof-of-concept trial of an enhanced response to treatment with pomaglumetad methionil (LY2140023 monohydrate) in Caucasian schizophrenia patients homozygous for T/T at single nucleotide polymorphism rs7330461 in the serotonin (5-hydroxytryptamine) 2A [...] Read more.
This study aims to confirm the initial pharmacogenetic finding observed within the clinical proof-of-concept trial of an enhanced response to treatment with pomaglumetad methionil (LY2140023 monohydrate) in Caucasian schizophrenia patients homozygous for T/T at single nucleotide polymorphism rs7330461 in the serotonin (5-hydroxytryptamine) 2A receptor gene compared to A/A homozygous patients. The effect of the rs7330461 genotype on the response to pomaglumetad methionil treatment was assessed in three additional clinical trials and in an integrated analysis. Overall, this study includes data from 1115 Caucasian patients for whom genotyping information for rs7330461 was available, consisting of 513 A/A homozygous, 466 A/T heterozygous and 136 T/T homozygous patients. Caucasian T/T homozygous patients showed significantly (p ≤ 0.05) greater improvement in Positive and Negative Syndrome Scale (PANSS) total scores during treatment with pomaglumetad methionil 40 mg twice daily compared to A/A homozygous patients. Additionally, T/T homozygous patients receiving pomaglumetad methionil had significantly (p ≤ 0.05) greater improvements in PANSS total scores compared to placebo and similar improvements as T/T homozygous patients receiving standard-of-care (SOC) treatment. The findings reported here in conjunction with prior reports show that in Caucasian patients with schizophrenia, the T/T genotype at rs7330461 is consistently associated with an increased treatment response to pomaglumetad methionil compared to the A/A genotype. Full article
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Communication
The Changing Landscape of Molecular Diagnostic Testing: Implications for Academic Medical Centers
by Heidi L. Rehm, Elizabeth Hynes and Birgit H. Funke
J. Pers. Med. 2016, 6(1), 8; https://doi.org/10.3390/jpm6010008 - 27 Jan 2016
Cited by 13 | Viewed by 9946
Abstract
Over the last decade, the field of molecular diagnostics has undergone tremendous transformation, catalyzed by the clinical implementation of next generation sequencing (NGS). As technical capabilities are enhanced and current limitations are addressed, NGS is increasingly capable of detecting most variant types and [...] Read more.
Over the last decade, the field of molecular diagnostics has undergone tremendous transformation, catalyzed by the clinical implementation of next generation sequencing (NGS). As technical capabilities are enhanced and current limitations are addressed, NGS is increasingly capable of detecting most variant types and will therefore continue to consolidate and simplify diagnostic testing. It is likely that genome sequencing will eventually serve as a universal first line test for disorders with a suspected genetic origin. Academic Medical Centers (AMCs), which have been at the forefront of this paradigm shift are now presented with challenges to keep up with increasing technical, bioinformatic and interpretive complexity of NGS-based tests in a highly competitive market. Additional complexity may arise from altered regulatory oversight, also triggered by the unprecedented scope of NGS-based testing, which requires new approaches. However, these challenges are balanced by unique opportunities, particularly at the interface between clinical and research operations, where AMCs can capitalize on access to cutting edge research environments and establish collaborations to facilitate rapid diagnostic innovation. This article reviews present and future challenges and opportunities for AMC associated molecular diagnostic laboratories from the perspective of the Partners HealthCare Laboratory for Molecular Medicine (LMM). Full article
(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)
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Editorial
Acknowledgement to Reviewers of Journal of Personalized Medicine in 2015
by Journal of Personalized Medicine Editorial Office
J. Pers. Med. 2016, 6(1), 7; https://doi.org/10.3390/jpm6010007 - 27 Jan 2016
Viewed by 5917
Abstract
The editors of Journal of Personalized Medicine would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2015. [...] Full article
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Technical Note
The Information Technology Infrastructure for the Translational Genomics Core and the Partners Biobank at Partners Personalized Medicine
by Natalie Boutin, Ana Holzbach, Lisa Mahanta, Jackie Aldama, Xander Cerretani, Kevin Embree, Irene Leon, Neeta Rathi and Matilde Vickers
J. Pers. Med. 2016, 6(1), 6; https://doi.org/10.3390/jpm6010006 - 21 Jan 2016
Cited by 15 | Viewed by 9353
Abstract
The Biobank and Translational Genomics core at Partners Personalized Medicine requires robust software and hardware. This Information Technology (IT) infrastructure enables the storage and transfer of large amounts of data, drives efficiencies in the laboratory, maintains data integrity from the time of consent [...] Read more.
The Biobank and Translational Genomics core at Partners Personalized Medicine requires robust software and hardware. This Information Technology (IT) infrastructure enables the storage and transfer of large amounts of data, drives efficiencies in the laboratory, maintains data integrity from the time of consent to the time that genomic data is distributed for research, and enables the management of complex genetic data. Here, we describe the functional components of the research IT infrastructure at Partners Personalized Medicine and how they integrate with existing clinical and research systems, review some of the ways in which this IT infrastructure maintains data integrity and security, and discuss some of the challenges inherent to building and maintaining such infrastructure. Full article
(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)
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Article
An eMERGE Clinical Center at Partners Personalized Medicine
by Jordan W. Smoller, Elizabeth W. Karlson, Robert C. Green, Sekar Kathiresan, Daniel G. MacArthur, Michael E. Talkowski, Shawn N. Murphy and Scott T. Weiss
J. Pers. Med. 2016, 6(1), 5; https://doi.org/10.3390/jpm6010005 - 20 Jan 2016
Cited by 24 | Viewed by 9114
Abstract
The integration of electronic medical records (EMRs) and genomic research has become a major component of efforts to advance personalized and precision medicine. The Electronic Medical Records and Genomics (eMERGE) network, initiated in 2007, is an NIH-funded consortium devoted to genomic discovery and [...] Read more.
The integration of electronic medical records (EMRs) and genomic research has become a major component of efforts to advance personalized and precision medicine. The Electronic Medical Records and Genomics (eMERGE) network, initiated in 2007, is an NIH-funded consortium devoted to genomic discovery and implementation research by leveraging biorepositories linked to EMRs. In its most recent phase, eMERGE III, the network is focused on facilitating implementation of genomic medicine by detecting and disclosing rare pathogenic variants in clinically relevant genes. Partners Personalized Medicine (PPM) is a center dedicated to translating personalized medicine into clinical practice within Partners HealthCare. One component of the PPM is the Partners Healthcare Biobank, a biorepository comprising broadly consented DNA samples linked to the Partners longitudinal EMR. In 2015, PPM joined the eMERGE Phase III network. Here we describe the elements of the eMERGE clinical center at PPM, including plans for genomic discovery using EMR phenotypes, evaluation of rare variant penetrance and pleiotropy, and a novel randomized trial of the impact of returning genetic results to patients and clinicians. Full article
(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)
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Article
Information Technology Support for Clinical Genetic Testing within an Academic Medical Center
by Samuel Aronson, Lisa Mahanta, Lei Lei Ros, Eugene Clark, Lawrence Babb, Michael Oates, Heidi Rehm and Matthew Lebo
J. Pers. Med. 2016, 6(1), 4; https://doi.org/10.3390/jpm6010004 - 20 Jan 2016
Cited by 8 | Viewed by 8535
Abstract
Academic medical centers require many interconnected systems to fully support genetic testing processes. We provide an overview of the end-to-end support that has been established surrounding a genetic testing laboratory within our environment, including both laboratory and clinician facing infrastructure. We explain key [...] Read more.
Academic medical centers require many interconnected systems to fully support genetic testing processes. We provide an overview of the end-to-end support that has been established surrounding a genetic testing laboratory within our environment, including both laboratory and clinician facing infrastructure. We explain key functions that we have found useful in the supporting systems. We also consider ways that this infrastructure could be enhanced to enable deeper assessment of genetic test results in both the laboratory and clinic. Full article
(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)
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Review
Molecular Pathology and Personalized Medicine: The Dawn of a New Era in Companion Diagnostics—Practical Considerations about Companion Diagnostics for Non-Small-Cell-Lung-Cancer
by Till Plönes, Walburga Engel-Riedel, Erich Stoelben, Christina Limmroth, Oliver Schildgen and Verena Schildgen
J. Pers. Med. 2016, 6(1), 3; https://doi.org/10.3390/jpm6010003 - 15 Jan 2016
Cited by 11 | Viewed by 11841
Abstract
Companion diagnostics (CDx) have become a major tool in molecular pathology and assist in therapy decisions in an increasing number of various cancers. Particularly, the developments in lung cancer have been most impressing in the last decade and consequently lung cancer mutation testing [...] Read more.
Companion diagnostics (CDx) have become a major tool in molecular pathology and assist in therapy decisions in an increasing number of various cancers. Particularly, the developments in lung cancer have been most impressing in the last decade and consequently lung cancer mutation testing and molecular profiling has become a major business of diagnostic laboratories. However, it has become difficult to decide which biomarkers are currently relevant for therapy decisions, as many of the new biomarkers are not yet approved as therapy targets, remain in the status of clinical studies, or still have not left the experimental phase. The current review is focussed on those markers that do have current therapy implications, practical implications arising from the respective companion diagnostics, and thus is focused on daily practice. Full article
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Article
Building the Partners HealthCare Biobank at Partners Personalized Medicine: Informed Consent, Return of Research Results, Recruitment Lessons and Operational Considerations
by Elizabeth W. Karlson, Natalie T. Boutin, Alison G. Hoffnagle and Nicole L. Allen
J. Pers. Med. 2016, 6(1), 2; https://doi.org/10.3390/jpm6010002 - 14 Jan 2016
Cited by 108 | Viewed by 10432
Abstract
The Partners HealthCare Biobank is a Partners HealthCare enterprise-wide initiative whose goal is to provide a foundation for the next generation of translational research studies of genotype, environment, gene-environment interaction, biomarker and family history associations with disease phenotypes. The Biobank has leveraged in-person [...] Read more.
The Partners HealthCare Biobank is a Partners HealthCare enterprise-wide initiative whose goal is to provide a foundation for the next generation of translational research studies of genotype, environment, gene-environment interaction, biomarker and family history associations with disease phenotypes. The Biobank has leveraged in-person and electronic recruitment methods to enroll >30,000 subjects as of October 2015 at two academic medical centers in Partners HealthCare since launching in 2010. Through a close collaboration with the Partners Human Research Committee, the Biobank has developed a comprehensive informed consent process that addresses key patient concerns, including privacy and the return of research results. Lessons learned include the need for careful consideration of ethical issues, attention to the educational content of electronic media, the importance of patient authentication in electronic informed consent, the need for highly secure IT infrastructure and management of communications and the importance of flexible recruitment modalities and processes dependent on the clinical setting for recruitment. Full article
(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)
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Article
Training the Future Leaders in Personalized Medicine
by Heather Mason-Suares, David A. Sweetser, Neal I. Lindeman and Cynthia C. Morton
J. Pers. Med. 2016, 6(1), 1; https://doi.org/10.3390/jpm6010001 - 7 Jan 2016
Cited by 11 | Viewed by 8274
Abstract
The era of personalized medicine has arrived, and with it a need for leaders in this discipline. This generation of trainees requires a cadre of new skill sets to lead the implementation of personalized medicine into mainstream healthcare. Traditional training programs no longer [...] Read more.
The era of personalized medicine has arrived, and with it a need for leaders in this discipline. This generation of trainees requires a cadre of new skill sets to lead the implementation of personalized medicine into mainstream healthcare. Traditional training programs no longer provide trainees with all the skills they will need to optimize implementation of this revolution now underway in medicine. Today’s trainees must manage clinical teams, act as clinical and molecular diagnostic consultants, train other healthcare professionals, teach future generations, and be knowledgeable about clinical trials to facilitate genomic-based therapies. To prepare trainees for the transition to junior faculty positions, contemporary genomic training programs must emphasize the development of these management, teaching, and clinical skills. Full article
(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)
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