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A special issue of Journal of Personalized Medicine (ISSN 2075-4426).

Deadline for manuscript submissions: closed (1 October 2015) | Viewed by 135731

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Special Issue Editor

Prof. Dr. Scott T. Weiss

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Guest Editor

Partners Center for Personalized Genetic Medicine, Partners Health Care, Boston, MA 02115, USA
Interests: whole genome sequencing; genetics; genomics; integrative genomics; microRNA; genetic association studies; pharmacogenomics

Special Issue Information

Dear colleagues,

Partners Health Care has over 60,000 employees including over 10,000 physicians and sees 4 million patients on an annual basis, making it the largest health care system in Massachusetts and one of the largest academic medical centers in the US. Personalized medicine is a Department of Partners Health Care that is responsible for enabling the use of genomics to subset patients for the best possible treatments. The Department also works to develop its solutions for Partners eCARE our electronic medical record and we provide core services to investigators to enhance research in personalized medicine. This issue of JPM will detail a variety of initiatives across Partners that are aimed at advancing the care of our patients with the most advanced genomic technologies.

Prof. Dr. Scott T. Weiss
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Personalized Medicine is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

personalized medicine
precision medicine
whole genome and whole exome sequencing
molecular diagnostics
genetic testing
biomarkers

Published Papers (14 papers)

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Editorial

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151 KiB

Open AccessEditorial

Implementing Personalized Medicine in the Academic Health Center

by Scott T. Weiss

J. Pers. Med. 2016, 6(3), 18; https://doi.org/10.3390/jpm6030018 - 21 Sep 2016

Cited by 5 | Viewed by 7403

Abstract

Recently we at Partners Health Care had a series of articles in the Journal of Personalized Medicine describing how we are going about implementing Personalized Medicine in an academic health care system [1–10].[...] Full article

(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)

Research

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1078 KiB

Open AccessArticle

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 14 | Viewed by 10468

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 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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637 KiB

Open AccessArticle

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 20 | Viewed by 10648

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 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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1336 KiB

Open AccessArticle

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 42 | Viewed by 10343

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 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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Graphical abstract

761 KiB

Open AccessArticle

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 6 | Viewed by 7716

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 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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634 KiB

Open AccessCommunication

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 9782

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 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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442 KiB

Open AccessFeature PaperArticle

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 8896

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 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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Open AccessArticle

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 8359

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 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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1176 KiB

Open AccessFeature PaperArticle

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 104 | Viewed by 10143

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 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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Open AccessFeature PaperArticle

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 - 07 Jan 2016

Cited by 10 | Viewed by 8082

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 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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Open AccessArticle

“Cancer 2015”: A Prospective, Population-Based Cancer Cohort—Phase 1: Feasibility of Genomics-Guided Precision Medicine in the Clinic

by John P. Parisot, Heather Thorne, Andrew Fellowes, Ken Doig, Mark Lucas, John J. McNeil, Brett Doble, Alexander Dobrovic, Thomas John, Paul A. James, Lara Lipton, David Ashley, Theresa Hayes, Paul McMurrick, Gary Richardson, Paula Lorgelly, Stephen B. Fox and David M. Thomas

J. Pers. Med. 2015, 5(4), 354-369; https://doi.org/10.3390/jpm5040354 - 29 Oct 2015

Cited by 9 | Viewed by 8941

Abstract

“Cancer 2015” is a longitudinal and prospective cohort. It is a phased study whose aim was to pilot recruiting 1000 patients during phase 1 to establish the feasibility of providing a population-based genomics cohort. Newly diagnosed adult patients with solid cancers, with residual tumour material for molecular genomics testing, were recruited into the cohort for the collection of a dataset containing clinical, molecular pathology, health resource use and outcomes data. 1685 patients have been recruited over almost 3 years from five hospitals. Thirty-two percent are aged between 61–70 years old, with a median age of 63 years. Diagnostic tumour samples were obtained for 90% of these patients for multiple parallel sequencing. Patients identified with somatic mutations of potentially “actionable” variants represented almost 10% of those tumours sequenced, while 42% of the cohort had no mutations identified. These genomic data were annotated with information such as cancer site, stage, morphology, treatment and patient outcomes and health resource use and cost. This cohort has delivered its main objective of establishing an upscalable genomics cohort within a clinical setting and in phase 2 aims to develop a protocol for how genomics testing can be used in real-time clinical decision-making, providing evidence on the value of precision medicine to clinical practice. Full article

(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)

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Review

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225 KiB

Open AccessFeature PaperReview

Personal Genome Sequencing in Ostensibly Healthy Individuals and the PeopleSeq Consortium

by Michael D. Linderman, Daiva E. Nielsen and Robert C. Green

J. Pers. Med. 2016, 6(2), 14; https://doi.org/10.3390/jpm6020014 - 25 Mar 2016

Cited by 47 | Viewed by 11599

Abstract

Thousands of ostensibly healthy individuals have had their exome or genome sequenced, but a much smaller number of these individuals have received any personal genomic results from that sequencing. We term those projects in which ostensibly healthy participants can receive sequencing-derived genetic findings and may also have access to their genomic data as participatory predispositional personal genome sequencing (PPGS). Here we are focused on genome sequencing applied in a pre-symptomatic context and so define PPGS to exclude diagnostic genome sequencing intended to identify the molecular cause of suspected or diagnosed genetic disease. In this report we describe the design of completed and underway PPGS projects, briefly summarize the results reported to date and introduce the PeopleSeq Consortium, a newly formed collaboration of PPGS projects designed to collect much-needed longitudinal outcome data. Full article

(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)

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Open AccessReview

Assessing the Costs and Cost-Effectiveness of Genomic Sequencing

by Kurt D. Christensen, Dmitry Dukhovny, Uwe Siebert and Robert C. Green

J. Pers. Med. 2015, 5(4), 470-486; https://doi.org/10.3390/jpm5040470 - 10 Dec 2015

Cited by 83 | Viewed by 13182

Abstract

Despite dramatic drops in DNA sequencing costs, concerns are great that the integration of genomic sequencing into clinical settings will drastically increase health care expenditures. This commentary presents an overview of what is known about the costs and cost-effectiveness of genomic sequencing. We discuss the cost of germline genomic sequencing, addressing factors that have facilitated the decrease in sequencing costs to date and anticipating the factors that will drive sequencing costs in the future. We then address the cost-effectiveness of diagnostic and pharmacogenomic applications of genomic sequencing, with an emphasis on the implications for secondary findings disclosure and the integration of genomic sequencing into general patient care. Throughout, we ground the discussion by describing efforts in the MedSeq Project, an ongoing randomized controlled clinical trial, to understand the costs and cost-effectiveness of integrating whole genome sequencing into cardiology and primary care settings. Full article

(This article belongs to the Special Issue Implementing Personalized Medicine in a Large Health Care System)

Other

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594 KiB

Open AccessTechnical 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 14 | Viewed by 9197

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 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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