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Journal of
Personalized
Medicine
Article
Infrastructure for Personalized Medicine at
Partners HealthCare
Scott T. Weiss
1,
* and Meini Sumbada Shin
2
1
Partners Personalized Medicine, Partners HealthCare System, Brigham and Women’s Hospital,
Harvard Medical School, Boston, MA 02115, USA
2
Partners Personalized Medicine, Partners HealthCare System, Boston, MA 02139, USA;
msumbadashin@partners.org
* Correspondence: Scott.weiss@channing.harvard.edu; Tel.: +1-617-525-5136
Academic Editor: Stephen B. Liggett
Received: 21 October 2015; Accepted: 3 February 2016; Published: 27 February 2016
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.
Keywords:
personalized medicine; academic medical centers; Partners HealthCare; biobank;
bioinformatics; laboratory testing; information technology infrastructure
1. Introduction
In this article we will describe the resources devoted to Personalized Medicine at Partners
HealthCare, how we integrate that set of resources with the existing infrastructure at the two academic
medical centers: Massachusetts General Hospital and Brigham and Women’s Hospital and how we
advance our mission to better integrate genomic data into clinical practice at Partners in a cost effective
way. This article will describe the center and its components and relate each element to our overall
vision and mission.
2. Results and Discussion
2.1. Partners HealthCare System
Partners HealthCare System (Partners) is a not-for-profit, integrated health care system in Boston,
Massachusetts founded by two of the nation’s leading academic medical centers (AMC), Massachusetts
General Hospital (MGH) and Brigham and Women’s Hospital (BWH), which have been ranked #1
and #6 respectively in the U.S. News and World Report 2015 Honor Roll of academic medical centers.
In addition to the two AMCs, Partners also includes community and specialty hospitals, a physician
network, community health centers, home care, and other health related services, cares for four
million patients with more than 7000 physicians attending and has 160,000 admissions per year. The
J. Pers. Med. 2016, 6, 13; doi:10.3390/jpm6010013 www.mdpi.com/journal/jpm
J. Pers. Med. 2016, 6, 13 2 of 9
composition of the patients in terms of race, gender and age is representative of the population of
eastern Massachusetts. In addition, Partners institutions maintain a total research budget of more than
$1.4 billion. MGH and BWH are the largest private hospital recipients of National Institutes of Health
(NIH) funding in the nation.
2.2. Partners HealthCare Personalized Medicine (PPM)
The mission of the PPM is to utilize genetics and genomics to improve the care of patients through
the promotion and implementation of personalized medicine in caring for patients throughout the
Partners HealthCare System and in healthcare nationally and globally in a cost effective manner.
Harvard Medical School (HMS) and Partners established the Harvard-Partners Center for Genetics and
Genomics (HPCGG) in 2001, recently renamed as Partners Personalized Medicine (PPM) to reflect a
heightened focus on translational issues related to moving genetics and genomics into clinical practice.
Figure 1 depicts the organizational structure of the Center. The arrows indicate informatics links
between the various Center components: the Biobank, the Translational Genomics Core (TGC), the
Laboratory for Molecular Medicine (LMM), and the Research Patient Data Registry (RPDR) to enable
data analysis and distribution to investigators across the health system. One of the keys to PPM’s
success is having a robust IT infrastructure that includes a sample management and tracking system
(StarLIMS) and a genomic results delivery system GeneInsight (described below) and a home-grown
LIMS System (GIGPAD). The details of this IT infrastructure are provided in subsequent sections. The
Center is physically located at 65 Landsdowne St. in Cambridge, MA approximately 15 min from BWH
and MGH. All staff are located onsite and each of the Labs (Biobank, LMM, and TGC) are contiguous
to allow the use of the same equipment and resources. We will describe each of the components in
Figure 1 in more detail.
Figure 1. Partners HealthCare Personalized Medicine (PPM) organizational structure.
2.2.1. The Laboratory for Molecular Medicine (LMM)
The LMM is a CLIA-certified molecular diagnostic laboratory, operating within the PPM. The
LMM was founded 13 years ago with the mission to bridge the gap between research and clinical
medicine, by accelerating the adoption of new molecular tests into clinical care. The current focus of
the LMM is on germ line mutation testing. Cancer testing is performed through molecular pathology
laboratories at each AMC affiliated with the two cancer centers associated with Partners i.e., the
Dana Farber Cancer Center and MGH Cancer Center. Major areas of expertise include inherited
J. Pers. Med. 2016, 6, 13 3 of 9
respiratory disorders, cardiomyopathies, hearing loss, connective tissue disorders, RASopathies, and
multi-organ genetic syndromes. Annually, the LMM performs about 5000 high complexity genetic
and genomics tests of disease-targeted NGS panels for a variety of disorders with genetic and clinical
heterogeneity, covering about 400 genes, as well as exome and genome sequencing. The lab consists
of six geneticists and 25 staff including genetic counselors and fellows. The LMM continues to
develop novel genetic tests in multiple areas, most recently, pulmonary and renal panels. An integral
component of the mission of the LMM is the incorporation of IT support into the dayto-day operations
of the clinical lab, as well as implementing innovative programs to help physicians stay current on
genetic information relevant to their patients. The LMM shares the lab instruments with TGC and
Biobank see Sections 2.2.2 and 2.2.3 below. In addition, the LMM’s close integration with the other
PPM components, especially with IT and bioinformatics teams, and its access to the AMCs physicians
have allowed the LMM to have a proven track record of developing and clinically implementing
novel, cutting-edge technologies, including bioinformatics tools, data analysis pipelines and novel
approaches to interpret and communicate medical genomic results to healthcare providers and patients
such as GeneInsight see Section 2.2.5 below. While many academic health centers have molecular
genetic clinical laboratories, what is unique at PPM is the close link with the other two center’s labs
(TGC and Biobank) and the common IT Infrastructure for all components [1].
2.2.2. Translational Genomics Core (TGC)
The Translational Genomics core of the PPM (Figure 1) performs high throughput next-generation
sequencing (NGS), library construction for NGS, genotyping, and gene expression analysis (both
chip and sequencing) for all Partners investigators and non-Partners researchers. The core
consists of one Director, one Lab Manager, one Project Manager, and four Technicians. The core
serves
over 200 customers
per year, performs over 400 individual projects annually, and supports
over $148 million
in NIH Grants. The core has one Illumina HiSeq 2500 and two Illumina MiSeq for
sequencing. It performs sequencing of large genomes and transcriptomes, whole exome, and whole
genome for both clinical (LMM) and research projects. The core provides flexible, high-throughput
SNP genotyping using the Illumina iScan platform. Both Illumina (HT-12) and Affymetrix chip based
microarray assays are supported as well as RNA seq. The core is currently developing end to end
services for sequencing of the human microbiome as well as RNA seq for microRNA in tissue, serum
and plasma. Genome Wide SNP genotyping with the Illumina Mega Chip (GWAS) is being performed
on the first 25,000 subjects in the Biobank. The first 5000 subjects have been available in the Fall of 2015
with the full 25,000 available in 2017 see (Figure 3 below) [2].
2.2.3. Partners HealthCare Biobank
Partners HealthCare Biobank is a large research data and sample repository operating within the
framework of PPM (Figure 1). It provides researchers access to high quality, consented samples to help
foster research, advance our understanding of the causes of common diseases, and advance the practice
of medicine. The Partners Biobank provides banked samples (plasma, serum and DNA) collected from
consented patients. These samples are available for distribution to Partners Healthcare investigators
with appropriate approval from the Partners Institutional Review board (IRB). They are linked to
phenotypic data stored in the Research Data Patient Registry (RPDR), as well as some additional health
information collected at the time of collection. To date, more than 35,000 patients have consented to
join the Partners Biobank. An additional 1000 to 2000 patients consent each month. The ultimate goal
is to reach 75,000 total subjects of whom samples are available on 50,000. Samples are collected at the
participating hospitals within Partners HealthCare. Samples are sent to the processing labs where the
plasma, serum, and buffy coats from each specimen are isolated, with the intention of being completed
within 4 h of collection to ensure highest quality for banking purposes. All specimens are shipped
to the Central Facility for DNA Extraction and long-term storage. One of the buffy coat aliquots is
extracted for DNA, quantitated and stored in both master tubes and tubes containing 50
µ
g of DNA.
J. Pers. Med. 2016, 6, 13 4 of 9
These specimen shipments are tracked by our internal software LIMS (STARLIMS), that interfaces with
other software maintaining specimen and data integrity. STARLIMS manages the collection, processing,
storage, distribution and billing of samples at the Central Facility. Samples are distributed in the
following manner. As noted above, investigators may request assistance from Biobank co-Principal
Investigators or complete specimen requests in the Biobank Portal of the Research Patient Data Portal.
These requests are routed through our custom software (EMSI) for parsing, and then forwarded to
the appropriate bank supervisor(s) for fulfillment. The Biobank Program Director is responsible for
managing the day-to-day operations including the distribution of the samples to the investigator
community, and ensuring that sample status is updated in Sunquest or Crimson the software used
to track specimens, as appropriate. To date, the Biobank has distributed >5000 specimens to >50
different investigators through the RPDR and outreach to different clinics within the cardiovascular
disease and various others. The Biobanks supports over $80 million in NIH research. The Biobank
staff includes five Faculty members, one Program Director, one Project Manager, two Recruitment
Managers, 18 Research Assistants, one Senior Lab Manager, and eight full time Technicians. As noted
above, the central facility is co-localized with the Translational Genomics Core (TGC), allowing for
tight integration and continuity of projects for investigators. Samples can be moved directly from the
Biobank to TGC for genotyping/sequencing before results are returned to investigators. The biobank
can accommodate >2 M specimens in 28.8 cubic-foot Revco Upright Ultra-low temperature freezers. To
ensure specimen integrity, freezers are all on emergency back-up power. Each individual freezer is also
monitored 24 h/7 days per week using the SIEMEN’s security system. This system is triggered when
there is a loss of normal power, a rise in temperature within the freezer, or a loss of communication
with the freezer’s alarm circuit. The storage space has two sources of cooling so that the back-up
system (the independent HVAC) can function automatically upon loss of normal power through the
use of an automatic transfer switch connected to the house standby generator. A copy of the Biobank
consent has been included as a supplement to this article [3].
2.2.4. PPM IT Infrastructure and Bioinformatics Team
PPM provides an integrated IT architecture supporting research and clinical activities, which
is directly connected to the Partners and Harvard Medical School networks and to the rest of the
academic community through the Internet. The PPM clinical IT team is responsible for IT support
for LMM and GeneInsight [
4
]. The PPM Research IT is responsible for IT support for Biobank and
TGC [
4
,
5
]. The PPM IT teams are part of Partners Research Computing group, which maintains
PPM’s high performance computing infrastructure database servers and virtual machine servers that
are currently used by our group in many applications. This includes ~100 Tb of dedicated primary
tier storage with access to >100 Tb of additional storage, as well as access to >300 Tb of long-term
replicated storage. We also have three dedicated computational clusters consisting of ten 128-core
nodes with 128 GB of memory each, fourteen 72-core nodes with 96 GB of memory each, and sixteen
32-core nodes with 16 GB of memory each. All systems are patched, monitored and scanned routinely
for vulnerabilities and intrusions by the systems administrator and Partners Information Security.
In addition to our IT hardware, PPM has a dedicated full-time IT staff of 21, including directors,
architects, analysts, developers, an implementation manager, implementation engineers, a quality
manager, genetic counselors and a geneticist.
Three pieces of software tie the LMM, TGC, and Biobank together: GeneInsight (described below),
GIGPAD, and StarLIMS. GIGPAD is the internal LIMS for LMM and TGC and handles samples
management for these two labs. StarLIMS handles sample management for the Biobank and can hand
these samples off to GIGPAD either in the LMM or in the TGC. StarLIMS is a commercial biobank
software while GIGPAD and GeneInsight are home-grown.
The bioinformatics team consists of one director, and seven bioinformaticians. The bioinformatics
team routinely processes and analyzes DNA sequencing, RNA sequencing, and microarray data,
supporting both our CLIA-certified lab and outside investigators via the translational genomics core.
J. Pers. Med. 2016, 6, 13 5 of 9
This includes a custom automated pipeline for generating sample-specific, demultiplexed fastq files
for all Illumina sequencing projects. For DNA-sequencing: (1) Quality Control steps are performed
using Picard and SAMtools; (2) alignment and variant calling use BWA and GATK for indels and small
SNVs; (3) coverage metrics are generated with a combination of GATK and custom scripts; and (4)
CNV calls are generated with a custom tool VisCap. Additionally, an evaluation of CNV calling using
XHMM, ExomeDepth, and others is underway. Our RNA-seq pipeline uses (1) FastQC for quality
steps and (2) the Tuxedo package for differential expression analysis and visualization, including
TopHat, Cufflinks, CuffDiff and CummeRbund. Microarray data is processed via (1) Affymetrix
Expression Console; (2) Illumina GenomeStudio; and (3) Heatmap2 package in R and custom scripts
for visualization. We are also in the process of implementing Beelin/Autoconvert, plink, and custom
software for high-throughput genotyping and annotation of Illumina data.
2.2.5. GeneInsight Suite
The GeneInsight Suite of IT tools has been developed by the PPM Clinical IT team, to address
some of the most critical challenges to enabling broad clinical utilization of genomic testing, a key
step towards the promise of personalized medicine. These challenges include the need to streamline
the clinical testing process, manage the vast amounts of data generated through genetic testing,
generate clinically useful interpretations from these data and channel this information efficiently
and effectively to clinicians to impact patient care. GeneInsight
®
assets have been developed
through close collaboration between LMM laboratory technicians, laboratory managers, geneticists, IT
developers and Partners hospitals practicing physicians to address the distinct, yet interrelated, needs
of laboratories and providers. GeneInsight delivers the IT infrastructure needed to overcome these
challenges (Figure 2).
Figure 2. GeneInsight workflow.
J. Pers. Med. 2016, 6, 13 6 of 9
IT applications include: GeneInsight Lab
®
(Boston, MA, USA), a laboratory tool to assist with
genetic variant knowledge management and interpretative report generation, GeneInsight Clinic
®
,
a standalone hosted clinician interface to enable delivery of patient genetic test results and future
variant updates to clinicians, and GeneInsight Network, a hub designed to enable high throughput
transfer of structured genetic data between and among laboratories and clinicians. The system has
been used to generate over 30,000 clinical reports. The GeneInsight Suite is registered with the FDA as
a Class I exempt medical device. It is subject to inspection and must comply with quality regulations.
Based on a set of IT assets designed to support genetic testing, the PPM IT team has built a solution
to provide broad support for the genetic testing processes in clinical settings. At present a strategic
alliance has been formed between Sunquest Information Systems and Partners HealthCare around
GeneInsight to collaborate on providing seamless genetic testing workflow capabilities to clinical
geneticists and pathologist and the goal to provide a wider dissemination of the software and its
continued development into the industry standard for delivery of genomic results to clinicians [6].
2.3. Partners Research Computing
Partners Research Computing is a Division of Academic Programs of Partners HealthCare. The
group occupies about 5000 square feet about 1200 yards from the MGH main campus and is physically
separate from the PPM space at 65 Lansdowne Street, Cambridge. This space is connected through
Ethernet with the main campus. The space houses offices for about 27 employees and staff members.
Dr. Murphy’s computer resources are located in the Needham Data Center of Partners HealthCare.
Over 40 powerful Windows 2003/2008 Pentium IV class servers are available on site, including several
that host large Oracle and SQL Server databases. These servers host both relational database (Oracle
and SQL Server) and Web server (Microsoft IIS and Tomcat/JBoss) software. Database servers include
RAID5 disk array capabilities. There are also redundant Pentium IV class Windows 2003 file servers
for shared use. In total the group hosts over 20 Terabytes of server disk storage. All servers are backed
up nightly to a Tivoli Storage Manager (TSM) system. Development and production servers reside in
the Partners corporate datacenter, which is, staffed 24/7. The main enterprise computer systems at
Partners are available through the network. All network activity at Partners occurs behind a Cisco
Firewall and traffic is constantly monitored. The group has over 50 desktop workstations ranging
from high-end Pentium multi-processor systems to moderate Pentiums. They include machines
with Microsoft Windows, Macintosh OS, and Linux operation systems. This group has built the
Research Patient Data Registry including the Biobank portal and the Phenotype Discovery Center as
described below.
2.3.1. Research Patient Data Registry (RPDR) and Biobank Portal
Developed by the Partners Research Computing group, the RPDR is a data warehouse that gathers
data from multiple hospital electronic record systems at Partners HealthCare and stores it in a SQL
Server database. The RPDR gathers clinical data from several hospital systems at Partners HealthCare.
(Enterprise Master Patient Index—EMPI, Hospital Decision Support System—EPSI (formerly TSI),
Physician Billing System—IDX and EPIC, Longitudinal Medical Record—LMR, Corporate Provider
Master—CPM, Clinical Data Repository—CDR, and Partners Personalized Medicine—PPM), and
stores the data in one central data warehouse. Researchers are able to query this data by using an
online query tool.
The query tool returns aggregate totals of patient data that are populated with appropriately
obfuscated, de-identified/encrypted data as per HIPPA privacy rules and the HHS Common Rule.
With the proper IRB approval, researchers may access the patients’ detailed medical records for
their specified cohorts of patients. The detailed medical records are returned to researchers in an
encrypted Microsoft Access file and text (.txt) files. Detailed medical records may include the following
types of data: transfusion, cardiology, contact information, demographics, diagnoses, discharge
notes, endoscopy, laboratory tests, PEAR allergies, LMR health maintenance, LMR medications,
J. Pers. Med. 2016, 6, 13 7 of 9
LMR notes, LMR problems, LMR vital signs, medications (RxNorm), microbiology, operative notes,
pathology reports, procedures (CPT codes), providers, pulmonary, radiology reports, radiology tests
and transfusion. Furthermore, images from hospital image repositories can be returned and viewed
online. The RPDR is able to obtain patient notes from hospital systems and create a secure database
for eMERGE III [
7
]. Security and privacy of the patients whose data are contained in RPDR are of
paramount importance in its operation. We have robust methods to protect the information while
maintaining its usability. We have developed methods of data obfuscation to allow users to have access
to aggregate data without threatening patient confidentiality. In addition to the RPDR, both genotype
data (GWAS) and survey data on Biobank participants are visible in the Biobank Portal that is the final
common pathway for investigators to get all of this integrated data. Figure 3 depicts the infrastructure
for the Biobank Portal [8].
Figure 3. Data Integration—Biobank Portal.
2.3.2. Phenotype Discovery Center (PDC)
The Partners Phenotype Discovery Center provides support to investigators to link phenotypes
with data on consented subjects in the Partners HealthCare Biobank. As part of the PDC, we have
created the Biobank Portal (see Figure 3) to combine specimen data with data from the electronic
medical record in a SQL Server database with a web-based application that enables users to query,
view and work with the data in a variety of ways. The Biobank Portal allows users to perform queries,
visualize longitudinal data (e.g., medication prescriptions, diagnoses, lab results), perform PheWAS
based on >1500 clinically grouped ICD9-CM codes, query phenotypes defined by i2b2 algorithms,
perform automated natural language processing (NLP), and request samples from cases and matched
controls. Data in the Biobank Portal database includes narrative data from doctors’ notes and other
hospital text reports (cardiology, pathology, radiology, operative, discharge summaries), as well as
coded data such as demographics, diagnoses, procedures, vital signs, lab values and medications. In
addition, patient reported data from the health information survey given to all Biobank subjects is
included in the Biobank Portal database and contains data on body mass index, occupational exposure,
sun exposure, physical activity, alcohol, smoking and sleep behaviors, family history of disease and
reproductive history for women.
Users of the Biobank Portal application can run queries on the aforementioned data to find
particular sets of patients and then view the query criteria in a timeline patient-by-patient to visualize
when phenomena of interest have occurred. Users can also review sets of patients in a Viewer that
J. Pers. Med. 2016, 6, 13 8 of 9
allows them to look at each patient’s data to determine whether or not to request specimen data
for that patient. Users can then use the application to request the set of patients selected using the
Timeline and Viewer from the Biobank. Another set of functions available in the Biobank Portal is
designed to help with phenotyping sets of patients. Existing validated phenotypes are available in the
user interface for eight diseases (Rheumatoid Arthritis, Ulcerative Colitis, Crohn’s Disease, Multiple
Sclerosis, Type2 Diabetes Mellitus, Coronary Heart Disease, Congestive Heart Failure, and Bipolar
Disorder), with an additional set of 12 planned to be completed over the next year. In addition, we
are creating a Validation Workbench to help users create their own phenotypes, which will require
creating a Natural Language Processing pipeline to help extract required features from narrative data,
creating further methods to help users annotate the data, providing basic statistical guidelines and
educating researchers about the nature of this work. Ultimately, genotyped results for the biobank
subjects will be added into the Biobank Portal data mart and made available for further investigation.
The Biobank is fully integrated with the Laboratory for Molecular Medicine, and the Translational
Genomics Core via the IT connections in the Biobank Portal (Figure 1). All of the work done within the
Biobank Portal and the Phenotype Discovery Center has been vetted by the IRB and abides by strict
security measures.
3. Conclusions
Although we do not provide a formal analysis of similar programs at other AMCs in this
description of the PPM, it is clear that the comprehensive nature of the infrastructure integration
is not common in AMCs. Investigators can utilize the PPM to obtain consented samples, have them
genotyped or sequenced, and then develop relevant diagnostic and prognostic indicators using the
structured IT system across the three labs. We propose this as one model that will facilitate progress in
this complex arena. We also note that the approach that we have taken is dynamic. We are moving in
the direction of having not just the LMM approved, but also the TGC core and the Biobank CLIA, thus
further strengthening the link between research and clinical care.
Acknowledgments:
We acknowledge the leaders of PPM: Heidi Rehm, PhD, Fellow American College of
Medical Genetics (FACMG); Sandy Aronson, MA, ALM; Sami Amr, PhD, FACMG; Matthew Lebo, PhD,
FACMG;
Elizabeth Karlson, MD;
Jordan Smoller, MD, ScD; Robert Green, MD, MPH; Birgit Funke, PhD, FACMG;
Natalie Boutin
and Lisa Mahanta for their contributions to the Center and to this manuscript. Grant support:
1 U01 HG008685-01 From the National Institute for Human Genome Research.
Author Contributions:
Scott T. Weiss wrote the first draft of the paper and Meini Sumbada Shin wrote the second
draft and edited the document.
Conflicts of Interest: The authors declare no conflict of interest.
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©
2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons by Attribution
(CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
