Pathology Informatics Education during the COVID-19 Pandemic at Memorial Sloan Kettering Cancer Center (MSKCC)
←
→
Page content transcription
If your browser does not render page correctly, please read the page content below
Clinical Science
Narrative Review
Acta Medica Academica 2021;50(x):xx-xx
DOI: 10.5644/ama2006-124.XX
Pathology Informatics Education during the COVID-19 Pandemic at Memorial
Sloan Kettering Cancer Center (MSKCC)
David Kim1, Matthew G. Hanna2, Chad Vanderbilt2, S. Joseph Sirintrapun2
1
Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States, 2Department of
Pathology and Warren Alpert Center for Computational and Digital Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, United States
Correspondence: dak9117@nyp.org; Tel.: + 1 212 746 2832; Fax: + 1 212 746 8545
Received: 20 January 2021; Accepted: 22 February 2021
Abstract
This review details the development and structure of a four-week rotation in pathology informatics for a resident trainee at
Memorial Sloan Kettering Cancer Center (MSKCC) in New York City so that other programs interested in such a rotation can
refer to. The role of pathology informatics is exponentially increasing in research and clinical practice. With an ever-expanding
role, training in pathology informatics is paramount as pathology training programs and training accreditation bodies recog-
nize the need for pathology informatics in training future pathologists. However, due to its novelty, many training programs are
unfamiliar with implementing pathology informatics training. The rotation incorporates educational resources for pathology
informatics, guidance in the development, and general topics relevant to pathology informatics training. Informatics topics
include anatomic pathology related aspects such as whole slide imaging, laboratory information systems, image analysis, and
molecular pathology associated issues such as the bioinformatics pipeline and data processing. Additionally, we highlight how
the rotation pivoted to meet the department’s informatics needs while still providing an educational experience during the onset
of the COVID-19 pandemic. Conclusion. As pathology informatics continues to grow and integrate itself into practice, infor-
matics education must also grow to meet the future needs of pathology. As informatics programs develop across institutions,
such as the one detailed in this paper, these programs will better equip future pathologists with informatics to approach disease
and pathology.
Key Words: Informatics Education Residency Digital Pathology Whole Slide Imaging Molecular and Genomic Pathology
Education.
Introduction identifies informatics as the application of infor-
mation management in healthcare to promote
Informatics in medicine and pathology has a long
safe, efficient, effective, personalized, and respon-
history. Medical informatics began in the 1950s as
sive care (2). The recent advent of electronic health
the “science of information” with pathology infor-
records and the digitization of medical informa-
matics introduced as a field a few decades later in
the 1990s. Many pathologist informaticians argue tion pushed medical informatics into the forefront
however, that technology and information man- as a critical and necessary aspect for education
agement has been a part of pathology since its and practice. Similarly, in recent years, pathol-
inception (1). Pathology at its core involves the ogy informatics is placed in the lead with expo-
identification, collection, and interpretation of nential and broad integration of advancements in
data, information, and knowledge in order to di- molecular pathology, genomics, digital imaging,
agnose, predict disease behavior, and guide treat- and artificial intelligence. Therefore, education in
ment. The College of American Pathology (CAP) pathology informatics is crucial now more than
Copyright © 2021 by the Academy of Sciences and Arts of Bosnia and Herzegovina.Acta Medica Academica 2021;50(x):xx-xx
ever for future clinical practice in pathology. The gaged in pathology informatics activities. Through
current gap, however, is the limited amount of on- input from these attendings, construction of the
line pathology informatics training resources and rotation began with the objective of maximizing
the few “hands-on” experiences in pathology in- the exposure of the resident to pathology informat-
formatics. Online pathology informatics training ics related aspects in a four-week period. MSKCC,
resources are evolving, and pathology residencies as an institution, also has many well-developed
still need training frameworks to keep up with the pathology informatics resources such as WSI and
rapid advancements and ever shifting landscape of molecular bioinformatics, combined with clinical
informatics education. Only a handful of articles and research initiatives to abundantly supplement
guideline pathology informatics education (3-6). a well-rounded experience in pathology informat-
Moreover, the few “hands-on” opportunities in- ics for the trainee.
clude a few U.S. academic centers and pathology An outline of general goals and objectives,
informatics fellowships where the focus is more to- though not necessary, is highly recommended
wards pathology informatics such as laboratory in- in developing an educational curriculum for the
formation systems (LIS) maintenance, whole slide trainee. An outline allows the trainee and faculty to
imaging (WSI), and bioinformatics compared to gauge the experience and address specific bench-
the more general field of medical informatics (7). marks throughout the rotation. Our outline of the
In our review, we detail the pathology infor- rotation goals and objectives of the four-week rota-
matics rotation in New York City at Memorial tion is shown in Table 1. The authors recognize that
Sloan Kettering Cancer Center (MSKCC), as a not every training environment has access to such
“hands-on” experience that supplements existing resources. Two accessible, free and comprehensive
pathology informatics training resources. We de- online pathology informatics training resources
tail the rotation’s construction, development, and formed the starting point for the rotation and is rec-
implementation at the trainee (e.g. resident/fel- ommended for training programs with and without
low) level, and also how the implementation of the resources. The two resources (Table 2) are the Pa-
rotation adapted because of the COVID-19 pan- thology Informatics Essentials for Residents (PIER)
demic in early 2020 to support remote pathologists curriculum (3) and Training Residents in Genomics
and clinical services. We provide our review as an (TRIG) (4). Both online curricula provide interac-
example of a successful framework for a pathology tive modules and recorded lectures but also serve
informatics rotation so that other institutions, for- as helpful guides for content and structure to ap-
mulating informatics curricula for their trainees, proach and teach the material during the rotation.
can leverage. Highlighted in this review are the PIER is an online informatics curriculum, devel-
online pathology informatics training resources oped by informatics experts, and focused towards
available to use by any institution for their train- residents in helping meet the Accreditation Coun-
ees. Such broad integration of pathology informat- cil for Graduate Medication Education (ACGME)
ics training assures the dissemination of necessary milestones in resident education/training in pathol-
knowledge and empowerment of informatics to ogy informatics. Developed in cooperation by the
the future pathologist community. College of American Pathologists (CAP), Associa-
tion of Pathology Chairs (APC), and Association for
Pathology Informatics (API), PIER details essential
Construction and Development of the topics in informatics that are essential for future pa-
Pathology Informatics Rotation thologists. Topics and objectives addressed by PIER
The setting for the pathology informatics rotation include fundamental principles of databases, data
was in the pathology department of MSKCC which and communication standards, digital imaging,
has the experience of attendings who have com- laboratory information systems, and the health
pleted pathology informatics training or have en- care information ecosystem to more advancedDavid Kim et al: Pathology Informatics at MSKCC
Table 1. The Listed Goals and Objectives to Be Met by the Resident Throughout the Rotation*
General Goals and Objectives
Informatics Knowledge:
Handling and management of medical data storage
Familiarity with basic information system terminology
Familiarity with different data structures and database architecture
Data analysis fundamentals
Digital imaging fundamentals
Whole slide imaging fundamentals
Information Systems:
User interface design
Familiarity of pathology workflows and processes
Structure of laboratory information systems and electronic medical/health record (EMR/EHR) systems
Familiarity of how data is stored, transferred, and accessed for information systems
Interpretation and analysis of molecular/genomic data of bioinformatics pipelines
Management:
Management of laboratory information systems and electronic medical/health record (EMR/EHR) systems
Management of operations and flow in pathology practice
Laboratory finance principles
Professionalism:
Proficiency in communicating with and presenting to clinicians and pathologists about informatics related matters
Education:
Prepare a 30-minute informatics based presentation to be presented at the Weill Cornell Clinical Pathology Resident Lecture
*
Having such an outline allows the resident and faculty involved in the rotation to have a clear goal as to the goals of the rotation. Therefore, by the end of the
rotation the trainee is able to concretely identify what they have gained through the experience.
Table 2. Easily accessible pathology informatics online curricula with their respective URL links
Henricks et al. (3) https://apc.memberclicks.net/index.php?option=com_content&view=article&id=152:pier&catid=20:si
te-content&Itemid=156Many
Haspel RL. (4) https://www.pathologylearning.org/trig
concepts like project management, clinical deci- National Society of Genetic Counselors and the
sion support, image analysis, and artificial intel- American College of Medical Genetics and Ge-
ligence. In addition, participatory interactions nomics. Through continual grant support from the
with pathology informatics attendings at MSKCC National Cancer Institute, the TRIG working group
helped solidify the didactic content of PIER holds workshops and courses at annual meetings
through actual “hands-on” practice in the rotation. of major pathology and oncology organizations.
Similarly, TRIG is an online curriculum, de- This four-week rotation was constructed and de-
veloped by an expert group in medical education, veloped for anatomic pathology related informat-
molecular pathology, and clinical genetics, that ics objectives. Clinical pathology related aspects
promotes genomic pathology education in mo- were not highlighted in the curriculum except for
lecular testing approaches and scenarios. TRIG is molecular and genomic pathology. Laboratory
a unique collaborative effort with major pathol- medicine related informatics activities in clinical
ogy organizations and representatives from the chemistry, microbiology, and blood banking wereActa Medica Academica 2021;50(x):xx-xx
not highlighted in the curriculum, because of the is a robust and well-integrated molecular/genom-
limited four-week time constraint, which was in- ics bioinformatics service within the department
sufficient to encompass those activities adequately. of pathology. This service allowed for an envi-
More time would have unlocked even more poten- ronment in which a trainee could easily integrate
tial for learning opportunities in these laboratory themselves and identify individuals to enrich their
medicine related areas in informatics as millions experience in molecular bioinformatics. This sec-
of data points are generated and interpreted for ond week exposes the trainee to how informat-
patient care. The focus on anatomic pathology in- ics aids in the organization and interpretation of
formatics as well as molecular genomic pathology molecular/genomic data and its practical role in
likewise fit the rotating residents’ interests. Given clinical care and patient treatments. Through the
the time constraint and the diversity of pathology integration of the bioinformatics pipeline, training
informatics rotations in informatics training can includes the understanding of the strengths and
be tailored to the trainee or pathologists’ interests. weaknesses of molecular/genomic testing.
Each week in the four-week rotation was devot- During this second week, the resident would at-
ed to a rotations/topic shown in Table 3. The first tend molecular/genomic sign outs, rotate with the
and last weeks were situated so the trainee would bioinformatics group, and attend quality assurance
work with whole slide imaging in the WSI scanner (QA)/quality control (QC) molecular/genomic
facilities to understand concepts, challenges, the meetings. MSKCC molecular/genomic sign out is
processes of digitizing diagnostic slides and their held with a bioinformatician, a molecular fellow,
utilization. In addition, the first and last weeks and a molecular attending. In reviewing molecu-
were set up so that the trainee would also be inte- lar/genomic reports and the associated molecular/
grated with the anatomic pathology laboratory in- genomic data output, a fluid dynamic dialogue ex-
formation system (AP-LIS) team. In this instance, ists as any QA/QC issues are addressed at the time
MSKCC utilizes Cerner CoPathPlus for its AP-LIS. of sign out. This fosters a learning environment
In these weeks the aspects of WSI, AP-LIS support, to how data is extracted as well as issues that may
automation of lab processes in anatomic pathology, arise in the process. Additionally, the weekly QA/
computer vision/artificial intelligence (AI) for WSI QC meetings allows the trainee to see how the mo-
were addressed; further solidifying the didactic lecular/genomic data output from molecular plat-
concepts serving as an adjunct to PIER. forms are filtered and analyzed computationally
The second week was dedicated to informat- as well as the challenges and pitfalls. Also sched-
ics in molecular and genomic pathology includ- uled for the resident during this second week, was
ing the bioinformatics pipeline and scripting. one-on-one didactics with a molecular/genomics
Understanding how sequencing data is processed attending. These didactic sessions further delved
and analyzed is integral to the future of pathology into the bioinformatics pipeline by going over the
practice as molecular and genomic pathology ex- code and architecture in further detail. Didactic
pands in testing and complexity. At MSKCC there topics included next generation sequencing (NGS)
Table 3. The Rotations and Topics Addressed for Each Week of the Rotation*
Week Rotations/Topics
Week 1 AP-LIS support and automation, WSI, computer vision/AI
Molecular and genomic informatics including
Week 2
bioinformatics pipeline and scripting
Rotations in Machine Learning Labs and
Week 3
Pathology Imaging Labs
Week 4 AP-LIS, WSI, Surgical Pathology Informatics, and Previous Rotations of Interest
Didactic lectures in pathology informatics by attending were performed throughout all the weeks. Any informatics related meetings were also attended to
*
when possible throughout the weeks (i.e., QA/QC meetings, molecular sign out, lab meetings, and vendor meetings).David Kim et al: Pathology Informatics at MSKCC
file formats, QA pitfalls, filtering variants, and in- On January 20th 2020, the first reported case of
troductions to using the programming language R COVID-19 infection was identified in the United
for analyzing data. States (8). On March 20th 2020, stay at home orders
The third week was designed as an anatomic were placed in New York City with strict gathering
pathology informatics research week in which the and social distancing measures in order to hinder
trainee would rotate through the Thomas Fuchs the spread of COVID-19 (9). By early April 2020,
Lab and the Yukako Yagi Lab. The Fuchs Lab is hospitals in New York City were overwhelmed, as
focused on computer vision and AI applications intensive care units were expanded and healthcare
to either WSI, tissue-micro arrays, and medical workers redeployed to meet the increasing num-
imaging. The Yagi Lab investigates novel innova- ber of individuals infected with COVID-19. Pa-
tive approaches to tissue processing and imag- thology departments in New York City also faced
ing such as 3D tissue imaging, multispectral im- difficulties in moving forward safely with clinical
age enhancement, and telepathology. During this operations.
third week, the trainee would attend lab meetings Though carefully developed and planned prior,
and team up with research scientists to help on the informatics rotation began right as COVID-19
their projects. Experience in both labs immerses hit New York City. By the second week of the rota-
the trainee in innovative approaches for pathology tion, all research labs had suspended in person activ-
and in fostering inspiration in academic pursuits ity with individuals working from home to decrease
in pathology informatics. exposure. At the same time discussions as to how
The entire four-week rotation was overseen pathology informatics could help in not only data
by multiple pathology informatics attendings. collection and investigation of COVID-19 but also
Integrated throughout the four-week rotation is remote sign out of WSI were discussed. MSKCC had
practice experience supplemented by individual in place a robust WSI lab and operation that was
one on one didactic lectures with informatics at- situated to aid pathology workflow in a safe manner
tendings on various informatics topics, infor- (10, 11). The focus of the trainee’s rotation adjusted
matics research projects, vendor meetings, and towards testing and validation of operational pro-
hospital wide informatics meetings. Two specific cesses adapted for pathologists to review and sign-
informatics projects were slated for involvement out pathology specimens remotely through WSI.
by the trainee during the four-week rotation. The Accomplishing such an endeavor meant promot-
first project was the validation of the Leica Aperio ing the safety of individuals in the lab and digital
LV1 for remote frozen section diagnosis. The Leica scanning, as well as pathologists, while continuing
Aperio LV1 (Leica Biosystems, Buffalo Grove, IL) clinical operations and responsibilities. The adap-
is a small footprint (e.g. 4 slide) hybrid robotic mi- tation of the rotation during the pandemic high-
croscope/whole slide scanner providing both WSI lights the flexibility as well as the wide applicability
capabilities and dynamic robotic telepathology of pathology informatics for training.
ideal for frozen sections (5). The second project
was analyzing component differences across dif- Testing and Validation of Remote Sign out
ferent WSI platforms to further investigate high Through WSI
power field quantification in digital pathology (6).
MSKCC has numerous WSI technologies, digital
scanning staffing, and existing processes to pilot a
Implementation and Adaptation of the larger WSI operation for remote sign out. Incor-
Rotation to the Covid-19 Pandemic porating WSI at scale during the pandemic for re-
mote sign out became the priority, though many
In December of 2019, cases of an unknown vi- operational questions remained that required
ral pneumonia were reported in Wuhan, China, tremendous efforts by the trainee in testing and
later identified as SARS-CoV-2 or COVID-19. validation in real time. In addition to these testingActa Medica Academica 2021;50(x):xx-xx
and validation efforts, one on one didactic lectures all CLIA-certified laboratories in NYS to have ap-
with informatics attendings continued via web proval for laboratory developed testing (LDT).
conferencing platforms (e.g. WebEx, Zoom Mi- LDT validation documentation was required for
crosoft Teams) on informatics topics such as mo- submission and approval, in order to perform re-
lecular/genomic bioinformatics, WSI, and labora- mote sign out using WSI. The application for vali-
tory information systems. dation by NYS was written and submitted during
For the validation, the Leica Aperio GT450 and the validation process and eventually granted ap-
Philips UltraFast Scanner were selected as high proval. By developing the process for remote WSI
throughput instruments to pilot remote sign out sign out along with participation in testing, valida-
of surgical pathology specimens. Initially, a select tion, and handling regulation around remote WSI
group of attendings began a remote sign out pilot sign out, the education of the trainee was greatly
using WSI for one specialty. Shortly after the initial enhanced. Familiarity with all the nuances around
pilot, a study protocol was developed to encompass digitization of glass slides, the steps required, and
all surgical pathology subspecialties on randomly the regulations of government and professional
selected service days (11). WSI was then expanded societies, brought unforeseen practical experience
to other services/specialties and attendings with the that would not have occurred without the pan-
eventual intent to scale operations to all glass slides demic forcing adaptions by MSKCC.
produced by the lab and all slides of cases received
as consultations. The trainee worked as part of the
team including digital imaging staff and operation- Conclusions
al directors to test and address issues that arose. As Pathology informatics continues to evolve with
there was no precedent, the trainee was actively process-driven technological solutions for an in-
involved in developing process frameworks for creasingly complex healthcare field. Advances in
slide scanning operations and workflows, address- WSI, computer vision/AI, and digital imaging in-
ing slide-reading errors; continual optimization of novations allow pathologists to not only work ef-
slide scanning workflows were addressed firsthand ficiently, but also yield new approaches to disease
without guidance from prior established examples. diagnostics and management. Likewise, informat-
Additionally, how digital slides were viewed and ics in molecular and genomic pathology plays a key
how to best optimize the required components for role in disease diagnostics and management with
WSI viewing, were also addressed directly without generations of insights through breakthroughs in
guidance from prior established examples. data analysis. Future pathologists need to know
Regulatory considerations were addressed in these aspects of informatics in in their practice.
the validation for remote WSI sign out. With the Therefore, training pathology residents and fel-
need for WSI remote sign out during COVID-19, lows in pathology informatics concepts are es-
Centers for Medicare and Medicaid Services sential for the future pathologist workforce. Such
(CMS) temporarily used their enforcement discre- essential training is acknowledged by the ACGME
tion to allow remote sites meeting specific criteria and CAP by their efforts to bolster informatics
to not require dedicated CLIA certifications; in or- education for trainees. The pathology informatics
der for pathologists to work remotely (12). Other rotation constructed, developed, and implement-
regulatory bodies in other countries also followed ed at MSKCC serves as a guide and example in
suit (13-15). The FDA also further provided guid- structuring a resident/fellow pathology informat-
ance with a temporary enforcement discretion on ics rotation. While the general goals, objectives,
the use of non-510(k) cleared devices, with valida- and designed activities pivoted to fit the needs of
tion prior to use (16). the department during the COVID-19 pandemic
In New York State (NYS), the NYS Department for remote WSI sign out, the rotation still yielded
of Health is the CLIA-deemed entity that requires valuable experience in learning about informaticsDavid Kim et al: Pathology Informatics at MSKCC
processes and core concepts. Having clear and well 8. World Health Organization. WHO Timeline - COVID-19.
thought out objectives prior to the rotation as well [cited 2020 Nov 5]. Available from: https://www.who.int/
news/item/27-04-2020-who-timeline---covid-19. Pub-
as dedicated mentors and attendings enhanced the lished 2020.
education experience. 9. New York State. New York State on PAUSE. 2020. [cited
2020 Nov 6]. Available from: https://coronavirus.health.
Conflict of Interest: David Kim, - None; Chad Vanderbilt, - ny.gov/new-york-state-pause.
DocDoc Pte. Ltd. (Provision of Services) and Paige.AI, Inc.
10. Hanna MG, Reuter VE, Hameed MR, Tan LK, Chiang S, Si-
(Ownership / Equity Interests; Provision of Services); Mat-
gel C, et al. Whole slide imaging equivalency and efficiency
thew Hanna, - Paige.AI, Inc. (Provision of Services) and Path-
study: experience at a large academic center. Mod Pathol.
Presenter (Provision of Services - uncompensated); S. Joseph
2019;32(7):916-28. doi:10.1038/s41379-019-0205-0
Sirintrapun, - None.
11. Hanna MG, Reuter VE, Ardon O, Kim D, Sirintrapun SJ,
Schüffler PJ, et al. Validation of a digital pathology system
References including remote review during the COVID-19 pandem-
ic. Mod Pathol. Published online June 2020. doi:10.1038/
1. Park S, Parwani AV, Aller RD, Banach L, Becich MJ, s41379-020-0601-5
Borkenfeld S, et al. The history of pathology informat- 12. Centers for Medicare & Medicaid Services. Centers for
ics: A global perspective. J Pathol Inform. 2013;4:7. doi: Medicare & Medicaid Services Memorandum, Clinical
10.4103/2153-3539.112689. Laboratory Improvement Amendments (CLIA) Labora-
2. College of American Pathologists. Clinical Informatics tory Guidance During COVID-19 Public Health Emer-
Resources. Published 2020. [cited 2020 Nov 5]. Available gency. [cited 2020 Nov 5]. Available from: https://www.
from: https://www.cap.org/member-resources/councils- cms.gov/medicareprovider-enrollment-and-certifica-
committees/informatics-committee/. tionsurveycertificationgeninfopolicy-and-memos-sta
3. Henricks WH, Karcher DS, Harrison JH, Sinard JH, Ri- tes-and/clinical-laboratory-improvement-amendments-
ben MW, Boyer PJ, et al. Pathology Informatics Essentials clia-laboratory-guidance-during-covid-19-public-health.
for Residents: A flexible informatics curriculum linked to Published 2020.
Accreditation Council for Graduate Medical Education 13. Williams BJ, Brettle D, Aslam M, Barrett P, Bryson G,
milestones. J Pathol Inform. 2016;7:27. doi: 10.4103/2153- Cross S, et al. Guidance for Remote Reporting of Digital
3539.185673. Pathology Slides During Periods of Exceptional Service
4. Haspel RL. Teaching Residents Genomic Pathology. Pressure: An Emergency Response from the UK Royal
Adv Anat Pathol. 2013;20(2):125-9. doi:10.1097/PAP. College of Pathologists. J Pathol Inform. 2020;11:12. doi:
0b013e31828629b2 10.4103/jpi.jpi_23_20.
5. Leica Biosystems. LEICA BIOSYSTEMS APERIO LV1 14. College of American Pathologists. COVID-19 - Re-
IVD APPROVED FOR REMOTE FROZEN SECTION mote Sign-Out Guidance. [cited 2020 Jan 12]. Available
AND TELEPATHOLOGY. 2018. [cited 2020 Nov 5]. from: https://documents.cap.org/documents/COVID19-
Available from: https://www.leicabiosystems.com/news- %0ARemote-Sign-Out-Guidance-vFNL.pdf. Published
events/news-details/article/leica-biosystems-aperio-lv1- 2020.
ivd-approved-for-remote-frozen-section-and-telepathol- 15. College of American Pathologists. Remote Sign-Out
ogy/News/detail/. FAQs. [cited 2020 Dec 1]. Available from: https://docu-
6. Hanna M, Pantanowitz L. Redefining the high power ments.cap.org/documents/Remote-Sign-Out-FAQs-
field when counting mitoses using digital pathology. Mod 42.%0AFINAL.pdf. Published 2020.
Pathol. 2017;30(S2):396A. 16. Food and Drug Administration. Enforcement Policy for
7. American Medical Informatics Association. Clinical Remote Digital Pathology Devices During the Coronavi-
Informatics Fellowship Programs. [cited 2020 Nov 5]. rus Disease 2019 (COVID19) Public Health Emergency.
Available from: https://amia.org/membership/academic- Guidance for Industry, Clinical Laboratories, Healthcare
forum/clinical-informatics-fellowships. Facilities, Pathologists, and Food and Drug Administra-
tion Staff. [cited 2020 Nov 23]. Available from: https://
www.fda.gov/media/137307/download.You can also read
