Journal:Bioinformatics education in pathology training: Current scope and future direction

Full article title	Bioinformatics education in pathology training: Current scope and future direction
Journal	Cancer Informatics
Author(s)	Clay, Michael R.; Fisher, Kevin E.
Author affiliation(s)	St. Jude Children’s Research Hospital, Baylor College of Medicine, Texas Children’s Hospital
Primary contact	Email: Kevin dot Fisher at bcm dot edu
Year published	2017
Volume and issue	16
Page(s)	1–6
DOI	10.1177/1176935117703389
ISSN	1176-9351
Distribution license	Creative Commons Attribution-NonCommercial 4.0 International
Website	http://insights.sagepub.com/
Download	http://insights.sagepub.com/redirect_file.php (PDF)

Abstract

Training anatomic and clinical pathology residents in the principles of bioinformatics is a challenging endeavor. Most residents receive little to no formal exposure to bioinformatics during medical education, and most of the pathology training is spent interpreting histopathology slides using light microscopy or focused on laboratory regulation, management, and interpretation of discrete laboratory data. At a minimum, residents should be familiar with data structure, data pipelines, data manipulation, and data regulations within clinical laboratories. Fellowship-level training should incorporate advanced principles unique to each subspecialty. Barriers to bioinformatics education include the clinical apprenticeship training model, ill-defined educational milestones, inadequate faculty expertise, and limited exposure during medical training. Online educational resources, case-based learning, and incorporation into molecular genomics education could serve as effective educational strategies. Overall, pathology bioinformatics training can be incorporated into pathology resident curricula, provided there is motivation to incorporate institutional support, educational resources, and adequate faculty expertise.

Keywords: Bioinformatics, informatics, residency, education, pathology, training

Introduction

Anatomic pathology (AP) and clinical pathology (CP) residents, fellows, and faculty dedicate countless hours in structured training environments equipped with textbooks, scientific literature, and professional expertise to achieve proficiency in the histopathologic diagnosis of disease and/or interpretation of laboratory data. With the emergence of genomics data and clinical data warehouses, laboratory professionals are now tasked with managing, interpreting, and leveraging data of unprecedented complexity. These complex data necessitate that educators rethink the skills and knowledge required for a graduating trainee to practice in the “information age” of diagnostic medicine.

Bioinformatics is defined as the management, acquisition, manipulation, and presentation of complex biological data sets, and clinical informatics is the application of information management in health care to promote safe, efficient, effective, personalized, and responsive care. Given the breadth of these definitions, it is not surprising that defining aspects germane to clinical training is a nontrivial task. In molecular pathology, in particular, these definitions are intricately linked; e.g., computational scripts manipulate raw data such that pathologists can review and interpret for clinical reporting. Here, we highlight the requisite baseline skill set a pathologist should acquire during training to remain facile in bioinformatics and still fulfill the necessary requirements to graduate from accredited pathology training programs. A few key questions, barriers, and proposed solutions to incorporate bioinformatics into general residency education will also be discussed.

Informatics education in pathology residency

The American College of Graduate Medical Education (ACGME) is a private organization that oversees all accredited medical residency training in the United States. Their primary role is to standardize program requirements and provide operational standards for the sponsoring institution, training hospitals, faculty and program directors, program resources, and duty hours. Also, the ACGME determines educational milestones that serve as specialty-specific data to facilitate improvements to curricula and resident performance and demonstrate the effectiveness of graduate medical education in meeting the needs of the public. Sponsoring institutions receive funds from the federal government to cover the costs of training physicians, and ACGME-accredited residents’ and fellows’ salaries are allocated from these monies. Notably, sponsoring institutions must demonstrate compliance with the ACGME’s educational recommendations to maintain accreditation and receipt of the federal funds.

The American Board of Pathology (ABP) partners with the ACGME to ensure that accredited pathology programs provide their trainees with the necessary requisites to become board eligible for the AP, CP, AP/CP, or AP/neuropathology (AP/NP) examinations, and all potential ABP examinees must complete 36 to 48 months of full-time training in an ACGME-accredited pathology program. Each trainee must receive at least 24 months of AP-only or CP-only training or 18 months each of structured AP and CP training. The remaining 12 months is flexible and may include AP, CP, or research rotations (up to six months). Furthermore, AP board-eligible examinees must complete at least 50 autopsies by the time the application for certification is submitted. An example of a typical 48-month AP/CP curriculum is provided in Table 1.

Table 1. A representative 48-month ACGME-accredited AP/CP residency curriculum; abbreviations: AP, anatomic pathology; CP, clinical pathology AP Rotations CP Rotations Other Rotations Year 1 Surgical pathology (4 mos.) Medical autopsy (2 mos.) Clinical chemistry (3 mos.) Medical microbiology (3 mos.) Year 2 Surgical pathology (3 mos.) Cytopathology (1 mo.) Medical autopsy (1 mo.) Pediatric pathology (1 mo.) Hematopathology (3 mos.) Transfusion medicine (3 mos.) Year 3 Surgical pathology (2 mos.) Cytopathology (2 mos.) Dermatopathology (1 mo.) Forensic pathology (1 mo.) Neuropathology (1 mo.) Gastrointestinal pathology (1 mo.) Gynecologic pathology (1 mo.) Genitourinary pathology (1 mo.) Flow cytometry (1 mo.) Molecular pathology (1 mo.) Year 4 Surgical pathology (2 mos.) Pulmonary pathology (1 mo.) Soft tissue pathology (1 mo.) Renal pathology (1 mo.) AP elective (1 mo.) Clinical informatics (1 mo.) Laboratory administration (1 mo.) CP elective (1 mo.) CP elective (1 mo.) Research (2 mos.) Total 28 mos. 18 mos. 2 mos.

Acknowledgements

Author contributions

MRC and KEF conceived and wrote the manuscript. All authors reviewed and approved the final manuscript.

Funding

The author(s) received no financial support for the research, authorship, and/or publication of this article.

Disclosures and ethics

As a requirement of publication, author(s) have provided to the publisher signed confirmation of compliance with legal and ethical obligations including but not limited to the following: authorship and contributorship, conflicts of interest, privacy and confidentiality, and (where applicable) protection of human and animal research subjects. The authors have read and confirmed their agreement with the ICMJE authorship and conflict of interest criteria. The authors have also confirmed that this article is unique and not under consideration or published in any other publication, and that they have permission from rights holders to reproduce any copyrighted material. Any disclosures are made in this section. The external blind peer reviewers report no conflicts of interest.

Declaration of conflicting interests

The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Notes

This presentation is faithful to the original, with only a few minor changes to presentation, grammar, and spelling. In some cases important information was missing from the references, and that information was added. In one case (the first citation), the original citation URL was dead, and an updated URL was substituted.