Clinical Informatics

Resource Guide

The Clinical Informatics Resource Guide highlights

resources that provide awareness and understanding
of clinical informatics topics.

VERSION 1.2.0.0 | ISSUE NO. 1 | 2018

 Opinions expressed in this document are the authors’ own
and do not necessarily reflect an endorsement by the CAP
of any organization, equipment, reagents, materials, or
services used by participating laboratories.

© 2018 College of American Pathologists. All rights reserved. None

of the contents of this publication may be reproduced, stored in a retrieval
system, or transmitted in any form or by any means (electronic, mechanical,
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the publisher.
Table of Contents Electronic Page Numbers

What is Clinical Informatics?  ||Page 8

Goals of this Resource Guide and How to Use It?  ||Page 10

What is the Clinial Informatics Resource Guide?  ||Page 10
How to Use This Clinical Informatics Resource Guide  ||Page 10
Versioning of the Clinical Informatics Resource Guide  ||Page 11
Clinical Informatics Resource Guide Revision Summary  ||Page 11
Editors and Contributors of the Clinical Informatics Resource Guide  ||Page 12

Section 1: Clinical Informatics - The Basics  ||Page 13

1.1 Overview  ||Page 13
1.2 What is Clinical Informatics and why is it important to me?  ||Page 14
1.3 How is Clinical Informatics different from Information Technology?  ||Page 19

Section 2: Understanding Information Technology Fundamentals  ||Page 22

2.1 The Basics  ||Page 22
2.1.1 What is an intranet? 
2.1.2 What is encryption? 
2.1.3 What is open source? 
2.1.4 What is HL7 and how does it relate to interfaces? 
2.1.5 What is Integrating the Healthcare Enterprise (IHE) and how does it relate
to the laboratory? 
2.2 VPNs and Authentications  ||Page 31
2.3 Specimen Identification and Tracking Technologies  ||Page 33
2.3.1 What are the pros and cons of 1D and 2D bar coding? 
2.3.2 What are the differences, advantages and disadvantages of using RFID
versus barcoding? 
2.3.3 How can barcodes and RFID be utilized in the Anatomic Pathology or
Biorepository laboratory? 
2.3.4 How can barcodes and RFID be utilized in Transfusion Medicine, and are
there additional uses for barcode and RFID technology within the laboratory? 
2.3.5 Insights from Adopters – Liron Pantanowitz, MD, FCAP 
2.3.6 Insights from Adopters – R. Ross Reichard, MD, FCAP 
2.3.7 Biometrics and Positive Patient Identification 

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2.3.8 Insights from Adopters – Raymond Aller, MD, FCAP

Section 3: Understanding Laboratory Data Structures and ||Page 65

Information Exchange 
3.1 Vocabularies  ||Page 65
3.1.1 LOINC - What is it and why do I need it? 
3.1.2 SNOMED CT-What are the uses for this in my laboratory results? 
3.1.3 What do I need to know about the Dublin Core and Common Data
Elements? 
3.1.4 What is UCUM (and why do I care)? Why is UCUM important? 
3.1.5 Are there guides I can use for implementing LOINC and SNOMED CT in
my laboratory? 
3.1.6 Insights from Adopters – Alexis Byrne Carter, MD, FCAP 
3.2 Reporting Standards  ||Page 87
3.2.1 What is free-text versus structured reporting? 
3.2.2 What is cCDA and how is it used? 
3.3 Using Data for Purposes Beyond Reporting the Result  ||Page 98
3.3.1 How do I use my LIS to get performance metrics? (e.g. TAT) 
3.3.2 How can I use the data in my LIS to improve patient care? 
3.4 What is the CMS Medicare’s Quality Payment Program (QPP)?  ||Page 102
3.4.1 Insights from Adopters – Walter H. Henricks, MD, FCAP 

Section 4: Selecting and Installing a Laboratory Information ||Page 116

System 
4.1 Selection and Purchasing Process  ||Page 116
4.1.1 How do I evaluate LISs, evaluate my needs, and write an RFP to
determine the best LIS for an institution? 
4.1.2 Should I choose a stand-alone LIS or lab modules incorporated into the
EHR? 
4.1.3 What are the performance and regulatory issues I need to be aware of
when selecting a new LIS, and what things do I need to consider so that my
new system will remain usable for many years? 
4.1.4 Insights from Adopters – John Sinard, MD, PhD, FCAP 
4.1.5 Insights from Adopters – Alexis Byrne Carter, MD, FCAP 
4.1.6 Insights from Adopters – Rajesh Dash, MD, FCAP and Alexis Byrne
Carter, MD, FCAP 
4.2 Installation Process and Vendor Collaboration  ||Page 157
4.2.1 How do I assess current and future workflows and why is it important? 
4.2.2 What factors should be considered and what is involved to purchase / add
/ bring a new analyzer LIVE and on-line? 
4.3 Validation and Documentation Considerations  ||Page 165
4.3.1 How do I validate my LIS and what are the different types of testing used

© 2018 College of American Pathologists. All rights reserved.
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in LIS implementations? (unit, integration, parallel, post-go-live) 

4.3.2 How do I validate my specialty systems such as Digital Pathology, Whole
Slide Imaging, and Next Generation Sequencing? 
4.3.3 How do I develop downtime processes and manage downtime in both
planned and unplanned situations? 
4.3.4 What procedure manuals for LIS are required? 
4.3.5 What should I know about Informatics and Laboratory Developed Tests
(LDTs)? 
4.4 Insights from Adopters – Mark Routbort, MD, PhD, FCAP  ||Page 196

Section 5: Integration and Management of Information Systems  ||Page 205

5.1 Interfaces and Middleware  ||Page 206
5.1.1 What are interfaces and middleware? 
5.1.2 How does my LIS interface with multiple EHRs? 
5.1.3 How does an LIS incorporate send-outs? 
5.1.4 How do I handle the electronic orders and results in an outreach setting? 
5.1.5 Are any implementation guides available from HL7 that provide
interoperability standards for use with orders and results interfaces? 
5.1.6 What is auto-verification and how do I get it implemented? 
5.1.7 What is a synthesized and/or integrated (composite) disease report and
how can I link to other systems? 
5.1.8 Will the reporting specialties—pathology and radiology-- join forces? Why
would they? 
5.2 Managing the Test Compendium  ||Page 223
5.2.1 How do I change a test and test definition in my test compendium? 
5.3 Managing Test Patients  ||Page 226
5.3.1 What are the best practices for test patients in the system? 
5.3.2 What are the best practices for PT testing? 
5.3.3 How do I avoid PT being labeled as a referral? 
5.4 Clinical Decision Rules  ||Page 228
5.4.1 What clinical decision rules can the lab develop? 
||Page 233
5.5 Patient Portals 
5.5.1 What are patient portals and what are the requirements to access lab
tests? 

Section 6: Accreditation and Regulatory Aspects of Information

||Page 236
Systems 
6.1 What are the CLIA and LAP Accreditation Requirements?  ||Page 238
6.1.1 How do I maintain my computer facility, and what do I have to do if it is
remote to my facility? 
6.1.2 What is the first downstream reporting system? 
6.1.3 How do I handle downtime for my electronic systems? 

© 2018 College of American Pathologists. All rights reserved. iii.
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6.1.4 What are the regulatory requirements to implement autoverification?

6.2 Insights from Adopters – William Castellani, MD, FCAP  ||Page 250
6.3 Outsource Storage and the Cloud  ||Page 255
6.3.1 What exactly is cloud computing? 
6.3.2 What are the existing standards relevant to cloud computing? 
6.3.3 Are virtualization and cloud computing the same? 
6.3.4 Are there security guidelines specific for clinical laboratories using cloud
application for in vitro diagnostic systems? 
6.3.5 What are the options for protecting privacy in cloud computing services? 
6.3.6 What concerns exist for outsourcing portions of organizational computing
services to a public cloud? 
6.3.7 What legal issues and topics should be addressed in cloud computing
contracts? 
6.3.8 How does “big data” relate to cloud computing? 

Section 7: Biobanking and Biorepositories  ||Page 267

7.1 Software Applications for Quality Biobanking  ||Page 267
7.2 Managing a Biobank  ||Page 270

7.3 Quality, Standards and Proficiency Testing  ||Page 271

7.4 Preanalytic Variables  ||Page 275

7.5 Integrating Biobanking Data into the practice of Medicine  ||Page 277

Section 8: Big Data and Metadata  ||Page 280

8.1 Big Data/Metadata  ||Page 280
8.1.1 What is metadata and what is its value? 
8.1.2 What is “big data” and what are its implications in my practice? 
8.1.3 Insights from Adopters – Ramy Arnaout, MD, DPhil, FCAP 
8.1.4 What is the role of precision medicine in cancer? 
8.1.5 What are the data sources for genomics? What are the challenges for
capturing, storing and analyzing this information? 
8.1.6 Insights from Adopters – Philip C. Chen, MD, PhD, FCAP 
8.2 Cost Implications  ||Page 318
8.2.1 How can I view financial data from my institution to calculate downstream
costs for what the laboratory does? 
8.2.2 What do I bring to the table that is valuable? 
8.3 The Value of Big Data in the Laboratory and in Value Based Care  ||Page 320
8.4 Insights from Adopters – Philip C. Chen, MD, PhD, FCAP  ||Page 326
8.5 Value of Informatics in the Laboratory  ||Page 329
8.5.1 How can I use informatics to determine cost-effectiveness and to better
allocate resources? 

© 2018 College of American Pathologists. All rights reserved. iv.
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Section 9: Futurematics  ||Page 332

9.1 Computational Pathology  ||Page 332
9.1.1 Anatomic Pathology 
9.1.2 Clinical Pathology 
9.1.3 Vision Statements 
9.2 Artificial Intelligence (AI)  ||Page 337
9.2.1 Tools 
9.2.2 Data Mining in Free Text 
9.2.3 Text Mining 
9.2.4 AI in Pathology Imaging 
9.3 Blockchain  ||Page 342
9.3.1 Blockchain in Healthcare Information Exchange (HIE) 
9.3.2 Blockchain in Population Health Research 
9.3.3 Blockchain in Interoperability 
9.4 Insights from Adopters – James Harrison, MD, PhD, FCAP  ||Page 347

Section 10: CAP Resources  ||Page 351

10.1 CAP Resource Guides  ||Page 351

10.2 CAP Cancer Protocols  ||Page 352
10.3 CAP Electronic Cancer Checklists (eCC)  ||Page 353
10.4 CAP LAP: Accreditation  ||Page 355
10.5 CAP’s Short Presentations on Emerging Concepts (SPECs)  ||Page 357

Section 11: CAP Clinical Informatics Educational Resources  ||Page 359

11.1 CAP Webinars  ||Page 359
11.1.1 Hot Topics in Pathology Webinars in 2017 and 2018 
11.1.2 Archived Non-CME Clinical Informatics Webinars 
11.2 CAP Annual Meeting  ||Page 360
11.3 CAP Education Resources  ||Page 361
11.4 Pathology Informatics Education for Residents (PIER)  ||Page 365

Section 12: Feedback  ||Page 367

How to Cite This Document 
Clinical Informatics Resource Guide Contributors 

Bibliography  ||Page 370

© 2018 College of American Pathologists. All rights reserved.
v.
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