ebook img

Cytogenetic laboratory management : chromosomal, FISH, and microarray-based best practices and procedures PDF

818 Pages·2016·6.134 MB·English
Save to my drive
Quick download
Download
Most books are stored in the elastic cloud where traffic is expensive. For this reason, we have a limit on daily download.

Preview Cytogenetic laboratory management : chromosomal, FISH, and microarray-based best practices and procedures

CytogenetiC laboratory management CytogenetiC laboratory management Chromosomal, FiSH and microarray‐based best Practices and Procedures SuSan maHler Zneimer Adjunct Professor, Moorpark College, California, USA CEO and Scientific Director, MOSYS Consulting, California, USA Copyright © 2017 by John Wiley & Sons, Inc. All rights reserved Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per‐copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750‐8400, fax (978) 750‐4470, or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748‐6011, fax (201) 748‐6008, or online at http://www.wiley.com/go/permissions. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages. For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at (800) 762‐2974, outside the United States at (317) 572‐3993 or fax (317) 572‐4002. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic formats. For more information about Wiley products, visit our web site at www.wiley.com. Library of Congress Cataloging‐in‐Publication data applied for ISBN: 9781119069744 Cover credit: © ttsz/Gettyimages Set in 10/12pt Times by SPi Global, Pondicherry, India 10 9 8 7 6 5 4 3 2 1 contents DeDication xi Preface xiii acknowleDgments xvii about the comPanion website xix section i: best Practices for laboratory oPerations 1 1 guidelines for good clinical laboratory Practice 3 1.1 Physical Facilities 4 1.2 Specimen Transport and Management 5 1.3 Personnel Safety 6 1.4 Laboratory Information System (LIS) 7 1.5 Quality Management 7 1.6 Organization and Personnel 10 1.7 Laboratory Equipment 10 1.8 Testing Operating Procedures 11 1.9 Safety Plan 12 1.10 Biosafety Plan 22 1.11 Chemical Hygiene Plan 31 1.12 Health Insurance Portability and Accountability Act (HIPAA) Incident Plan 55 Appendix 1.A: OSHA’s Form 300 60 Appendix 1.B: OSHA’s Form 300A 61 Appendix 1.C: Information on HMIS and NFPA Labeling Systems used in Laboratories 62 v vi CONTENTS Further Reading 66 More Resources 69 HIPAA Reference 70 2 Quality management 71 2.1 QC Program 74 2.2 Individualized QC Plan (IQCP) 80 2.3 Standards for Test Records and Reporting 81 2.4 Overview of General Culturing Issues 83 2.5 QI Program 95 2.6 Proficiency Testing 101 2.7 Inspection Preparation 110 2.8 Calibration Verification 112 Further Reading 121 3 Design control of tests and fDa guidelines for laboratory Developed tests (lDts) 125 3.1 Design Control of Tests 125 3.2 FDA Guideline Summary for LDTs 139 Further Reading 157 4 Preclinical Validation studies 159 4.1 Validation Plans and Protocols 159 4.2 Validation Reports 179 4.3 Example Validation Plan and Report—Analysis of FISH Probes for Chromosome 5 Deletion and Monosomy 181 4.4 Example Validation Plan and Report for the FDA‐Approved Vysis ALK FISH Probe 192 Further Reading 206 5 reagents, instruments, and equipment 209 5.1 Reagents 209 5.2 Instruments and Equipment 227 5.3 IQ, OQ, and PQ Procedures 237 5.4 Example Equipment Process Validation Protocol 245 Further Reading 250 section ii: best Practices for staffing anD training 253 6 cost of testing and staffing requirements 255 6.1 Labor Costs 256 6.2 Time and Cost Assessment 260 6.3 Staffing Hiring Needs 260 6.4 Staff Task Requirements 262 Further Reading 267 CONTENTS vii 7 Process improvement: six sigma approach to laboratory improvement 269 7.1 Introduction 269 7.2 DMAIIC Tools 273 7.3 Defining the Project 274 7.4 Measuring Variables 279 7.5 Analyze Data for the Project 282 7.6 Innovate and Improve the Project 287 7.7 Controlling the Results of the Project 289 Appendix 7.A Raw Baseline Data 295 Appendix 7.B Raw Control Data 295 Further Reading 296 8 staff training and competency for a cytogenetics laboratory 299 8.1 Technician (Nonlicensed/Certified Lab Personnel) Training and Competency 300 8.2 Technologist (Licensed/ASCP‐Certified) Training and Competency 303 8.3 General Supervisor/Manager Training and Competency 307 8.4 Cytogenetic Technical Supervisor/Director Training and Competency 310 Further Reading 316 9 training Program for cytogenetic and fish technologists 319 9.1 Training Program Overview and Objectives 320 9.2 Program Content 323 9.3 Practical Component 332 9.4 Lectures, Quizzes, and Assignments 335 9.5 Trainee Competency and Completion of the Program 335 9.6 Trainee Handbook 336 9.7 Logs, Competency Forms, and Evaluation Forms 344 Further Reading 356 10 training Program for molecular genetic technologists 357 10.1 Training Overview and Objectives 358 10.2 Program Content 361 10.3 Practical Component 367 10.4 Lectures, Quizzes, and Assignments 370 10.5 Trainee Competency and Completion of the Training Program 370 10.6 Trainee Handbook 371 10.7 Logs, Competency Forms, and Evaluations Forms 379 Further Reading 383 section iii: stanDarD oPerating ProceDures 385 11 general soP information by test and Preanalytic Procedures 387 11.1 Definition of an SOP 387 11.2 Example Template for Writing an SOP 390 viii CONTENTS 11.3 CAP and ACMG Guidelines for Writing SOPs 393 11.4 Preanalytic Procedures: Accessioning Specimens for all Specimen Types 396 Further Reading 402 12 analytic Procedures: chromosome analysis 405 12.1 Peripheral Blood and Percutaneous Umbilical Blood Specimen for Constitutional Disorders 410 12.2 Amniotic Fluid Specimens 440 12.3 Chorionic Villus Sampling 479 12.4 Solid Tissue Samples: Tissue Biopsies and Products of Conception 505 12.5 Bone Marrow and Blood for Hematologic Malignancies 534 12.6 Lymph Nodes and Solid Tumors 565 12.7 Breakage Syndromes 592 Appendix 12.A Cytogenetics Blood Culture and Harvest Worksheet 597 Appendix 12.B Daily Harvest Log 598 Appendix 12.C Test Slide Banding Log 599 Appendix 12.D Batch Banding Log 600 Appendix 12.E Analysis Sheet 601 Appendix 12.F Prenatal Culture and Harvest Worksheet 602 Appendix 12.G Culture Failure Log 603 Appendix 12.H Amniotic Fluid Count Guidelines—for Normal and Extended Studies 604 Appendix 12.I Hematologic Culture Log 605 Appendix 12.J Specimen Setup—Hematologic Malignancies 606 Appendix 12.K Solid Tumor Culture Worksheet 607 Further Reading 608 13 analytic Procedures: fluorescence in situ hybridization (fish) analysis 613 13.1 General Information 613 13.2 CAP and ACMG Guidelines for Performing FISH Analyses 617 13.3 Cell Sorting for Plasma Cell Disorders for FISH Analysis 619 13.4 General Procedure for Direct Labeling of FISH Probes 624 13.5 Prenatal Multicolor Probes 641 13.6 ToTelVysion™ Multicolor DNA Probe Mixtures 654 13.7 Multicolor: Telomere, Centromere, and Paint Probes (Cytocell) 666 13.8 Microscope Analysis for Metaphase Scoring 680 13.9 Microscope Analysis for Interphase Scoring 685 13.10 Formalin‐Fixed Paraffin‐Embedded Procedure for FISH Analysis 693 13.11 HER2/ERBB2 FISH Analysis 700 13.12 UroVysion (Vysis) Bladder Cancer FISH Analysis 711 Appendix 13.Aa Constitutional FISH Probes 722 Appendix 13.Ab Hematologic FISH Assays 723 Appendix 13.B Probe Chart: Panels of Probes 724 Appendix 13.C FISH Direct Harvest Log 725 Appendix 13.D Batch Hybridization Log 726 Appendix 13.E General FISH Probe Analysis Sheet 727 CONTENTS ix Appendix 13.F FISH Probe Analysis Sheet—AML Panel 728 Appendix 13.G FISH Probe Analysis Sheet—MDS Panel 729 Appendix 13.H FISH Probe Analysis Sheet—CLL Panel 730 Appendix 13.I FISH Probe Analysis Sheet—NHL Panel 731 Appendix 13.J FISH Probe Analysis Sheet—MM Panel 732 Appendix 13.K FISH Probe Analysis Sheet—ALL Panel 733 Appendix 13.L FISH Analysis Sheet—BCR/ABL/ASS Triple Fusion 734 Appendix 13.M HER2 Analysis Sheet 735 Appendix 13.N UroVysion Analysis Sheet 736 Further Reading 736 14 analytic Procedures: chromosomal microarray analysis (cma) 739 14.1 Test Principle 739 14.2 Comparing Conventional Chromosome Analysis, FISH Analysis and Chromosomal Microarray Analysis 741 14.3 Interpretation 745 14.4 Procedure Overview 747 Further Reading 752 15 Postanalytic Procedures 755 15.1 Reviewing and Reporting Cases for Chromosome Analysis 756 15.2 Reviewing and Reporting Cases for FISH Analysis 762 15.3 Reviewing and Reporting Cases for Microarray Analysis 765 15.4 Procedure for Avoidance and Detection of Clerical Errors Post Reporting 772 15.5 Specimen, Material and Record Retention, and Specimen Disposal 774 Appendix 15.A Record of Results Correspondence Log 778 Further Reading 779 glossary 781 inDex 811 DeDication I dedicate this book to my daughters, Mira and Alana, who since they were born have changed my life forever and for the better. They have given me strength, inspired me to do great things, and have given me abounding love. I hope I have done the same for them. Mira and Alana, I wish you both a life of good health, happiness, and profound significance. And may you strive for Tikkun Olam. And to my dear friend and colleague, Lauren Jenkins, whom I have known for most of my life. Your time on this earth was much too short. I miss you with all my heart. Lauren died on Rosh Hashanah 5776 (September 14, 2015). xi Preface For the last 25 years, I have been the director of different cytogenetic laboratories. Like most directors, I started out in academia for my American Board of Medical Genetics fellowship, but then moved on to various commercial laboratories for the next 20 years, and now currently to consulting for different genetic laboratories, both commercial and academic. After all these years, I realize that my daily work consists of two main tasks, signing out cytogenetic cases and managing the clinical laboratory. I wrote my first book, Cytogenetic Abnormalities, Chromosomal, FISH and Microarray‐Based Clinical Reporting, published by Wiley Publishers in 2014, to reflect all the information that I have learned in signing out cases throughout my career. In this book I want to focus on the other aspects of my laboratory duties, namely, laboratory management. Managing or directing a lab requires vastly different skills than what we learn as scientists who need to perform, review, and interpret cytogenetic laboratory results. As scientists, we generally receive lit- tle training in the field of management, let alone laboratory management. As geneticists, we rely on our scientific knowledge base and experience in genetic procedures to perform and sign out test results. We acquire those skills after years of working in the laboratory in graduate school and postdoctoral programs. However, laboratory management uses other skills that we usually learn “on the job.” We learn that to be a good director or manager, we need to be good at interpersonal relations, organization, and time management. We learn to be supportive of the laboratory staff yet be good disciplinarians when performance is not acceptable. We learn to be inno- vative and strive to be as productive as possible. We learn to be conscious of interpreting patient results and performing genetic analyses with complete accuracy, yet to also be aware of the “bottom line” in order to be within a specific budget. It is a balancing act that we must perform daily and get right every time. Genetic results require 100% accuracy in diagnostic testing as well as being business savvy to be always within a budget; otherwise, our jobs may be in jeopardy. For these reasons, I decided to write this book on laboratory management. I know what most lab directors and managers face with regards to “running a lab.” So I want to share as xiii

See more

The list of books you might like

Most books are stored in the elastic cloud where traffic is expensive. For this reason, we have a limit on daily download.