Cytogenetic Laboratory Management – Chromosomal, FISH, and Microarray–Based Best Practices and Procedures
Chromosomal, FISH and Microarray–Based Best Practices and Procedures
Samenvatting
Cytogenetic Laboratory Management: Chromosomal, FISH and Microarray–Based Best Practices and Procedures is a practical guide that describes how to develop and implement best practice processes and procedures in the genetic laboratory setting. The text first describes good laboratory practices, including quality management, design control of tests and FDA guidelines for laboratory developed tests, and pre–clinical validation study designs. The second focus of the book describes best practices for staffing and training, including cost of testing, staffing requirements, process improvement using Six Sigma techniques, training and competency guidelines and complete training programs for cytogenetic and molecular genetic technologists. The third part of the text provides step–wise standard operating procedures for chromosomal, FISH and microarray–based tests, including pre–analytic, analytic and post–analytic steps in testing, and divided into categories by specimen type, and test–type.
All three sections of the book include example worksheets, procedures, and other illustrative examples that can be downloaded from the Wiley website to be used directly without having to develop prototypes in your laboratory.
Providing both a wealth of information on laboratory management and molecular and cytogenetic testing, Cytogenetic Laboratory Management will be an essential tool for laboratorians world–wide in the field of laboratory testing and genetics testing in particular.
This book gives the essentials of:
Developing and implementing good quality management programs in laboratories
Understanding design control of tests and pre–clinical validations studies and reports
FDA guidelines for laboratory developed tests
Use of reagents, instruments and equipment
Cost of testing assessment and process improvement using Six Sigma methodology
Staffing training and competency objectives
Complete training programs for molecular and cytogenetic technologists
Standard operating procedures for all components of chromosomal analysis, FISH and microarray testing of different specimen types
This volume is a companion to Cytogenetic Abnormalities: Chromosomal, FISH and Microarray–Based Clinical Reporting. The combined volumes give an expansive approach to performing, reporting and interpreting cytogenetic laboratory testing and the necessary management practices, staff and testing requirements.
Specificaties
Inhoudsopgave
<p>PREFACE xiii</p>
<p>ACKNOWLEDGMENTS xvii</p>
<p>ABOUT THE COMPANION WEBSITE xix</p>
<p>SECTION I: BEST PRACTICES FOR LABORATORY OPERATIONS 1</p>
<p>1 Guidelines for Good Clinical Laboratory Practice 3</p>
<p>1.1 Physical Facilities 4</p>
<p>1.2 Specimen Transport and Management 5</p>
<p>1.3 Personnel Safety 6</p>
<p>1.4 Laboratory Information System (LIS) 7</p>
<p>1.5 Quality Management 7</p>
<p>1.6 Organization and Personnel 10</p>
<p>1.7 Laboratory Equipment 10</p>
<p>1.8 Testing Operating Procedures 11</p>
<p>1.9 Safety Plan 12</p>
<p>1.10 Biosafety Plan 22</p>
<p>1.11 Chemical Hygiene Plan 31</p>
<p>1.12 Health Insurance Portability and Accountability Act (HIPAA) Incident Plan 55</p>
<p>Appendix 1.A: OSHA s Form 300 60</p>
<p>Appendix 1.B: OSHA s Form 300A 61</p>
<p>Appendix 1.C: Information on HMIS and NFPA Labeling Systems used in Laboratories 62</p>
<p>Further Reading 66</p>
<p>More Resources 69</p>
<p>HIPAA Reference 70</p>
<p>2 Quality Management 71</p>
<p>2.1 QC Program 74</p>
<p>2.2 Individualized QC Plan (IQCP) 80</p>
<p>2.3 Standards for Test Records and Reporting 81</p>
<p>2.4 Overview of General Culturing Issues 83</p>
<p>2.5 QI Program 95</p>
<p>2.6 Proficiency Testing 101</p>
<p>2.7 Inspection Preparation 110</p>
<p>2.8 Calibration Verification 112</p>
<p>Further Reading 121</p>
<p>3 Design Control of Tests and FDA Guidelines for Laboratory Developed Tests (LDTs) 125</p>
<p>3.1 Design Control of Tests 125</p>
<p>3.2 FDA Guideline Summary for LDTs 139</p>
<p>Further Reading 157</p>
<p>4 Preclinical Validation Studies 159</p>
<p>4.1 Validation Plans and Protocols 159</p>
<p>4.2 Validation Reports 179</p>
<p>4.3 Example Validation Plan and Report Analysis of FISH Probes for Chromosome 5 Deletion and Monosomy 181</p>
<p>4.4 Example Validation Plan and Report for the FDA–Approved Vysis ALK FISH Probe 192</p>
<p>Further Reading 206</p>
<p>5 Reagents, Instruments, and Equipment 209</p>
<p>5.1 Reagents 209</p>
<p>5.2 Instruments and Equipment 227</p>
<p>5.3 IQ, OQ, and PQ Procedures 237</p>
<p>5.4 Example Equipment Process Validation Protocol 245</p>
<p>Further Reading 250</p>
<p>SECTION II: BEST PRACTICES FOR STAFFING AND TRAINING 253</p>
<p>6 Cost of Testing and Staffing Requirements 255</p>
<p>6.1 Labor Costs 256</p>
<p>6.2 Time and Cost Assessment 260</p>
<p>6.3 Staffing Hiring Needs 260</p>
<p>6.4 Staff Task Requirements 262</p>
<p>Further Reading 267</p>
<p>7 Process Improvement: Six Sigma Approach to Laboratory Improvement 269</p>
<p>7.1 Introduction 269</p>
<p>7.2 DMAIIC Tools 273</p>
<p>7.3 Defining the Project 274</p>
<p>7.4 Measuring Variables 279</p>
<p>7.5 Analyze Data for the Project 282</p>
<p>7.6 Innovate and Improve the Project 287</p>
<p>7.7 Controlling the Results of the Project 289</p>
<p>Appendix 7.A Raw Baseline Data 295</p>
<p>Appendix 7.B Raw Control Data 295</p>
<p>Further Reading 296</p>
<p>8 Staff Training and Competency for a Cytogenetics Laboratory 299</p>
<p>8.1 Technician (Nonlicensed/Certified Lab Personnel) Training and Competency 300</p>
<p>8.2 Technologist (Licensed/ASCP–Certified) Training and Competency 303</p>
<p>8.3 General Supervisor/Manager Training and Competency 307</p>
<p>8.4 Cytogenetic Technical Supervisor/Director Training and Competency 310</p>
<p>Further Reading 316</p>
<p>9 Training Program for Cytogenetic and FISH Technologists 319</p>
<p>9.1 Training Program Overview and Objectives 320</p>
<p>9.2 Program Content 323</p>
<p>9.3 Practical Component 332</p>
<p>9.4 Lectures, Quizzes, and Assignments 335</p>
<p>9.5 Trainee Competency and Completion of the Program 335</p>
<p>9.6 Trainee Handbook 336</p>
<p>9.7 Logs, Competency Forms, and Evaluation Forms 344</p>
<p>Further Reading 356</p>
<p>10 Training Program for Molecular Genetic Technologists 357</p>
<p>10.1 Training Overview and Objectives 358</p>
<p>10.2 Program Content 361</p>
<p>10.3 Practical Component 367</p>
<p>10.4 Lectures, Quizzes, and Assignments 370</p>
<p>10.5 Trainee Competency and Completion of the Training Program 370</p>
<p>10.6 Trainee Handbook 371</p>
<p>10.7 Logs, Competency Forms, and Evaluations Forms 379</p>
<p>Further Reading 383</p>
<p>SECTION III: STANDARD OPERATING PROCEDURES 385</p>
<p>11 General SOP Information by Test and Preanalytic Procedures 387</p>
<p>11.1 Definition of an SOP 387</p>
<p>11.2 Example Template for Writing an SOP 390</p>
<p>11.3 CAP and ACMG Guidelines for Writing SOPs 393</p>
<p>11.4 Preanalytic Procedures: Accessioning Specimens for all Specimen Types 396</p>
<p>Further Reading 402</p>
<p>12 Analytic Procedures: Chromosome Analysis 405</p>
<p>12.1 Peripheral Blood and Percutaneous Umbilical Blood Specimen for Constitutional Disorders 410</p>
<p>12.2 Amniotic Fluid Specimens 440</p>
<p>12.3 Chorionic Villus Sampling 479</p>
<p>12.4 Solid Tissue Samples: Tissue Biopsies and Products of Conception 505</p>
<p>12.5 Bone Marrow and Blood for Hematologic Malignancies 534</p>
<p>12.6 Lymph Nodes and Solid Tumors 565</p>
<p>12.7 Breakage Syndromes 592</p>
<p>Appendix 12.A Cytogenetics Blood Culture and Harvest Worksheet 597</p>
<p>Appendix 12.B Daily Harvest Log 598</p>
<p>Appendix 12.C Test Slide Banding Log 599</p>
<p>Appendix 12.D Batch Banding Log 600</p>
<p>Appendix 12.E Analysis Sheet 601</p>
<p>Appendix 12.F Prenatal Culture and Harvest Worksheet 602</p>
<p>Appendix 12.G Culture Failure Log 603</p>
<p>Appendix 12.H Amniotic Fluid Count Guidelines for Normal and Extended Studies 604</p>
<p>Appendix 12.I Hematologic Culture Log 605</p>
<p>Appendix 12.J Specimen Setup Hematologic Malignancies 606</p>
<p>Appendix 12.K Solid Tumor Culture Worksheet 607</p>
<p>Further Reading 608</p>
<p>13 Analytic Procedures: Fluorescence in situ Hybridization (FISH) Analysis 613</p>
<p>13.1 General Information 613</p>
<p>13.2 CAP and ACMG Guidelines for Performing FISH Analyses 617</p>
<p>13.3 Cell Sorting for Plasma Cell Disorders for FISH Analysis 619</p>
<p>13.4 General Procedure for Direct Labeling of FISH Probes 624</p>
<p>13.5 Prenatal Multicolor Probes 641</p>
<p>13.6 ToTelVysion Multicolor DNA Probe Mixtures 654</p>
<p>13.7 Multicolor: Telomere, Centromere, and Paint Probes (Cytocell) 666</p>
<p>13.8 Microscope Analysis for Metaphase Scoring 680</p>
<p>13.9 Microscope Analysis for Interphase Scoring 685</p>
<p>13.10 Formalin–Fixed Paraffin–Embedded Procedure for FISH Analysis 693</p>
<p>13.11 HER2/ERBB2 FISH Analysis 700</p>
<p>13.12 UroVysion (Vysis) Bladder Cancer FISH Analysis 711</p>
<p>Appendix 13.Aa Constitutional FISH Probes 722</p>
<p>Appendix 13.Ab Hematologic FISH Assays 723</p>
<p>Appendix 13.B Probe Chart: Panels of Probes 724</p>
<p>Appendix 13.C FISH Direct Harvest Log 725</p>
<p>Appendix 13.D Batch Hybridization Log 726</p>
<p>Appendix 13.E General FISH Probe Analysis Sheet 727</p>
<p>Appendix 13.F FISH Probe Analysis Sheet AML Panel 728</p>
<p>Appendix 13.G FISH Probe Analysis Sheet MDS Panel 729</p>
<p>Appendix 13.H FISH Probe Analysis Sheet CLL Panel 730</p>
<p>Appendix 13.I FISH Probe Analysis Sheet NHL Panel 731</p>
<p>Appendix 13.J FISH Probe Analysis Sheet MM Panel 732</p>
<p>Appendix 13.K FISH Probe Analysis Sheet ALL Panel 733</p>
<p>Appendix 13.L FISH Analysis Sheet BCR/ABL/ASS Triple Fusion 734</p>
<p>Appendix 13.M HER2 Analysis Sheet 735</p>
<p>Appendix 13.N UroVysion Analysis Sheet 736</p>
<p>Further Reading 736</p>
<p>14 Analytic Procedures: Chromosomal Microarray Analysis (CMA) 739</p>
<p>14.1 Test Principle 739</p>
<p>14.2 Comparing Conventional Chromosome Analysis, FISH Analysis and Chromosomal Microarray Analysis 741</p>
<p>14.3 Interpretation 745</p>
<p>14.4 Procedure Overview 747</p>
<p>Further Reading 752</p>
<p>15 Postanalytic Procedures 755</p>
<p>15.1 Reviewing and Reporting Cases for Chromosome Analysis 756</p>
<p>15.2 Reviewing and Reporting Cases for FISH Analysis 762</p>
<p>15.3 Reviewing and Reporting Cases for Microarray Analysis 765</p>
<p>15.4 Procedure for Avoidance and Detection of Clerical Errors Post Reporting 772</p>
<p>15.5 Specimen, Material and Record Retention, and Specimen Disposal 774</p>
<p>Appendix 15.A Record of Results Correspondence Log 778</p>
<p>Further Reading 779</p>
<p>GLOSSARY 781</p>
<p>INDEX 811</p>