Description
Book SynopsisCytogenetic Laboratory Management Cytogenetic Laboratory Management
Chromosomal, FISH and Microarray-Based Best Practices and Procedures
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 preclinical validation study designs. The second focus of the book is on 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 stepwise standard operating procedures for chromosomal
Trade Review
"From beginning to end, this book provides relevant concepts, procedures and strategies that give the reader a complete overview of good laboratory practices. In addition to providing an excellent guide for setting up a new clinical lab, Zneimer's book should be considered as a useful guide for any laboratory because it provides a wealth of practical information that can be used on a daily basis. All of the spreadsheets, guides, examples and templates in the book are useful bonus features and represent a valuable legacy of the author's extensive experience." (Phenotype June 2017)
Table of ContentsDedication xiii
Preface xvii
Acknowledgments xix
About the Companion Website v
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
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
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
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
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
