Scientific equipment, experiments and techniques Books

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 chromosomalTrade 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

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Book SynopsisChemoinformatics draws upon techniques from many disciplines including computer science, mathematics, computational chemistry and data visualisation to tackle these problems.Trade ReviewThis is a rather remarkable little book. Just as its title promises, it provides an introduction to a very wide variety of chemoinformatic and CADD topics. Allthough the book is written for beginning graduate students and advanced undergraduates, it could certainly provide a very helpful overview for professionals with no prior knowledge of the subject matter. Robert S. Pearlman, University of Texas at Austin. J.Am. Chem. Soc., Vol 126, No. 4, 2004.Table of ContentsPreface. Acknowledgements. 1: Representation and Manipulation of 2D Molecular Structures. 1. Introduction. 2. Computer Representations of Chemical Structures. 3. Structure Searching. 4. Substructure Searching. 5. Reaction Databases. 6. The Representation of Patents and Patent Databases. 7. Relational Database Systems. 8. Summary. 2: Representation and Manipulation of 3D Molecular Structures. 1. Introduction. 2. Experimental 3D databases. 3. 3D Pharmacophores. 4. Implementation of 3D database Searching. 5. Theoretical 3D Databases. 6. Methods to Derive 3D Pharmacophores. 7. Applications of 3D Pharmacophore Mapping and 3D Database Searching. 8. Summary. 3: Molecular Descriptors. 1. Introduction. 2. Descriptors Calculated from the 2D Structure. 3. Descriptors Based on 3D Representations. 4. Data Verification and Manipulation. 5. Summary. 4: Computational Models. 1. Introduction. 2. Historical Overview. 3. Deriving a QSAR Equation: Simple and Multiple Linear Regression. 4. Designing a QSAR 'Experiment'. 5. Principal Components Regression. 6. Partial Least Squares. 7. Molecular Field Analysis and Partial Least Squares. 8. Summary. 5: Similarity Methods. 1. Introduction. 2. Similarity Based on 2D Fingerprints. 3. Similarity Coefficients. 4. Other 2D Descriptor Methods. 5. 3D Similarity. 6. Summary. 6: Selecting Diverse SetsOf Compounds. 1. Introduction. 2. Cluster Analysis. 3. Dissimilarity-Based selection methods. 4. Cell-Based Methods. 5. Optimisation Methods. 6. Comparison and Evaluation of Selection Methods. 7. Summary. 7: Analysis of High-Throughput Screening Data. 1. Introduction. 2. Data Visualisation. 3. Data Mining Methods. 4. Summary. 8: Virtual Screening. 1. Introduction. 2. 'Drug-Likeness' and Compound Filters. 3. Structure-Based Virtual Screening. 4. The Prediction of ADMET Properties. 5. Summary. 9: Combinatorial Chemistry and Library Design. 1. Introduction. 2. Diverse and Focussed Libraries. 3. Library Enumeration. 4. Combinatorial Library Design Strategies. 5. Approaches to Product-Based Library Design. 6. Multiobjective Library Design. 7. Practical Examples of Library Design. 8. Summary. Appendix 1: Matrices, Eigenvectors and Eigenvalues. Appendix 2: Conformation, Energy Calculations and Energy Surfaces. Further Reading. References. Index.

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Book Synopsis

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