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9780521517713

Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-Scale RNAi Research

by
  • ISBN13:

    9780521517713

  • ISBN10:

    0521517710

  • Edition: 1st
  • Format: Hardcover
  • Copyright: 2011-02-21
  • Publisher: Cambridge University Press

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Summary

This concise, self-contained, and cohesive book focuses on commonly used and recently developed methods for designing and analyzing high-throughput screening (HTS) experiments from a statistically sound basis. Combining ideas from biology, computing, and statistics, the author explains experimental designs and analytic methods that are amenable to rigorous analysis and interpretation of RNAi HTS experiments. The opening chapters are carefully presented to be accessible both to biologists with training only in basic statistics and to computational scientists and statisticians with basic biological knowledge. Biologists will see how new experiment designs and rudimentary data-handling strategies for RNAi HTS experiments can improve their results, whereas analysts will learn how to apply recently developed statistical methods to interpret HTS experiments.

Table of Contents

Preface pagep. ix
Acknowledgmentsp. xv
Acronyms and Abbreviationsp. xvii
RNAi HTS and Data Analysis
Introduction to Genome-Scale RNAi Researchp. 3
RNAi: An Effective Tool for Elucidating Gene Functions and a New Class of Drugsp. 3
High-Throughput Screening: A Vital Technology in Drug Discoveryp. 5
Genome-Scale RNAi Screensp. 7
An Example of Genome-Scale RNAi Researchp. 9
Challenges in Genome-Scale RNAi Researchp. 10
Experimental Designsp. 13
siRNA Designsp. 13
Control Designsp. 15
Plate Designsp. 16
Designs of siRNA Delivery and Optimization of Transfectionp. 24
Design of Sample Sizep. 24
Conclusionsp. 25
Data Display and Normalizationp. 27
Data Display Using Graphicsp. 27
Transformation of Measured Raw aluesp. 32
Identification and Adjustment of Systematic Spatial Effectsp. 33
Strategy for Data Display and Normalizationp. 41
Quality Control in Genome-Scale RNAi Screensp. 42
Introductionp. 42
Quality Assessment Metricsp. 42
Quality Control Criteriap. 47
Adoption of Effective Plate Designsp. 53
Integration of Experimental and Analytic Approaches to Improve Data Qualityp. 56
Applicationp. 57
Discussion and Conclusionsp. 60
Hit Selection in Genome-Scale RNAi Screens without Replicatesp. 62
Introduction
Methods for Hit Selection in Primary Screens without Replicatesp. 63
Decision Rules for Hit Selection in RNAi Screensp. 69
Sample Size Determinationp. 74
Applicationsp. 77
Conclusionsp. 82
Hit Selection in Genome-Scale RNAi Screens with Replicatesp. 83
Metrics for Hit Selection in Screens with Replicatesp. 83
Dual-Flashlight Plotp. 86
Decision Rules for Hit Selection in Screens with Replicatesp. 88
False Discovery Rate, False Non-Discovery Rate, q-Value, and q*-Valuep. 90
Sample Size Determinationp. 92
Analytic Methods Adjusting for Off-Target Effectsp. 93
Applicationsp. 98
Discussion and Conclusionsp. 106
Methodological Development for Analyzing RNAi HTS Screens
Statistical Methods for Group Comparisonp. 111
Illustration of Issues in Traditional Contrast Analysisp. 112
Contrast Variable, Smcv, and c+ -Probabilityp. 114
A Classifying Rule for Interpreting Strength of Group Comparisonsp. 116
A Theorem to Facilitate the Estimation and Inference of Smcvp. 119
Estimation of Smcv and c+ -Probabilityp. 127
Contrasts in Multifactor Anovap. 133
Case Studies and Simulationp. 142
Discussion and Conclusionsp. 152
Statistical Methods for Assessing the Size of siRNA Effectsp. 154
SSMD and d+-Probabilityp. 154
Estimation of SSMDp. 156
Comparing SSMD with Standardized Mean Difference and Classical t-Statisticp. 159
SSMD-Based Ranking Methods for Hit Selection in Genome-Scale RNAi Screensp. 165
SSMD-Based FPR, FNR, and Powerp. 166
FDR and FNDR in RNAi Screensp. 176
Analytic Methods Adjusting for Off-Target Effectsp. 179
Discussion and Conclusionsp. 186
Referencesp. 189
Indexp. 201
Table of Contents provided by Ingram. All Rights Reserved.

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The New copy of this book will include any supplemental materials advertised. Please check the title of the book to determine if it should include any access cards, study guides, lab manuals, CDs, etc.

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