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A Litigator’s Guide to DNA This page intentionally left blank A Litigator’s Guide to DNA From the Laboratory to the Courtroom Ron C. Michaelis, PhD, FACMG Robert G. Flanders, Jr., Esq. Paula H. Wulff, JD Amsterdam • Boston • Heidelberg • London • New York • Oxford Paris • San Diego • San Francisco • Singapore • Sydney • Tokyo Academic Press is an imprint of Elsevier Acquisitions Editor: Jennifer Soucy Associate Developmental Editor: Kelly Weaver Project Manager: Christie Jozwiak Publishing Services Manager: Sarah Hajduk Marketing Manager: Kristin Banach Design Direction: Joanne Blank Cover Design: Brian Moore Cover image  Chris Dascher/iStockphoto. Academic Press is an imprint of Elsevier 30 Corporate Drive, Suite 400, Burlington, MA 01803, USA 525 B Street, Suite 1900, San Diego, California 92101-4495, USA 84 Theobald’s Road, London WC1X 8RR, UK 1 This book is printed on acid-free paper.  Copyright  2008 Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone: (þ44) 1865 843830, fax: (þ44) 1865 853333, E-mail: permissions@elsevier.com. You may also complete your request online via the Elsevier homepage (http://elsevier.com), by selecting ‘‘Support & Contact’’ then ‘‘Copyright and Permission’’ and then ‘‘Obtaining Permissions.’’ Library of Congress Cataloging-in-Publication Data Application Submitted British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. ISBN: 978- 0-12-374036-6 For information on all Academic Press publications visit our website at books.elsevier.com Printed in the United States of America 08 09 10 9 8 7 6 5 4 3 2 1 Working together to grow libraries in developing countries www.elsevier.com | www.bookaid.org | www.sabre.org Please direct all correspondence regarding this book to Dr. Michaelis at litigatorsguidetodna@gmail.com. Dedication I would like to dedicate this book to my parents, Robert and Dorothy Michaelis. I am keenly aware of, and deeply grateful for, the many ways in which they provided the foundation for this work (and all my other works as well). I would also like to dedicate the book to my children, Matt and Kathryn. They serve as a never-ending source of motivation and inspiration for me in everything I do. Finally, this book is dedicated to Ellen Boyd. Without her kindness and generosity there would have been no beginning; this book would have ended up as one of those things I should have done. –Ron C. Michaelis I dedicate this book to my wife, Ann I. Flanders, whose love and friendship have been and remain indispensable to all that I am and do. –Robert G. Flanders, Jr. I would like to acknowledge the dedication of the many state and local prosecutors who routinely carry full case loads and mentor others through the complexities of preparing a criminal case. Specifically I would like to thank Martha Bashford, Robert Biancavilla, Norm Gahn, Rockne Harmon, Ted Hunt, Robert Laurino, Hon. Mitch Morrissey, Melissa Mourges, Steve Redding, Hon. Matt Redle and Brian Zubel for their ceaseless energy and dedication to helping others understand the challenges presented in DNA cases. I would also like to thank my husband, John, and son, Matt, for their patience. –Paula H. Wulff v This page intentionally left blank Table of Contents ACKNOWLEDGMENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi INTRODUCTION. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii CHAPTER 1 The Structure of DNA and the Variability of the Human DNA Sequence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 You Are Out of Your Field, But Not Out of Your Depth . . . . . . . . . . . . 1 Markers, Alleles, Genotypes and Profiles. . . . . . . . . . . . . . . . . . . . . . . . 2 The Two Sources of DNA in Human Cells . . . . . . . . . . . . . . . . . . . . . . . 5 The Structure of DNA and RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Variability Is the Rule, Not the Exception . . . . . . . . . . . . . . . . . . . . . . 11 Polymorphisms Commonly Used for Forensic Testing . . . . . . . . . . . . 15 Using the DNA Profile to Identify an Unknown Perpetrator . . . . . . . 24 References and Additional Readings . . . . . . . . . . . . . . . . . . . . . . . . . . 25 CHAPTER 2 The Molecular Biological Basis of Forensic DNA Tests. . . . .27 Extraction and Quantification of DNA . . . . . . . . . . . . . . . . . . . . . . . . . 27 Polymerase Chain Reaction (PCR)-Based Tests . . . . . . . . . . . . . . . . . 32 Variable Number of Tandem Repeats (VNTR) Testing . . . . . . . . . . . . 50 Direct Sequencing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 References and Additional Readings . . . . . . . . . . . . . . . . . . . . . . . . . . 53 CHAPTER 3 Quality Control, Quality Assurance and Sources of Uncertainty in the Data. . . . . . . . . . . . . . . . . . . . . . . . . . .55 Laboratory Accreditation, Personnel Certification and Proficiency Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Validation Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 The Inevitable Nemeses: Suboptimal Samples and Human Error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 Allele Dropout Due to Degradation, Preferential Amplification and Stochastic Effects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 Artifacts Inherent in STR Analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 Hybridization Specificity in Dot-Blot Tests . . . . . . . . . . . . . . . . . . . . . 87 References and Additional Readings . . . . . . . . . . . . . . . . . . . . . . . . . . 88 vii viii Table of Contents CHAPTER 4 Population Genetics, Probability Calculations and the Proper Interpretation of the Evidence . . . . . . . . . . .91 The Common Logical Fallacies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 Databanks and Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 Allele Frequencies, Genotype Probabilities and the Product Rule for Independent Events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106 The Principles of Population Genetics that Impact Forensic DNA Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113 Applying the Product Rule—Compensating for Population Substructure and Possible Allele Dropout . . . . . . . . . . . . . . . . . . . . . 119 The Likelihood Ratio (LR) Allows the Analyst to Compare the Strength of Competing Hypotheses . . . . . . . . . . . . . . . . . . . . . . . 135 The Application of Bayes’ Theorem to Paternity Disputes . . . . . . . 142 Recommended Procedure for Analyzing Mixed Samples . . . . . . . . . 147 References and Additional Readings . . . . . . . . . . . . . . . . . . . . . . . . . 167 CHAPTER 5 Mitochondrial DNA (mtDNA) Analyses . . . . . . . . . . . . . . .171 The mtDNA Molecule—Abundant and Durable but Less Variable than nDNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171 Laboratory Analysis of mtDNA Haplotypes . . . . . . . . . . . . . . . . . . . . 174 Matrilineal Inheritance and a Lack of Recombination . . . . . . . . . . . 178 A High Mutation Rate Leads to Mitochondrial Heteroplasmy . . . . . 180 Statistical Analysis of mtDNA Haplotype Data . . . . . . . . . . . . . . . . . 187 References and Additional Readings . . . . . . . . . . . . . . . . . . . . . . . . . 193 CHAPTER 6 Y Chromosome Analyses . . . . . . . . . . . . . . . . . . . . . . . . .197 Y Chromosome Evolution and its Consequences for Forensic Analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197 Laboratory Analysis of Y Chromosome Haplotypes . . . . . . . . . . . . . . 204 Statistical Analysis of Y Chromosome Haplotypes . . . . . . . . . . . . . . 207 References and Additional Readings . . . . . . . . . . . . . . . . . . . . . . . . . 212 CHAPTER 7 DNA in Court . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .215 The Evolution of Standards for Admissibility of Experts and Evidence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 The Ongoing Controversy Regarding Laboratory Error Rates . . . . . . 225 Counsels’ Obligations Regarding Discovery . . . . . . . . . . . . . . . . . . . . 228 Expert Witnesses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232 The Durability of DNA Presents Problems for Statutes of Limitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237 Rape Shield Laws May Limit the Use of DNA Evidence . . . . . . . . . 238 Table of Contents Judges’ and Jurors’ Perceptions of DNA Evidence . . . . . . . . . . . . . . 239 References and Additional Readings . . . . . . . . . . . . . . . . . . . . . . . . . 253 CHAPTER 8 Arguing for the Prosecution . . . . . . . . . . . . . . . . . . . . . . .255 Obtaining DNA Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255 DNA in the Courtroom: The Essentials of the Prosecution’s Presentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279 References and Additional Readings . . . . . . . . . . . . . . . . . . . . . . . . . 312 CHAPTER 9 Arguing for the Defense . . . . . . . . . . . . . . . . . . . . . . . . .313 The Defense’s Choice of Strategy . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313 Elements of a Competent Defense . . . . . . . . . . . . . . . . . . . . . . . . . . . 326 When the Defendant Has Been Identified by a Databank Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 362 References and Additional Readings . . . . . . . . . . . . . . . . . . . . . . . . . 367 CHAPTER 10 Postconviction DNA Testing . . . . . . . . . . . . . . . . . . . . . .369 DNA has the Power to Exonerate the Innocent . . . . . . . . . . . . . . . . . 369 Avenues for Relief . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370 There Are Many Procedural Obstacles . . . . . . . . . . . . . . . . . . . . . . . . 373 New Evidence May Justify a New Theory of the Case . . . . . . . . . . . 379 Accessing the Necessary Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . 380 Know the Specific Provisions of the Controlling Statute . . . . . . . . . 383 References and Additional Readings . . . . . . . . . . . . . . . . . . . . . . . . . 386 APPENDIX I: Using the Chi-Square Test to Determine if a Population Conforms to HWE Expectations . . . . . . . . . . . . . . . . . . . .389 APPENDIX II: How the RMP, Prior Odds of Guilt, and the PFP Influence the Posterior Odds of Guilt (POG) . . . . . . . . . . .393 APPENDIX III: Paternity Index (PI) Calculations for Different Combinations of Maternal, Child and Alleged Father Genotypes . . . . . . . . . . . . . . . . . . . . . . . .397 APPENDIX IV: A Sample Consent Form to Collect an Oral Swab, Which Allows the Profile Obtained to Be Entered Into a Databank for Use in Additional Investigations . . . . . . . .399 APPENDIX V: Doing Your Own Research: Useful References, Websites and Strategies for Finding Current Information . .401 GLOSSARY OF KEY TERMS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .411 INDEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .423 ix