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ADVANCED TOPICS IN
FORENSIC DNA TYPING
 This work was funded in part by the National Institute of Justice (NIJ) through an interagency
agreement with the NIST Law Enforcement Standards Office. Points of view in this document
are those of the author and do not necessarily represent the official position or policies of the U.S.
Department of Justice or the National Institute of Standards and Technology. Certain commercial
equipment, instruments, and materials are identified in order to specify experimental procedures
as completely as possible. In no case does such identification imply a recommendation or endorse-
ment by the National Institute of Standards and Technology, nor does it imply that any of the
materials, instruments, or equipment identified are necessarily the best available for the purpose.
 ADVANCED
TOPICS IN
FORENSIC DNA
TYPING:
INTERPRETATION
JOHN M. BUTLER
National Institute of Standards and Technology
Gaithersburg, Maryland, USA

AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW YORK

OXFORD • PARIS • SAN DIEGO • SAN FRANCISCO
SINGAPORE • SYDNEY • TOKYO
Academic Press is an imprint of Elsevier
Academic Press is an imprint of Elsevier
The Boulevard, Langford Lane, Kidlington, Oxford, OX5 1GB
525 B Street, Suite 1800, San Diego, CA 92101-4495, USA

Contribution of the National Institute of Standards and Technology 2015 Published by Elsevier Inc.

No part of this publication may be reproduced or transmitted in any form or by any means, electronic
or mechanical, including photocopying, recording, or any information storage and retrieval system,
without permission in writing from the publisher. Details on how to seek permission, further information
about the Publisher’s permissions policies and our arrangement with organizations such as the Copyright
Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/
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This book and the individual contributions contained in it are protected under copyright by the Publisher
(other than as may be noted herein).

Notices
Knowledge and best practice in this field are constantly changing. As new research and experience
broaden our understanding, changes in research methods, professional practices, or medical treatment
may become necessary.

Practitioners and researchers must always rely on their own experience and knowledge in evaluating
and using any information, methods, compounds, or experiments described herein. In using such
information or methods they should be mindful of their own safety and the safety of others, including
parties for whom they have a professional responsibility.

To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume
any liability for any injury and/or damage to persons or property as a matter of products liability,
negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas
contained in the material herein.

British Library Cataloguing in Publication Data

A catalogue record for this book is available from the British Library

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A catalog record for this book is available from the Library of Congress

ISBN: 978-0-12-405213-0

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visit our website at store.elsevier.com

Printed and bound in China

15 16 17 18 10 9 8 7 6 5 4 3 2 1
 Dedication

To my parents Doug and Marsha Butler

who instilled in me an important worldview of education and service
by which I interpret everything around me
and to Bruce Budowle
who helped me to become a better writer when I was a graduate student
and since then has challenged me to become a better scientist and a better man.
This page intentionally left blank
 Contents

Foreword ix
Introduction xi
Acknowledgments xvii
About the Author xix

I
DATA INTERPRETATION
1. Data Interpretation Overview 3
2. Data, Models, Thresholds 25
3. STR Alleles and Amplification Artifacts 47
4. STR Genotypes 87
5. STR Profiles 109
6. DNA Mixtures 129
7. Low-Level DNA and Complex Mixtures 159
8. Troubleshooting Data Collection 183

II
STATISTICAL INTERPRETATION
9. Statistical Interpretation Overview 213
10. STR Population Data Analysis 239
11. DNA Profile Frequency Estimates and Match Probabilities 281
12. DNA Mixture Statistics 309
13. Coping with Potential Missing Alleles 333
14. Relationship Testing: Kinship Statistics 349
15. Lineage Marker Statistics 403
16. Laboratory Reports: Communicating Results and Conclusions 445

vii
viii CONTENTS

Appendix 1: STR Allele Frequencies from U.S. Population Data 497

Appendix 2: NRC I & NRC II Recommendations 519
Appendix 3: DAB Recommendations on Statistics 529
Appendix 4: Worked Mixture Example 537

Index 569
 Foreword

Another book from the prolific writings of John Butler that keeps pace with the rapidly changing
world of DNA profiling in forensic science e it reminds me of the “Red Queen’s Race” in Lewis
Carroll’s Alice Through the Looking-Glass: “.it takes all the running you can do, to keep in the
same place. If you want to get somewhere else, you must run at least twice as fast as that!” Over
the past few years there have been major changes in DNA profiling technology and interpretation.
The introduction of more sensitive instrumentation, coupled with the introduction of modern multi-
plexed loci from the manufacturers that employ up to 24 loci with new biochemistry and detection
platforms, also realizes the dream of approaching the ultimate in sensitivity e it is almost a matter of
routine to detect DNA profiles from a handful of cells. Such advances are not without significant
challenges, particularly in the area of interpretation of the evidence. Fortunately there have been
significant advances in this area too, although the complete adoption by the community is yet to
be realized.
The book is divided into 16 chapters and 4 appendices that describe the “state of the art” and
beyond. Starting with an overview of data interpretation, subsequent chapters lead onto a discussion
of the characterization of DNA profiles in terms of heterozygote balance, stutter, artifacts, and muta-
tion and stochastic effects. There is an introduction to the phenomenon of allele drop-out, a character-
istic of low-template DNA that results in “false homozygotes.” To interpret DNA profiles, a system of
thresholds (e.g. stochastic threshold, stutter threshold, limit of detection) has evolved. However,
there are limitations and risks to consider. There is an extensive discussion on the deliberation of
the scientific societies that is linked to an outline of the steps to interpret mixtures, before moving
onto challenging “complex DNA profiles,” i.e. those profiles that are mixtures of two or more contrib-
utors, where allele drop-out, secondary transfer, and contamination are additional complications.
There has been a fundamental shift by the forensic community towards the analysis of these kinds
of profiles. In one laboratory we are informed that the proportion of submissions of samples with
<100 pg DNA has increased from 19% in 2004 to 45% in 2008. Chapters 9e13 are devoted to the inter-
pretation of evidence complemented by Appendix 1, which has a complete list of STR loci used in the
U.S. and their respective allele frequencies. There is a comprehensive review of statistical theory and
methods e this leads to a complete description of various programmed solutions that have recently
evolved to interpret “complex DNA profiles.” Appendix 4 has a worked example, concisely written
by Mike Coble, that further explains the rationale, theory, and benefits of the practical use of prob-
abilistic methods. The reader is able to use the book as a handy one-stop guide to everything that
is currently available (and where to find out more information).
Chapter 14 turns to relationship testing, providing an outline of the theory, a summary of recom-
mendations from the scientific societies, a list of available software, along with an outline of the use of
high-density SNP arrays to identify distant relationships. The penultimate Chapter 15 deals with
lineage markers, including mitochondrial DNA, and Y-chromosomal and X-chromosomal DNA.

ix Copyright Ó 2015 Elsevier Inc. All rights reserved.

x FOREWORD

These markers are useful in missing persons, disaster victim identification, and other complex
inquires.
Finally, Chapter 16 explores the most contentious area in forensic science, namely, the interpreta-
tion of the evidence. It isn’t just the fact of the DNA profile to consider. With the introduction of
methods that are ever more sensitive, the focus turns to how and when the DNA profile was trans-
ferred. Is it possible that a contamination event, or secondary transfer is possible? How can cognitive
(psychological) bias be avoided in reporting? A useful way to think about evidence is described by
the “hierarchy of propositions” e can we ascribe a “source,” such as blood, or an “activity,” such as
stabbing, to the DNA profiling evidence? To prepare this chapter, John Butler has consulted widely
with practitioners, gathering their views, cross-referenced to historical and recent deliberations of the
scientific societies and advisory boards (Appendices 2 and 3), distilling the information into a treatise
on how to write a report for the court.
This book complements John Butler’s previous works with the most comprehensive and
up-to-date text of its kind. As such, it will readily be adopted by the forensic community as the defin-
itive guide to the galaxy of forensic DNA-typing technologies.

Peter Gill, Ph.D.

April 2014
 Introduction

“Writing is thinking. To write well is to think clearly. That’s why it’s so hard.”
David McCullough (NEA 2003)

The third edition of Forensic DNA Typing has been divided up into three volumes: a basic
volume for students and beginners in the field and two advanced volumes for professionals/
practitioners who may be interested in more detail. The basic volume was released in September
2009 (with a publication date of 2010) and is entitled Fundamentals of Forensic DNA Typing. The first
advanced volume, Advanced Topics in Forensic DNA Typing: Methodology, was released in August
2011 (with a 2012 publication date). The present book, Advanced Topics in Forensic DNA Typing:
Interpretation, is intended as volume 3 of the third edition, with a focus on data interpretation
and statistical analysis.
Several reasons exist for dividing the material. First and foremost, people use books more
frequently if they are less bulky. I have heard from more than one colleague at conferences that
they prefer to carry the smaller first edition with them to court or other teaching situations. Second,
by having multiple books, each volume can be focused on its intended audience rather than trying to
be all things to all readers. Third, the books will enable both undergraduate and graduate studies,
with each building upon the previous volumes.
There is only minor overlap in subject matter among the various volumes. The basic Fundamentals
volume contains the simpler “starter” information, while most of the “updates” to the field are found
in the Advanced Topics volumes. It is my intention that the three volumes together provide a compre-
hensive view of the current state of forensic DNA analysis. With a field advancing as rapidly as
forensic DNA typing is, this is a challenge.
The present book has been divided into two primary sections: data interpretation (Chapters 1e8)
and statistical interpretation and reporting (Chapters 9e16). The first part covers data analysis
and factors impacting a DNA profile, while the second part examines evidence evaluation and
interpretation e essentially what information exists in a DNA profile and what does this information
mean in the context of variability expected from the DNA results obtained. In this edition, I again
utilize Data, Notes, and Applications (D.N.A.) Boxes to cover specific topics of general interest, to
review example calculations, or to cover a topic that serves to highlight information needed by
a DNA analyst.

NEW MATERIAL IN THIS VOLUME

Advanced Topics in Forensic DNA Typing: Interpretation is substantially enhanced with additional
information beyond what was available in the second edition of Forensic DNA Typing, which was

xi
xii INTRODUCTION

completed in June 2004. Much has happened to advance our understanding of DNA evidence inter-
pretation in the past decade.
I am grateful to have had three years between writing the Methodology and this Interpretation
volume. During this additional time, I have learned a great deal as I have responded to numerous
questions from forensic scientists around the world via email or in person. I have also had the priv-
ilege of preparing and presenting hundreds of slides on DNA mixture interpretation. Materials from
these training workshops are available at the NIST website (NIST 2014a). In addition, recent publi-
cations have provided new research and perspectives on DNA interpretation. For example, the Inter-
national Society for Forensic Genetics DNA Commission published recommendations on DNA
mixtures and probabilistic approaches in the December 2012 issue of Forensic Science International:
Genetics.
As with previous books, a fairly comprehensive list of references is included at the end of each
chapter that serves as a foundation for citations in the chapter as well as a launching point where
interested readers can go for additional information. More than 2,000 references are provided,
enabling readers to expand their study beyond the information contained between the covers of
this book. References to journal articles include titles to enhance value.
More than 80% of this book is completely new. Figures, tables, and D.N.A. Boxes have been
created (>200 in total) to help illustrate the principles being taught. Since I do not now write or
review laboratory reports, I sought and received valuable input from more than a dozen laboratory
analysts, laboratory directors, police investigators, lawyers (prosecution and defense), and private
consultants who regularly review laboratory reports. Their collective wisdom and insights are
captured in Chapter 16. Numerous others have contributed to information contained in this volume,
and their input is gratefully appreciated and acknowledged.
Throughout this book I have prepared teaching examples with the STR locus D18S51, which is one
of the original U.S. core markers and also is used in Europe, China, Australia, and elsewhere around
the world. I have endeavored to mind my Ps and Qs in using a consistent allele nomenclature in
statistical equations. In some areas, material in this book may not be as advanced as readers might
like. There is, however, enough information to help provide a bridge to more detailed work already
available or soon to be available from authors like John Buckleton and Peter Gill.
At points throughout the text, I quote from the 2010 SWGDAM Interpretation Guidelines for
Autosomal STR Typing by Forensic DNA Testing Laboratories. Although I chaired the group that
prepared these guidelines, the opinions expressed in this book are mine alone and in no way should
be thought of as the official opinion of SWGDAM or the SWGDAM Autosomal STR Interpretation
Committee.

OVERVIEW OF BOOK CHAPTERS

Chapters 1 to 8 cover data interpretation. Chapter 1 provides an overview and perspective on
principles, protocols, and practice in an effort to understand the “why,” “what,” and “how” of
forensic DNA typing. Autosomal and Y-chromosome STR loci and kits are reviewed. Chapter 2
describes data generation by the Applied Biosystems Genetic Analyzers as well as introducing
the role of statistical models in setting thresholds such as the analytical threshold. Chapter 3
covers issues surrounding measurement of STR alleles and distinguishing alleles from artifacts
such as stutter products. Chapter 4 reviews peak height ratios (heterozygote balance) and null
 INTRODUCTION xiii
alleles that can impact STR genotypes. Stochastic thresholds and allele drop-out are introduced.
Chapter 5 focuses on evaluation of multi-locus STR profiles, tri-allelic patterns, and issues with
amelogenin as a sex-typing marker. Chapter 6 considers DNA mixtures and steps for interpreting
them, including determining the number of contributors. Chapter 7 explores complex DNA
mixture issues, including allele sharing and allele drop-out due to low-level DNA contributors.
Chapter 8 seeks to inform readers regarding principles and processes involved with capillary elec-
trophoresis so that high-quality data may be obtained and common problems avoided. It
discusses how troubleshooting improves as close attention is paid to details in the laboratory
data produced.
Chapters 9 to 16 involve statistical interpretation and reporting. Chapter 9 introduces the role of
statistics in forensic DNA analysis with a review of the individuals who have influenced the field.
The laws of probability are introduced along with likelihood ratios and Bayesian versus frequentist
approaches to statistics. Chapter 10 describes principles of population genetics and how population
data are used to estimate STR profile frequencies. Chapter 11 covers approaches and assumptions
made with generating STR profile frequency estimates. Chapter 12 involves DNA mixture statistics
and contrasts combined probability of inclusion methods with likelihood ratio calculations.
Chapter 13 deals with situations where allele drop-out from stochastic effects with low-level DNA
present challenges in comparing evidentiary profiles to reference profiles. Chapter 14 reviews kinship
analysis used in relationship testing. Paternity testing, mutations, and disaster victim identification
are among the topics discussed. Chapter 15 addresses Y-chromosome, X-chromosome, and mito-
chondrial DNA lineage markers and how their different genetic transmission influences statistical
interpretation of results. Finally, Chapter 16 covers laboratory reports and the importance of effec-
tively communicating results and conclusions. Input from more than a dozen laboratory report
providers and users enhanced this material.

Appendices
There are four appendices at the back of the book that provide helpful supplemental material:
• Appendix 1 provides U.S. population data in the form of STR allele frequencies based on studies
performed at NIST. This information is utilized in worked examples throughout the book.
• Appendix 2 lists the recommendations made by both National Research Council reports (NRC I
and NRC II) in their 1992 and 1996 publications entitled “DNA Technology in Forensic Science”
and “The Evaluation of Forensic DNA Evidence.”
• Appendix 3 contains the FBI’s DNA Advisory Board recommendations on statistics that were
released in February 2000 to provide a historical perspective.
• Appendix 4 is a DNA mixture example prepared by Dr. Mike Coble, a valued colleague within the
Applied Genetics Group at the National Institute of Standards and Technology.
A brief “cross-walk” of major topics covered across the various editions of Forensic DNA Typing is
shown in Table I.1 with chapters (Ch.) and appendices (App.) indicated. In a few cases, information
was limited to a single D.N.A. Box.
In my Interpretation book, I have included information from the latest articles as well as insights I
have gained over the past two decades of working in the field. Writing these books on forensic
DNA typing has been richly rewarding as I must carefully think through each issue and decide
how to best address it. As David McCullough points out in the quote at the beginning of this
xiv INTRODUCTION

TABLE I.1 “Cross-Walk” of Major Topics

3rd edition, 3rd edition, 3rd edition,

volume 1 volume 2 volume 3

1st edition 2nd edition Fundamentals Advanced Topics: Advanced Topics:

Topic (2001) (2005) (2010) Methodology (2012) Interpretation (2015)

Amelogenin Ch. 5 Ch. 5 Ch. 8 Ch. 5 Ch. 5

Capillary Ch. 9 & 11 Ch. 12 & 14 Ch. 9 Ch. 6 Ch. 8
electrophoresis
Data interpretation Ch. 6 & 13 Ch. 6 & 15 Ch. 10 e Ch.1e8

Disaster victim Ch. 17 Ch. 24 Ch. 17 Ch. 9 Ch. 14

identification
DNA basics Ch. 2 Ch. 2 Ch. 2 e e
DNA databases Ch. 16 Ch. 18 Ch. 12 Ch. 8 e
DNA extraction Ch. 3 Ch. 3 Ch. 5 Ch. 2 e

DNA quantitation Ch. 3 Ch. 3 Ch. 6 Ch. 3 e

Expert witness e e e Ch. 18, App. 4 e
testimony
Familial searching e e Ch. 12 (p. 282) App. 2 D.N.A. Box 14.9

FBI Quality App. 3 App. 4 e e e

Assurance Standards (1998/99) (1998/99)

FMBIO gel imaging Ch. 12 Ch. 14 D.N.A. Box 9.2 e e

system

Glossary e e App. 1 e e
History of DNA Ch. 1 Ch. 1 Ch. 1 & 3 e e

Kinship analysis e Ch. 23 Ch. 17 e Ch. 14

Low copy number e Ch. 7 Ch. 14 Ch. 11 Ch. 7
DNA testing
Match probability e Ch. 21 Ch. 11 e Ch. 11
calculations

Mixtures Ch. 7 Ch. 7 Ch. 14 e Ch. 6 & 7, App. 4

Mixture statistics e Ch. 22 D.N.A. Box 14.2 e Ch. 12 & 13
Mitochondrial DNA Ch. 8 Ch. 10 Ch. 16 Ch. 14 Ch. 15

New technologies Ch. 15 Ch. 17 Ch. 18 Ch. 17 e

Non-human DNA Ch. 8 Ch. 11 Ch. 15 Ch. 16 e
Null alleles Ch. 6 Ch. 6 D.N.A. Box 10.3 Ch. 5 Ch. 4

PCR Ch. 4 Ch. 4 Ch. 7 Ch. 4 e

 INTRODUCTION xv
TABLE I.1 “Cross-Walk” of Major Topics (cont'd)
3rd edition, 3rd edition, 3rd edition,
volume 1 volume 2 volume 3

1st edition 2nd edition Fundamentals Advanced Topics: Advanced Topics:

Topic (2001) (2005) (2010) Methodology (2012) Interpretation (2015)

Population data e Ch. 20 Ch. 11 e Ch. 10

Report writing e e e e Ch. 16

Sample collection Ch. 3 Ch. 3 Ch. 4 Ch. 1 e

SNP testing Ch. 8 Ch. 8 Ch. 15 Ch. 12 e

Statistics & e Ch. 19 App. 3 e Ch. 9
probability
STR alleles App. 1 App. 1 e App. 1 Ch. 3

STR kits Ch. 5 Ch. 5 Ch. 8 Ch. 5 Ch. 1

STR markers Ch. 5 Ch. 5 Ch. 8 Ch. 5 Ch. 1
Stutter products Ch. 6 Ch. 6 Ch. 10 e Ch. 3
Thresholds e e Ch. 10 e Ch. 2

Tri-allelic patterns Ch. 6 Ch. 6 D.N.A. Box 10.2 e Ch. 5

Validation Ch. 14 Ch. 16 Ch. 13 Ch. 7 Ch. 5

Variant alleles Ch. 6 Ch. 6 D.N.A. Box 10.1 App. 1 Ch. 3
X-STRs e e e Ch. 15 Ch. 15

Y-STRs Ch. 8 Ch. 9 Ch. 16 Ch. 13 Ch. 15

Introduction, writing is hard work. This hard work has been beneficial to my personal learning but
comes at the price of significant time away from my family and other responsibilities. I am grateful
for the support of others, especially my wife, who have permitted me the time needed to complete
this book.
My father, Doug Butler, has written about a dozen textbooks and spent his career teaching and
helping to shape his profession. He is an amazing teacher because of his dedication to learning
and excelling at the highest level. Recently when I told him some of the things I was learning while
working on this book and other presentations that I was giving to the forensic DNA community, he
shared an important lesson: “You never really learn anything until you have to teach it to someone
else.” While I hope the information in this book helps the field, I know that I have been the main bene-
ficiary of this effort in terms of what I have learned during the process of trying to teach the concepts
to others.
The pressure to carefully craft each phrase so that my words are less likely to be misunderstood
has increased with the widespread use of my books, particularly in courts of law. I do not take lightly
the opportunity to share my thoughts and perspective in this book. While I have benefited from
discussions and input from many people, I alone am responsible for the content. My goal in
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