C H A P T E R

1
Data Interpretation Overview
“We see the world, not as it is, but as we are e or, as we are conditioned to see it.”
Stephen R. Covey (The 7 Habits of Highly Effective People, p. 28)

PURPOSE OF THIS BOOK

This book is primarily intended for DNA analysts or those trying to understand what a DNA
analyst does in his or her review of forensic DNA data that was obtained by polymerase chain reaction
(PCR) amplification and short tandem repeat (STR) typing via capillary electrophoresis (CE). A DNA
analyst, according to the FBI Quality Assurance Standards (QAS) that govern U.S. laboratories, is an
individual who “conducts and/or directs the analysis of forensic samples, interprets data and reaches
conclusions” (QAS 2011, definitions). Many laboratories employ technicians to perform the analytical
techniques required to obtain a DNA profile from a biological sample e typically under the supervi-
sion of a trained and qualified analyst. However, as noted by the QAS, “technicians do not interpret
data, reach conclusions on typing results, or prepare final reports” (QAS 2011, definitions). Thus, there
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

is an expectation that DNA analyst training involves developing an understanding and mastery of
data interpretation as well as report writing and statistical analysis used in reaching conclusions on
typing results.
The general steps and workflow involved in forensic DNA typing are illustrated in Figure 1.1.
The companion volume to this book entitled Advanced Topics in Forensic DNA Typing: Methodology

Understanding
Results Obtained
Gathering the Data & Sharing Them
Collection/Storage/ Extraction/ Amplification/ Separation/
Data Stats Report
Characterization Quantitation Marker Sets Detection

Advanced Topics: Methodology Interpretation

Advanced Topics: Interpretation

FIGURE 1.1 Steps involved in the overall process of forensic DNA typing. This book focuses on understanding the data
through data interpretation and statistical interpretation.

Advanced Topics in Forensic DNA Typing: Interpretation

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 4 1. DATA INTERPRETATION OVERVIEW

(Butler 2012) covered many aspects of gathering the data used in DNA testing. Picking up where that
book left off, the purpose of this book, Advanced Topics in Forensic DNA Typing: Interpretation, is to
help readers understand data obtained from the STR typing process, with a focus on interpreting
and reporting results. Data interpretation is covered in Chapters 1 through 8 where we address
the question, “What are the data obtained from a set of samples?” Statistical interpretation is
reviewed in Chapters 9 through 15 to help discuss, “How significant are the data?” Chapter 16 fo-
cuses on drawing conclusions and report writing to assess, “What do the data mean when compar-
isons are made between evidentiary and reference sample results?”
Everyone may think that their way of DNA analysis is correct. However, misinterpretations of
some fundamental principles have given rise to a variety of approaches being undertaken in labs
today, some of which are not optimal, or even border on being incorrect for certain scenarios of
use. Unfortunately, often times the approaches taken for interpretation are subjective, and therefore
become the weakest part of the overall DNA typing process. I have written this book because I
believe that a better understanding of fundamental principles will aid consistency and quality of
work being performed in forensic DNA laboratories around the world.
In February 2009, the U.S. National Academy of Sciences released a report entitled “Strengthening
Forensic Science in the United States” (NAS 2009). The report emphasized that good (forensic) science
includes: (1) valid and reliable methodologies, and (2) practices that minimize the threat of bias in
data interpretation. My Methodology volume demonstrates that valid and reliable methodologies
can be achieved with forensic DNA typing. This Interpretation volume seeks to help minimize the
threat of bias in data interpretation.
Good science takes time and effort to do well. It is worth noting that some measurements and in-
terpretations are more reliable than others. Hence, uncertainty in measurements and interpretation
should be reflected in the reports generated in a forensic case investigation. As will be described
throughout this book, it is important that assumptions made during the interpretation process be
documented and conveyed as clearly as possible. This documentation will aid those individuals
reviewing the lab report to appropriately assess the results obtained and the conclusions drawn. It
is important for analysts to offer what they know from the data obtained in a case in a fashion
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

that is as clear and unbiased as possible.

That being said, I recognize that there are two areas of forensic DNA interpretations that are partic-
ularly challenging: (1) low-level DNA samples where sensitivity is an issue, and (2) complex mixtures
where specificity is an issue. In other words, how much DNA is needed to obtain a reliable result and
how well can the number of contributors to a sample be estimated to limit the uncertainty or ambi-
guity in the conclusions drawn. Chapters 7 and 13 will discuss some potential approaches to
handling difficult interpretations. Unfortunately, in many situations involving complex results where
uncertainty in the interpretation is large, the only scientifically responsible conclusion is “inconclu-
sive” to avoid the chance of inappropriately including or excluding a potential contributor from
an evidentiary result.

THE INTERPRETATION PROCESS

If the companion volume entitled Advanced Topics in Forensic DNA Typing: Methodology begins with
an evidentiary biological sample from a crime scene, then this book begins with a computer file. This
computer file contains data points corresponding to time and fluorescence intensity at various

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 THE INTERPRETATION PROCESS 5
wavelengths of light that represent the digital signature of a DNA profile. When these data points are
plotted with time on the x-axis and fluorescence intensity on the y-axis, an electropherogram is
created. This electropherogram, sometimes referred to as an EPG or e-gram, is then evaluated using
STR genotyping software to produce a final results table representing the biological sample’s DNA
profile.
An overview of the components and processes involved in data interpretation are illustrated in
Figure 1.2. A sample data file contains time and fluorescence information for a PCR-amplified sample
along with an internal size standard. The sample data file, which has a file extension of .fsa or .hid, is
loaded into genotyping software along with an allelic ladder data file containing the same internal
size standard to enable the sample and allelic ladder results to be correlated. Along with the allelic
ladder sample, STR kit manufacturers provide a computer file specific for each STR kit containing
bins (that define the allele repeat number for each STR locus) and panels (that define the STR loci pre-
sent in the kit). When combined with the allelic ladder data file, bins and panels provide genotyping
software with the capability to transform DNA size information into an STR allele repeat number for
each observed peak.

Laboratory Protocols to Aid Interpretation

Laboratory protocols, which are often referred to as standard operating procedures (SOPs), are
step-by-step instructions used to provide a consistent framework to gather and interpret information
from analyzed samples. As part of a quality assurance system, accredited forensic laboratories will
have written SOPs. Laboratory personnel are trained to understand and follow their laboratory-
specific SOPs.
As will be described in more detail in Chapter 2, laboratories define parameters as part of their
SOPs that act as thresholds within the genotyping software to filter information and aid analyst de-
cisions that are made in determining the final sample DNA profile. These SOPs should be created
based on validation data and then verified to work properly with control samples before being
put into routine use.
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

A primary purpose of SOPs is to provide consistent results across DNA analysts within a labora-
tory as well as across cases analyzed by the same DNA analyst. The hope is that by following well-
defined directions in a laboratory’s SOP, the same result can be obtained on a particular DNA sample
by any qualified analyst or data reviewer.

Overview of Data Interpretation Process FIGURE 1.2 Overview of DNA

interpretation process illustrating
Allelic Ladder Data File that sample data files, at least one
(with internal size standard) allelic ladder data file, and informa-
Bins & Panels tion from laboratory SOPs are
entered into genotyping software.
Sample Data File Genotyping Analyst or Sample Analysts (or expert system software)
(with internal size standard) Software Expert System DNA Profile review the information from the
Decisions software to produce the final sample
DNA profile.
Laboratory SOPs
with parameters/thresholds
established from validation studies

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 6 1. DATA INTERPRETATION OVERVIEW

Decisions during Data Interpretation

An analyst must make decisions about whether electrophoretic data from an evidentiary or a refer-
ence sample represent peaks or noise, whether peaks are alleles or artifacts, whether alleles can be
confidently paired to form genotypes, whether genotypes from individual loci can be combined to
create a contributor profile, whether the data are too weak or too complex to be reliably interpreted,
and if overall data quality is appropriate for obtaining reliable results. Table 1.1 correlates the discus-
sion of further details on these decisions with the various chapters in the first half of this book.
A DNA profile produced from the evidentiary sample, often referred to as the question (Q) sam-
ple, is then compared to a reference, or known (K) sample, which must also undergo data analysis
and the same interpretation decision process. Reference samples may come directly from a suspect
or indirectly from a DNA database search of previous offenders. Fortunately, expert system software
programs have been validated and implemented in many labs to help rapidly evaluate single-source
samples (see Butler 2012, Table 8.4).
Following comparison of the Q and K sample profile results, conclusions are drawn regarding a
potential match or not, and a report is written (see Chapter 16). If there is deemed to be a match
(or some kind of kinship association) between the Q and K samples, then statistical interpretation
is performed to estimate the weight-of-evidence. Chapters 9 through 15 describe approaches for
statistical interpretation and issues involved. A summary of the steps and decisions in STR data
interpretation are illustrated in Figure 1.3.

The DNA Profile Computer File

The computer file extension for a DNA result produced by an Applied Biosystems Genetic
Analyzer will be either .fsa or .hid depending on the instrument used to collect data from separated
components of PCR-amplified STR markers. The .fsa (fragment size analysis) files are produced with
ABI 310, 3100, 3130, 3700, and 3730 series CE instruments, while the .hid (human identity) files are
produced with ABI 3500 series CE systems.
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

TABLE 1.1 Information Flow in the Data Interpretation Process Correlated with Chapters in This Book

Chapter Input Information Decision to be made How decision is made

2 Data file Peak or Noise Analytical threshold

3 Peak Allele or Artifact Stutter threshold; precision sizing bin

4 Allele Heterozygote or Homozygote or Allele(s) Peak heights and peak height ratios;
missing stochastic threshold

5 Genotype/full profile Single-source or Mixture Numbers of peaks per locus

6 Mixture Deconvolution or not Major/minor mixture ratio
7 Low level DNA Interpret or not Complexity/uncertainty threshold
8 Poor quality data Replace CE components (buffer, polymer, Review size standard data quality with
array) or call service engineer understanding of CE principles

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 THE INTERPRETATION PROCESS 7

Steps in DNA Interpretation FIGURE 1.3 Steps in DNA interpreta-

Match probability
tion. The evidentiary (Q) sample and
Question sample reference (K) sample are processed from
peaks to profile and then compared. If Q
Weight
Peak Allele Genotype Profile and K match, then a match probability is
(vs. noise) (vs. artifact) (allele pairing) (genotype combining)
of
computed to assess the weight of this
Evidence
evidence. Finally, a report is written
Known sample describing the results obtained. A separate
technical review by another analyst in the
originating laboratory is performed prior
to the casework report being finalized and
Report Written released by the laboratory.
& Reviewed

As described in D.N.A. Box 1.1, the .fsa files are in a binary file format known as ABIF (Applied
Biosystems, Inc. Format) and are similar to Tag Image File Format (TIFF), which has been used for
graphics files (Applied Biosystems Genetic Analysis Data File Format 2009). Although we will
focus on the electronic information used to create a DNA profile, it is worth noting that other
diagnostic information, such as laser power and run current, is also stored in the computer file
during data collection; this information can be helpful in troubleshooting efforts described in
Chapter 8.
During the process of data analysis and genotyping, information from the .fsa or .hid data
file is converted from time (scan) points to DNA size relative to an internal size standard
and then to an STR allele call relative to STR typing kit-specific bins and panels and allelic
ladders.

Software for Analysis of DNA Profile Computer Files

Copyright © 2014. Elsevier Science & Technology. All rights reserved.

Sophisticated software has been developed to take sample electrophoretic data rapidly through
the STR genotyping process (Ziegle et al. 1992). Life Technologies/Applied Biosystems (Foster
City, CA), which manufactures the Genetic Analyzer CE instruments used in forensic DNA lab-
oratories, supplies software for processing the .fsa or .hid files generated by their CE instruments.
This software enables peaks to be defined and STR alleles designated using kit-specific allelic
ladders and bins and panels. GeneScan and Genotyper software programs were used originally
with early Mac and NT versions of data collection from the ABI 310 and 3100 series instruments.
In more recent years, GeneMapperID v3.2 and GeneMapperID-X v1.1 or 1.2 have replaced
GeneScan/Genotyper functions (in 2012, GeneMapperID-X v1.4 expanded data analysis capabil-
ities to 6-dyes).
GeneMarkerHID software (Holland & Parson 2011) from Soft Genetics (State College, PA) can also
process .fsa and .hid files directly as can Cybergenetics’ TrueAllele (Pittsburgh, PA; see also Kadash
2004) and Qualitype’s GenoProof (Dresden, Germany). In addition, the National Center for Biotech-
nology Information (NCBI) has produced an open-source STR genotyping software program (Goor
et al. 2011) called OSIRIS, which stands for Open Source Independent Review and Interpretation
System (OSIRIS 2014).

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Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
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 8 1. DATA INTERPRETATION OVERVIEW

D.N.A. BOX 1.1

WHAT INFORMATION IS STORED IN THE .FSA

AND .HID DNA PROFILE COMPUTER FILE?
ABI 310, 3100, 3100-Avant, 3130, 3130xl, instruments. It appears that the .fsa data file
and 3730 Genetic Analyzer instruments (Life structure has storage room for up to 99 different
Technologies/Applied Biosystems, Foster City, fluorescent dyes, so there is room to grow beyond
CA) produce .fsa files during capillary electro- the four, five, or even six dyes that STR kit
phoresis data collection. ABI 3500 and 3500xl in- chemistry currently provide! The .fsa file format
struments produce .hid files for human identity has two sets of tags that point to the same elec-
applications and .fsa files for other applications. tropherogram data, while the .hid format consists
During analysis with the Applied Biosystems of four sets of tags e three essentially in .fsa
software GeneMapperID and GeneMapperID-X format containing the same data, and a fourth set
programs, the .fsa or .hid sample files are im- of tags that are proprietary to Applied Biosystems
ported into an Oracle database along with allelic software for use in signal normalization. The
ladders and other controls for further analysis fluorescence signal collected by the charged-
(Applied Biosystems 2003, 2004). These Gene- coupled device (CCD) camera is stored in a
Mapper projects can be then be exported as .ser 2-byte format-enabling signal to be collected
files (Java serialized file) for storage. While .fsa between þ32,767 and 32,767. Spectral calibra-
files can be read by all versions of GeneMapperID tion, known as “multi-componenting,” is applied
and ID-X, the .hid files can only be read by to enable color correction with a mathematical
GeneMapperID-X v1.2 or above. matrix involving the fluorescent dyes used.
The .fsa files are written in a binary file format With the introduction of the ABI 3500 and
known as ABIF (Applied Biosystems, Inc. 3500xl Genetic Analyzers in 2010, the .fsa file
Format) and are similar to the TIFF files (Tag format was replaced by .hid files. Initially these
Image File Format) that are sometimes used for files could only be read by Applied Biosystems
graphics files. Applied Biosystems has published software GeneMapperID-X v1.2 or higher. Now
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

various versions of their .fsa file format schema, alternative genotyping software programs such
most recently in September 2009, to enable other as GeneMarkerHID (SoftGenetics, State College,
software developers to create products that can PA), GenoProof (QualiType, Dresden, Germany),
utilize Genetic Analyzer data. Unfortunately, the TrueAllele (Cybergenetics, Pittsburgh, PA), and
full details of their .hid file format have not yet OSIRIS (National Center for Biotechnology
been publicly released. Information, Bethesda, MD) can process .hid file
However, both .fsa and .hid files appear to formats. The new .hid file format captures addi-
consist of the same basic structure: (1) a header tional information in the sample file including the
that points to (2) a directory of tags which then 3500 radio frequency identification (RFID) infor-
points via a file offset to (3) electrophoretic data. mation used for instrument consumables, such as
The electrophoretic data are collected by scan the polymer and buffer lot numbers. In addition,
number (time) and fluorescence signal in speci- normalization capabilities exist with ABI 3500
fied dye-channels. In the developer toolkit on the .hid files. Normalization, which enables signal to
Applied Biosystems website, a detailed descrip- be equalized between different ABI 3500 or 3500xl
tion of the file tags are provided for (a) ABI 3100 instruments, is performed by multiplying the
and 3100-Avant, (b) ABI 3130 and 3130xl, (c) ABI data points by a factor calculated from the in-
3500 and 3500xl, and (d) ABI 3730 and 3730xl tensity of some of the internal size standard

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 THE INTERPRETATION PROCESS 9

peaks in the LIZ600v2 size standard. This feature how programs perform baseline subtraction and
is only available with ABI STR kits. With ABI other forms of signal processing.
3500 .hid files, GeneMapperID-X and other non-
Applied Biosystems software programs show Source: Applied Biosystems Genetic Analysis Data File
Format, Sept 2009 (available at http://www.appliedbiosystems.
similar-sized peaks for data displayed without com/absite/us/en/home/support/software-community/tools-for-
the 3500 normalization feature turned on. How- accessing-files.html); information shared by George Riley, Douglas
ever, minor differences in relative fluorescence Hoffman, and Robert Goor from OSIRIS development (see http://
www.ncbi.nlm.nih.gov/projects/SNP/osiris/)
unit (RFU) peak heights may exist depending on

Data Processing and Analysis

Following the steps of DNA extraction, DNA quantitation, PCR amplification, and CE separation
and detection of the STR alleles, a computer file becomes the electronic representation of the DNA
information obtained from a crime scene (Q e question) or reference (K e known) biological sample.
As noted previously, a trained DNA analyst using compatible software or a validated expert
system software program then reviews the results following laboratory-established parameters
(see Chapter 2).
The data collected and stored in the sample .fsa or .hid file is transformed from time and fluores-
cence intensity at specific wavelengths to size and peak height by dye color to STR allele and peak
height by locus information (Figure 1.4). This information is then compiled for each individual locus

Expert System
(for single-source samples)

Software (e.g., GeneMapperID)

Copyright © 2014. Elsevier Science & Technology. All rights reserved.

Analyst Manual Review

Color-separated
Raw Data Time Points DNA Sizes STR Alleles Genotype
Color separation

Interpretation
Allele Calling
Sizing

14,16

Scan numbers Scan numbers Nucleotide length Repeat number

FIGURE 1.4 An example of the transformation of sample information that occurs at a single STR locus during the course of
data interpretation. This same transformation occurs with all other STR loci that are PCR-amplified in a multiplex kit.
Additional information (indicated across the bottom) helps convert the initial data through steps of color separation, sizing,
and allele calling. An analyst must review the initial software results as part of the interpretation process. Expert system
software can take a sample from raw data to genotype for high-quality, single-source samples.

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 10 1. DATA INTERPRETATION OVERVIEW

to determine the overall STR profile representative of the original DNA template. Understanding
each step facilitates the troubleshooting efforts that reviewed in Chapter 8.
Through calibration to an internal size standard run with every sample, data points measured in
time (scan number) on the x-axis are converted to a relative size typically expressed to the one-
hundredth of a nucleotide. While we may sometimes refer to the DNA size of a PCR product in
base pairs (bp), in the denaturing environment of the capillary electrophoresis instrument we are
actually examining single-stranded DNA so nucleotides (nt) is a more correct unit of size. Thus,
example DNA size results might be 107.23 nt or 315.02 nt.
Different sizing algorithms are available in the GeneMapperID software, with the default method
being local Southern sizing (Elder & Southern 1983, Mayrand et al. 1992). Local Southern involves
determining the size of a DNA fragment by utilizing two peaks from the size standard larger and
two peaks smaller than the DNA fragment being sized.

Validation Studies
The purpose of validation studies is to observe, document, and understand variation in the data
generated under specific laboratory conditions. Validation helps define the scope or range of condi-
tions under which reliable results may be obtained. Throughout this book, suggestions are made for
validation studies that can be performed and the means for translating this information into param-
eters and thresholds used to assess and interpret data. By operating within validated ranges, uncer-
tainty in measurements made on evidentiary samples with the technique can be accurately conveyed
in laboratory reports.

CHARACTERISTICS OF IDEAL DATA

In physics and physical chemistry, important concepts are often introduced with ideal situations
(e.g. a perfect sphere) that are easier to model than the real world with all of its complexity and
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

uncertainty. In this manner, theoretical principles can be taught more effectively.

The same is true for DNA analysis. By starting with an example of ideal data, we can more effec-
tively see throughout this book why and to what extent data is non-ideal in the real-world, particu-
larly the poor quality DNA templates containing mixtures of multiple contributors often examined in
forensic casework. Starting with the ideal enables examination of the primary principles in data inter-
pretation and statistical analysis. Throughout this book we will see the challenges, difficulties, and
uncertainties that exist when working with and attempting to interpret non-ideal, real-world data.
Figure 1.5 illustrates what an ideal DNA profile might look like for four loci from a single dye
channel of an STR electropherogram. In this artificial example, each allele possesses a signal of
1,000 relative fluorescence units (RFUs). At this signal level, the tops of peaks are well above the back-
ground noise and analytical threshold (see Chapter 2), but not too high where we might have to
worry about off-scale data and bleedthrough into adjacent color channels. Note that all four loci
have nice, well-defined peaks, and that all peaks size within the shaded bins defined by the allelic
ladder alleles enabling definitive allele calls to be made. The two alleles present in Locus 1, Locus
2, and Locus 4 are identical in height. In other words, these heterozygotes all have a 100% peak height
ratio (PHR). No difference exists with the intralocus PHR depending on the heterozygous allele
spread e all are 100% regardless if the difference is one repeat (Locus 1), two repeats (Locus 2), or

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 CHARACTERISTICS OF IDEAL DATA 11
Locus 1 Locus 2 Locus 3 Locus 4
2500
8,8
2000

1500

13 14 29 31 10 13
1000

500

FIGURE 1.5 An artificial electropherogram with ideal STR typing data demonstrating perfect intra-locus (100% peak
height ratios) and perfect inter-locus balance (heterozygous alleles from different loci are the exact same height). With this
electropherogram, homozygous alleles in Locus 3 stack to produce a peak height exactly twice that of heterozygous alleles in
other loci. Shaded vertical bins reflect potential alleles defined by a previously run allelic ladder. Horizontal dashed lines
represent potential stochastic and analytical thresholds. Numbers above the peaks represent STR allele calls. The y-axis is in
relative fluorescence units (RFUs). Hypothetical data image created with EPG Maker (SPM v3) kindly provided by Steven
Myers.

three repeats (Locus 4). The homozygous alleles in Locus 3 (each possessing 8 repeats and a signal of
1,000 RFU) stack to produce a signal of 2,000 RFU.
In this example, there is 100% interlocus balance between all four loci. Peak heights of the alleles
present in the three heterozygous loci are all 1,000 RFU. Within each locus, the sum of alleles present
is 2,000 RFU. This perfect interlocus balance enables the double signal from stacked homozygous
alleles to be easily recognized. Furthermore, no observable stutter artifacts interfere with the ability
to decipher whether a minor component from a second contributor might be present in this sample
result. In fact, the absence of any other detectable alleles provides great confidence in assuming that
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

this sample originates from a single source.

A major benefit of ideal data without artifacts such as stutter products would be the ability to
detect and decipher mixtures more readily and at lower contributor amounts. With all observed
data on-scale (i.e. well below typical signal saturation levels), no signal bleedthrough peaks
(commonly referred to as pull-up artifacts) are expected in the dye channels that are not shown.
In an ideal world, we might have genetic markers that are so polymorphic that all DNA profiles
are fully heterozygous with distinguishable alleles to better enable mixture detection and interpreta-
tion when multiple contributors are present in a mixed sample. However, with such highly variable
markers, the mutation rate would likely be high for each locus, making it difficult to establish links
across generations in kinship testing. The reality is that some loci contain relatively few common
alleles, and thus more homozygotes are present in the general population (e.g. the 8,8 result at Locus
3 in Figure 1.5).
Completely repeatable peak heights from injection to injection on the same or other CE instru-
ments in the lab or other labs would enable greater confidence in correlating DNA amounts to the
observed fluorescence signal. If all CE instruments and PCR amplifications within a laboratory or be-
tween different laboratories produced the same 1,000 RFU peaks and clean DNA profile allele calls on
this same sample, then comparisons between evidentiary and reference samples would be trivial

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 12 1. DATA INTERPRETATION OVERVIEW

whether performed within a single laboratory or with database results generated from different
laboratories. Unfortunately, with real-world data, the situation is more complex and interpretation
is more challenging.

Real-World Challenges
Stochastic (random) variation in sampling each allele at a locus during PCR amplification leads to
variation in peak heights and peak height ratios for heterozygous samples (see Chapter 4). DNA
quality and quantity play a major factor in the degree of stochastic variation. Degraded DNA tem-
plates may make some STR allele targets unavailable. Alleles may fail to amplify if a sequence differ-
ence exists (due to mutation relative to the standard template sequence) in a PCR primer binding
region. These alleles, which are present in the original sample but fail to amplify, are termed “silent”
or “null” (see Chapter 4). PCR inhibitors present in forensic evidentiary samples may reduce effi-
ciency in amplifying some loci and/or alleles resulting in an imbalance in the signal obtained across
the DNA profile. The PCR process is also highly dependent on DNA sample quantity; this can lead to
great variability in amplifying individual alleles (if retesting the identical DNA extract) when ampli-
fying smaller amounts of DNA.
The existence of PCR amplification artifacts, such as stutter products or STR alleles that are not
fully adenylated and possess A peaks (see Chapter 3), complicates interpretation, particularly
when a mixture of DNA templates from more than one individual may be present. The possibility
of tri-allelic patterns (see Chapter 5) can further complicate the ability to recognize and discern
whether a DNA profile originates from more than one individual.
Technological artifacts can arise due to fluorescent dye impurities in the primer synthesis (dye
blobs), failure of the spectral calibration due to signal saturation (pull-up or bleedthrough between
dye channels), and other anomalies such as electrophoretic spikes. See Chapter 8 for more informa-
tion on these artifacts.
To complicate factors even more, variability exists between CE instruments due to the individual
instruments’ optics used to detect the fluorescence signal arising from the dye-labeled PCR products.
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

GUIDANCE FOR DNA INTERPRETATION

With a technique as powerful as forensic DNA testing to help establish guilt or innocence in the
context of criminal investigations, it is imperative that measures are in place to create confidence
in the results obtained. Around the world a number of organizations exist that work on a local,
national, or international level to aid quality assurance and to promote accurate forensic DNA
testing. These organizations are primarily made up of select working scientists who coordinate their
efforts to benefit the DNA typing community as a whole.
One of the primary groups that the forensic DNA community looks to for guidance regarding
topics such as validation and data interpretation is the Scientific Working Group on DNA Analysis
Methods, or SWGDAM (D.N.A. Box 1.2).
In 1994, the United States Congress established a DNA Advisory Board (DAB) that operated for
five years, from 1995 to 2000, to develop the initial Quality Assurance Standards (QAS) used in
the U.S. Since 2000, SWGDAM has inherited the role of the DAB, and during its semiannual meetings

I. DATA INTERPRETATION
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 GUIDANCE FOR DNA INTERPRETATION 13

D.N.A. BOX 1.2

WHAT ROLE DOES SWGDAM HAVE IN PRODUCING

GUIDANCE DOCUMENTS?
The Technical Working Group on DNA Analysis polymorphism (RFLP), polymerase chain reac-
Methods (TWGDAM) was established in tion (PCR), Combined DNA Index System
November 1988 under FBI Laboratory sponsor- (CODIS), mitochondrial DNA, short tandem
ship to aid forensic DNA scientists in North repeat (STR) interpretation, training, validation,
America. After its first decade of existence, Y-chromosome, expert systems, quality assur-
TWGDAM’s name was changed in 1998 to ance, missing persons/mass disasters, mixture
SWGDAM, which stands for the Scientific Work- interpretation, mass spectrometry, enhanced
ing Group on DNA Analysis Methods. method detection and interpretation, and rapid
SWGDAM is a group of approximately 50 DNA analysis. TWGDAM issued guidelines for
scientists representing federal, state, and local quality assurance in DNA analysis in 1989, 1991,
forensic DNA laboratories in the United States and 1995. Revised SWGDAM validation guide-
and Canada. A representative of the European lines were published in 2004, and 2012 and
Network of Forensic Science Institutes (ENFSI) interpretation guidelines for autosomal short
DNA Working Group often attends as well. tandem repeat (STR) typing were released in
Meetings are held twice a year, usually in January 2010. Several ad hoc working groups have pro-
and July. For several years, public SWGDAM duced recommendations on such topics as the
meetings were held in conjunction with the In- review of outsourced data and partial matches.
ternational Symposium on Human Identification, SWGDAM documents were originally made
sponsored each fall by the Promega Corporation. available through Forensic Science Communica-
Since 2006, the public SWGDAM meeting has tions, an on-line journal sponsored by the FBI
been held as part of the FBI-sponsored National Laboratory. More recently, a SWGDAM website
CODIS Conference (FBI 2012). enables the community to access SWGDAM
Over the years, a number of TWGDAM or work products and resources.
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

SWGDAM Committees have operated to bring

recommendations before the entire group. These Source: SWGDAM, http://www.swgdam.org; Butler, J.M.
(2013). Forensic DNA advisory groups: DAB, SWGDAM,
Committees have included (at different times) the ENFSI, and BSAG. Encyclopedia of Forensic Sciences, 2nd
following topics: restriction fragment length Edition. Elsevier Academic Press: New York.

discusses methods and produces guidance documents to aid the forensic DNA community
(including revisions to the QAS). A helpful guidance document is the 2010 SWGDAM Interpretation
Guidelines for Autosomal STR Typing by Forensic DNA Testing Laboratories (SWGDAM 2010). The
September 2011 Quality Assurance Standards for Forensic DNA Laboratories are available online
(QAS 2011).
Other groups around the world that play a similar role as SWGDAM include the DNA Commis-
sion of the International Society for Forensic Genetics, the European Network of Forensic Science
Institute’s (ENFSI 2014) DNA Working Group, and the Australia/New Zealand Biology Specialist
Advisory Group (BSAG).

I. DATA INTERPRETATION
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 14 1. DATA INTERPRETATION OVERVIEW

NRC I and NRC II Recommendations

The U.S. National Academy of Science’s National Research Council (NRC) issued two reports
during the 1990s commonly referred to as NRC I and NRC II that provide guidance on quality assur-
ance and recommendations for appropriate statistical methods in DNA analysis. Appendix 2 lists the
memberships and recommendations of NRC I and NRC II, as well as a number of references that
provide background and criticism of the reports.

The FBI Quality Assurance Standards

Several sections of the FBI Quality Assurance Standards for Forensic DNA Testing Laboratories
focus on the importance of interpretation. For example, U.S. forensic DNA laboratories are required
to have and follow written guidelines for interpretation of data (QAS 9.6), to verify that control
results meet the laboratory guidelines for all reported results (QAS 9.6.1), to use internal validation
experiments to help define laboratory interpretation guidelines including approaches for mixture
interpretation (QAS 8.3.2), and to perform validation prior to implementation and when changes
are made to collection or analysis software that may impact data interpretation (QAS 8.7).
The QAS also require U.S. forensic DNA laboratories to have and follow a documented procedure
for mixture interpretation that addresses major and minor contributors, inclusions and exclusions,
and policies for the reporting of results and statistics (QAS 9.6.4), and to follow NRC II recommen-
dations (see Appendix 2) with statistical analysis of autosomal STR data using a documented popu-
lation database appropriate for the calculation (QAS 9.6.2). Furthermore, laboratories are required to
“retain, in hard or electronic format, sufficient documentation for each technical analysis to support
the report conclusions such that another qualified individual could evaluate and interpret the data”
(QAS 11.1).

DNA Commission of the International Society for Forensic Genetics

The International Society for Forensic Genetics (ISFG) is an organization of over 1,100 scientists
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

from more than 60 countries promoting scientific knowledge in the field of genetic markers as applied
to forensic science. Since 1989, the ISFG has issued recommendations on a variety of important topics
in forensic DNA analysis through a DNA Commission. These recommendations have included
naming of STR variant alleles and STR repeat nomenclature, mitochondrial DNA and Y-STR issues,
DNA mixture interpretation, paternity testing biostatistics, disaster victim identification, use of ani-
mal DNA in forensic genetic investigations, and coping with potential allele drop-out and drop-in
through probabilistic genotyping. For more information on the ISFG DNA Commission, see their
website (ISFG 2014).

SWGDAM Interpretation Guidelines

While the QAS provide requirements (the “what”), in many cases they do not provide many
details that might enable further guidance (the “how”). SWGDAM guidelines offer guidance on
important topics related to validation and interpretation. While the QAS provide policies, SWGDAM
guidelines focus more on principles that impact lab protocols and how analysts put SOPs into
practice (D.N.A. Box 1.3).

I. DATA INTERPRETATION
Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
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 GUIDANCE FOR DNA INTERPRETATION 15

D.N.A. BOX 1.3

PRESCRIPTIONS AND PERSPECTIVES ON

HOW PRINCIPLES, PROTOCOLS, AND PRACTICE
IMPACT PERSONAL PERFORMANCE
WITH INTERPRETING DNA DATA
Our perspective impacts how well we see
everything around us. Since I wear eyeglasses and Example Who is Based on
cannot see well without them, I understand what it is impacted
like going from not having my glasses on (or having Policies QAS Community Decisions from
ones with the wrong prescription) to putting on organizations
glasses with the right prescription. About age 10, like SWGDAM
when I first obtained a pair of eyeglasses containing Principles SWGDAM Community (hopefully)
the correct prescription to focus light appropriately Guidelines Good science
into my near-sighted eyes, I suddenly become aware Protocols Lab SOPs Laboratory Validation
of what I was not seeing previously. Hazy objects experiments
come into focus. This was especially evident at night Practice Casework Individual Training &
when the fuzzy blurs of streetlights in the distance in a specific analysts experience
became discrete pinpoints of light with corrected case
eyesight. Eyeglasses help me see better, which in
turn has helped improve my understanding of the
world around me.
Throughout this book, we try to identify a
Similarly, an appropriate “prescription” to aid
D.N.A. pattern where the “D” of dogma or a
understanding of basic principles underlying
fundamental law of biology, chemistry, or phys-
forensic DNA concepts can help an analyst better
ics addresses answers to “why” questions, the
“see” how to interpret and report data. A primary
“N” of notable principles covers answers to
purpose of SWGDAM guidelines (D.N.A. Box 1.2)
“what” questions, and the “A” of application
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

is to provide principles and best practices to enable

within a specific laboratory environment deals
a framework of good science. Following the
with the “how” questions. For example, peak
precepts of these principles, laboratories then
height ratio measurements with heterozygous
develop written protocols e or standard operating
alleles (the “how”) permit assessment of potential
procedures (SOPs) e based on experience gained
allele pairing into genotypes (the “what”) because
from their internal validation studies. Finally,
offspring receive one allele from each parent in
analysts put these SOPs into practice on individual
normal diploid individuals (the “why”).
cases based on their training and experience.
The hope of this approach is that by under-
Within the United States, laboratories and analysts
standing the “why” better, the “what” and “how”
are audited according to their performance against
will come into an improved focus. Analysts
specific policies established by the FBI Quality
armed with a better “prescription” can then “see”
Assurance Standards (QAS). Thus, as noted in the
more clearly an appropriate scientific solution as
table below, a pattern of policy, principles, pro-
they interpret their DNA profiles, develop con-
tocols, and practice exists and impacts how forensic
clusions, and write reports.
DNA analysis and interpretation is performed.
Ideally, analysts with appropriate training within a Source: Rudin, N., & Inman, K. (2012). The discomfort of
laboratory and across the community will interpret thought: a discussion with John Butler. The CAC News, 1st
forensic DNA cases in a consistent and high-quality Quarter 2012, pp. 8e11. Available at http://www.cacnews.org/
news/1stq12.pdf.
manner.

Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
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 16 1. DATA INTERPRETATION OVERVIEW

In early 2010, SWGDAM approved and released “SWGDAM Interpretation Guidelines for
Autosomal STR Typing by Forensic DNA Testing Laboratories.” With the availability of these inter-
pretation guidelines, laboratories were “encouraged to review their standard operating procedures
and validation data and to update their procedures as needed” (SWGDAM 2010).
As will be emphasized throughout this book, a forensic DNA laboratory should develop STR
interpretation guidelines based upon its own validation studies. Information from STR kit and instru-
ment manufacturers and results reported in the literature can be helpful. Practical experience with
instrumentation and results from performing casework are also important factors in developing an
interpretation strategy.

A MATCH OR NOT A MATCH: THAT IS THE QUESTION.

Generally, the process of comparing two or more samples is limited to one of three possible
outcomes that are submitted in a case report (see Chapter 16):
1. Inclusion (Match) e Peaks between the compared STR profiles have the same genotypes, and no
unexplained differences exist between the samples. Statistical evaluation of the significance of the
match is usually cited in the match report. Alternatives for presentation of a match range from
statements of identity, to computations of the likelihood ratio for the hypothesis that the defendant
is the source, to descriptions of random-match probabilities in various populations.
2. Exclusion (Non-match) e The genotype comparison shows profile differences that can only be
explained by the two samples originating from different sources.
3. Inconclusive e The data does not support a conclusion whether the profiles match. This finding
might be reported if two analysts remain in disagreement after review and discussion of the data
and it is felt that insufficient information exists to support any conclusion. Poor quality evidentiary
samples or lack of a reference sample for comparison purposes can be other reasons for an
inconclusive result.
As noted in the 2010 SWGDAM STR Interpretation Guideline 4.1, “the laboratory must perform
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

statistical analysis in support of any inclusion that is determined to be relevant in the context of a
case, irrespective of the number of alleles detected and the quantitative value of the statistical anal-
ysis” (SWGDAM 2010). Providing an appropriate weight to the evidence provides an opportunity to
reflect the uncertainty in the result obtained e particularly with partial profiles where more ambigu-
ity may exist.
If a match is observed between a suspect (known sample “K”) and crime-scene evidence (question
sample “Q”), then three possibilities exist: (1) the suspect deposited the sample, (2) the suspect did
not provide the sample but has the profile by chance, and (3) the suspect did not provide the sample
and the matching result is a false positive due to a sample switch or some other kind of error.
The first explanation is the basis behind the use of DNA testing in the criminal justice system. The
second possibility depends on population genetics principles, covered in the second half of this book,
specifically Chapter 10, from which the probability of a random match is determined. The third
explanation of why a match might occur concerns the possibility of laboratory mistakes. Chapter 7
in Advanced Topics: Methodology (Butler 2012) discusses quality assurance measures that are in place
to prevent or reduce the possibility of error in performing DNA testing. Generally speaking, a great
deal of effort goes into ensuring reliable forensic DNA testing.

I. DATA INTERPRETATION
Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
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 A MATCH OR NOT A MATCH: THAT IS THE QUESTION. 17
TABLE 1.2 Characteristics of Autosomal STR Loci Present in 31 Commercially Available STR Kits

Autosomal STR Kits

Autosomal

Identifiler (Direct, Plus)

STR Loci

Hexaplex ESS
Nonaplex ESS

Decaplex SE
ESSplex SE
NGM SElect
GlobalFiler
SEfiler Plus
SGM Plus

SinoFiler

ESSplex
MiniFiler

VeriFiler
Profiler

IDplex
NGM
Promega STR kits Life Technologies (ABI) STR kits Qiagen STR kits
1q31 F13B AAAT 6 to 11 2

1q42 D1S1656 TAGA 10 to 19.3 3 2 3 2 3 3 2 3 3 2 2 2 3 2

2p25.3 TPOX AATG 5 to 13 4 4 6 6 3 3 3 5 1

2p14 D2S441 TCWA 8 to 17 5 1 5 1 4 1 1 1 1 1 1 1 1

2q35 D2S1338 TKCC 15 to 27 2 4 3 4 3 3 3 4 4 5 2 5 2 4 4 4 5 5 4 5

3p21.31 D3S1358 TCTR 11 to 20 1 1 2 2 2 2 2 2 1 1 1 1 1 1 1 2 2 1 3 3 3 3 3

4q31.3 FGA YTYY 16.2 to 43.2 5 5 2 4 2 4 4 2 4 3 3 3 3 3 2 3 4 4 4 4 3 4 2 4

5q23.2 D5S818 AGAT 7 to 15 1 1 5 5 1 1 2 2 2 4

5q33.1 CSF1PO AGAT 7 to 15 5 5 4 4 4 4 4 1 4 4 2

6p24 F13A01 AAAG 3.2 to 17 4

6q14 SE33 AAAG 6.3 to 36 3 4 3 5 5 4 3 1

6q15 D6S1043 AGAY 8 to 26 4 2 2

7q21.11 D7S820 GATA 6 to 14 3 3 4 4 3 1 3 3 2 3 4 2

8p22 LPL AAAT 7 to 15 1

8q24.13 D8S1179 TCTR 8 to 18 3 3 1 3 1 3 1 3 1 2 2 2 1 1 2 2 3 4 4 2 3 2

9p13 Penta C AAAAC 5 to 16 1

10q26.3 D10S1248 GGAA 8 to 19 4 1 4 1 5 1 1 1 1 1 1 2 1

11p15.5 TH01 TCAT 5 to 11 2 2 1 3 1 3 1 1 1 2 2 2 2 2 3 3 3 3 2 2 1 2 2 2

12p13.31 vWA TCTR 11 to 21 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 4 4 4 4

12p13.2 D12S391 AGAY 14 to 27 4 2 4 2 2 2 3 3 4 4 3 3 3 2 3

13q31.1 D13S317 TATC 8 to 15 2 2 5 6 2 2 3 1 3 3 3

15q25 FESFPS ATTT 5 to 14 3

15q26.2 Penta E AAAGA 5 to 25 5 5 6 1 7

16q24.1 D16S539 GATA 5 to 15 4 4 1 4 1 4 1 1 2 3 3 4 1 4 3 3 3 1 1 1 1

18q21.33 D18S51 AGAA 9 to 28 4 4 2 5 2 5 2 2 2 4 4 2 4 2 4 4 4 5 2 2 1 1 1

Copyright © 2014. Elsevier Science & Technology. All rights reserved.

19q12 D19S433 WAGG 9 to 18.2 1 3 3 3 3 3 3 1 1 1 1 2 2 2 2 3 3 2 3

21q21.1 D21S11 TCTR 24.2 to 39 3 3 3 4 3 4 3 3 3 3 1 2 3 2 3 3 4 5 5 5 5 5

21q22.3 Penta D AAAGA 2.2 to 17 6 6 5 5 5

22q12.3 D22S1045 ATT 8 to 19 5 1 5 1 5 1 1 1 1 2 2 2 2

Xp, Yp Amelogenin -- -- 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1

Yq11.21 DYS391 TCTA 7 to 13 7 6

Yq11.221 Yindel TTCTC/- "1" or "2" 1

autosomal STRs amplified 15 17 15 15 16 16 20 7 4 22 9 6 9 10 11 15 8 15 9 15 16 22 15 16 6 13 11 15

Allele range is from the NIST 1036 data set (D.N.A. Box 1.4). Numbers inside the colored boxes indicate relative size position for that locus within a dye
channel for the specific STR kit.

When utilizing data comparisons with DNA databases that may have data coming from many
sources, it is important to recognize that different PCR primer sets may detect or not detect an allele
(allele dropout) due to primer binding site mutations (see Chapter 4).
In forensic DNA Q-K comparisons (as currently practiced in many parts of the world), if any STR
locus fails to match when comparing the genotypes between two or more samples, then the compar-
ison of profiles between the questioned and reference sample is usually declared a non-match,

I. DATA INTERPRETATION
Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
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 18 1. DATA INTERPRETATION OVERVIEW

TABLE 1.3 Characteristics of Y-STR Loci and Y-Chromosome Sex-Typing Markers in Commercial Kitsa

ChrY Y-STR Present in

Position (Mb) Marker Repeat Motif Allele Rangeb Y-STR Kit

3.13 DYS393 AGAT 7 to 18 PPY, Yfiler, PPY23, Yfiler Plus

4.27 DYS456 AGAT 11 to 23 Yfiler, PPY23, Yfiler Plus
6.74 AMEL Y þAAAGTG Fusion, GlobalFiler,d etc.
6.86 DYS570 TTTC 10 to 25 PPY23, Yfiler Plus
7.05 DYS576 AAAG 11 to 23 PPY23, Yfiler Plus

7.87 DYS458 GAAA 10 to 24 Yfiler, PPY23, Yfiler Plus

c
8.22 DYS449 TTTC 22 to 40 Yfiler Plus
8.43 DYS481 CTT 17 to 32 PPY23, Yfiler Plus
c
8.65 DYS627 AAAG 11 to 27 Yfiler Plus
9.52 DYS19 TAGA 9 to 19 PPY, Yfiler, PPY23, Yfiler Plus
14.10 DYS391 TCTA 5 to 16 PPY, Yfiler, PPY23, Yfiler Plus,
Fusion, GlobalFiler
14.38 DYS635 TSTA 15 to 28 Yfiler, PPY23, Yfiler Plus
14.47 DYS437 TCTR 11 to 18 PPY, Yfiler, PPY23, Yfiler Plus

14.51 DYS439 AGAT 6 to 17 PPY, Yfiler, PPY23, Yfiler Plus

14.61 DYS389 I/II TCTR 9 to 17/ PPY, Yfiler, PPY23, Yfiler Plus
24 to 35
14.94 DYS438 TTTTC 6 to 16 PPY, Yfiler, PPY23, Yfiler Plus
15.51 M175 [TTCTC/] “1” or “2” GlobalFilerd Y-InDel (Y)
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

17.27 DYS390 TCTR 17 to 29 PPY, Yfiler, PPY23, Yfiler Plus

c
17.32 DYS518 AAAG 32 to 49 Yfiler Plus
17.43 DYS643 CTTTT 6 to 17 PPY23

18.39 DYS533 ATCT 7 to 17 PPY23, Yfiler Plus

18.74 GATA-H4 TAGA 8 to 18 Yfiler, PPY23, Yfiler Plus
20.80, 20.84 DYS385 a/b GAAA 7 to 28 PPY, Yfiler, PPY23, Yfiler Plus
c
21.05 DYS460 ATAG 7 to 14 Yfiler Plus
21.52 DYS549 GATA 7 to 17 PPY23
22.63 DYS392 TAT 4 to 20 PPY, Yfiler, PPY23, Yfiler Plus

24.36 DYS448 AGAGAT 14 to 24 Yfiler, PPY23, Yfiler Plus

c
25.93, 28.03 DYF387S1 a/b RAAG 30 to 44 Yfiler Plus
a
See Figure 1.8 for loci layouts in Y-STR kits. Markers in bold font are the 11 recommended by SWGDAM and are present in all kits. Shaded markers are present in
some newer autosomal STR kits. The Y-chromosome positions were determined using the February 2009 human reference sequence and BLAT (2014)
b
Allele range listed is for PowerPlex Y23 allelic ladders (Promega 2012)
c
Range of Yfiler Plus allelic ladder alleles
d
GlobalFiler (2014).

I. DATA INTERPRETATION
Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
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 D.N.A. BOX 1.4

NIST 1036 DATA SET

Since 2002, the Applied Genetics Group at the from the NIST 1036 data set. The full set of allele
National Institute of Standards and Technology frequencies is found in Appendix 1. Information
(NIST) has worked with a set of U.S. population and data on these DNA samples are available
DNA samples for purposes of understanding ge- from the NIST Population Data section of
netic marker variability and performance. These STRBase (NIST Population Data 2014). An
samples have been extensively studied with extensive description of the results from the NIST
numerous autosomal and Y-chromosome STR 1036 data set is found in Profiles in DNA (Butler
commercial kits and assays developed at NIST. et al. 2012), which is freely available on the
Although more than 1,450 samples have been Promega website.
studied in some cases, the full set of samples in-
cludes related individuals such as fathers and sons. Sources: Butler, J.M., et al. (2012). Variability of new STR loci
and kits in U.S. population groups. Profiles in DNA. Available
In 2012, a set of 1,036 unrelated individuals, at http://www.promega.com/resources/articles/profiles-in-dna/
termed the NIST 1036 data set (Butler et al. 2012), 2012/variability-of-new-str-loci-and-kits-in-us-population-groups/;
was established that includes 1,032 males and four Coble, M.D., et al. (2013). Haplotype data for 23 Y-chromosome
markers in four U.S. population groups. Forensic Science
females examined with 29 autosomal STR loci (Hill International: Genetics, 7, e66ee68.; Hill, C.R., et al. (2013).
et al. 2013) and 23 Y-STR loci (Coble et al. 2013). U.S. population data for 29 autosomal STR loci. Forensic
Throughout this book, allele frequencies used Science International: Genetics, 7, e82ee83.

in examples will come from information derived

Life Technologies/ABI STR Kits (Internal Size Standard LIZ GS500 – 5-dye; LIZ GS600 – 6-dye)

100 bp 200 bp 300 bp 400 bp

D8S1179 D21S11 D7S820 CSF1PO

16plex
Identifiler

D3S1358 TH01 D13S317 D16S539 D2S1338 (5-dye)

Copyright © 2014. Elsevier Science & Technology. All rights reserved.

D19S433 vWA TPOX D18S51

AM D5S818 FGA

D10S1248 vWA D16S539 D2S1338

17plex
NGM SElect

AM D8S1179 D21S11 D18S51 (5-dye)

D22S1045 D19S433 TH01 FGA

D2S441 D3S1358 D1S1656 D12S391 SE33

D3S1358 vWA D16S539 CSF1PO TPOX 24plex

(6-dye)
Y± AM D8S1179 D21S11 D18S51 DYS391
GlobalFiler

D2S441 D19S433 TH01 FGA

D22S1045 D5S818 D13S317 D7S820 SE33

D10S1248 D1S1656 D12S391 D2S1338

Butler, John M..FIGURE

<i>Advanced1.6TopicsLayout ofDNA
in Forensic lociTyping:
by dyeInterpretation</i>,
channel and relative size in& selected
Elsevier Science Life
Technology, Technologies
2014. (Applied
ProQuest Ebook Central, Biosystems, ABI) STR kits.
http://ebookcentral.proquest.com/lib/uam-ebooks/detail.action?docID=1770238.
Created from uam-ebooks on 2019-08-16 06:11:08.
 20 1. DATA INTERPRETATION OVERVIEW

Promega STR Kits (Internal Size Standard CXR ILS600 – 4-dye; CXR ILS 550 – 5-dye)
200 bp 300 bp 400 bp
100 bp
16plex
(4-dye)
16

D3S1358 TH01 D21S11 D18S51 Penta E

PowerPlex

D5S818 D13S317 D7S820 D16S539 CSF1PO Penta D

AM vWA D8S1179 TPOX FGA

ESI 17 Pro

AM D3S1358 D19S433 D2S1338 D22S1045 17plex

D16S539 D18S51 D1S1656 D10S1248 D2S441 (5-dye)

TH01 vWA D21S11 D12S391

PowerPlex

D8S1179 FGA SE33

24plex
Fusion

AM D3S1358 D1S1656 D2S441 D10S1248 D13S317 Penta E (5-dye)

D16S539 D18S51 D2S1338 CSF1PO Penta D

PowerPlex

TH01 vWA D21S11 D7S820 D5S818 TPOX DYS391

D8S1179 D12S391 D19S433 FGA D22S1045

FIGURE 1.7 Layout of loci by dye channel and relative size in selected Promega PowerPlex STR kits (Promega 2012).
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

regardless of how many other loci match. This binary (match/no-match) approach becomes problem-
atic with low-level evidentiary DNA samples where stocastic allele dropout is likely. Probabilistic
approaches are under development to help with these difficult situations (Gill et al. 2012).
As noted in Chapter 14, paternity testing is an exception to this “single mismatch leads to exclu-
sion” rule because of the possibility of mutational events. When analyzing and reporting the results
of parentage cases, an allowance for one or even two possible mutations is often made. In other
words, if 13 loci are used and the questioned parentage is included for all but one locus, the data
from the non-inclusive allele is usually attributed to a possible mutation.
In the end, interpretation of results in forensic casework is a matter of professional judgment and
expertise. Interpretation of results within the context of a case is the responsibility of the case analyst
with supervisors or technical leaders conducting a follow-up verification of the analyst’s interpreta-
tion of the data as part of the technical and administrative review process (see Chapter 16). When
coming to a final conclusion regarding a match or exclusion between two or more DNA profiles,
laboratory interpretation guidelines should be adhered to by both the case analyst and the supervi-
sor. However, as experience using various analytical procedures grows, interpretation guidelines
will evolve and improve. These guidelines should always be based on the proper use of controls
and validated methods.

I. DATA INTERPRETATION
Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
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 STR LOCI, KITS, AND POPULATION DATA 21
STR LOCI, KITS, AND POPULATION DATA
At the time this book is being written, three commercial manufacturers provide more than two
dozen different STR kits. These kits examine subsets of markers from a total of 29 autosomal STR
loci, a sex-typing marker named amelogenin, and a Y-STR marker DYS391. Table 1.2 lists the char-
acteristics of these STRs, including their chromosomal location, primary repeat motif, and allele
range. For Y-chromosome analysis, up to 29 Y-STR loci can be examined with commercial kits avail-
able as of early 2014 (Table 1.3).
U.S. population data from 1,036 individuals has been collected on these 29 autosomal STR loci and
23 Y-STR loci (D.N.A. Box 1.4). Data generated from these DNA samples will be used throughout
the book.
The STR locus dye color and size range for several commonly used STR kits are laid out in
Figure 1.6 for Life Technologies kits (Life Technologies 2012), Figure 1.7 for Promega kits (Promega
2012), and Figure 1.8 for Y-STR kits from Life Technologies and Promega. As these STR kits will be
referred to in many of the following chapters, we include them here as a helpful reference.

Y-STR Kits
(Internal Size Standard CXR 600 – 4-dye; LIZ GS500 or CC5 ILS 500 – 5-dye)

100 bp 200 bp 300 bp 400 bp

DYS456 DYS389I DYS390 DYS389II

DYS458 DYS19 DYS385 a/b

17plex
Yfiler

DYS393 DYS391 DYS439 DYS635 DYS392 (5-dye)

Y-GATA-H4 DYS437 DYS438 DYS448

Copyright © 2014. Elsevier Science & Technology. All rights reserved.

DYS576 DYS389I DYS448 DYS389II DYS19

PowerPlex Y23

DYS391 DYS481 DYS549 DYS533 DYS438 DYS437

23plex
DYS570 DYS635 DYS390 DYS439 DYS392 (5-dye)
DYS643

DYS393 DYS458 DYS385 a/b DYS456 Y-GATA-H4

DYS576 DYS389I DYS635 DYS389II DYS627

DYS460 DYS458 DYS19 Y-GATA-H4 DYS448 DYS391

Yfiler Plus

DYS456 DYS390 DYS438 DYS392 DYS518 27plex

(6-dye)
DYS570 DYS437 DYS385 a/b DYS449

DYS393 DYS439 DYS481 DYF387S1a/b DYS533

FIGURE 1.8 Layout of loci by dye channel and relative size in Y-chromosome STR kits from Life Technologies and
Promega.

I. DATA INTERPRETATION
Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
http://ebookcentral.proquest.com/lib/uam-ebooks/detail.action?docID=1770238.
Created from uam-ebooks on 2019-08-16 06:11:08.
 22 1. DATA INTERPRETATION OVERVIEW

SUMMARY
DNA interpretation with STR markers involves utilizing genotyping software and laboratory
SOPs to evaluate CE data. Peaks in multi-colored CE electropherograms generated as CE mobility
time points are translated into DNA size information and then to allele repeat number for each
STR locus. In both evidentiary and reference samples, decisions are made for each peak above an
analytical threshold regarding whether or not the peak is an allele or an artifact, whether or not alleles
at an STR locus can be paired to form a genotype, whether it is possible for some alleles to be missing
from the data, and whether or not the sample originated from a single-source or a mixture of multiple
contributors. Validation studies are essential for setting parameters used in a laboratory’s SOPs to
make these decisions. Guidance on validation studies and data interpretation has been provided
from organizations such as SWGDAM and the ENFSI.

Reading List and Internet Resources

Purpose of This Book
Butler, J. M. (2012). Advanced Topics in Forensic DNA Typing: Methodology. New York: Elsevier Academic Press.
National Academies of Science. (2009). Strengthening Forensic Science in the United States: A Path Forward. Washington, D.C: The
National Academies Press.
QAS. (2011). Quality Assurance Standards for Forensic DNA Testing Laboratories effective 9-1-2011. See http://www.fbi.gov/
about-us/lab/codis/qas-standards-for-forensic-dna-testing-laboratories-effective-9-1-2011. Accessed March 18, 2014.

The Interpretation Process

STR Data Analysis and Interpretation (on-line training): http://www.dna.gov/training/strdata/

Computer Files and Genotyping Software

Applied Biosystems. (2003). GeneMapper ID Software Version 3.1 Human Identification Analysis User Guide. Foster City,
California.
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

Applied Biosystems. (2004). GeneMapperID Software Version 3.2: Human Identification Analysis Tutorial. Foster City,
California.
Applied Biosystems. (2009). Genetic Analysis Data File Format, Sept 2009. Available at http://www.appliedbiosystems.com/
absite/us/en/home/support/software-community/tools-for-accessing-files.html. Accessed March 18, 2014.
BatchExtract. ftp://ftp.ncbi.nih.gov/pub/forensics/BATCHEXTRACT. Accessed March 18, 2014.
GeneMapperID-X (from Applied Biosystems): http://www.lifetechnologies.com/us/en/home/technical-resources/
software-downloads/genemapper-id-x-software.html. Accessed March 18, 2014.
GeneMarker HID (from Soft Genetics): http://www.softgenetics.com/GeneMarkerHID.html. Accessed March 18, 2014.
GenoProof (from Qualitype AG): http://www.genoproof.de/en/. Accessed March 18, 2014.
Goor, R. M., et al. (2011). A mathematical approach to the analysis of multiplex DNA profiles. Bulletin of Mathematical Biology,
73(8), 1909e1931.
Holland, M. M., & Parson, W. (2011). GeneMarkerÒ HID: a reliable software tool for the analysis of forensic STR data. Journal
of Forensic Sciences, 56(1), 29e35.
Kadash, K., et al. (2004). Validation study of the TrueAllele automated data review system. Journal of Forensic Sciences, 49,
660e667.
OSIRIS (Open Source Independent Review and Interpretation System). http://www.ncbi.nlm.nih.gov/projects/SNP/osiris/.
Accessed March 18, 2014.
TrueAllele (from Cybergenetics). http://www.cybgen.com. Accessed March 18, 2014.

I. DATA INTERPRETATION
Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
http://ebookcentral.proquest.com/lib/uam-ebooks/detail.action?docID=1770238.
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 READING LIST AND INTERNET RESOURCES 23
DNA Sizing
Elder, J. K., & Southern, E. M. (1983). Measurement of DNA length by gel electrophoresis II: comparison of methods for
relating mobility to fragment length. Analytical Biochemistry, 128, 227e231.
Mayrand, P. E., et al. (1992). The use of fluorescence detection and internal lane standards to size PCR products automatically.
Applied and Theoretical Electrophoresis, 3(1), 1e11.
Rosenblum, B. B., et al. (1997). Improved single-strand DNA sizing accuracy in capillary electrophoresis. Nucleic Acids Research,
25, 3925e3929.
Ziegle, J. S., et al. (1992). Application of automated DNA sizing technology for genotyping microsatellite loci. Genomics, 14(4),
1026e1031.

Guidance for DNA Interpretation

Butler, J. M. (2013). Forensic DNA advisory groups: DAB, SWGDAM, ENFSI, and BSAG. Encyclopedia of Forensic Sciences
(2nd ed.). New York: Elsevier Academic Press.
DNA Commission of the ISFG (2014). http://www.isfg.org/Publications/DNAþCommission. Accessed March 18, 2014.
European Network of Forensic Science Institutes (ENFSI) DNA Working Group (2014): http://www.enfsi.eu/page.php?
uid¼98. Accessed March 18, 2014.
Gill, P., et al. (2012). The interpretation of DNA evidence (including low-template DNA). Available at http://www.homeoffice.gov.
uk/publications/agencies-public-bodies/fsr/interpretation-of-dna-evidence. Accessed March 18, 2014.
Gill, P., et al. (2012). DNA commission of the International Society of Forensic Genetics: recommendations on the evaluation of
STR typing results that may include drop-out and/or drop-in using probabilistic methods. Forensic Science International:
Genetics, 6, 679e688.
Hobson, D., et al. (1999). STR analysis by capillary electrophoresis: development of interpretation guidelines for the
Profiler Plus and COfiler systems for use in forensic science. Proceedings of the 10th International Symposium on Human
Identification. Available at http://www.promega.com/products/pm/genetic-identity/ishi-conference-proceedings/10th-
ishi-oral-presentations/. Accessed March 18, 2014.
International Society of Forensic Genetics (ISFG): http://www.isfg.org/. Accessed March 18, 2014.
Puch-Solis, R., et al. (2012). Assessing the probative value of DNA evidence: guidance for judges, lawyers, forensic scientists
and expert witnesses. Practitioner Guide No. 2. Prepared under the auspices of the Royal Statistical Society’s Working
Group on Statistics and the Law (Chairman: Colin Aitken). Available at http://www.rss.org.uk/uploadedfiles/userfiles/
files/Practitioner-Guide-2-WEB.pdf. Accessed March 18, 2014.
Quality Assurance Standards (QAS) for Forensic DNA Laboratories. September 2011. Available online at http://www.fbi.
gov/about-us/lab/biometric-analysis/codis. Accessed March 18, 2014.
Rudin, N., & Inman, K. (2012). The discomfort of thought: a discussion with John Butler. The CAC News, 1st Quarter, 2012.
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

pp. 8e11. Available at http://www.cacnews.org/news/1stq12.pdf. Accessed March 18, 2014.

SWGDAM website: http://www.swgdam.org. Accessed March 18, 2014.
SWGDAM. (2010). SWGDAM Interpretation Guidelines for Autosomal STR Typing by Forensic DNA Testing Laboratories. Available
at http://www.swgdam.org/Interpretation_Guidelines_January_2010.pdf. Accessed March 18, 2014.

A Match or Not a Match: That is the Question.

Gill, P., et al. (2012). DNA commission of the International Society of Forensic Genetics: recommendations on the evaluation of
STR typing results that may include drop-out and/or drop-in using probabilistic methods. Forensic Science International:
Genetics, 6, 679e688.

STR Kits, Loci, and Population Data

BLAT Search Genome: http://genome.ucsc.edu/cgi-bin/hgBlat. Accessed March 18, 2014.
Budowle, B., et al. (1998). CODIS and PCR-based short tandem repeat loci: law enforcement tools. Proceedings of the Second European
Symposium on Human Identification. pp. 73e88. Madison, Wisconsin: Promega Corporation. Available at http://www.
promega.com/products/pm/genetic-identity/ishi-conference-proceedings/2nd-eshi-oral-presentations/. Accessed March
18, 2014.

I. DATA INTERPRETATION
Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
http://ebookcentral.proquest.com/lib/uam-ebooks/detail.action?docID=1770238.
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 24 1. DATA INTERPRETATION OVERVIEW

Butler, J. M. (2006). Genetics and genomics of core short tandem repeat loci used in human identity testing. Journal of Forensic
Sciences, 51, 253e265.
Butler, J. M., & Hill, C. R. (2012). Biology and genetics of new autosomal STR loci useful for forensic DNA analysis. Forensic
Science Review, 24(1), 15e26.
FBI. (2012). Planned process and timeline for implementation of additional CODIS core loci. Available at http://www.fbi.gov/about
e us/lab/codis/planned e process e and e timeline e for e implementation e of e additional e codis e core e loci.
Gill, P., et al. (2006a). The evolution of DNA databases e Recommendations for new European STR loci. Forensic Science
International, 156, 242e244.
Gill, P., et al. (2006b). New multiplexes for Europe e amendments and clarification of strategic development. Forensic Science
International, 163, 155e157.
Hares, D. R. (2012a). Expanding the CODIS core loci in the United States. Forensic Science International: Genetics, 6(1), e52ee54.
Hares, D. R. (2012b). Addendum to expanding the CODIS core loci in the United States. Forensic Science International: Genetics,
6(5), e135.
Life Technologies (2012). http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Human-
Identification/globalfiler_str_kit.html. Accessed March 18, 2014.
GlobalFiler information (2014). http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/
Human-Identification/globalfiler_str_kit/resources.html. Accessed March 18, 2014.
Mulero, J. J., & Hennessy, L. K. (2012). Next-generation STR genotyping kits for forensic applications. Forensic Science Review,
24(1), 1e13.
Promega. (2012). PowerPlex Fusion System. http://www.promega.com/products/pm/genetic-identity/powerplex-fusion.
Accessed March 18, 2014.
Ruitberg, C. M., et al. (2001). STRBase: a short tandem repeat DNA database for the human identity testing community.
Nucleic Acids Res., 29, 320e322.
STRBase: http://www.cstl.nist.gov/strbase. Accessed March 18, 2014.

Population Data on NIST U.S. Samples

Butler, J. M., et al. (2012). Variability of new STR loci and kits in U.S. population groups. Profiles in DNA. Available at http://
www.promega.comz/resources/articles/profiles-in-dna/2012/variability-of-new-str-loci-and-kits-in-us-population-
groups. Accessed March 18, 2014.
Coble, M. D., et al. (2013). Haplotype data for 23 Y-chromosome markers in four U.S. population groups. Forensic Science
International: Genetics, 7, e66ee68.
Diegoli, T. M., et al. (2011). Allele frequency distribution of twelve X-chromosomal short tandem repeat markers in four U.S.
population groups. Forensic Science International: Genetics Supplement Series, 3, e481ee483.
Copyright © 2014. Elsevier Science & Technology. All rights reserved.

Hill, C. R., et al. (2013). U.S. population data for 29 autosomal STR loci. Forensic Science International: Genetics, 7, e82ee83.
NIST Population Data (2014). http://www.cstl.nist.gov/strbase/NISTpop.htm. Accessed March 18, 2014.

I. DATA INTERPRETATION
Butler, John M.. <i>Advanced Topics in Forensic DNA Typing: Interpretation</i>, Elsevier Science & Technology, 2014. ProQuest Ebook Central,
http://ebookcentral.proquest.com/lib/uam-ebooks/detail.action?docID=1770238.
Created from uam-ebooks on 2019-08-16 06:11:08.