Forensic DNA Profiling

A Practical Guide to Assigning Likelihood Ratios

Jo-Anne Bright, Michael Coble

• Publisher: CRC Press
• Year: 2019
• Print ISBN: 9781032082318
• eBook ISBN: 9780429671425
• Edition: 1
• Topic: Ciencias biológicas
• Subtopic: Ciencias forenses

DNA testing and its forensic analysis are recognized as the "gold standard" in forensic identification science methods. However, there is a great need for a hands-on step-by-step guide to teach the forensic DNA community how to interpret DNA mixtures, how to assign a likelihood ratio, and how to use the subsequent likelihood ratio when reporting interpretation conclusions.

Forensic DNA Profiling: A Practical Guide to Assigning Likelihood Ratios will provide a roadmap for labs all over the world and the next generation of analysts who need this foundational understanding. The techniques used in forensic DNA analysis are based upon the accepted principles of molecular biology. The interpretation of a good-quality DNA profile generated from a crime scene stain from a single-source donor provides an unambiguous result when using the most modern forensic DNA methods. Unfortunately, many crime scene profiles are not single source. They are described as mixed since they contain DNA from two or more individuals.

Interpretation of DNA mixtures represents one of the greatest challenges to the forensic DNA analyst. As such, the book introduces terms used to describe DNA profiles and profile interpretation. Chapters explain DNA extraction methods, the polymerase chain reaction (PCR), capillary electrophoresis (CE), likelihood ratios (LRs) and their interpretation, and population genetic models—including Mendelian inheritance and Hardy-Weinberg equilibrium. It is important that analysts understand how LRs are generated in a probabilistic framework, ideally with an appreciation of both semicontinuous and fully continuous probabilistic approaches.

KEY FEATURES:
• The first book to focus entirely on DNA mixtures and the complexities involved with interpreting the results
• Takes a hands-on approach offering theory with worked examples and exercises to be easily understood and implementable by laboratory personnel
• New methods, heretofore unpublished previously, provide a means to innovate deconvoluting a mixed DNA profile, assign an LR, and appropriately report the weight of evidence
• Includes a chapter on assigning LRs for close relatives (i.e., "It's not me, it was my brother"), and discusses strategies for the validation of probabilistic genotyping software

Forensic DNA Profiling fills the void for labs unfamiliar with LRs, and moving to probabilistic solutions, and for labs already familiar with LRs, but wishing to understand how they are calculated in more detail. The book will be a welcome read for lab professionals and technicians, students, and legal professionals seeking to understand and apply the techniques covered.

1

An Introduction and Review of DNA Profile Interpretation

DNA testing is recognized as the “gold standard” in forensic identification science methods. The techniques used in forensic DNA analysis are based upon the accepted principles of molecular biology, including DNA extraction methods, the polymerase chain reaction (PCR), capillary electrophoresis (CE), and population genetic models including Mendelian inheritance and the Hardy–Weinberg equilibrium. The interpretation of a good-quality DNA profile generated from a crime scene stain from a single donor (termed “single source”) provides an unambiguous result when using the most modern forensic DNA methods.

Many crime scene profiles however are not single source. They are described as mixed as they contain DNA from two or more individuals. Interpretation of DNA mixtures represents one of the greatest challenges to the forensic DNA analyst. In this chapter, we introduce some important terms used to describe DNA profiles and profile interpretation. We cover the very basics of DNA mixture interpretation by introducing the threshold-based interpretation approach called the “binary” method. We include two worked examples, describe different methods of assigning the strength of a match, and finally discuss some of the limitations of these methods.

1.1 A Very Basic Review of a DNA Profile

The DNA markers tested for forensic analysis are known as short tandem repeats, or STRs, and are found throughout the human genome. We refer to these specific “locations” as a locus (a single position of interest) or loci (two or more markers of interest). The names of the loci can tell us a little bit about themselves. For example, the forensic STR marker D8S1179 refers to a location on the DNA chromosome 8, that is a single-copy marker (i.e., this is the only place in the genome where this marker is found), and was the 1179th marker that was identified on the chromosome. The STR marker TPOX refers to a location within the intron (noncoding region) of the thyroid peroxidase gene.

STR markers contain a repeating unit (called the motif) that is composed of four nucleotide bases, such as AGTC or ATTC. These “tetranucleotide” markers (tetra meaning four) make up the majority of STRs used in forensic testing, although there is now a common locus that has three nucleotide repeats (D22S1045, a trinucleotide repeat [tri meaning three]). Having three, four, or five repeating nucleotides within the repeating structure is why these markers are called “short” tandem repeats.

The term “tandem” within STR refers to the fact that the short sequences are repeated sequentially at a locus. For example, at the locus D8S1179, the sequence TCTA may be repeated in tandem 9 times on one chromosome and 12 times on the other chromosome (chromosomes are in pairs, one inherited from each parent).

This highlights an important characteristic of STRs; the number of repeats at a locus can vary among individuals and is useful for the discrimination of individuals within the population. We refer to these alternate forms (variants) of STRs as alleles. The genotype is the combination of alleles found on both chromosomes. A locus with two different alleles, such as 9,12 at D8S1179 as described in the previous paragraph, is called a “heterozygous” genotype. If an individual has inherited the same number of repeating alleles from each parent at a locus (e.g., 13,13 – where both chromosomes have 13 repeats) the locus is described as being “homozygous.”

Multiple STRs are combined in the one forensic testing kit, called a multiplex. Most modern-day multiplexes combine upwards of 15 loci with larger kits (called megaplexes) containing over 20 loci. The ability to combine many discriminatory loci within the one test makes modern-day DNA testing a very quick and powerful tool for human identification.

1.1.1 Molecular Biology Review

A physical examination of a bloodstain from the crime scene does not simply send out a message to alert the analyst the genotype is a 9,12 at D8S1179. It will be necessary to convert this information within the stain into something we can visualize (a digital representation of the evidence). The analysis of DNA for forensic use is a multistep process. We must first extract the DNA from the stain, and then quantify the amount of DNA present in the sample. Using PCR, we then target and amplify the STR markers in the sample.

The process of PCR requires the generation of two specific primer sequences that are complementary to a sequence of DNA upstream and downstream of the STR marker of interest (these are often called “forward” and “reverse” primers). Attached to one of the primers is a fluorescent dye. For example, the FAM fluorescent dye is one of the most commonly used dyes in molecular biology and will emit a color signal in the blue portion of the visible spectrum. With each cycle of PCR, the targeted amplicons (the products of PCR) are copied through a process in which the double-stranded DNA is opened, the primers bind to their targeted sequences, and an enzyme (Taq polymerase) then extends the newly formed sister strand. The resulting product is two copies of DNA from the one initial amplicon. This is repeated over a...

Table of contents

• Cover
• Half Title
• Title Page
• Copyright Page
• Contents
• Foreword
• Preface
• Acknowledgments
• Authors
• 1. An Introduction and Review of DNA Profile Interpretation
• 2. An Introduction to Statistics and Proposition Setting
• 3. Assigning the LR: Single-Source Examples and Population Genetic Models
• 4. Application of the Binary LR for Mixtures
• 5. LRs Considering Relatives as Alternate Contributors
• 6. Probabilistic Genotyping: Semicontinuous Models
• 7. Probabilistic Genotyping: Continuous Models
• 8. Considerations on Validation of Probabilistic Genotyping Software
• Appendix 1: Allele Frequencies
• Appendix 2: Model Answers
• References
• Index