Forensic DNA Evidence Interpretation

John S. Buckleton, Jo-Anne Bright, Duncan Taylor, John S. Buckleton, Jo-Anne Bright, Duncan Taylor

• Publisher: CRC Press
• Year: 2018
• ISBN:
  9781315360126
• Edition: 2
• Topic: Law
• Subtopic: Forensic Science
• Index: Law

Now in its second edition, Forensic DNA Evidence Interpretation is the most comprehensive resource for DNA casework available today. Written by leaders in the fields of biology and statistics, including a contribution from Peter Gill, the father of DNA analysis, the book emphasizes the interpretation of test results and provides the necessary formulae in an easily accessible manner. This latest edition is fully updated and includes current and emerging techniques in this fast-moving field.

The book begins by reviewing all pertinent biology, and then provides information on every aspect of DNA analysis. This includes modern interpretation methods and contemporary population genetic models available for estimating DNA frequencies or likelihood ratios. Following a chapter on procedures for validating databases, the text presents overviews and performance assessments of both modern sampling uncertainty methods and current paternity testing techniques, including new guidelines on paternity testing in alignment with the International Society for Forensic Genetics. Later chapters discuss the latest methods for mixture analysis, LCN (ultra trace) analysis and non-autosomal (mito, X, and Y) DNA analysis. The text concludes with an overview of procedures for disaster victim identification and information on DNA intelligence databases.

Highlights of the second edition include:

• New information about PCR processes, heterozygote balance and back and forward stuttering
• New information on the interpretation of low template DNA, drop models and continuous models
• Additional coverage of lineage marker subpopulation effects, mixtures and combinations with autosomal markers

This authoritative book provides a link among the biological, forensic, and interpretative domains of the DNA profiling field. It continues to serve as an invaluable resource that allows forensic scientists, technicians, molecular biologists and attorneys to use forensic DNA evidence to its greatest potential.

1

Biological Basis for DNA Evidence

Duncan Taylor, Jo-Anne Bright and John S. Buckleton^*

* Based on an earlier version by Peter Gill and John Buckleton.

Contents

Historical and Biological Background

DNA Profiling Technology

Short Tandem Repeat Analysis

Next-Generation Sequencing

Understanding STR Profiles

Genetic Anomalies

Trisomy and Gene Duplication

Somatic Mutation

PCR Effects

Analytical Threshold

Heterozygote Balance

Allelic Dropout

Degradation Slopes

Back Stutter

Forward Stutter

Drop-In Alleles

Additivity or Stacking

Non-Specific Artefacts

Pull-Up

Capillary Carryover

Suppression of Amplification Efficiency, Silent or Null Alleles

Summary

This book deals in large part with the interpretation of DNA evidence, mixed or unmixed, after it has been collected, stored, transferred and finally analyzed in the laboratory. The supposition throughout is that the earlier stages in the chain that leads to evidence in court have been undertaken correctly. The inference at the final end of the chain is practically useless unless all these earlier aspects have been undertaken with due attention to continuity and integrity.¹

This chapter gives a brief background to the biotechnology relevant to the interpretation of short tandem repeat (STR) samples. For an extended discussion see the excellent work by Rudin and Inman^2,3 as well as Butler.⁴

Historical and Biological Background

Modern forensic DNA history begins with the first DNA case, which was processed by the then-34-year-old professor Sir Alec Jeffreys from Leicester University, UK. This case involved the murders of two 15-year-old girls, Lynda Mann and Dawn Ashworth.⁵ The police were convinced that the perpetrator was a local man. Consequently, blood samples were requested from all males of a certain age group from three villages within the area of the two murders. These samples were analyzed using a combination of classical blood-typing techniques and multi-locus probe DNA profiling. The first mass screening of individuals using DNA technology led to the arrest and confession of Colin Pitchfork, a cake decorator with a history of flashing.⁶

This pioneering case demonstrated the potential of DNA profiling^{7, 8, 9, 10} and firmly pointed towards its future as the most important forensic investigative tool to be developed in the twentieth century.

DNA is the genetic code of most organisms. The DNA of humans and many other organisms has been used in forensic work. Human primers can also be used to amplify the DNA from some other primates.¹¹ Much of the work discussed here focuses on the analysis of modern human DNA. However many of the principles apply to all organisms and to ancient DNA.¹²

Most human DNA is present in the nucleus of the cell. It is packaged in the 46 chromosomes of most cells. This DNA is termed nuclear DNA. However a small portion of the DNA complement of each cell is housed in the mitochondria. This mitochondrial DNA is inherited by a different mechanism and is treated differently in the forensic context. A separate section in a subsequent chapter 10, non-autosomal forensic markers is devoted to this topic.

Most human cells are diploid, meaning that they have two copies of each chromosome. Exceptions include the sex cells (sperm or ova), which are haploid (having a single copy of each chromosome), and liver cells, which are polyploid. Diploid cells contain 46 chromosomes in 23 pairs (the count was given as 48 for over 40 years). The human chromosomes are numbered from 1 to 22 starting with the largest numbered 1 and the second largest numbered 2. The 23rd pair is the X and Y chromosomes, which dictate the sex of the individual. This pair may be referred to as non-autosomal or as gonosomal.

Each chromosome possesses a centromere. This structure is involved in organizing the DNA during cell division. It is always off-centre and hence produces the short arm and long arm of the chromosome.

A normal female has two X chromosomes, whereas a normal male has one X and one Y chromosome. One of the female X chromosomes is deactivated in each cell, forming a Barr body structure visible through the microscope. The X chromosome that is deactivated may differ for each cell.¹³ In mammals possession of the Y chromosome determines the organism to be male. In fact possession of even a small section of the short arm of the Y chromosome will result in a male. Other orders of life, such as reptiles, determine sex using other mechanisms. One chromosome of each of the 23 pairs has been inherited from the mother and one from the father.

It was historically not possible, from the examination of a single individual, to tell which chromosome had come from which parent, with the exception that a Y chromosome must have come from a male individual’s father and hence the X chromosome of a male must have come from his mother. However there are reports utilizing paternally imprinted allele typing that suggest that the ability to determine the parental origin of a chromosome may be possible for some loci.^{13, 14, 15, 16} In mammals some genes undergo parental imprinting and either the maternal or the paternal allele may be preferentially expressed in the offspring. The reason for this is currently unknown. Imprinting appears to be associated with differential methylation upstream from the allele. This difference gives the potential to determine the parental origin of some alleles in the vicinity of any imprinted gene. Seventy-six human genes have been identified as undergoing paternal imprinting, although more are under investigation.¹⁷

When most individuals are DNA profiled, they show either one or two alleles at each locus. If they show one we assume that they are homozygotic, meaning that they have received two copies of the same allele, one from each parent. If an individual shows two alleles, he or she is usually assumed to be heterozygotic. In such cases the individual has inherited different alleles from each parent. An exception is caused by null or silent alleles. Heterozygotic individuals bearing one silent allele may easily be mistaken for homozygotes. Silent alleles most probably occur when an allele is actually present but the system is unable to visualize it. Alternative methods may in fact be able to visualize the allele. Hence the term silent allele is preferable instead of the term null, although uptake of this preferred term is patchy.

There are a few genetic exceptions that may lead to people having more than two alleles. These include trisomy (three chromosomes), translocation of a gene (a copy of the gene has been inserted somewhere else on the genome), somatic mutation (the individual has different genotypes in different cells) and chimerism (coexistence of two genetically distinct cell populations).¹⁸

It is thought that all humans except identical twins differ in their nuclear DNA. Even identical twins may differ in minor ways. There is no formal proof of this concept of underlying uniqueness and it h...