Molecular Photofitting

Predicting Ancestry and Phenotype Using DNA

Tony Frudakis Ph.D., Tony Frudakis, Ph.D.

• Publisher: Academic Press
• Year: 2010
• Print ISBN: 9780120884926
• eBook ISBN: 9780080551371
• Topic: Law
• Subtopic: Forensic Science
• Index: Law

In the field of forensics, there is a critical need for genetic tests that can function in a predictive or inferential sense, before suspects have been identified, and/or for crimes for which DNA evidence exists but eye-witnesses do not. Molecular Photofitting fills this need by describing the process of generating a physical description of an individual from the analysis of his or her DNA. The molecular photofitting process has been used to assist with the identification of remains and to guide criminal investigations toward certain individuals within the sphere of prior suspects. Molecular Photofitting provides an accessible roadmap for both the forensic scientist hoping to make use of the new tests becoming available, and for the human genetic researcher working to discover the panels of markers that comprise these tests. By implementing population structure as a practical forensics and clinical genomics tool, Molecular Photofitting serves to redefine the way science and history look at ancestry and genetics, and shows how these tools can be used to maximize the efficacy of our criminal justice system. - Explains how physical descriptions of individuals can be generated using only their DNA - Contains case studies that show how this new forensic technology is used in practical application - Includes over 100 diagrams, tables, and photos to illustrate and outline complex concepts

Chapter 1

Forensic DNA Analysis: From Modest Beginnings to Molecular Photofitting, Genics, Genetics, Genomics, and the Pertinent Population Genetics Principles

With an Introduction by, Mark D. Shriver

PART I: INTRODUCTION: BRIEF HISTORY OF DNA IN FORENSIC SCIENCES

The forensic analysis of DNA is one of the clear successes resulting from our rapidly increasing understanding of human genetics. Perhaps much of this success is because this particular application of the molecular genetic revolution is ultimately pragmatic and because the genetic information required for efforts such as the Combined DNA Index System (CODIS) and The Innocence Project (www.innocenceproject.org) are relatively simple. Although the requirements of DNA in these instances, namely individualization, are indeed, relatively simple, they are somewhat technical, especially for the reader unfamiliar with molecular methods or population genetics. They nonetheless provide an important framework for the bulk of the material presented in this book. Though they are important for the rest of our discussion in the book, in this chapter, we provide only a brief summary of the standard forensic DNA methods, because these are well documented in other recent texts (Budowle et al. 2000; Butler 2001; Rudin & Inman 2002).

Modern forensic DNA analysis began with Variable Number of Tandem Repeats (VNTR), or minisatellite techniques. First discovered in 1985 by Sir Alex Jeffreys, these probes, when hybridized to Southern blot membranes (see Box 1-A), produced highly variable banding patterns that are known as DNA fingerprints (Jeffreys et al. 1985). Underlying these complex multibanded patterns are a number of forms (alleles) of genetic loci that simultaneously appear in a given individual. The particular combinations of alleles in a given individual are highly specific, yet each is visible because they share a common DNA sequence motif that is recognized by the multilocus molecular probe through complementary base pairing. These multilocus probes are clearly very individualizing, but problematic when it comes to quantifying results. Some statistics can be calculated on multilocus data, but certain critical calculations cannot be made unless individual-locus genotype data are available. In answer to this need, a series of single-locus VNTR probe systems were developed, and these became standard in U.S. forensic labs from the late 1980s through the early 1990s.

Box 1-A

The Southern Blot is named after Edwin Southern, who developed this important first method for the analysis of DNA in 1975. This method takes advantage of several fundamental properties of DNA in order to assay genetic variation, generally called polymorphism. The first step is to isolate high molecular weight DNA, a process known as genomic DNA extraction. Next, the DNA is digested with a restriction enzyme, which makes double-stranded cuts in the DNA at every position where there is a particular base pair sequence. For example, the restriction enzyme, EcoRI, derived from the bacteria, Escherichia coli strain RY13, has the recognition sequence, GAATTC, and will cut the DNA at every position where there is a perfect copy of this sequence. Importantly, sequences that are close to this sequence (e.g., GATTTC) will not be recognized and cut by the enzyme. The restriction digestion functions to reduce the size of the genomic DNA in a systematic fashion, and originally evolved in the bacteria as a defense mechanism as the bacteria’s own genomic complement was protected at these sequences through the action of other enzymes.

After DNA extraction the DNA is generally a series of large fragments averaging 25,000 to 50,000 bp in length. Because of the immense size and complexity of the genome, the results of a restriction enzyme digestion are a huge mix of fragments from tens of base pairs to tens of thousands of base pairs. When these fragments are separated by size on agarose gels using the process known as electrophoresis, they form a heavy smear. Although it’s hard to tell by looking at these smears since all the fragments are running on top of each other, everyone has basically the same smear since all our DNA sequences are 99.9% identical. Places where the restriction patterns differ because of either changes in the sequence of the restriction sites (e.g., GAATTC → GATTTC) or the amount of DNA between two particular restriction sites are called Restriction Fragment Length Polymorphisms (RFLPs).

The key advancement of the Southern Blot was to facilitate the dissection of these restriction enzyme smears through the ability of DNA to denature (become single-stranded) and renature (go back to the double-stranded configuration), and to do so in a sequence-specific fashion such that only DNA fragments that have complementary sequences will hybridize or renature. The DNA in the gel is denatured using a highly basic solution and then transferred by capillary action, using stacks of paper towels onto a thin membrane, usually charged nylon. After binding the digested DNA permanently to the membrane, we can scan it by annealing short fragments of single-stranded DNA, called probes, which are labeled in such a way that we can detect their presence. The probes will anneal with DNA at locations on the genomic smear to which they have complete, or near complete complementarity depending on the stringency of the hybridization and wash conditions. Since the probes are radiolabeled or chemiluminescently labeled, the result is a banding pattern where the location of particular sequences on the genome emerge as blobs called bands. The lengths of the bands can be estimated as a function of the position to which they migrated on the gel relative to size standards which are run in adjacent lanes.

The single-locus forensic VNTR systems are highly informative, with each marker having tens to hundreds of alleles. At every locus each person has only two alleles, which together constitute the genotype, one received from the mother and one from the father. Given such a large number of alleles in the population, most genotypes are very rare. A standard analysis wit...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright page
• Foreword
• Preface
• Acknowledgments
• Chapter 1: Forensic DNA Analysis: From Modest Beginnings to Molecular Photofitting, Genics, Genetics, Genomics, and the Pertinent Population Genetics Principles
• Chapter 2: Ancestry and Admixture
• Chapter 3: Biogeographical Ancestry Admixture Estimation—Theoretical Considerations
• Chapter 4: Biogeographical Ancestry Admixture Estimation—Practicality and Application
• Chapter 5: Characterizing Admixture Panels
• Chapter 6: Apportionment of Autosomal Diversity with Continental Markers
• Chapter 7: Apportionment of Autosomal Diversity with Subcontinental Markers
• Chapter 8: Indirect methods for Phenotype Inference
• Chapter 9: Direct Method of Phenotype Inference
• Chapter 10: The first case studies of molecular photofitting
• Chapter 11: The Politics and Ethics of Genetic Ancestry Testing
• Bibliography
• Index