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Reference Guide on DNA Identification Evidence--David H. Kaye and George Sensabaugh
Pages 129-210

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From page 129...
... contents I. Introduction, 131 A. Summary of Contents, 131 B. A Brief History of DNA Evidence, 132 C. Relevant Expertise, 134 II. Variation in Human DNA and Its Detection, 135 A. What Are DNA, Chromosomes, and Genes?
From page 130...
... Source or uniqueness testimony, 175 V. Special Issues in Human DNA Testing, 176 A. Mitochondrial DNA, 176 B. Y Chromosomes, 181 C. Mixtures, 182 D. Offender and Suspect Database Searches, 186 1.  Which statistics express the probative value of a match to a defendant located by searching a DNA database?
From page 131...
... To assist the courts in understanding the extent to which the results incriminate the defendant, it enumerates the hypotheses that need to be considered before concluding that the defendant is the source of the crime scene samples, and it explores the 1.  For a discussion of other forensic identification techniques, see Paul C Giannelli et al., Reference Guide on Forensic Identification Expertise, in this manual.
From page 132...
... These include the detection and interpretation of mixtures, Y-STR testing, mitochondrial DNA testing, and the evidentiary implications of DNA database searches of various kinds. Finally, Section VI discusses the forensic analysis of nonhuman DNA.
From page 133...
... to include or exclude individuals as the source of crime scene DNA. 7.  Moreover, a minority of courts, perhaps concerned that DNA evidence might be conclusive in the minds of jurors, added a "third prong" to the general-acceptance standard of Frye v.
From page 134...
... As a result, this guide describes not only the predominant STR technology, but also newer analytical techniques that can be used for forensic DNA identification.
From page 135...
... Given the penetration of molecular technology into all areas of biological inquiry, it is likely that individuals can be found who know both the technology and the population biology of the organism in question. Finally, when samples come from crime scenes, the expertise and experience of forensic scientists can be crucial.
From page 136...
... usually are abbreviated as A, T, G, and C The physical structure of DNA is often described as a double helix because the molecule has two spiraling strands connected to each other by weak bonds between the nucleotide bases.
From page 137...
... This small percentage may not sound like a lot, but it adds up to some three million sites for variation among individuals. The process that gives rise to this variation among people starts with the production of special sex cells -- sperm cells in males and egg cells in females.
From page 138...
... The diverse variations occur both within the genes and in the regions of DNA sequences between the genes. A gene can be defined as a segment of DNA, usually from 1000 to 10,000 base pairs long, that "codes" for a protein.
From page 139...
... By determining which alleles are present at strategically chosen loci, the forensic scientist ascertains the genetic profile, or genotype, of an individual (at those loci)
From page 140...
... A small number of repeats in the VNTR region gives rise to a small "restriction fragment," and a large number of repeats yields a large fragment. A substantial quantity of DNA from a crime scene sample is required to give a detectable number of VNTR fragments with this procedure.
From page 141...
... or microsatellites. STRs have very short core repeats, two to seven base pairs in length, and they typically extend for only some 50 to 350 base pairs.20 Like the larger VNTRs, which extend for thousands of base pairs, STR sequences do not code for proteins, and the ones used in identity testing convey little or no information about an individual's propensity for disease.21 Because STR alleles 17.  It would be clearer to call it RFLP-VNTR testing, because the fragments being measured contain the VNTRs rather than some simpler polymorphisms that were used in genetic research and disease testing.
From page 142...
... Because the amplified fragments are shorter, electrophoretic detection permits the exact number of base pairs in an STR to be determined, allowing alleles to be defined as discrete entities. Figure 2 illustrates the nature of allelic variation at an STR locus found on chromosome 16.
From page 143...
... is warmed to a comfortable working temperature for the polymerase to insert the complementary base pairs one at a time, building a matching second strand bound to the original "template" and thus replicating part of the DNA strand that was separated from its partner in the first step. The same replication occurs with the separated partner as the template.
From page 144...
... These soon would be used to build England's National DNA Database. The database system allows a computer to check the STR types of millions of known or suspected criminals against thousands of crime 25.  A null allele will not lead to a false exclusion if the two DNA samples from the same individual are amplified with the same primer system, but it could lead to an exclusion at one locus when searching a database of STR profiles if the database profile was determined with a different PCR kit than the one used to analyze the crime scene DNA.
From page 145...
... A six-locus STR profile can be represented as a string of 12 digits; each digit indicates the number of repeat units in the alleles at each locus. These discrete, numerical DNA profiles are far easier to compare mechanically than the complex patterns of fingerprints.
From page 146...
... The bottom panel is a "sizing standard" -- a set of peaks from DNA sequences of known lengths (in base pairs)
From page 147...
... The copy on the X chromosome is 112 bp long. The copy onfixed image has a string of six base pairs deleted, making it slightly shorter (106 bp)
From page 148...
... Finally, the population genetics of the system should be characterized. As new systems are discovered, researchers typically analyze convenient collections of DNA samples from various human populations and publish studies of the relative frequencies of each allele in these population samples.
From page 149...
... Advances in the years since 2004 suggest that this goal will be achieved before the target date of 2014,31 and the successful innovations could provide major advances in forensic DNA testing. However, it is too soon to identify which of the nascent sequencing technologies might emerge from the pack.
From page 150...
... Is it simply an extension of existing technologies, or does it invoke entirely new concepts? Is the new technology used in research or clinical applications independent of forensic science?
From page 151...
... the extent to which it is degraded. Generally speaking, if a sufficient quantity of reasonable quality DNA can be extracted from a crime scene sample, no matter what the nature of the sample, DNA typing can be done without problem.
From page 152...
... The primary determinant of DNA quality for forensic analysis is the extent to which the long DNA molecules are intact. Within the cell nucleus, each molecule of DNA extends for millions of base pairs.
From page 153...
... But environmental insult does not result in the selective loss of an allele at a locus or in the creation of a new allele at that locus. 45.  For a review of the history of quality assurance in forensic DNA testing, see J.L.
From page 154...
... ;46 a number of states require forensic DNA laboratories to be accredited;47 and federal law requires accreditation or other safeguards of laboratories that receive certain federal funds48 or participate in the national DNA database system.49 a. Documentation Quality assurance guidelines normally call for laboratories to document laboratory organization and management, personnel qualifications and training, facilities, evidence control procedures, validation of methods and procedures, analytical procedures, equipment calibration and maintenance, standards for case documentation and report writing, procedures for reviewing case files and testimony, proficiency testing, corrective actions, audits, safety programs, and review of subcontractors.
From page 155...
... Developmental validation is undertaken to determine the applicability of a new test to crime scene samples; it defines conditions that give reliable results and identifies the limitations of the procedure. For example, a new genetic marker being considered for use in forensic analysis will be tested to determine if it can be typed reliably in both fresh samples and in samples typical of those found at crime scenes.
From page 156...
... Sample mishandling, mislabeling, or contamination, whether in the field or in the laboratory, is more likely to compromise a DNA analysis than is an error in genetic typing. For example, a sample mixup due to mislabeling reference blood samples taken at the hospital could lead to incorrect association of crime scene samples to a reference individual or to incorrect exclusions.
From page 157...
... Finally, laboratories must retain, when feasible, portions of the crime scene samples and extracts to allow reanalysis.55 However, retention is not always possible. For example, retention of original items is not to be expected when the items are large or immobile (e.g., a wall or sidewalk)
From page 158...
... First, the crime scene samples by their nature may contain a mixture of fluids or tissues from different individuals. Examples include vaginal swabs collected as sexual assault evidence and bloodstain evidence from scenes where several individuals shed blood.
From page 159...
... With discrete allele systems, such as STRs, it is natural to speak of "matching" and "nonmatching" profiles. If the genetic profile obtained from the biological sample taken from the crime scene or the victim (the "trace evidence sample")
From page 160...
... The prosecution's hypothesis is that the defendant is the source of the crime scene sample.61 Conceivably, other hypotheses could account for the matching profiles. One possibility is laboratory error -- the genotypes are not actually the same even though the laboratory thinks that they are.
From page 161...
... The former hypothesis we shall refer to as kinship, and the latter as coincidence. To infer that the defendant is the source of the crime scene DNA, one must reject these alternative hypotheses of laboratory error, kinship, and coincidence.
From page 162...
... With enough loci to test, all individuals except identical twins should be distinguishable. With existing technology and small sample sizes of DNA recovered from crime scenes, however, this ideal is not always attainable.
From page 163...
... Could an Unrelated Person Be the Source? Another rival hypothesis is coincidence: The defendant is not the source of the crime scene DNA but happens to have the same genotype as an unrelated individual who is the true source.
From page 164...
... However, the frequencies of most alleles can be determined accurately by sampling the population to construct databases that reveal how often each allele occurs. Principles of population genetics then can be applied to combine the estimated allele frequencies into an estimate of the probability that a person born in the population will have the multilocus genotype.
From page 165...
... . 76. In the formative years of forensic DNA testing, defendants frequently contended that forensic databases were too small to give accurate estimates, but this argument generally proved unpersuasive.
From page 166...
... Courts applying the Daubert and Frye rules for scientific evidence issued conflicting opinions as to the admissibility of basic product-rule estimates.79 A 1992 report from a committee of the National Academy of Sciences did not resolve the question, but a second committee concluded in 1996 that the basic product rule provided reasonable estimates in most cases, and it described a modified version of the product rule 78. The use of a range of estimates conditioned on race is defended, and several alternatives are discussed in Kaye, supra note 3, at 192–97; David H Kaye, The Role of Race in DNA Evidence: What Experts Say, What California Courts Allow, 37 Sw.
From page 167...
...  rgument: Frequencies or probabilities are prejudicial because they are so small A The most common form of expert testimony about matching DNA involves an explanation of how the laboratory ascertained that the defendant's DNA has the profile of the forensic sample plus an estimate of the profile frequency or random-match probability. It has been suggested, however, that jurors do not understand probabilities in general, and that infinitesimal match probabilities will so bedazzle jurors that they will not appreciate the other evidence in the case or any innocent explanations for the match.82 Empirical research into this hypothesis has been limited,83 and commentators have noted that remedies short of exclusion 80. The 1996 committee's recommendations for computing random-match probabilities with broad populations and particular subpopulations are summarized in the previous edition of this guide.
From page 168...
... The r ­andom-match probability is the probability that the suspect has the DNA genotype of the crime scene sample if he is not the true source of that sample (and is unrelated to the true source)
From page 169...
... . The committee suggested the following instruction to define the random-match probability: In evaluating the expert testimony on the DNA evidence, you were presented with a number indicating the probability that another individual drawn at random from the [specify]
From page 170...
... Koehler et al., The Random Match Probability in DNA Evidence: Irrelevant and Prejudicial? 35 Jurimetrics J
From page 171...
... Morris, An Empirical Assessment of Presentation Formats for Trace Evidence with a Relatively Large and Quantifiable Random Match Probability, 42 Jurimetrics J
From page 172...
... Adequate safeguards and checks for possible laboratory error make that explanation of the finding of matching genotypes implausible. The inference that the defendant is the source of the crime scene DNA is then secure.
From page 173...
... are the odds as they were known prior to receiving the data times the likelihood ratio. More succinctly, posterior odds = likelihood ratio × prior odds.104 For example, if the relevant match probability105 were 1/100,000, and if the chance that the laboratory would report a match between samples from the same source were 0.99, then the likelihood ratio would be 99,000, and the jury could be told how the DNA evidence raises various prior probabilities that the defendant's DNA is in the evidence sample.106 102.  For legal commentary and additional cases upholding the admission of likelihood ratios over objections based on Frye and Daubert, see Kaye et al., supra note 1, § 14.2.2.
From page 174...
... Verbal Expressions of Probative Value Having surveyed the issues related to the value and dangers of probabilities and statistics for DNA evidence, we turn to a related issue that can arise under Rules 702 and 403: Should an expert be permitted to offer a nonnumerical judgment about the DNA profiles? Many courts have held that a DNA match is inadmissible unless the expert attaches a scientifically valid number to the match.
From page 175...
... . There might already be cases in which it is defensible for an expert to assert that, assuming that there has been no sample mishandling or laboratory error, the profile's probable uniqueness means that the two DNA samples come from the same person."112 Before concluding that a DNA profile is unique in a given population, however, a careful expert also should consider not only the random-match probability (which pertains to unrelated individuals)
From page 176...
... Mitochondria have a small genome -- a circle of 16,569 nucleotide base pairs within the mitochondrion -- that bears no relation to the comparatively monstrous chromosomal genome in the cell nucleus.115 Mitochondrial DNA (mtDNA) has four features that make it useful for forensic DNA testing.
From page 177...
... The small mitochondrial genome can be analyzed with a PCR-based method that gives the order of all the base pairs.121 The sequences of two samples -- say, DNA extracted from a hair shaft found at a crime scene and hairs plucked from a suspect -- then can be compared. Most analysts describe the results in terms on 116. A third, somewhat less polymorphic, region in the D-loop can be used for additional discrimination.
From page 178...
... Pappas,125 the reference database consisted of 1219 mtDNA sequences from whites, and it did not include the sequence that was present in the hairs near the crime scene and in the defendant. Thus, this particular sequence was observed once (at the crime scene)
From page 179...
... Kaestle et al., Database Limitations on the Evidentiary Value of Forensic Mitochondrial DNA Evidence, 43 Am.
From page 180...
... If it is identical to one of the suspect's sequences, then the suspect is included, and a suitable reference database should indicate how infrequent such an inclusion would be. If crime scene DNA is one base pair removed from either of the suspect's sequences, then the result is inconclusive.
From page 181...
... In this third scenario, multiple sequences are seen in each sample. To keep track of things, we can call the sequences in the crime scene sample C1 and C2, and those in the suspect's sample S1 and S2.
From page 182...
... Mixtures Samples of biological trace evidence recovered from crime scenes often contain a mixture of fluids or tissues from different individuals. Examples include vaginal swabs collected as sexual assault evidence and bloodstain evidence from scenes where several individuals shed blood.
From page 183...
... Because the vast bulk of ­ the amplified STRs will come from the defendant's DNA, the electropherogram should show only one STR profile. In these situations, the interpretation of the single DNA profile is the same as when 100% of the DNA molecules in the sample are the defendant's.
From page 184...
... 2006) (testing for Y-STRs on "the genital swab with the DNA profile from the Defendant's buccal swab, .
From page 185...
... . 148.  See, e.g., Tim Clayton & John Buckleton, Mixtures, in Forensic DNA Evidence Interpretation 217 (John Buckleton et al.
From page 186...
...  hich statistics express the probative value of a match to a defendant W located by searching a DNA database? States and the federal government are amassing huge databases consisting of the DNA profiles of suspected or convicted offenders.152 If the DNA profile from a crime scene stain matches one of those on file, the person identified by this "cold hit" will become the target of the investigation.
From page 187...
... DNA Advisory Board, Statistical and Population Genetics Issues Affecting the Evaluation of the Frequency of Occurrence of DNA Profiles Calculated from Pertinent Population Database(s) , 2 Forensic Sci.
From page 188...
... 931 (1999) ; Kaye, supra note 109; Simon Walsh & John Buckleton, DNA Intelligence Databases, in Forensic DNA Evidence Interpretation 439 (John Buckleton et al.
From page 189...
... Indeed, the rules of evidence sometimes prohibit this proof over the objection of the defendant.164 Another search pro identified through a database trawl is the source of a crime scene DNA sample, see Yun S Song et al., Average Probability That a "Cold Hit" in a DNA Database Search Results in an Erroneous Attribution, 54 J
From page 190...
... The policy question is whether exposing relatives to the possibility of being investigated on the basis of genetic leads from their kin is appropriate.165 In receiving the DNA evidence, courts might consider having the prosecution describe the match without revealing that the defendant's close relative is a known or suspected criminal. In addition, if database trawls degrade the probative value of a perfect match in the database -- a theory discussed in the previous subsection -- then the usual random-match probability or estimated frequency exaggerates the value of the match derived from a database search.
From page 191...
... Section IV.E explained how population genetics models and reference samples for determining allele frequencies are used to estimate DNA genotype frequen cies. Large databases can be used to check these theoretical computations.
From page 192...
... Curran et al., Empirical Support for the Reliability of DNA Evidence Interpretation in Australia and New Zealand, 40 Australian J Forensic Sci.
From page 193...
... However, inasmuch as DNA analysis might be informative in any kind of case involving biological material, DNA analysis has found application in such diverse situations as identification of individual plants and animals that link suspects to crime scenes, enforcement of endangered species and other wildlife regulations, investigation of patent issues involving specific animal breeds and plant cultivars, identification of fraudulently labeled foodstuffs, identification of sources of bacterial and viral epidemic outbreaks, and identification of agents of bioterrorism.173 These applications are directed either at identifying the species origin of an item or at distinguishing among individuals (or subgroups) within a species.
From page 194...
... In particular, this gene sequence previously had been used to determine the evolutionary placement of sturgeons among other species of fish.179 Likewise, the use of phylogenetic analysis for assessing relationships among HIV strains has provided critical insights into the biology of this deadly virus. 175.  Dep't of Justice, Caviar Company and President Convicted in Smuggling Conspiracy, available at http://www.usdoj.gov/opa/pr/2002/January/02_enrd_052.htm.
From page 195...
... Nonetheless, a match between the DNA at a crime scene and the organism that could be the source of that trace evidence still may be informative. In these cases, a court may consider admitting testimony about the matching features along with circumscribed, qualitative explanations of the significance of the similarities.182 Such cases began appearing in the 1990s.
From page 196...
... at 521. Furthermore, unbeknownst to the experimenter, two apparently distinct samples were prepared from the tree at the crime scene that appeared to have been abraded by the defendant's truck.
From page 197...
... Craft et al., Application of Plant DNA Markers in Forensic Botany: Genetic Comparison of Quercus Evidence Leaves to Crime Scene Trees Using Microsatellites, 165 Forensic Sci.
From page 198...
... But if mating is nonrandom, as occurs when individuals within a species are selectively bred to obtain some property such as coat color, body type, or behavioral repertoire, or as occurs when a species exists in geographically distinct subpopulations, the inheritance of loci may no longer be independent. Because it cannot be assumed a priori that a crime scene sample originates from a mixed-breed animal, inbreeding normally must be accounted for.194 A different approach is called for if the species is not sexually reproducing.
From page 199...
... amplified fragment length polymorphism (AMP-FLP) . A DNA iden tification technique that uses PCR-amplified DNA fragments of varying lengths.
From page 200...
... along the double helix "backbone" of the DNA molecule.The length of a DNA fragment often is measured in numbers of base pairs (1 kilobase (kb)
From page 201...
... (A sequence of three base pairs specifies a particular one of the 20 possible amino acids in the protein. The mapping of a set of three nucleotide bases to a particular amino acid is the genetic code.
From page 202...
... See genotype. DNA sequence.  The ordered list of base pairs in a duplex DNA molecule or of bases in a single strand.
From page 203...
... genome.  The complete genetic makeup of an organism, including roughly 23,000 genes and many other DNA sequences in humans. Over three billion nucleotide base pairs comprise the haploid human genome.
From page 204...
... See independence, linkage disequilibrium. heteroplasmy, heteroplasty. The condition in which some copies of mito chondrial DNA in the same individual have different base pairs at certain points.
From page 205...
... is the reciprocal of the random-match probability. Legal scholars have introduced the likelihood ratio as a measure of the probative value of evidence.
From page 206...
... See primer. paternity index.  A number (technically, a likelihood ratio)
From page 207...
... Significant structure can lead to allele frequencies being different in the subpopulations. primer.  An oligonucleotide that attaches to one end of a DNA fragment and provides a point for more complementary nucleotides to attach and replicate the DNA strand.
From page 208...
... See also random-match probability. random-match probability. The chance of a random match.
From page 209...
... given that someone other than the defendant is the source of the crime scene DNA (B) as if it were the probability of someone else being the source (B)
From page 210...
... . National Research Council Committee on DNA Forensic Science: An Update, The Evaluation of Forensic DNA Evidence (1996)


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