Genetic Justice

by Sheldon Krimsky

  Chapter 5

  Forensic DNA Phenotyping

  Scientists now have the ability to identify an indefinite number of physical traits including height, eye color, sex and race from a trace of DNA material. Recent breakthroughs in the Human Genome Project (HGP) mandate an expansion of DNA evidence as an investigative tool.

  —Lindsy Elkins1

  A few years from now we’re going to have figured out so many traits that a criminal might as well leave his driver’s license at the scene of the crime.

  —Tony Frudakis2

  An unidentified girl, presumed to be 3 or 4 years old, was found decapitated in Kansas City, Missouri, in 2001. Local residents had given her the name “Precious Doe” in order to humanize her tragic fate and draw public interest to her case. The police sent her DNA to be analyzed for clues to her ethnic heritage. Results of her DNA test indicated that Precious Doe was of mixed ancestry, approximately 40 percent Caucasian and 60 percent African American. From the tests, forensic specialists in DNA analysis estimated that Precious Doe had a white grandparent. Police also had a tip from an Oklahoma man who said that he was a relative of the slain girl and knew who killed her. They also sought out people who had failed to report the disappearance of a child. From the tips they narrowed the suspects to one woman who had not reported her child as missing and had one black and one white parent. When they ran a DNA test of the woman, they discovered that she was the biological mother of Precious Doe. Both she and her husband, the girl’s stepfather, were charged with her homicide. Writing about the case for USA Today, Richard Willing noted, “Advances in DNA testing are allowing investigators to learn more about suspects whose profiles are not in the databases. Tests that can identify a suspect’s ancestry are being used not to identify the suspect by name, but rather to give police the idea of what he or she looks like.”3

  The term “DNA profiling” first came into use when Alec Jeffreys discovered how to use DNA samples to determine identity or paternity. “DNA profiling” became synonymous with terms like “DNA typing,” “DNA fingerprinting,” “DNA identification,” and “forensic DNA testing.” In this sense DNA profiling means sequencing the DNA loci that can be used to compare two samples to determine if they came from the same person. The DNA profile is the set of 26 numbers that characterize the short tandem repeats (STRs) at 13 loci in the human genome (see chapter 1).

  However, the genetic age has brought with it a new usage of DNA profiling that is similar to visual profiling of crime suspects. In a visual profile an eyewitness identifies some characteristics of the alleged perpetrator of a crime, such as height, hair color, distinguishing marks, skin color, and body size and shape. A composite sketch (profile) is created from bits of eyewitness information. In forensic DNA phenotyping forensic scientists analyze DNA from a crime scene in an attempt to determine certain aspects of the individual’s physical characteristics. This “second generation” of DNA profiling goes well beyond examining the 13 loci that are used and stored in the U.S. Combined DNA Index System (CODIS) database. Instead, one or more genetic tests are run to glean information from the DNA that might provide clues about the suspect’s physical features. Lindsy Elkins describes DNA phenotyping as follows: “Scientists can now discern from DNA a virtually indefinite number of physical traits possessed by an individual from height, eye color, sex and race, down to the shapes of a person’s toes. In addition, genetic typing permits inferences as to inherited disorders and may offer clues to facial or other bodily features.”4

  Forensic DNA phenotyping is not without socioethical concerns. These include the following: Does DNA phenotyping by police infringe on civil liberties? Will DNA phenotyping exacerbate racial or ethnic stereotypes? Will it help law enforcement solve crimes? Will DNA phenotyping reduce the use of prejudicial and subjective (based on eyewitness reports) profiling?5 How scientifically credible is phenotyping by DNA? Because the technology of DNA phenotyping is still in its early stages of development, the answers to these questions must be tentative.

  Linking Genotype to Phenotype

  Lindsy Elkins in her law review article on physical profiling based on genetics is far too optimistic about the relationship between the DNA and the phenotype (“down to the shapes of a person’s toes”).6 There are significant uncertainties associated with predicting racial or ethnic origins or physical qualities on the basis of DNA. The remaining sections of this chapter discuss the current possibilities and limitations for “phenotyping” DNA. Can we draw inferences about physical appearance or the medical condition of an individual from his or her DNA? What are the possibilities of creating a physical profile of an individual exclusively from crime-scene data?

  Three research programs in genetics have provided the scientific foundations behind forensic genotype-to-phenotype profiling: ancestral testing, behavioral genetics, and medical genetics. In each case scientists seek to find links between components of the human genome and an individual’s physical characteristics, behavior, or response to environmental factors such as medication or antigens.

  Ancestral Genotyping

  The Human Genome Diversity Project, an outcome of the Human Genome initiative, has been used to identify genetic patterns that reveal one’s biogeographical ancestry. Population-specific alleles (PSAs) enable geneticists to distinguish the genotypes of a select number of ethnic populations, such as Europeans, Africans, Native Americans, and Asians. And although there are more genetic variations within ethnic/racial groups than between groups, some researchers have found that there are sufficiently stable genetic segments (haplotypes) that can distinguish among several ancestral population groups. These are called ethnic geographical markers of ancestral origin, or Ancestry Informative Markers:

  Ancestry informative markers (AIMs) . . . are autosomal genetic markers that show substantial differences in allele frequency across population groups. . . . Factors such as isolation by distance, range expansions, land bridges, maritime technologies, ice ages, and cultural and linguistic barriers have all affected human migration and mating patterns in the past and have therefore shaped the present worldwide distribution of genetic variation.7

  Current ancestry tests examine upwards of 176 genetic markers in which the DNA varies at only one position. These single-nucleotide polymorphisms (SNPs) have been found to occur more frequently in certain population groups than in others—the result of centuries of geographical separation and group intermarriage.8

  Because most people have mixed biogeographical ancestral origins, the programs that yield information of this kind provide percentages (such as 80 percent African and 20 percent European). The composite percentages typically cannot yield definitive information about the phenotype of specific individuals falling within these biogeographical categories, but the question of probabilities for populations is left open.

  According to Susanne Haga, assistant research professor at the Duke Institute for Genome Science and Policy, because admixture confounds the prediction of ancestral origins, “a substantial gap remains between ancestry and/or race and physical appearance. . . . Knowing an individual’s race [percentage of racial origin] can be misleading if used to predict certain physical traits.”9 When someone is told they are 60 percent Asian and 40 percent European it is based on large segments of DNA. We do not know what the 60 percent Asian DNA will express itself as; therefore we cannot from those percentages say anything about the phenotype of the individual. But if we had probability figures, such as “90 percent of the people who are tested by DNA ancestry as 60 percent Asian have ‘yellow’ skin tone,” then we may be able to draw some probabilistic predictions about phenotype.

  Ancestral Genomics in Law Enforcement

  Ancestral genomics is beginning to find a place in law enforcement. In March 2003 a company known as DNAPrint Genomics of Sarasota, Florida, analyzed the DNA of a serial killer in Louisiana using a genetic ancestry technique trademarked as DNA Witness. The company concluded that the killer’s “biogeographical ances
try” was 85 percent sub-Saharan African and 15 percent Native American. Until then, police had been seeking a Caucasian male in a pickup truck. The analysis of biological evidence at the crime scene by DNA Witness concluded that the Louisiana task force’s search was misguided, and that the individual they were looking for was more likely to be a “lighter skinned black man.” This description was inferred from probabilistic ancestry percentages revealed in the perpetrator’s DNA. The Louisiana police were dubious about the reliability of DNA Witness in profiling the serial killer. They sent the company 20 other DNA samples of individuals of whom they alone knew the ethnic or racial identification. According to the research director at DNAPrint Genomics, the company correctly identified the ancestry of all the samples.10 As a result of the analysis, Louisiana police shifted the focus of their investigation and identified Derrick Todd Lee, an African American man, as a possible suspect in the crime. Lee became the first person in the United States to be identified as a possible murder suspect through the use of a DNA test that racially profiled his DNA. On August 11, 2004, Lee was convicted in the first of a series of murder and rape cases.

  DNAPrint Genomics used its success in Louisiana to aggressively market its services to police departments, investigators, and agencies.11 Toward the end of 2004 it started offering “RETINOME,” a genetic test to infer eye color, to law-enforcement agencies in addition to ancestry testing.12 Here is how the company described its forensic profiling services:

  Testing DNA to create a physical description from crime scene DNA and providing a photo database array of representatives closely matching the analyzed DNA, allows detectives a means of describing “persons of interest.” This presumptive test method is a new market based on evolving DNAPrint™ Genomics technologies. Common hereditary traits such as skin pigmentation, eye color, hair color, facial geometry and even height can be predicted through analysis of DNA sequences. This can be done indirectly, through an extensive knowledge of ancestry admixture or for certain genetic traits, directly through knowledge of the underlying genes. At DNA-Print™ we use both methods. Our goal is to continue to lead the field of forensic presumptive testing using our DNA Witness™ line of products and services.13

  The DNA Witness software technology was contracted out by the Boulder, Colorado, Police Department in 2004 to develop suspects in the highly publicized investigation of the rape-murder of a 23-year-old woman. In December 1997 Susannah Chase was walking home after getting a pizza when she was savagely raped and beaten to death with a baseball bat. When her murder investigation failed to lead to any suspects, it was put in the cold-case file. Six years later, in December 2003, the Boulder Police Department contacted DNAPrint Genomics to acquire some phenotypic information from the male sperm preserved from the victim’s body. In its January 2004 report the company stated that the source of the DNA was a person of Hispanic or Native American background. According to Boulder police chief Mark Beckner, “This technology gave our detectives a focus and direction that turned out to be right on the mark.”14

  Police arrested a prime suspect in January 2008 by the name of Diego Olmos-Alcalde, a Chilean native who had an uncertain U.S. immigration status. DNAPrint Genomics appeared to have correctly identified the Hispanic ancestry of the person whose sperm was found at the crime scene. But what role did the ancestry information have in solving the crime? Did the phenotype “Hispanic or Native American” help police narrow the lead to the prime suspect?

  As it turned out, it was not the phenotyping of the DNA that solved the case, but a match on CODIS, albeit a delayed one. The suspect was known to both Colorado and Wyoming police authorities for other felony arrests. He was arrested in 1998 in Denver on charges of attempted sexual assault and carrying a concealed weapon. However, prosecutors dropped the sexual assault charge in exchange for a guilty plea to the weapon charge.15 In May 2001, while in Wyoming, Olmos-Alcalde was given a 12- to 20-year prison term for kidnapping a Cheyenne woman in a parking lot near her apartment. Because of errors made by the trial judge, the Wyoming Supreme Court overturned the conviction and ordered a new trial, whereupon Olmos-Alcalde was resentenced in September 2004 to 7 to 10 years, with credit for time served.16 The defendant was paroled in the summer of 2007.

  When the Denver police got around to loading the crime-scene DNA profile into CODIS, there was no match, that is, not until six months after Olmos-Alcalde was released from prison. If Olmos-Alcalde’s DNA profile had been uploaded to CODIS as soon as he entered prison, the police would not have needed the services of DNAPrint Genomics. There are two likely explanations for the delay. It is possible that his DNA was not profiled when he entered the Wyoming penal system but only after he was released. Alternatively, the profile of his DNA was not loaded into CODIS until he got out of prison or after some combination of delays. One report stated that officials were not sure when his DNA was profiled: “Melinda Brazalle, spokesperson for the Wyoming Department of Corrections, said the Department’s policy calls for collecting DNA from inmates during the intake process. But she wasn’t certain when Alcalde’s genetic information was obtained.”17 Colorado loaded the DNA sample taken from Chase’s body into CODIS as early as 2002 without a match, while Wyoming entered Olmos-Alcalde’s profile into CODIS in January 2008.18 The reason for the delay was the backlog of samples awaiting DNA processing. At the time there was a backlog of about 180,000 federal convicted-offender samples awaiting DNA processing and about 50,000 samples that were already processed but were waiting to be entered into CODIS.

  There are two points to this story. First, DNAPrint Genomics’s ancestry analysis did not help solve this case; rather, it was solved from a DNA profile match in CODIS. Second, had there been no backlog in processing convicted felon DNA, police would have had no reason to consult DNAPrint Genomics.19

  When the National DNA Advisory Board was considering the alleles it would recommend for use in forensic testing of crime-scene samples, its members made a deliberate choice to avoid any sequence that had known phenotypic properties or that disclosed ancestral origins. According to Ranajit Chakraborty, a board member and director of the University of Cincinnati’s Center for Genome Information, “In 1997, when members of the national DNA Advisory Board officially selected the gene markers for DNA evidence matching, they could have included a few markers associated with ancestral geographical origins (European, East Asian, Sub-Saharan African), which are a good indicator of race and ethnicity.” But the board instead decided against using racial markers because of the political sensitivity they represented.20 During the period in which CODIS was being developed, there was a heightened sensitivity both in law enforcement and among scientists that there were privacy issues involved in decoding people’s DNA that law enforcement should steer clear of. Although it was the board’s noble intention to use DNA exclusively for identification purposes, scientists continue to investigate methods that link allele variations in the STRs with racial and ethnic ancestry.21

  Behavioral Genetics and Profiling

  Research in behavioral genetics seeks to find links between genotype and certain human behaviors, specifically, but not exclusively, criminal behaviors.22 Thus, if genes could be strongly correlated with a person’s “fits of anger” or one’s pedophiliac tendencies, police could use genetic screening to narrow—or generate—a list of suspects in the search for a perpetrator of a violent and/or sexually deviant crime. Claims made by behavioral geneticists have sparked vigorous debates. Some scientists have critiqued the underlying science, pointing out the inherent limitations in studies of simple correlations that occur between genetic factors and complex behaviors.23 Others have cautioned that the miscommunications and misapplication of behavioral genetic research to policy could result in grave social consequences, especially in the area of criminal justice.24 Still others view the new field of behavioral genetics as a reincarnation of widely disavowed beliefs in genetic determinism and eugenics.25

  In 1965 a study published in Nature found that a s
ignificantly higher number of inmates in a prison hospital in Edinburgh, Scotland, described as “dangerously violent” had an extra Y chromosome (XYY males), compared with the general population.26 The authors hypothesized that the presence of an extra Y chromosome produces extra aggressiveness and concluded that this condition increased the chances that an individual would be institutionalized. In 1970 President Richard Nixon’s personal medical adviser suggested that the country make use of this science, proposing a massive program of genetic screening for every 6-year-old to detect the “criminal potential” of preadolescents. Moreover, he suggested that every “hard-core 6-year-old” be sent to “therapeutic” camps where they could learn to be “good social animals.”27

  The XYY study and other similar early studies lacked a satisfactory control group. When the studies were replicated with the proper methodology, scientists learned that XYY males tended to be taller, less intelligent, and more hyperactive but not necessarily more violent than their XY counterparts.28 The search for biological markers for social deviance has been a central theme in behavioral genetics. If such markers were discovered and their reliability were demonstrated, their forensic use would be nearly impossible to prevent so long as the entire human genome remains within the reach of law enforcement.