Forensic DNA data banking by state crime laboratories.

This article reports the results of a survey of the responsible crime laboratories in the first 19 states with legislation establishing forensic DNA data banks. The survey inquired into the labs' policies and procedures regarding the collection, storage, and analysis of samples; the retention of samples and data; search protocols; access to samples and data by third parties; and related matters. The research suggests that (1) the number of samples collected from convicted offenders for DNA data banking has far surpassed the number that have been analyzed; (2) data banks have already been used in a small but growing number of cases, to locate suspects and to identify associations between unresolved cases; (3) crime labs currently plan to retain indefinitely the samples collected for their data banks; and (4) the nature and extent of security safeguards that crime labs have implemented for their data banks vary among states. The recently enacted DNA Identification Act (1994) will provide $40 million in federal matching grants to states for DNA analysis activities, so long as states comply with specified quality-assurance standards, submit to external proficiency testing, and limit access to DNA information. Although these additional funds should help to ease some sample backlogs, it remains unclear how labs will allocate the funds, as between analyzing samples for their data banks and testing evidence samples in cases without suspects. The DNA Identification Act provides penalties for the disclosure or obtaining of DNA data held by data banks that participate in CODIS, the FBI's evolving national network of DNA data banks, but individual crime labs must also develop stringent internal safeguards to prevent breaches of data-bank security.     

Comparison of three methods to estimate genetic ancestry and control for stratification in genetic association studies among admixed populations

Population stratification may confound the results of genetic association studies among unrelated individuals from admixed populations. Several methods have been proposed to estimate the ancestral information in admixed populations and used to adjust the population stratification in genetic association tests. We evaluate the performances of three different methods: maximum likelihood estimation, ADMIXMAP and Structure through various simulated data sets and real data from Latino subjects participating in a genetic study of asthma. All three methods provide similar information on the accuracy of ancestral estimates and control type I error rate at an approximately similar rate. The most important factor in determining accuracy of the ancestry estimate and in minimizing type I error rate is the number of markers used to estimate ancestry. We demonstrate that approximately 100 ancestry informative markers (AIMs) are required to obtain estimates of ancestry that correlate with correlation coefficients more than 0.9 with the true individual ancestral proportions. In addition, after accounting for the ancestry information in association tests, the excess of type I error rate is controlled at the 5% level when 100 markers are used to estimate ancestry. However, since the effect of admixture on the type I error rate worsens with sample size, the accuracy of ancestry estimates also needs to increase to make the appropriate correction. Using data from the Latino subjects, we also apply these methods to an association study between body mass index and 44 AIMs. These simulations are meant to provide some practical guidelines for investigators conducting association studies in admixed populations.     

“They want to know where they came from”: population genetics,identity, and family genealogy

This paper discusses the changing relationship between population genetics, family genealogy and identity. It reports on empirical research with participants in a genetic study who anticipated that personal feedback on the analysis of their donated samples would elucidate aspects of their own family genealogies. The paper also documents how geneticists, building on the practices of offering personal feedback to research participants, have developed genetic tests marketed directly to people wishing to trace their ancestry. Some of the social and ethical issues raised by this development in the use of genetic testing are considered.     

Assessment of the Relationship between Self-Declared Ethnicity,Mitochondrial Haplogroups and Genomic Ancestry in Brazilian Individuals

In populations that have a high degree of admixture, such as in Brazil, the sole use of ethnicity self-declaration information is not a good method for classifying individuals regarding their ethnicity. Here, we evaluate the relationship of self-declared ethnicities with genomic ancestry and mitochondrial haplogroups in 492 individuals from southeastern Brazil. Mitochondrial haplogroups were obtained by analyzing the hypervariable regions of the mitochondrial DNA (mtDNA), and the genomic ancestry was obtained using 48 autosomal insertion-deletion ancestry informative markers (AIM). Of the 492 individuals, 74.6% self-declared as White, 13.8% as Brown and 10.4% as Black. Classification of the mtDNA haplogroups showed that 46.3% had African mtDNA, and the genomic ancestry analysis showed that the main contribution was European (57.4%). When we looked at the distribution of mtDNA and genomic ancestry according to the self-declared ethnicities from 367 individuals who self-declared as White, 37.6% showed African mtDNA, and they had a high contribution of European genomic ancestry (63.3%) but also a significant contribution of African ancestry (22.2%). Of the 68 individuals who self-declared as Brown, 25% showed Amerindian mtDNA and similar contribution of European and African genomic ancestries. Of the 51 subjects who self-declared as black, 80.4% had African mtDNA, and the main contribution of genomic ancestry was African (55.6%), but they also had a significant proportion of European ancestry (32.1%). The Brazilian population had a uniform degree of Amerindian genomic ancestry, and it was only with the use of genetic markers (autosomal or mitochondrial) that we were able to capture Amerindian ancestry information. Additionally, it was possible to observe a high degree of heterogeneity in the ancestry for both types of genetic markers, which shows the high genetic admixture that is present in the Brazilian population. We suggest that in epidemiological studies, the use of these methods could provide complementary information.     

"They want to know where they came from": population genetics, identity, and family genealogy

This paper discusses the changing relationship between population genetics, family genealogy and identity. It reports on empirical research with participants in a genetic study who anticipated that personal feedback on the analysis of their donated samples would elucidate aspects of their own family genealogies. The paper also documents how geneticists, building on the practices of offering personal feedback to research participants, have developed genetic tests marketed directly to people wishing to trace their ancestry. Some of the social and ethical issues raised by this development in the use of genetic testing are considered.     

Development of two multiplex mini-sequencing panels of ancestry informative SNPs for studies in Latin Americans: an application to populations of the State of Minas Gerais (Brazil)

Admixture occurs when individuals from parental populations that have been isolated for hundreds of generations form a new hybrid population. Currently, interest in measuring biogeographic ancestry has spread from anthropology to forensic sciences, direct-to-consumers personal genomics, and civil rights issues of minorities, and it is critical for genetic epidemiology studies of admixed populations. Markers with highly differentiated frequencies among human populations are informative of ancestry and are called ancestry informative markers (AIMs). For tri-hybrid Latin American populations, ancestry information is required for Africans, Europeans and Native Americans. We developed two multiplex panels of AIMs (for 14 SNPs) to be genotyped by two mini-sequencing reactions, suitable for investigators of medium-small laboratories to estimate admixture of Latin American populations. We tested the performance of these AIMs by comparing results obtained with our 14 AIMs with those obtained using 108 AIMs genotyped in the same individuals, for which DNA samples is available for other investigators. We emphasize that this type of comparison should be made when new admixture/population structure panels are developed. At the population level, our 14 AIMs were useful to estimate European admixture, though they overestimated African admixture and underestimated Native American admixture. Combined with more AIMs, our panel could be used to infer individual admixture. We used our panel to infer the pattern of admixture in two urban populations (Montes Claros and Manhua?u) of the State of Minas Gerais (southeastern Brazil), obtaining a snapshot of their genetic structure in the context of their demographic history.     

Consumer (dis-)interest in genetic ancestry testing: the roles of race,immigration, and ancestral certainty

Genetic ancestry testing (GAT) is marketed as a way to make up for missing knowledge about one’s ancestry. Previous research questions the GAT industry’s ability to fulfill this promise in terms of the validity and reliability of test results. We instead explore the demand side of GAT, evaluating who is most and least likely to express interest in GAT. Using data from an original, nationwide survey of over 100,000 American adults, we find that GAT interest is related to both self-identified race and immigrant generation, with Asian Americans and first-generation immigrants expressing the least interest. Our quantitative and qualitative evidence suggests interest is further shaped by a pre-existing sense of ancestral certainty, leading some individuals to decline GAT, even if it were free. How interest and ancestral certainty are patterned has implications for who is included in – and thus for the conclusions that can be drawn from – genetic ancestry databases.     

The breakdown of genomic ancestry blocks in hybrid lineages given a finite number of recombination sites

When a lineage originates from hybridization genomic blocks of contiguous ancestry from different ancestors are fragmented through genetic recombination. The resulting blocks are delineated by so called junctions, which accumulate with every generation that passes. Modeling the accumulation of ancestry block junctions can elucidate processes and timeframes of genomic admixture. Previous models have not addressed ancestry block dynamics for chromosomes that consist of a finite number of recombination sites. However, genomic data typically consist of informative markers that are interspersed with fragments for which no ancestry information is available. Hence, repeated recombination events may occur between markers, effectively removing existing junctions. Here, we present an analytical treatment of the dynamics of the mean number of junctions over time, taking into account the number of recombination sites per chromosome, population size, genetic map length, and the frequency of the ancestral species in the founding hybrid swarm. We describe the expected number of junctions using equidistant molecular markers and estimate the number of junctions using random markers. This extended theory of junctions thus reflects properties of empirical data and can serve to study the genomic patterns following admixture.     

The anthropometric legacy of Franz Boas

Franz Boas was responsible for obtaining anthropometric data from approximately 27,000 subjects living around the turn-of-the-century. The subjects are of Native American, Siberian and European ancestry. These data have been entered into databases and are available for research. This paper describes the circumstances under which these data were collected and discusses their research potential.     

Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture.

Genes that underlie ethnic differences in disease risk can be mapped in affected individuals of mixed descent if the ancestry of the alleles at each marker locus can be assigned to one of the two founding populations. Linkage can be detected by testing for association of the disease with the ancestry of alleles at the marker locus, by conditioning on the admixture (defined as the proportion of genes that have ancestry from the high-risk population) of both parents. With regard to exploiting the effects of admixture, this test is more flexible and powerful than the transmission-disequilibrium test. Under the assumption of a multiplicative model, the statistical power for a given sample size depends only on parental admixture and the risk ratio r between populations that is generated by the locus. The most informative families are those in which mean parental admixture is .2-.7 and in which admixture is similar in both parents. The number of markers required for a genome search depends on the number of generations since admixture and on the information content for ancestry (f) of the markers, defined as a function of allele frequencies in the two founding populations. Simulations using a hidden Markov model suggest that, when admixture has occurred 2-10 generations earlier, a multipoint analysis using 2,000 biallelic markers, with f values of 30%, can extract 70%-90% of the ancestry information for each locus. Sets of such markers could be selected from libraries of single-nucleotide polymorphisms, when these become available.     

Estimation of allele frequencies for VNTR loci

VNTR loci provide valuable information for a number of fields of study involving human genetics, ranging from forensics (DNA fingerprinting and paternity testing) to linkage analysis and population genetics. Alleles of a VNTR locus are simply fragments obtained from a particular portion of the DNA molecule and are defined in terms of their length. The essential element of a VNTR fragment is the repeat, which is a short sequence of basepairs. The core of the fragment is composed of a variable number of identical repeats that are linked in tandem. A sample of fragments from a population of individuals exhibits substantial variation in length because of variation in the number of repeats. Each distinct fragment length defines an allele, but any given fragment is measured with error. Therefore the observed distribution of fragment lengths is not discrete but is continuous, and determination of distinct allele classes is not straightforward. A mixture model is the natural statistical method for estimating the allele frequencies of VNTR loci. In this article we develop nonparametric methods for obtaining the distribution of allele sizes and estimates of their frequencies. Methods for obtaining maximum-likelihood estimates are developed. In addition, we suggest an empirical Bayes method to improve the maximum-likelihood estimates of the gene frequencies; the empirical Bayes procedure effects a local smoothing. The latter method works particularly well when measurement error is large relative to the repeat size, because the estimated distribution of allele frequencies when maximum likelihood is used is unreliable because of an alternating pattern of over- and underestimation. We define alleles and estimate the allele frequencies for two VNTR loci from the human genome (D17S79 and D2S44), from data obtained from Lifecodes, Inc.     

Parental attitudes toward genetic testing for pediatric deafness

Recent molecular genetic advances have resulted in genetic testing becoming an option for deaf individuals and their families. However, there is little information about the interest in such testing. To investigate this issue, parents with normal hearing who have one or more deaf children were surveyed about their attitudes toward diagnostic, carrier, and prenatal genetic testing for deafness. This population was chosen because it represents the majority of individuals who are encountered in clinical practice, given that 90%-95% of deaf individuals are born to persons with normal hearing. Of 328 surveys distributed, 96 were completed and returned. Of the respondents, 96% recorded a positive attitude toward genetic testing for deafness, including prenatal testing, although none would use this information to terminate an affected pregnancy. All respondents had a poor understanding of genetics, with 98% both incorrectly estimating the recurrence risk of deafness and misunderstanding the concept of inheritance. Notably, these findings were similar in the group who had had genetic testing for their children and in the group who had not, suggesting either that the parents who received genetic testing did not receive genetic counseling or that the counseling was not effective. On the basis of these results, it was concluded that this population is interested in the use of genetic testing and that testing should not be done without first providing formal genetic counseling. Appropriate counseling can help parents to understand the risks, benefits, and limitations of genetic testing.     

Geographic patterns of genome admixture in Latin American Mestizos

The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region.     

Crossing disciplinary lines: reconciling social and genomic perspectives on the histories and legacies of the transatlantic trade in enslaved Africans

Over the past two decades, advances in the field of genomics have presented new opportunities to shed light upon the origins of enslaved Africans and their contemporary descendants. While this possibility has caused enthusiasm among members of the public, it has provoked contention within the academic sphere. This paper represents an attempt to reconcile these opposing disciplinary divisions, by examining, explaining, and discussing the processes involved in the production of genetic “ancestry” estimates, in order to moderate the aura of absolute “truth” that is often associated with such techniques. Our discussion focuses on two case studies – the academic use of ancient DNA analyses to estimate the geographic origins of historically enslaved individuals, and the commercialization of DNA “ancestry” testing techniques aimed at African-American roots-seekers – and draws upon recent ethnographic data relating to the experiences of test creators and test-takers, in order to contribute to this debate.     

DNA from the Past Informs Ex Situ Conservation for the Future: An “Extinct” Species of Galápagos Tortoise Identified in Captivity

Background

Although not unusual to find captive relicts of species lost in the wild, rarely are presumed extinct species rediscovered outside of their native range. A recent study detected living descendents of an extinct Galápagos tortoise species (Chelonoidis elephantopus) once endemic to Floreana Island on the neighboring island of Isabela. This finding adds to the growing cryptic diversity detected among these species in the wild. There also exists a large number of Galápagos tortoises in captivity of ambiguous origin. The recently accumulated population-level haplotypic and genotypic data now available for C. elephantopus add a critical reference population to the existing database of 11 extant species for investigating the origin of captive individuals of unknown ancestry.

Methodology/Findings

We reanalyzed mitochondrial DNA control region haplotypes and microsatellite genotypes of 156 captive individuals using an expanded reference database that included all extant Galápagos tortoise species as well as the extinct species from Floreana. Nine individuals (six females and three males) exhibited strong signatures of Floreana ancestry and a high probability of assignment to C. elephantopus as detected by Bayesian assignment and clustering analyses of empirical and simulated data. One male with high assignment probability to C. elephantopus based on microsatellite genotypic data also possessed a “Floreana-like” mitochondrial DNA haplotype.

Significance

Historical DNA analysis of museum specimens has provided critical spatial and temporal components to ecological, evolutionary, taxonomic and conservation-related research, but rarely has it informed ex situ species recovery efforts. Here, the availability of population-level genotypic data from the extinct C. elephantopus enabled the identification of nine Galápagos tortoise individuals of substantial conservation value that were previously misassigned to extant species of varying conservation status. As all captive individuals of C. elephantopus ancestry currently reside at a centralized breeding facility on Santa Cruz, these findings permit breeding efforts to commence in support of the reestablishment of this extinct species to its native range.     

Risk reversals in predictive testing for Huntington disease.

The first predictive testing for Huntington disease (HD) was based on analysis of linked polymorphic DNA markers to estimate the likelihood of inheriting the mutation for HD. Limits to accuracy included recombination between the DNA markers and the mutation, pedigree structure, and whether DNA samples were available from family members. With direct tests for the HD mutation, we have assessed the accuracy of results obtained by linkage approaches when requested to do so by the test individuals. For six such individuals, there was significant disparity between the tests. Three went from a decreased risk to an increased risk, while in another three the risk was decreased. Knowledge of the potential reasons for these changes in results and impact of these risk reversals on both patients and the counseling team can assist in the development of strategies for the prevention and, where necessary, management of a risk reversal in any predictive testing program.     

Disclosure of personal medical information: differences among parents and affected adults for genetic and nongenetic conditions

Protecting the confidentiality of medical information has been an issue of great interest in the fields of bioethics, public policy, and law. Few empirical studies have addressed patient experiences and attitudes toward disclosure of private medical information in multiple contexts such as health insurance, employment, and the family. Furthermore, it is unclear whether differences exist in experiences and attitudes about privacy between those living with a serious medical condition versus those who have a child with a medical condition. The study sought to determine whether attitudes and experiences related to medical privacy and confidentiality differ between affected adults and parents of affected children. Interviews were conducted with 296 adults and parents of children with sickle cell disease (SCD), cystic fibrosis (CF), or diabetes mellitus (DM). This cross-sectional study collected data regarding their experiences, attitudes, and beliefs concerning medical privacy and confidentiality. Multinomial logistic regression analysis was conducted on quantitative data. Qualitative analysis was conducted on data from open-ended response items. Parents disclose their child's diagnosis to others more often than affected adults disclose their own disease status. Parents are less likely than affected adults to regret their disclosure, to hope others do not find out, to have been pressured to share information, and to be asked about their disease by employers. Affected adults express greater concern about disclosure, a greater prevalence and greater fear of discrimination, and experience greater pressure from family members to disclose. Clinicians and researchers working with these populations should consider these differences in privacy and disclosure. Further study is necessary to examine the implications of these differences in attitudes and experiences concerning insurance, employment, and social interactions among persons with these conditions.     

Laws restricting health insurers' use of genetic information: impact on genetic discrimination

Since 1991, 28 states have enacted laws that prohibit insurers' use of genetic information in pricing, issuing, or structuring health insurance. This article evaluates whether these laws reduce the extent of genetic discrimination by health insurers. From the data collected at multiple sites, we find that there are almost no well-documented cases of health insurers either asking for or using presymptomatic genetic test results in their underwriting decisions, either (a) before or after these laws have been enacted or (b) in states with or without these laws. By using both in-person interviews with insurers and a direct market test, we found that a person with a serious genetic condition who is presymptomatic faces little or no difficulty in obtaining health insurance. Furthermore, there are few indications that the degree of difficulty varies according to whether a state regulates the use of genetic information. Nevertheless, these laws have made it less likely that insurers will use genetic information in the future. Although insurers and agents are only vaguely aware of these laws, the laws have shaped industry norms and attitudes about the legitimacy of using this information.     

Lack of interest by nonpregnant couples in population-based cystic fibrosis carrier screening.

We used signs and letters to offer free cystic fibrosis (CF) carrier screening to nonpregnant adults in stable relationships who visited numerous clinical and nonclinical sites in Nashville. A total of 179 individuals (<<1% of those eligible) elected to be tested. To understand this observation, we used questionnaires to assess individuals' attitudes about genetic testing in general and about CF carrier screening in particular (n=873). Participants expressed conflicting views about carrier screening. More than 90% of people thought that genetic testing should at least be available. Most respondents said that the views of their partners and physicians were important in their decision making, and most believed that these others favored genetic testing. Yet, more than two-thirds indicated that such factors as insurability, being "at risk," what they would need to learn, abortion, and religious beliefs were important in their decision making, opinions that mitigated against genetic testing. In particular, one-third feared that carriers would lose their health insurance, one-quarter said that they would have been more interested had they been able to provide DNA by buccal swab rather than by finger stick, and less than one-sixth believed that genetic testing was meddling in God's plan. In the face of both the low level of use of free CF carrier screening by nonpregnant couples when it was not offered in person by health-care professionals and the wide variety of concerns demonstrated, we believe that clinicians should not routinely offer carrier screening to nonpregnant individuals who do not have a family history of CF.     

Genotoxicity testing of biotechnology-derived products. Report of a GUM task force. Gesellschaft für Umweltmutationsforschung

Various aspects of genotoxicity testing of biotechnology-derived products are discussed based on information gathered from a questionnaire which was sent to about 30 predominantly European companies. Feedback was received from 13 companies on 78 compounds, mostly recombinant proteins but also on a number of nonrecombinant proteins, which had been assessed for genotoxicity in a total of 177 tests. Four of the 78 compounds appeared to elicit reproducible genotoxic effects. For one of these compounds, the activity could be related to a nonpeptidic linker molecule. No scientifically convincing rationale for the other three compounds could be established, although, at least for two compounds, their activity may be connected with the enzymatic/hormonal activity. In addition to the survey, published reports on genotoxicity testing of biotechnology products were reviewed. The data are discussed relative to whether genotoxicity testing is a valuable exercise when assessing potentially toxic liabilities of biotechnology-derived compounds. It is concluded that genotoxicity testing is generally inappropriate and unnecessary, a position which is in accordance with the available guidelines addressing this area. For the 'average' protein, electrophilic reactions are difficult to envision. Indirect reactions via DNA metabolism and growth regulation seem possible for only very specific proteins such as nucleases, growth factors, cytokines. No information on testing of different types of biotechnology-derived products (e.g., ribozymes, antisense-oligonucleotides, DNA vaccines) has been received in the questionnaires. Discussion of their potential to cause genotoxic changes was based on literature reports. Even for those products for which concerns of genotoxic/tumourigenic potential cannot be completely ruled out, e.g., because of their interaction with DNA metabolism or proliferation control, the performance of standard genotoxicity assays generally appears to be of little value. All information, including also information on the occurrence of genotoxic impurities, has been utilized to formulate a decision tree approach for the genotoxicity testing of biotechnology-derived products.