Returning genetic research results to individuals: points-to-consider

This paper is intended to stimulate debate amongst stakeholders in the international research community on the topic of returning individual genetic research results to study participants. Pharmacogenetics and disease genetics studies are becoming increasingly prevalent, leading to a growing body of information on genetic associations for drug responsiveness and disease susceptibility with the potential to improve health care. Much of these data are presently characterized as exploratory (non-validated or hypothesis-generating). There is, however, a trend for research participants to be permitted access to their personal data if they so choose. Researchers, sponsors, patient advocacy groups, ethics committees and regulatory authorities are consequently confronting the issue of whether, and how, study participants might receive their individual results. Noted international ethico-legal guidelines and public policy positions in Europe and the United States are reviewed for background. The authors offer 'Points-to-Consider' regarding returning results in the context of drug development trials based on their knowledge and experience. Theses considerations include: the clinical relevance of data, laboratory qualifications, informed consent procedures, confidentiality of medical information and the competency of persons providing results to participants. The discussion is framed as a benefit-to-risk assessment to balance the potential positive versus negative consequences to participants, while maintaining the integrity and feasibility of conducting genetic research studies.     

Identifying mutation regions for closely related individuals without a known pedigree

ABSTRACT: BACKGROUND: Linkage analysis is the rst step in the search for a disease gene. Linkage studies have facilitated the identication of several hundred human genes that can harbor mutations leading to a disease phenotype. In this paper, we study a very important case, where the sampled individuals are closely related, but the pedigree is not given. This situation happens very often when the individuals share a common ancestor 6 or more generations ago. To our knowledge, no algorithm can give good results for this case. RESULTS: To solve this problem, we rst developed some heuristic algorithms for haplotype inference without any given pedigree. We propose a model using the parsimony principle that can be viewed as an extension of the model rst proposed by Dan Guseld. Our heuristic algorithm uses Clark's inference rule to infer haplotype segments. CONCLUSIONS: We ran our program both on the simulated data and a set of real data from the phase II HapMap database. Experiments show that our program performs well. The recall value is from 90% to 99% in various cases. This implies that the program can report more than 90% of the true mutation regions. The value of precision varies from 29% to 90%. When the precision is 29%, the size of the reported regions is three times that of the true mutation region. This is still very useful for narrowing down the range of the disease gene location. Our program can complete the computation for all the tested cases, where there are about 110,000 SNPs on a chromosome, within 20 seconds.     

African elephant age determination from teeth: validation from known individuals

We assess tooth‐based age criteria for African elephants developed by Laws in relation to known‐aged individuals in the Amboseli elephant population. Laws’s technique remains a robust and useful mechanism for age determination, although we suggest revisions to the oldest age categories. Blind age assignment to jaws of unknown sex using the Laws criteria resulted in misclassification of M4 and M5; measures overlapped too much to differentiate these teeth by sex. Sexes could be reliably distinguished after age 30 or XIX in tooth category by two measures: mandible thickness and width of the ascending ramus, but individuals of the same known age differed in tooth wear and progression rates. Such variation needs to be incorporated in the error assigned to tooth age categories. Ages at death of found jaws (n = 266) were similar to results of survival analysis from all demographic data (n = 2455), excluding calves whose jaws decompose because of weathering and scavengers. Jaw‐based models of age at death need correction for the inability to detect this early mortality, which artificially extends mean longevity by up to 6 years.     

Accurate partition of individuals into full-sib families from genetic data without parental information.

Two Markov chain Monte Carlo algorithms are proposed that allow the partitioning of individuals into full-sib groups using single-locus genetic marker data when no parental information is available. These algorithms present a method of moving through the sibship configuration space and locating the configuration that maximizes an overall score on the basis of pairwise likelihood ratios of being full-sib or unrelated or maximizes the full joint likelihood of the proposed family structure. Using these methods, up to 757 out of 759 Atlantic salmon were correctly classified into 12 full-sib families of unequal size using four microsatellite markers. Large-scale simulations were performed to assess the sensitivity of the procedures to the number of loci and number of alleles per locus, the allelic distribution type, the distribution of families, and the independent knowledge of population allelic frequencies. The number of loci and the number of alleles per locus had the most impact on accuracy. Very good accuracy can be obtained with as few as four loci when they have at least eight alleles. Accuracy decreases when using allelic frequencies estimated in small target samples with skewed family distributions with the pairwise likelihood approach. We present an iterative approach that partly corrects that problem. The full likelihood approach is less sensitive to the precision of allelic frequencies estimates but did not perform as well with the large data set or when little information was available (e.g., four loci with four alleles).     

The meaning of genetic variation within and between subpopulations

Summary Argumentation is presented which indicates that the additive decomposition of the total genetic variation of a population into variation within and between (among) its subpopulations suffers from conceptual inconsistency. While the measurement of variation between subpopulations can be shown to be identical to the measurement of subpopulation differentiation, the notion of variation within subpopulations, when viewed as a single measurement, cannot be derived as an independent and cogent concept. Rather, it appears to be merely technically defined as the arithmetic difference between the total variation and the variation between subpopulations, and this difference happens to be non-negative for concave measures of variation such as the (statistical) variance or certain measures of genetic diversity. In order to overcome the conceptual inconsistency, variation between subpopulations could be regarded as subpopulation differentiation and the notion of variation within subpopulations could be replaced by measurements of the degree to which the variation in the total population is represented within the subpopulations. A complementary situation with respect to total variation is thus realized once more, and appropriate measures can be directly derived from existing ones.     

Risky individuals and the politics of genetic research into aggressiveness and violence

New genetic technologies promise to generate valuable insights into the aetiology of several psychiatric conditions, as well as a wider range of human and animal behaviours. Advances in the neurosciences and the application of new brain imaging techniques offer a way of integrating DNA analysis with studies that are looking at other biological markers of behaviour. While candidate 'genes for' certain conditions, including schizophrenia and bipolar disorders, are said to be 'un-discovered' at a faster rate than they are discovered, many studies are being conducted on personality traits such as aggressiveness and anti-social traits. The clinical applicability and implications of these studies are often discussed within the scientific community. However, little attention has so far been paid to their possible policy implications in relation to criminality management and to Criminal Law itself. Similarly, the related ethical issues arising in the field of crime control, and the tensions between enhancing security for society and protecting civil liberties, are currently under-explored. This paper investigates these ethical issues by focusing on the views of those professionals - including judges, lawyers, probation officers and social workers - who work with individuals 'deemed at risk' of violent and aggressive behaviours. It also discusses and problematizes mainstream rhetoric and arguments around the notion of 'risky individuals'.     

What research participants want to know about genetic research results: the impact of "genetic exceptionalism"

The disclosure of individual genetic results has generated an ongoing debate about which rules should be followed. We aimed to identify factors related to research participants' preferences about learning the results of genomic studies using their donated tissue samples. We conducted a cross-sectional survey of 279 patients from the United States and Spain who had volunteered to donate a sample for genomic research. Our results show that 48% of research participants would like to be informed about all individual results from future genomic studies using their donated tissue, especially those from the U.S. (71.4%) and those believing that genetic information poses special risks (69.7%). In addition, 16% of research participants considered genetic information to be riskier than other types of personal medical data. In conclusion, our study demonstrates that a high proportion of participants prefer to be informed about their individual results and that there is a higher preference among those research subjects who perceive their genetic information as riskier than other types of personal medical data.     

Upward squatting in individuals with and without patellofemoral pain syndrome: a biomechanical study

The purpose of the study was to test the hypothesis on whether individuals with patellofemoral pain syndrome (PFPS) try to avoid knee position during upward squatting so as not to aggravate this syndrome. Also, we tested whether PFPS would generate changes in the kinetic and electromyographic (EMG) strategies used to perform this task. Eight healthy subjects and 8 subjects with PFPS, but without a history of pain for at least 30 days, took part in the experiment. They were asked to perform upward squatting with knees initially flexed at 60° (very flexed) until reaching an upright position. Angle, velocity, and acceleration (kinematic) were reconstructed for knee and ankle joints. The torques at these joints were calculated using inverse dynamics, taking into account anthropometric and inertial characteristics of each subject, including records from force data. Only activities of major muscles were recorded. The kinetic and EMG profiles were quantified during acceleration and deceleration phases of the upward squatting. Both healthy and PFPS subjects used the same kinetic and EMG strategies to perform the upward squatting, even though the magnitude of the muscle activities were decreased for the latter group. Compared to the control group, the PFPS subjects presented larger joint ankle torques and smaller knee joint torques. However, the subjects avoided keeping their knees very flexed at the initial position. Group differences in the kinetic and EMG strategies can be explained by differences in the initial position, suggesting a protective strategy used by subjects with PFPS. Therefore, for these subjects, coaches and therapists should avoid using this exercise when the knee is required to move above 40° flexion.     

Estimation of average heterozygosity and genetic distance from a small number of individuals

The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the number of individuals to be used for estimating average heterozygosity can be very small if a large number of loci are studied and the average heterozygosity is low. The number of individuals to be used for estimating genetic distance can also be very small if the genetic distance is large and the average heterozygosity of the two species compared is low.     

Factors determining dissemination of results and uptake of genetic testing in families with known BRCA1/2 mutations

BACKGROUND: Uptake of genetic testing remains low, even in families with known BRCA1 and BRCA2 (BRCA1/2) mutations, despite effective interventions to reduce risk. We report disclosure and uptake patterns by BRCA1/2-positive individuals to at-risk relatives, in the setting of no-cost genetic counseling and testing. METHODS: Relatives of BRCA1/2-positive individuals were offered cost-free and confidential genetic counseling and testing. If positive for a BRCA1/2 mutation, participants were eligible to complete a survey about their disclosure of mutation status and the subsequent uptake of genetic testing by at-risk family members. RESULTS: One hundred and fifteen of 142 eligible individuals responded to the survey (81%). Eighty-eight (77%) of those surveyed disclosed results to all at-risk relatives. Disclosure to first-degree relatives (FDRs) was higher than to second-degree relatives (SDRs) and third-degree relatives (TDR) (95% vs. 78%; p < 0.01). Disclosure rates to male versus female relatives were similar, but reported completion of genetic testing was higher among female versus male FDRs (73% vs. 49%; p < 0.01) and SDRs (68% vs. 43%; p < 0.01), and among members of maternal versus paternal lineages (63% vs. 0%; p < 0.01). Men were more likely than women to express general difficulty discussing positive BCRA1/2 results with at-risk family members (90% vs. 70%; p = 0.03), while women reported more emotional distress associated with disclosure than men (48% vs. 13%; p < 0.01). DISCUSSION: We report a very high rate of disclosure of genetic testing information to at-risk relatives. However, uptake of genetic testing among at-risk individuals was low despite cost-free testing services, particularly in men, SDRs, and members of paternal lineages. The complete lack of testing among paternally related at-risk individuals and the lower testing uptake among men signify a significant barrier to testing and a challenge for genetic counselors and physicians working with high-risk groups. Further research is necessary to ensure that family members understand their risk and the potential benefits of genetic counseling.     

The use of stored tissue samples from minors for genetic research: interviews with professionals

Stored tissue sample collections from minors are useful for genetic research. The ethics of the use of stored tissue samples for genetic research continues be a much debated topic of discussion. The use of pediatric samples poses specific ethical questions. Although a substantial corpus of empirical literature exists on the use of samples from adults, not much is known about the opinion of professionals on the use of samples from children. We conducted ten interviews with professionals in the field. Their primary concerns were the fact that consent procedures should not be too bureaucratic, the need for proper research design and privacy protections, the fact that research should not burden children and guidance from ethics committees.     

Prenatal diagnosis of trisomy 21: registration results from a single genetic center

This is a retrospective review of all collected amniotic fluid samples, chorionic villus samples and other fluid-aspirations (hygroma colli fluid/urine from megacystis) over an 11-year period (1996-2006) in a single Genetic Center (University Hospital Gasthuisberg, Leuven), looking at the prenatal diagnosis of trisomy 21. In this study a total of 404 diagnoses of trisomy 21 were made on 29696 samples (1.4%). The prenatal diagnosis of trisomy 21 increased over the years with 0.88% (21/2363) in 1996 and 1.99% (50/2512)in 2006. Also the type of invasive testing changed over the years with an increase of the proportion of trisomy 21- diagnoses by chorionic villussampling from 2001. Looking at the registry for perinatal activities in Flanders for the year 2006 the live birth incidence for trisomy 21 was 1/1782 and this is lower than the often reported incidence oftrisomy 21 at birth of 1/800: it is likely that the use of more sensitive screening methods for the prenatal detection of trisomy 21 and the election of termination for most affected pregnancies affects the birth incidence oftrisomy 21.     

Epilepsy patient-participants and genetic research results as "answers"

Better understanding of how research participants with a known condition ascribe meaning to individual genetic results is important to help researchers and institutional review boards evaluate the potential benefits and harms of disclosing results in the context of genotype-driven research recruitment. Based on 29 in-depth interviews with epilepsy patients participating in a genetic study, we found that this population of research subjects anticipated that genetic research results would provide answers to a range of questions about the research process and their condition. Their multi-layered interpretations underscore the need for clear communication about the nature and limitations of results if individual or aggregate genetic results are returned in the process of recruitment for additional research.     

Hare's affairs: Lessons learnt from a noninvasive genetic monitoring for tracking mountain hare individuals

Systematic monitoring of individuals and their abundance over time has become an important tool to provide information for conservation. For genetic monitoring studies, noninvasive sampling has emerged as a valuable approach, particularly so for elusive or rare animals. Here, we present the 5‐year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in a protected area in the Swiss Alps. We used nuclear microsatellites and a sex marker to identify individuals and assign species to noninvasively collected feces samples. Through including a marker for sex identification, we were able to assess sex ratio changes and sex‐specific demographic parameters over time. Male abundance in the area showed high fluctuations and apparent survival for males was lower than for females. Generally, males and females showed only little temporary migration into and out of the study area. Additionally, using genotyped tissue samples from mountain hares, European hares (Lepus europaeus) and their hybrids, we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2,300 m a.s.l. in spring 2016. For future monitoring studies, we suggest to include complementary analysis methods to reliably infer species identities of the individuals analyzed and, thus, not only monitor mountain hare individual abundance, but also assess the potential threats given through competitive exclusion by and hybridization with the European hare.     

MicroRNA expression profiling of human islets from individuals with and without type 2 diabetes: promises and pitfalls

Recent studies in mouse, involving the β-cell-specific deletion of Dicer1, have highlighted the crucial role of miRNAs (microRNAs) in regulating insulin secretion and consequently Type 2 diabetes. Identifying the individual miRNAs involved in human islet dysfunction may be of diagnostic and therapeutic interest. miRNA expression profiling of human islets isolated from donors with and without Type 2 diabetes may represent one of the first steps in the discovery of these specific miRNAs. The present review discusses some of the potential pitfalls and promises of such an approach.     

The effects of a known family-size distribution on the estimation of genetic parameters.

We consider the question: In a segregation analysis, can knowledge of the family-size distribution (FSD) in the population from which a sample is drawn improve the estimators of genetic parameters? In other words, should one incorporate the population FSD into a segregation analysis if one knows it? If so, then under what circumstances? And how much improvement may result? We examine the variance and bias of the maximum likelihood estimators both asymptotically and in finite samples. We consider Poisson and geometric FSDs, as well as a simple two-valued FSD in which all families in the population have either one or two children. We limit our study to a simple genetic model with truncate selection. We find that if the FSD is completely specified, then the asymptotic variance of the estimator may be reduced by as much as 5%-10%, especially when the FSD is heavily skewed toward small families. Results in small samples are less clear-cut. For some of the simple two-valued FSDs, the variance of the estimator in small samples of one- and two-child families may actually be increased slightly when the FSD is included in the analysis. If one knows only the statistical form of the FSD, but not its parameter, then the estimator is improved only minutely. Our study also underlines the fact that results derived from asymptotic maximum likelihood theory do not necessarily hold in small samples. We conclude that in most practical applications it is not worth incorporating the FSD into a segregation analysis. However, this practice may be justified under special circumstances where the FSD is completely specified, without error, and the population consists overwhelmingly of small families.