Quality control in molecular genetic testing

DNA-based testing for genetic diseases has developed from nothing into a principal part of laboratory medicine over the past 15 years. In the rush to bring these powerful new technologies into medical use, issues of quality have not always been given sufficient attention. Efforts are now being made to assess the quality of the output of genetic testing laboratories, and the results show that there is room for improvement.     

Knowledge, attitudes, and utilization of BRCA1/2 testing among women with early-onset breast cancer

A total of 2,400 questionnaires were mailed to members of two mid-Atlantic breast cancer awareness/support groups to investigate the association between attitudes, knowledge, and use of BRCA1/2 testing among women with early-onset breast cancer. Of the 493 (21%) questionnaires returned, 406 respondents had a diagnosis of breast cancer, of whom 248 were diagnosed prior to age 50 and included in the analyses. Eighty-three percent (206/248) of these women had heard of BRCA1/2 testing and 12.5% (31/248) had undergone BRCA1/2 testing. Among women who had heard of BRCA1/2 testing, women who had been tested were younger (p = 0.03), more likely to have a college education (p = 0.03), more likely to have a family member who had undergone BRCA1/2 testing (p = 0.005), and had greater knowledge, more positive attitudes, and fewer negative attitudes about BRCA1/2 testing (p = 0.02, p = 0.004, and p = 0.004, respectively). In this sample, knowledge regarding BRCA1/2 testing is high, but uptake of genetic testing is low. Lack of information regarding how genetic testing might alter health-care decisions and fear about the genetic testing procedure, its costs, and possible false-positive results are associated with low uptake of genetic testing. Further education regarding these specific points may enhance the use of genetic testing.     

Review of capture-recapture methods applicable to noninvasive genetic sampling

The use of noninvasive genetic sampling to identify individual animals for capture-recapture studies has become widespread in the past decade. Strong emphasis has been placed on the field protocols and genetic analyses with fruitful results. Little attention has been paid to the capture-recapture application for this specific type of data beyond stating the effects of assumption violations. Here, we review the broad class of capture-recapture methods that are available for use with DNA-based capture-recapture data, noting the array of biologically interesting parameters such as survival, emigration rates, state transition rates and the finite rate of population change that can be estimated from such data. We highlight recent developments in capture-recapture theory specifically designed for noninvasive genetic sampling data.     

Attitudes to genetic testing in families with multiple cases of bipolar disorder

OBJECTIVES: This study assesses interest in genetic testing for gene variations associated with bipolar disorder and associated information needs. METHODS: Two hundred individuals (95 unaffected and 105 affected with either bipolar disorder, schizoaffective disorder--manic type, or recurrent major depression) from families with multiple cases of bipolar disorder were assessed, using mailed, self-administered questionnaires. RESULTS: The percentage of participants reporting interest in genetic testing was associated with the degree of certainty with which any test would indicate the development of bipolar disorder. Interest in genetic testing, given a 25% lifetime risk scenario, was lowest (with 77% of participants indicating interest), and highest for the 100% lifetime risk scenario (92%). Eighty percent of participants indicated interest in genetic testing of their own children; of these 30% reported wanting their children tested at birth, and 33% in early childhood. Forty-one percent of participants reported that they would be interested in preimplantation genetic diagnosis, and 54% in prenatal testing. LIMITATIONS: The possibility of ascertainment bias cannot be ruled out. Interest in hypothetical genetic testing for bipolar disorder may not necessarily translate into actual utilization. CONCLUSIONS: These results indicate that uptake of genetic testing for genotyping for low-risk alleles related to bipolar disorder is likely to be lower than for testing for high-penetrance gene mutations that follow Mendelian inheritance. The discrepancy between the desired age of testing children and the accepted current practice may be a source of distress and conflict for parents and health professionals alike.     

Attitudes toward genetic testing in patients at risk for HNPCC/FAP and the German population

Adequate knowledge regarding hereditary diseases and genetics, as well as personal attitudes toward gene tests, are major determinants of optimal utilization of genetic testing. In the present study, we aimed to explore the general attitudes toward genetic testing in a sample representative of the German general population (n = 2,076) and to compare the attitudes of persons at risk for hereditary non-polyposis colorectal cancer/familial adenomatous polyposis (HNPCC/FAP) (n = 36) who had attended a university genetic counseling service, with a matched general population sample. We administered a subset of a questionnaire previously used in a Finnish study (Jallinoja et al., 1998). The 12 statements pertain to approval, disapproval, and concern for genetic testing. Overall, the results reveal high approval of genetic testing in the German population and in at-risk persons. In accordance with other studies, we find that the attitudes of individuals for whom hereditary disease is a salient issue of personal relevance and the attitudes of the general public are very similar. Only a few significant differences between these two samples emerged, indicating that at-risk persons hold a more favourable view of the testing. One intriguing finding was the high rate of "don't know" responses, especially in the general population sample. Compared to results from Finland, approval of genetic testing is lower in the German population, and endorsement of "don't knows" is remarkably higher. We argue for increased attention to the issue of attitude change after genetic counseling and for the need of comparative cross-cultural research on attitudes toward gene technology.     

Genotype-based screening for hereditary hemochromatosis: II. Attitudes toward genetic testing and psychosocial impact--a report from a German pilot study

In collaboration with the German Sickness Fund (Kaufm?nnische Krankenkasse-KKH), we conducted a pilot study on DNA-based population screening of hereditary hemochromatosis (HH) in Germany. The health insurance organization KKH briefly informed their members about the possibility to participate voluntarily in this pilot project. A total of 5882 KKH members contacted us and received detailed information on the aim of the project and clinical and genetic aspects of HH. Of these individuals, 3961 requested HFE genotyping. After genotype results had been communicated to the participants' general practitioner, we sent a self-administered questionnaire to all homozygous (n = 67) and heterozygous (n = 485) as well as 448 wild-type study participants (sigma = 1000) to assess the psychosocial impact of HFE genotyping. In addition, questionnaires were sent to 8000 randomly selected members of the KKH to investigate their attitude toward genetic testing. Six hundred thirty-one (63.1%) of the test participants and 2141 (26.8%) of the randomly chosen KKH members responded. A total of 59.1% of the members would generally accept predictive genetic testing and 3.7% objected to such tests in principle. Individuals with higher educational status accepted predictive testing significantly more often than individuals with less education. Of the tested individuals, 69.9% thought that participation in the pilot study was probably beneficial for them and 1% (5 heterozygotes and 1 wild-type) thought that it was probably harmful. Of the participants, 94.6% judged their decision to have participated in the pilot study as right and 0.3% (2 heterozygotes) as probably wrong. Only very few of the tested individuals underwent pretest (1 case) or posttest (11 cases) genetic counseling. We conclude that genotype- based screening for HH is generally accepted and was perceived as beneficial. Negative psychosocial consequences are rare and could presumably have been prevented by delivering appropriate pretest and posttest information.     

Preimplantation genetic diagnosis in Saudi Arabia

Preimplantation genetic diagnosis (PGD) testing is the practice of obtaining a cellular biopsy sample from a developing human oocyte or embryo, acquired via a cycle of in vitro fertilization (IVF); evaluating the genetic composition of this sample; and using this information to determine which embryos will be optimal for subsequent uterine transfer. PGD has become an increasingly useful adjunct to IVF procedures. The ability to provide couples who are known carriers of genetic abnormalities the opportunity to deliver healthy babies has opened a new frontier in reproductive medicine. The purpose of the PGD is enables us to choose which embryos will be implanted into the mother. In the present study 137 families who had undergone IVF at Habib Medical Centre, were enrolled for the PGD analysis. The couple visited the clinic for the sex selection, recurrent fetal loss and with the recurrent IVF failure. 802 embryos were tested by the biopsy method and 512 are found to be normal and 290 were abnormal embryos. In this study only 24% of the embryos were transferred and the remaining was not transferred because of the abnormalities or undesired sex of the embryos. The structural and numerical abnormalities were found to be 16.8%.     

The role of financial factors in acceptance of clinical BRCA genetic testing

Many women who are offered BRCA genetic testing by genetics professionals do not have the test, possibly for financial reasons. We explored financial factors implicated in non-uptake of BRCA testing in women who had received genetic counseling in a clinical setting. Specifically, we described financial factors (affordability, health insurance, other) involved with BRCA testing; compared nonfinancial factors (disease, sociodemographic, risk assessment) in women who did not have BRCA testing (nontesters) with women who had the test (testers); showed associations of financial and nonfinancial factors with BRCA testing; and identified predictors of non-uptake of BRCA testing. The sample of 100 women (64 nontesters and 36 testers) completed an anonymous mailed survey on financial factors; 52 of the nontesters answered questions about nonfinancial factors. Testers had significantly better affordability and insurance coverage (p < 0.001), more diagnoses of breast or ovarian cancer (p < 0.05) and higher rates of receiving post-counseling risk estimates (p < 0.05), than nontesters. Non-uptake was 5.5-fold more likely in women that could not afford full or partial payment for the test and was 15.5-fold more likely in women that did not recall receiving risk estimates post-counseling. For many women having risk factors for breast/ovarian cancer, affordability of BRCA testing and insurance coverage for the test remain problematic. Post-counseling reminders of risk estimates may contribute to uptake of testing.     

Differences between African Americans and Whites in their attitudes toward genetic testing for Alzheimer's disease

The possibility of predictive genetic testing for Alzheimer's disease (AD) has prompted examination of public attitudes toward this controversial new health-care option. This is the first study to examine differences between Whites and African Americans with regard to: (1) interest in pursuing genetic testing for AD, (2) reasons for pursuing testing, (3) anticipated consequences of testing, and (4) beliefs about testing. We surveyed a convenience sample of 452 adults (61% white; 39% African American; 78% female; mean age = 47 years; 33% with family history of AD). Both racial groups indicated general interest in predictive genetic testing for AD, viewed it as having many potential benefits, and believed it should be offered with few restrictions. However, in comparison to whites, African Americans showed less interest in testing (p < 0.01), endorsed fewer reasons for pursuing it (p < 0.01), and anticipated fewer negative consequences from a positive test result (p < 0.001). These preliminary findings show important distinctions between whites and African Americans in their attitudes toward genetic testing for AD. These differences may have implications for how different racial and ethnic groups will respond to genetic testing programs and how such services should be designed. Future research in real-life testing situations with more representative samples will be necessary to confirm these racial and cultural differences in perceptions of genetic testing.     

Ethical issues in the diagnostic genetic testing process

The diagnostic genetic testing process has certain unique ethical features and deserves special consideration. The purpose of this study was to determine through empirical research, using focussed interview, what ethical issues are involved in the diagnostic genetic testing process. This article describes views and perceptions of adult patients, parents of child patients and various personnel groups (n = 30). The ethical issues were analysed classified into three main categories: a) personnel characteristics, including personality, professional skills, morals and values; b) realization of ethical principles in the examination process, with subcategories of knowledge, autonomy, data protection and equity; and c) consequences of genetic testing, including patients' control over their own lives, manifestation of heterogeneity and outlook on the world. Problematic ethical issues in all three main categories were described in a more many‐sided way by parents and personnel than by adult patients. In the future, attention should be paid to the content areas highlighted by the study, in both clinical practice and further studies.     

Ethical issues in the diagnostic genetic testing process

The diagnostic genetic testing process has certain unique ethical features and deserves special consideration. The purpose of this study was to determine through empirical research, using focussed interview, what ethical issues are involved in the diagnostic genetic testing process. This article describes views and perceptions of adult patients, parents of child patients and various personnel groups (n=30). The ethical issues were analysed classified into three main categories: a) personnel characteristics, including personality, professional skills, morals and values; b) realization of ethical principles in the examination process, with subcategories of knowledge, autonomy, data protection and equity; and c) consequences of genetic testing, including patients' control over their own lives, manifestation of heterogeneity and outlook on the world. Problematic ethical issues in all three main categories were described in a more many-sided way by parents and personnel than by adult patients. In the future, attention should be paid to the content areas highlighted by the study, in both clinical practice and further studies.     

Comparison between RAPD and SSR molecular markers in detecting genetic variation in kiwifruit (Actinidia deliciosa A. Chev)

Two different DNA-based techniques, random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers, were used for fingerprinting kiwifruit genotypes and for detecting undesirable genetic variation in micropropagated plants. The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Two cluster analyses were performed to express - in the form of dendrograms - the relationships among the genotypes and the genetic variability detected. Both DNA-based techniques were able to amplify all of the genotypes, but only SSR markers could detect genetic variation induced in micropropagated plants of cv. Tomuri. Two hypotheses were formulated to explain these results, both of them are in agreement with the results obtained using these two types of molecular markers. We conclude that when the tissue culture technique is used, the analysis of somaclonal variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for SSR and RAPD markers.     

Advances in genetic analysis and biotechnology of the cultivated button mushroom, Agaricus bisporus

During the last decade several major breakthroughs have been achieved in mushroom biotechnology, which greatly enhanced classical mushroom breeding. DNA-based technologies such as restriction fragment length polymorphisms and randomly amplified polydisperse DNA sequences have allowed for a measure of genetic diversity, for the isolation of homokaryons, for the determination of inheritance of nuclear and mitochondrial markers, and for the production of a genetic linkage map. The recent availability of ready-to-use and affordable DNA technologies has resulted in a substantial increase in the number of Agaricus bisporus genes that have been identified and characterized. A major breakthrough was achieved in 1996 when the first successful and stable transformation system of A. bisporus was reported. Together, the availability of an increasing number of known genes and the possibility to produce transgenic mushrooms will result in a better understanding of the molecular, physiological and biochemical processes that are essential for mushroom production, shelf life and quality aspects such as flavor, texture and disease resistance. Some potential targets for strain improvement are discussed, such as the genes involved in brown discoloration, substrate utilization, carbon and nitrogen metabolism, and fruit body development. Received: 19 January 1999 / Received revision: 27 May 1999 / Accepted: 4 June 1999     

Correlates of genetic monogamy in socially monogamous mammals: insights from Azara's owl monkeys

Understanding the evolution of mating systems, a central topic in evolutionary biology for more than 50 years, requires examining the genetic consequences of mating and the relationships between social systems and mating systems. Among pair-living mammals, where genetic monogamy is extremely rare, the extent of extra-group paternity rates has been associated with male participation in infant care, strength of the pair bond and length of the breeding season. This study evaluated the relationship between two of those factors and the genetic mating system of socially monogamous mammals, testing predictions that male care and strength of pair bond would be negatively correlated with rates of extra-pair paternity (EPP). Autosomal microsatellite analyses provide evidence for genetic monogamy in a pair-living primate with bi-parental care, the Azara''s owl monkey (Aotus azarae). A phylogenetically corrected generalized least square analysis was used to relate male care and strength of the pair bond to their genetic mating system (i.e. proportions of EPP) in 15 socially monogamous mammalian species. The intensity of male care was correlated with EPP rates in mammals, while strength of pair bond failed to reach statistical significance. Our analyses show that, once social monogamy has evolved, paternal care, and potentially also close bonds, may facilitate the evolution of genetic monogamy.     

Amplified fragment length polymorphisms as a tool for DNA fingerprinting sunflower germplasm: genetic diversity among oilseed inbred lines

 Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints. The AFLP diversity of sunflower has not been described, and much of the public germ plasm of sunflower has not yet been fingerprinted. Our objectives were to: (1) estimate genetic similarities, polymorphism rates, and polymorphic information contents (PICs) for AFLP markers among elite public oilseed inbred lines, and (2) assess the genetic diversity of inbred lines using genetic similarities estimated from AFLP fingerprints. We produced fingerprints for 24 public inbred lines of sunflower (Helianthus annuus L.) using six AFLP primer combinations. These primers produced a total of 359 AFLP markers or about 60 markers per primer combination. Genetic similarities ranged from 0.70 to 0.91, polymorphism rates ranged from 7 to 24%, and PICs ranged from 0.0 to 0.5. Genetic similarities were lower overall for maintainer (B)×restorer (R) crosses than for B×B or R×R crosses. Principal-coordinate and cluster analyses separated lines into two groups, one for B-lines and another for R-lines. These groupings illustrate the breeding history and basic heterotic pattern (B×R) of sunflower and the widespread practice of using B×B and R×R crosses to develop new lines. There were, nevertheless, distinct subgroups within these groups. These subgroups may represent unique heterotic groups and create a basis for formally describing heterotic patterns in sunflower. Received: 10 June 1996 / Accepted: 4 April 1997     

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.     

Speciation in reverse: morphological and genetic evidence of the collapse of a three-spined stickleback (Gasterosteus aculeatus) species pair

Historically, six small lakes in southwestern British Columbia each contained a sympatric species pair of three-spined sticklebacks (Gasterosteus aculeatus). These pairs consisted of a 'benthic' and 'limnetic' species that had arisen postglacially and, in four of the lakes, independently. Sympatric sticklebacks are considered biological species because they are morphologically, ecologically and genetically distinct and because they are strongly reproductively isolated from one another. The restricted range of the species pairs places them at risk of extinction, and one of the pairs has gone extinct after the introduction of an exotic catfish. In another lake, Enos Lake, southeastern Vancouver Island, an earlier report suggested that its species pair is at risk from elevated levels of hybridization. We conducted a detailed morphological analysis, as well as genetic analysis of variation at five microsatellite loci for samples spanning a time frame of 1977 to 2002 to test the hypothesis that the pair in Enos Lake is collapsing into a hybrid swarm. Our morphological analysis showed a clear breakdown between benthics and limnetics. Bayesian model-based clustering indicated that two morphological clusters were evident in 1977 and 1988, which were replaced by 1997 by a single highly variable cluster. The most recent 2000 and 2002 samples confirm the breakdown. Microsatellite analysis corroborated the morphological results. Bayesian analyses of population structure in a sample collected in 1994 indicated two genetically distinct populations in Enos Lake, but only a single genetic population was evident in 1997, 2000, and 2002. In addition, genetic analyses of samples collected in 1997, 2000, and 2002 showed strong signals of 'hybrids'; they were genetically intermediate to parental genotypes. Our results support the idea that the Enos Lake species pair is collapsing into a hybrid swarm. Although the precise mechanism(s) responsible for elevated hybridization in the lake is unknown, the demise of the Enos Lake species pair follows the appearance of an exotic crayfish, Pascifasticus lenisculus, in the early 1990s.     

Principles of formalizing a quantitative evaluation of the genetic danger of chemical compounds for man

Specific characteristics of the mutagenic effect of chemicals, which must be taken into account in developing the test system to assess the potential genetic risk caused by chemical substances, are considered. The organizational principles of the procedures currently available for testing and ranking chemicals by their mutagenic and carcinogenic hazard to humans are discussed. The use of selective information suggested by Wiener and Shannon as an efficiency measure of testing and estimating the potential genetic hazard of chemical substances is substantiated. The feasibility of this approach was demonstrated by testing the efficiency of the battery of two short-term in vitro tests as an example. It was shown that selective information is able to serve as an integral universal criterion of the efficiency of testing, if either one test or the test battery were used.     

Comparative analysis of genetic diversity in pea assessed by RFLP- and PCR-based methods

DNA-based molecular-marker techniques have been proven powerful in genetic diversity estimations. Among them, RFLP was the first and is still the most commonly used in the estimation of genetic diversity of eukaryotic species. The recently developed PCR-based multiple-loci marker techniques, which include RAPD, AFLP, Microsatellite-AFLP and inter-SSR PCR, are playing increasingly important roles in this type of research. Despite the wide application of these techniques, no direct comparison of these methods in the estimation of genetic diversity has been carried out. Here we report a direct comparison of DNA-based RFLP with various PCR-based techniques regarding their informativeness and applicability for genetic diversity analysis. Among ten pea genotypes studied, all the PCR-based methods were much more informative than cDNA-RFLP. Genetic diversity trees were derived from each marker technique, and compared using Mantel's test. By this criterion, all trees derived from the various molecular marker techniques, except for the tree derived from inter-SSR PCR, were significantly correlated, suggesting that these PCR-based techniques could replace RFLP in the estimation of genetic diversity. On the basis of this result, AFLP analysis was applied to assess the genetic diversity of a sample of accessions representing the various species and subspecies within the genus Pisum.     

Destination‐based seed dispersal homogenizes genetic structure of a tropical palm

As the dominant seed dispersal agents in many ecosystems, frugivorous animals profoundly impact gene movement and fine‐scale genetic structure of plants. Most frugivores engage in some form of destination‐based dispersal, in that they move seeds towards specific destinations, resulting in clumped distributions of seeds away from the source tree. Molecular analyses of dispersed seeds and seedlings suggest that destination‐based dispersal may often yield clusters of maternal genotypes and lead to pronounced local genetic structure. The long‐wattled umbrellabird Cephalopterus penduliger is a frugivorous bird whose lek mating system creates a species‐specific pattern of seed dispersal that can potentially be distinguished from background dispersal processes. We used this system to test how destination‐based dispersal by umbrellabirds into the lek affects gene movement and genetic structure of one of their preferred food sources Oenocarpus bataua, a canopy palm tree. Relative to background dispersal processes, umbrellabird mating behaviour yielded more diverse seed pools in leks that included on average five times more seed sources and a higher incidence of long‐distance dispersal events. This resulted in markedly lower fine‐scale spatial genetic structure among established seedlings in leks than background areas. These species‐specific impacts of destination‐based dispersal illustrate how detailed knowledge of disperser behaviour can elucidate the mechanistic link driving observed patterns of seed movement and genetic structure.