Estimating the Total Pathogenic Allele Frequency of Autosomal Recessive Disorders in Case of Consanguinity.

OBJECTIVE: Estimating the total allele frequency of all pathogenic alleles of an autosomal recessive disease is not possible if only mutational data of a sample of affected individuals are available. However, if the affected individuals come from a population where consanguinity is not uncommon, this total allele frequency can be estimated by additionally using the positive individual inbreeding coefficients or an estimate of the population inbreeding coefficient. In this paper, we propose two estimators. METHODS/RESULTS: We propose to estimate the total allele frequency by a conditional maximum likelihood estimator if a part of the affected individuals in the sample comes from consanguineous marriages with known inbreeding coefficients. A simulation study shows that this estimator is unbiased and robust. We propose a second estimator which is based on an estimate of the population inbreeding coefficient. The method is applied to mutational data and individual inbreeding coefficients of Tunisian patients with congenital adrenal hyperplasia. CONCLUSION: Additionally using individual inbreeding coefficients or an estimate of the population inbreeding coefficient makes it possible to estimate the total allele frequency. Since consanguinity is commonly practiced in many parts of the world, the estimators proposed in the paper are of practical importance.

Consanguinity and endogamy in the Netherlands: demographic and medical genetic aspects.

This paper reviews what is currently known about the presence of consanguinity and endogamy in the Netherlands, in the past and today, and concludes with a discussion of medical genetic aspects. First geographic characteristics, the demographic history, the genetic make-up of the native population, legal aspects and the public opinion are reviewed. Then data on the prevalence of consanguinity in the native population are presented for marriages since 1840, followed by data on consanguineous marriages among immigrants from countries with a tradition of close-kin marriages. It is estimated that approximately 1% of at-risk consanguineous couples are referred to clinical genetic centres for prospective genetic counselling in the Netherlands. This picture will change dramatically if and when next-generation sequencing is introduced to identify couples at ≥ 25% risk prospectively.

Challenges in the care for consanguineous couples: an exploratory interview study among general practitioners and midwives.

BACKGROUND: It is often suggested that an effort must be made to increase awareness among consanguineous couples of their reproductive risk, and to refer them for genetic counseling if needed. Primary care professionals are considered most appropriate for addressing the subject and identifying couples at risk during consultations in their practice. This Dutch study aims to explore the experiences, attitudes and beliefs of such professionals regarding their care for consanguineous couples. METHODS: Sixteen semi-structured interviews were conducted with midwives and general practitioners. RESULTS: Although most primary care professionals considered it their task to inform couples about the risks of consanguinity, during consultations the topic was generally only briefly touched upon and quickly abandoned. Important reasons for this were professionals' beliefs about religious and social values of couples, their low perception of the couples' reproductive risk and expected limited feasibility of referral. Feelings of embarrassment regarding addressing consanguinity did not seem to play a significant role. CONCLUSIONS: Primary care professional beliefs about their clients' religious and social values, their attitudes toward the risk, and perceived limited options for referral seem to conflict with the professional norm to address the topic of consanguinity.

Preconceptional genetic carrier testing and the commercial offer directly-to-consumers.

Recently, a number of commercial companies are offering preconceptional carrier tests directly-to-consumers. This offer raises a number of concerns and issues above and beyond those encountered with preconceptional tests offered within the traditional health care setting. In order to bring some of these issues to light and to initiate dialogue on this topic, this article discusses the following issues: the current offer of preconceptional carrier tests (until the end of 2010) through online commercial companies; the implications for the informed consent procedure and the need for good information; the need for medical supervision and follow-up; and the appropriate use of existing resources. The article concludes with some reflections about the potential sustainability of the offer of preconceptional carrier tests directly-to-consumers.

TP53 germline mutation testing in 180 families suspected of Li-Fraumeni syndrome: mutation detection rate and relative frequency of cancers in different familial phenotypes.

BACKGROUND Li-Fraumeni syndrome (LFS) is a rare autosomal dominant cancer predisposition syndrome. Most families fulfilling the classical diagnostic criteria harbour TP53 germline mutations. However, TP53 germline mutations may also occur in less obvious phenotypes. As a result, different criteria are in use to decide which patients qualify for TP53 mutation analysis, including the LFS, Li-Fraumeni-like (LFL) and Chompret criteria. We investigated which criteria for TP53 mutation analysis resulted in the highest mutation detection rate and sensitivity in Dutch families. We describe the tumour spectrum in TP53-positive families and calculated tumour type specific relative risks. METHOD A total of 180 Dutch families referred for TP53 mutation analysis were evaluated. Tumour phenotypes were verified by pathology reports or clinical records. RESULTS A TP53 germline mutation was identified in 24 families. When the Chompret criteria were used 22/24 mutations were detected (sensitivity 92%, mutation detection rate 21%). In LFS and LFL families 18/24 mutations were found (sensitivity 75%). The two mutations detected outside the 'Chompret group' were found in a child with rhabdomyosarcoma and a young woman with breast cancer. In the mutation carriers, in addition to the classical LFS tumour types, colon and pancreatic cancer were also found significantly more often than in the general population. CONCLUSION We suggest TP53 mutation testing for all families fulfilling the Chompret criteria. In addition, TP53 mutation testing can be considered in the event of childhood sarcoma and breast cancer before 30 years. In addition to the risk for established LFS tumour types, TP53-positive individuals may also have an elevated risk for pancreatic and colon cancer.

Do consanguineous parents of a child affected by an autosomal recessive disease have more DNA identical-by-descent than similarly-related parents with healthy offspring? Design of a case-control study.

BACKGROUND: The offspring of consanguineous relations have an increased risk of congenital/genetic disorders and early mortality. Consanguineous couples and their offspring account for approximately 10% of the global population. The increased risk for congenital/genetic disorders is most marked for autosomal recessive disorders and depends on the degree of relatedness of the parents. For children of first cousins the increased risk is 2-4%. For individual couples, however, the extra risk can vary from zero to 25% or higher, with only a minority of these couples having an increased risk of at least 25%. It is currently not possible to differentiate between high-and low-risk couples. The quantity of DNA identical-by-descent between couples with the same degree of relatedness shows a remarkable variation. Here we hypothesize that consanguineous partners with children affected by an autosomal recessive disease have more DNA identical-by-descent than similarly-related partners who have only healthy children. The aim of the study is thus to establish whether the amount of DNA identical-by-descent in consanguineous parents of children with an autosomal recessive disease is indeed different from its proportion in consanguineous parents who have healthy children only. METHODS/DESIGN: This project is designed as a case-control study. Cases are defined as consanguineous couples with one or more children with an autosomal recessive disorder and controls as consanguineous couples with at least three healthy children and no affected child. We aim to include 100 case couples and 100 control couples. Control couples are matched by restricting the search to the same family, clan or ethnic origin as the case couple. Genome-wide SNP arrays will be used to test our hypothesis. DISCUSSION: This study contains a new approach to risk assessment in consanguineous couples. There is no previous study on the amount of DNA identical-by-descent in consanguineous parents of affected children compared to the consanguineous parents of healthy children. If our hypothesis proves to be correct, further studies are needed to obtain different risk figure estimates for the different proportions of DNA identical-by-descent. With more precise information about their risk status, empowerment of couples can be improved when making reproductive decisions.

Three-month follow-up of Western and non-Western participants in a study on preconceptional ancestry-based carrier couple screening for cystic fibrosis and hemoglobinopathies in the Netherlands.

OBJECTIVE: To study psychological outcomes, knowledge, recall and understanding of test-results, satisfaction, and reproductive intentions among 97 Western and 46 non-Western participants in a unique preconceptional carrier screening study for both cystic fibrosis and hemoglobinopathies in a multiethnic population the Netherlands, in which a couple's eligibility for cystic fibrosis and/or hemoglobinopathies testing was based on both partners' ancestry. METHODS: Questionnaires before and after pretest consultation, and 1 week and 3 months after receiving test-results. Three cystic fibrosis and seven hemoglobinopathy carriers were identified, but no carrier couples. RESULTS: Overall, anxiety levels were low, knowledge improved after pretest consultation but decreased after 3 months. Ninety-four percent remembered their test-results. Western compared with non-Western participants had higher knowledge-scores and better understanding of test-results. None of the carriers felt less healthy, six felt relieved, and one felt disappointed. Four carriers were unaware of the residual risk of having an affected child. Participants intended to draw reproductive decisions from test-results, were satisfied, did not regret participation, and did not report major feelings of discrimination or stigmatization. CONCLUSIONS: Similar to previous studies, no major adverse psychological effects were demonstrated among the Western and non-Western participants in this study, and they would draw reproductive decisions on test-results. No arguments for rejecting a combined offer of preconceptional ancestry-based cystic fibrosis and hemoglobinopathies carrier screening were found. An extensive implementation study should be carried out, in which understanding of test-results needs further attention, to investigate whether or not this type of screening should be implemented on a large scale in the Netherlands.

Assessing educational priorities in genetics for general practitioners and specialists in five countries: factor structure of the Genetic-Educational Priorities (Gen-EP) scale.

PURPOSE: A scale assessing primary care physicians' priorities for genetic education (The Gen-EP scale) was developed and tested in five European countries. The objective of this study was to determine its factor structure, to test scaling assumptions and to determine internal consistency. METHODS: The sample consisted of 3686 practitioners (general practitioners, gyneco-obstetricians, pediatricians) sampled in France, Germany, the Netherlands, Sweden, and United Kingdom. We first determined the factor structure of the Gen-EP scale (30 items) on the whole sample. Scaling assumptions were then tested on each country using multitrait scaling analysis. Internal consistency was assessed across the five countries. RESULTS: Six factors were identified accounting for 63.3% of the variance of the items. They represented the following priorities for genetic education: "Genetics of Common Diseases"; "Ethical, Legal, and Public Health Issues"; "Approaching Genetic Risk Assessment in Clinical Practice"; "Basic Genetics and Congenital Malformations"; "Techniques and Innovation in Genetics" and "Psychosocial and Counseling Issues." In each country, convergent and discriminant validity were satisfactory. Internal-consistency reliability coefficients (Cronbach's alpha) were all above the acceptable threshold (0.70). CONCLUSION: The Gen-EP scale could be a helpful instrument in different countries to organize and evaluate the impact of genetic educational programs for primary care providers.

CFTR mutations in Turkish and North African cystic fibrosis patients in Europe: implications for screening.

AIMS: To obtain more insight into the variability of the CFTR mutations found in immigrant cystic fibrosis (CF) patients who are living in Europe now, and to estimate the test sensitivity of different frequently used methods of DNA analysis to detect CF carriers or patients among these Turkish or North African immigrants. METHODS: A survey among 373 European CF centers asking which CFTR mutations had been found in Turkish and North African CF patients. RESULTS: 31 and 26 different mutations were reported in Turkish and North African patients, identifying 64.2% (113/176) and 87.4% (118/135) alleles, respectively (p < 0.001). The mean sensitivity (detection rate) of three most common CFTR mutation panels to detect these mutations differed between Turkish and North African people, 44.9% (79/176) versus 69.6% (94/135) (p < 0.001), and can be increased to 57.4% (101/176) and 79.3% (107/135) (p < 0.001), respectively, by expanding these panels with 13 mutations which have been found on two or more alleles. CONCLUSION: 35.8% and 12.6%, respectively, of CF alleles in Turkish and North African patients living in Europe now had not been identified. Among these populations, the test sensitivity of common CFTR mutation panels is insufficient for use in screening programs in Europe, even after expansion with frequent Turkish and North African mutations. This raises questions about whether and how to implement CF carrier and neonatal screening in a multiethnic society.

With expanded carrier screening, founder populations run the risk of being overlooked.

Genetically isolated populations exist worldwide. Specific genetic disorders, including rare autosomal recessive disorders may have high prevalences in these populations. We searched for Dutch genetically isolated populations and their autosomal recessive founder mutations. We investigated whether these founder mutations are covered in the (preconception) expanded carrier screening tests of five carrier screening providers. Our results show that the great majority of founder mutations are not covered in these screening panels, and these panels may thus not be appropriate for use in founder populations. It is therefore important to be aware of founder mutations in a population when offering carrier tests.

Segregation ratio in cranio-cerebello-cardiac syndrome.

According to several authors cranio-cerebello-cardiac (3C) syndrome is an autosomal recessive disorder. This opinion was based on pedigree inspection without formal segregation analysis. Recently, the assumption of autosomal recessive inheritance was challenged by the observation of overlapping features with 6p deletions. We therefore performed segregation analysis by means of methods described by Li and Mantel, Davie and Lange on 27 pedigrees selected from literature. The results of all three methods are consistent with autosomal recessive inheritance but their broad confidence intervals leave room for other explanations as well. Reporting of 3C cases without evaluation of 6p copy number should be discouraged from now on.

Informed decision making in the context of prenatal screening.

OBJECTIVE: This study aimed to construct a measure of informed decision making that includes knowledge, deliberation, and value-consistency, and to assess the level of informed decision making about prenatal screening, and differences between test acceptors and test decliners. METHODS: Women attending one of 44 midwifery and gynaecology practices were asked to fill out postal questionnaires before and after the prenatal screening offer. The principal outcome was the level of informed decision making. For this purpose, knowledge about prenatal screening, deliberation about the pros and cons of the alternatives, test uptake, and attitude towards having a prenatal screening test were measured. RESULTS: Eighty-four percent of the participants were sufficiently knowledgeable about prenatal screening, 75% of the decisions were deliberate, and 82% were value-consistent. Fifty-one percent of the participants made an informed decision. Test acceptors made less informed decisions as compared to test decliners. This difference was mainly caused by the lower rate of deliberation in this group. CONCLUSION: It appears from this study that prenatal screening decisions are often not informed decisions. This is inconsistent with the main objective of offering screening, which is to enable people to make informed decisions. PRACTICE IMPLICATIONS: Decision makers should be encouraged during the counselling to deliberate about the various alternatives.

The difference between observed and expected prevalence of MCAD deficiency in The Netherlands: a genetic epidemiological study.

Medium chain acyl coenzyme A dehydrogenase (MCAD) deficiency is assumed to be the most common inherited disorder of mitochondrial fatty acid oxidation. Few reports mention the difference between the expected and observed prevalence of MCAD deficiency on the basis of the carrier frequency in the population. We performed a population-wide retrospective analysis of all known MCAD-deficient patients in The Netherlands. In this study, the observed prevalence of MCAD deficiency in The Netherlands was 1/27 400 (95% confidence interval (CI) 1/23 000-1/33 900), significantly different from the expected prevalence of 1/12 100 (95% CI 1/8450-1/18 500). The observed prevalence of MCAD deficiency showed a remarkable north-south trend within the country. From the patients in this cohort, it can be observed that underdiagnosis contributes to a larger extent to the difference between the expected and observed prevalences of MCAD deficiency in our country, than reduced penetrance. We determined estimates of the segregation proportion in a cohort of 73 families under the assumption of complete ascertainment (p(LM) = 0.41, 95% CI 0.31-0.51) and single ascertainment (p(D) = 0.28, 95% CI 0.19-0.37). With the expectation-maximization algorithm, a third estimate was obtained (p(EM) = 0.28, 95% CI 0.20-0.37). The agreement between the latter two estimates supports incomplete selection and the segregation proportions were in agreement with normal mendelian autosomal recessive inheritance.

Personal experiences of cystic fibrosis (CF) carrier couples prospectively identified in CF families.

This qualitative study explores the experiences of cystic fibrosis (CF) carrier couples, prospectively identified in CF families, and the impact of the resulting genetic risk on reproductive behavior. Of the 12 couples identified until 1997, seven couples participated in semistructured interviews and two couples filled in a questionnaire, two to eight years after receipt of the test-results. After receiving the results, most couples reported that they were shocked, because they did not expect to both be carriers. More anxiety was expressed by those who were pregnant (n = 4) at the time of testing. There were reported difficulties in disclosing the results to family members, and the reactions of family members were not always supportive. After testing, some couples had problems with reproductive decision-making. All viable pregnancies (17 in 8 couples) were monitored by prenatal diagnosis; all affected pregnancies were terminated (6 in 4 couples). Couples who have live-born children after testing may subsequently have concerns during infancy about the correctness of the results of prenatal diagnosis and how to inform their children. Most couples did not regret the testing and, in general, the counseling was experienced positively, although some dissatisfaction was reported with regard to the psychological support received during pregnancy. Couples supported the idea of carrier screening in the general population, although various concerns were expressed. The results indicate a preference for testing before pregnancy. These findings may be useful in investigating possible dilemmas caused by the introduction of population carrier screening. Observations reported here might also apply to other recessively inherited disorders.

Preconceptional cystic fibrosis carrier screening: opinions of general practitioners, gynecologists, and pediatricians in the Netherlands.

Knowledge of the opinions of physicians with regard to preconceptional cystic fibrosis (CF) carrier screening and the possible factors that are associated with their opinions is important for the implementation of such a screening program. Data were obtained from a study in which genetic knowledge, opinions with regard to genetic testing and related skills were investigated. A questionnaire, developed and used by American researchers, was adapted to the Dutch health care situation, and sent to randomly selected general practitioners (GPs) (n = 200), gynecologists (GYNs) (n = 300), and pediatricians (PEDs) (n = 265). In this part of the study, their opinions with regard to genetic preconceptional CF carrier screening in different situations were assessed. The response rate for the GPs, GYNs, and PEDs was 64%, 69%, and 72%, respectively. In total, 63% of the GPs, 69% of the GYNs and 72% of the PEDs supported preconceptional CF carrier testing if a couple requested a test. Sixteen percent, 19% and 25%, respectively, were in favor of actively offering a test with 95% test sensitivity to all couples who were planning a pregnancy. A positive opinion on preconceptional CF carrier screening was associated with the following variables: "considering the test sensitivity as less important" (GPs, GYNs), "high perceived risk of having a child with CF" (GYNs), "providing genetic counselling in their own practice" (PEDs) and "reassurance when both partners test negative" (PEDs). Physicians are sympathetic toward preconceptional CF carrier screening if the couples themselves request a test. Physicians had reservations about routinely offering a CF carrier test.

Preconceptional cystic fibrosis carrier screening: attitudes and intentions of the target population.

The aim of this study was to assess the attitudes and intentions of individuals planning a pregnancy with regard to preconceptional cystic fibrosis (CF) carrier screening and to determine factors associated with a positive and negative/neutral intention to have the test. A survey, based on a questionnaire, was conducted among a stratified random sample of 303 recently married couples (606 individuals). Of the eligible individuals, 70% (n = 380) participated. Of the respondents, 73% had a positive attitude toward a routine offer of preconceptional CF carrier screening, and 56% had the intention to participate in a screening program. A positive intention to have the test was associated with high perceived anticipation of regret, intended preconceptional behavior, high perceived pressure from experts, high perceived consequences of the test results, low perceived barriers, and low perceived negative consequences for family members. These results suggest that the offer of routine preconceptional CF carrier screening would lead to substantial acceptance among couples planning a pregnancy. Several variables related with intention were identified.

Comparison of activities and attitudes of general practitioners concerning genetic counseling over a 10-year time-span.

The aim of this study was to investigate whether the activities and attitudes of general practitioners (GPs) concerning genetic counseling have changed between 1989 and 1999. In 1989 a random sample of 124 GPs in The Netherlands was selected. Of these GPs, 98 were contacted again in 1999 and 71 completed the questionnaire. The study showed an increase in the percentage of GPs who provided genetic counseling when a risk factor for having a child with a congenital disorder was present and known. In both 1989 and 1999, the GPs seldom used a recommended combination of oral and written information, and only data that was available in the databases on the risk indicator 'use of medication' increased over the years. GPs are still supporters of a directive method of counseling, and seem to believe that the main goal of genetic counseling is to prevent hereditary and congenital disorders. Although, between 1989 and 1999 more GPs provided genetic counseling when a risk indicator was present and known or referred to a clinical geneticist, only limited improvement was found in the activities of GPs to attempt to collect these data.

Linkage and association studies of IL1B and IL1RN gene polymorphisms in preeclampsia.

OBJECTIVE: To determine whether preeclampsia is either associated with or linked to two polymorphisms in the IL1B gene (IL1B-TaqI and IL1B-511) and one polymorphism in the IL1RN gene (IL1RN-IVS2). METHODS: Genotyping was performed in 150 affected sib-pair families and 104 healthy Dutch blood donors. Genotype and allele frequencies as well as allelic associations were assessed in three groups of unrelated women from these 150 families; 133 with either eclampsia, preeclampsia or the haemolysis, elevated liver enzymes, low platelets (HELLP) syndrome, 101 with preeclampsia only, and 63 with HELLP syndrome only. These frequencies were compared to those in controls. Frequencies of transmitted and nontransmitted haplotypes, inferred from the three polymorphisms, were compared. Allele sharing between affected siblings from all 150 families was assessed by means of multipoint nonparametric affected sib-pair analyses. RESULTS: No significant differences in genotype and allele frequencies were found between the unrelated study groups and controls. No allelic associations were apparent, nor were there differences in frequencies of transmitted and nontransmitted haplotypes within affected families. Excess allele sharing for any of the three polymorphic markers was absent in affected sib-pairs. CONCLUSIONS: None of the IL1B and IL1RN polymorphisms provided evidence for either association or linkage with the risk for (pre)eclampsia/HELLP syndrome, preeclampsia only or HELLP syndrome only.