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Vehicle-based tire testing can potentially make it easier to reparametrize tire models for different road surfaces. A passenger car equipped with external sensors was used to measure all input and output signals of the standard tire interface during a ramp steer maneuver at constant velocity. In these measurements, large lateral force vibrations are observed for slip angles above the lateral peak force with clear peaks in the frequency spectrum of the signal at 50 Hz and at multiples of this frequency. These vibrations can lower the average lateral force generated by the tires, and it is therefore important to understand which external factors influence these vibrations. Hence, when using tire models that do not capture these effects, the operating conditions during the testing are important for the accuracy of the tire model in a given maneuver. An Ftire model parameterization of tires used in vehicle-based tire testing is used to investigate these vibrations. A simple suspension model is used together with the tire model to conceptually model the effects of the suspension on the vibrations. The sensitivity of these vibrations to different operating conditions is also investigated together with the influence of the testing procedure and testing equipment (i.e., vehicle and sensors) on the lateral tire force vibrations. Note that the study does not attempt to explain the root cause of these vibrations. The simulation results show that these vibrations can lower the average lateral force generated by the tire for the same operating conditions. The results imply that it is important to consider the lateral tire force vibrations when parameterizing tire models, which does not model these vibrations. Furthermore, the vehicle suspension and operating conditions will change the amplitude of these vibrations and must therefore also be considered in maneuvers in which these vibrations occur.

The demand for reduced development time and cost for passenger cars increases the strive to replace physical testing with simulations. This leads to requirements on the accuracy of the simulation models used in the development process. The tyres, the only components transferring forces from the road to the vehicle, are a challenge from a modelling and parameterization perspective. Tests are typically performed on flat belt tyre testing machines. Flat belt machines offers repeatable and reliable measurements. However, differences between the real world road surface and the flat belt can be expected. Hence, when using a tyre model based on flat belt measurements in full vehicle simulations, differences between the simulations and real prototype testing can be expected as well. Vehicle-based tyre testing can complement flat belt measurements by allowing reparameterization of tyre models to a new road surface. This paper describes an experimental vehicle-based tyre testing approach that aims to parameterize force and moment tyre models compatible with the standard tyre interface. Full-vehicle tests are performed, and the results are compared to measurements from a mobile tyre testing rig on the same surface and to measurements on a flat belt machine. The results show that it is feasible to measure the inputs and outputs to the standard tyre interface on a flat road surface with the used experimental setup. The flat belt surface and the surface on the test track show similar characteristics. The maximum lateral force is sensitive to the chosen manoeuvres, likely due to temperature differences and to vibrations at large slip angles. For tyre models that do not model these effects, it is vital to test the tyres in a manoeuvre that creates comparable conditions for the tyres as the manoeuvre in which the tyre model will be used.

Objective measurements and computer-aided engineering simu- lations cannot be exploited to their full potential because of the high importance of driver feel in vehicle development. Further- more, ...

Key Clinical Message We report a novel KRT13 germ line variant that causes white sponge nevus (WSN) with mucosal dysplasia. Genital, vaginal, and cervical WSN were observed in four female patients, of whom two had premalignant cervical lesions at young age. Two of the 12 patients with oral WSN developed oral squamous cell carcinoma.

Objective testing of vehicle handling in winter conditions has not been implemented yet because of its low repeatability and its low signal-to-noise ratio. Enabling this testing, by identifying rob ...

This paper focuses on increasing the available knowledge about correlations between objective metrics and subjective assessments in steering feel and vehicle handling. Linear and non-linear correlations have been searched for by means of linear regression and neural network training, complemented by different statistical tools. For example, descriptive statistics, the t-distribution and the normal distribution have been used to define the 95% confidence interval for expected subjective assessments and their mean, which makes it possible to predict the subjective rating related to a given objective metric and its area of confidence. Single- and multi-driver correlations have been investigated, as well as how the use of different databases and different vehicle classes affects the results. A method for automatizing the search for correlations when using the driver-by-driver strategy is also explained and evaluated. Ranges of preferred objective metrics for vehicle dynamics have been defined. Vehicles with characteristics within these ranges of values are expected to receive a higher subjective rating when evaluated. Finally, linear correlations between objective metrics have been studied, linear dependency between objective metrics has been identified and its consequences have been presented.

In order to develop and verify the steering system, especially during parking manoeuvres with numerical methods, a tyre model that generates accurate lateral force and self-aligning moment is definitely essential. This paper first reviews the tyre parking measurements from the recently developed tyre test rig at Camber Ridge. After that, a new method is introduced to describe the tyre force and moment for parking as an extension of the combined slip Magic Formula. The turn slip effect is implicitly incorporated by shifting the acting point with an effective width and length of the contact patch. The validations between the measurements and simulations suggest that proposed method is promising for improving the correlation of measured tyre force and moment generation for parking manoeuvres over the standard Magic Formula tyre model.

This paper investigates subjective assessments (SA) of vehicle handling and steering feel tests, both numerical and verbal, to understand drivers’ use of judgement scales, rating tendencies and spread. Two different test methods are compared: a short multi-vehicle first-impression test with predefined-driving vs the standard extensive single-vehicle free-driving tests, both offering very similar results but with the former saving substantial testing time. Rating repeatability is evaluated by means of a blind test. Key SA questions are identified by numerical subjective assessment autocorrelations and by generating word clouds from the most used terms in verbal assessments, with both methods leading to similar key parameters. The results exposed in this paper enable better understanding of SA, allowing improving the overall subjective testing and evaluation process, and improving the data collection and analysis process needed before identifying correlations between SA and objective metrics.

OBJECTIVE: With a shift towards noninvasive testing, we have explored and validated the use of noninvasive prenatal diagnosis (NIPD) for Huntington disease (HD). METHODS: Fifteen couples have been included, assessing a total of n = 20 pregnancies. Fetal paternally inherited CAG repeat length was determined in total cell-free DNA from maternal plasma using a direct approach by PCR and subsequent fragment analysis. RESULTS: All fetal HD (n = 7) and intermediate (n = 3) CAG repeats could be detected in maternal plasma. Detection of repeats in the normal range (n = 10) was successful in n = 5 cases where the paternal repeat size could be distinguished from maternal repeat patterns after fragment analysis. In all other cases (n = 5), the paternal peaks coincided with the maternal peak pattern. All NIPD results were concordant with results from routine diagnostics on fetal genomic DNA from chorionic villi. CONCLUSION: In this validation study, we demonstrated that all fetuses at risk for HD could be identified noninvasively in maternal plasma. Additionally, we have confirmed results from previously described case reports that NIPD for HD can be performed using a direct approach by PCR. For future diagnostics, parental CAG profiles can be used to predict the success rate for NIPD prior to testing. (c) 2015 John Wiley & Sons, Ltd.

The objective of this study was to expand and study the molecular spectrum of β-thalassemia (β-thal) mutations in Oman by examining cases from seven different regions and comparing the prevalence with neighboring countries. A total of 446 cases of β hemoglobinopathies was obtained and analyzed to determine the frequency and distribution of the different β alleles. The molecular spectrum of β-thal in Oman revealed the presence of 32 mutations from different origins and 11 alleles are reported for the first time in the Omani population. The wide heterogeneous spectrum of β-thal mutations found can be associated with the history of trade and migration as well as the past domination from other countries. The presented data will facilitate the development of a comprehensive prevention strategy in Oman.

We describe the molecular characterization of α-globin gene defects in a cohort of 634 Omani patients. A total of 21 different α gene mutations were found in 484 subjects. Overall, we identified three different large deletions, three small deletions, 11 point mutations [two on the α2 polyadenylation signal (polyA) (HBA2: c.*94A>G), and nine α chain variants], three αααanti 3.7 triplication, a 21 nucleotide (nt) duplication on the α1 gene and two novel (presumed) polymorphisms on the α 3.7 kb hybrid gene, namely −5 (C>T) and +46 (C>A). Of these defects, 15 have not been previously reported in the Omani population. This large heterogeneity of α-thalassemia (α-thal) observed in the Omani population could be expected in neighboring Arab countries. The high frequency of α-thal, solely or in association with β-globin gene defects, emphasize the necessity of adding α-thal testing to pre marital programs for accurate genetic counseling.

The characteristics of steering perception are decisive factors for overall driver preference and for vehicle safety. Car manufacturers are continuously required to tune the characteristics of the vehicle and have a strong need to be more effective in the design and evaluation of cars. Using only objective metrics (OM) can result in unwanted steering feel and using only subjective assessments (SA) is time-consuming, costly and non-repetitive. Before a tool can be built to predict the steering feel in front-end development and to improve design knowledge from the full vehicle level to the component level, links between subjective assessments and objective metrics must be found and analysed. The data collected for the study presented in this paper include subjective ratings from expert drivers and objective measurements made with steering robots, involving twelve expert drivers and over twenty vehicles across four different vehicle classes. Linear regression and neural network analysis (NN) have been used to explore reliable subjective-objective links. The tools and methods used in this research showed promising results. Most of the links found concern response and torque feedback. The preferred ranges of some crucial objective metrics leading to more desirable steering feel have been defined and presented. The results indicate that it would be possible for car manufacturers to develop new vehicles more effectively with a steering feel in line with the design criteria by using the tools and methods investigated in this paper.

Healthy carriers of severe Hemoglobinopathies are usually asymptomatic and only efficiently detected through screening campaigns. Based upon epidemiological data, screenings have been offered for decades to populations of endemic Southern Europe for primary prevention of Thalassemia Major, while for many populations of the highly endemic African and Asian countries prevention for Sickle Cell Disease and Thalassemia Major is mainly unavailable. The massive migrations of the last decades have brought many healthy carriers of these diseases to live and reproduce in non-endemic immigration areas changing the epidemiological pattern of the local recessive diseases and bringing an urgent need for treatment and primary prevention in welfare countries. Nonetheless, no screening for an informed reproductive choice is actively offered by the healthcare systems of most of these welfare countries. As a consequence more children affected with severe Hemoglobinopathies are born today in the immigration countries of Northern Europe than in the endemic Southern European area. Following the Mediterranean example, some countries like the UK and The Netherlands have been offering early pregnancy carrier screening at different levels and/or in specific areas but more accessible measures need to be taken at the national level in all immigration countries. Identification of carriers using simple and inexpensive methods should be included in the Rhesus and infectious diseases screening which is offered early in pregnancy in most developed countries. This would allow identification of couples at risk in time for an informed choice and for prenatal diagnosis if required before the first affected child is born.

During the development of new vehicles, finding correlation links between subjective assessments (SA) and objective metrics (OM) is an important part of the vehicle evaluation process. Studying different correlation links is important in that the knowledge gained can be used at the front end of development, during testing and when creating new systems. Both SA from expert drivers using a rating scale of 1–10 and OM from different tests measured by a steering robot were collected using standard testing protocols at an automotive manufacturer. The driver ratings were evaluated and the correlations were analysed using regression analysis and neural networks through a case study approach. Links were identified and were compared with related research.

Objective: Universal newborn screening for hemoglobinopathies started in The Netherlands in 2007. Herewith severe conditions, such as sickle cell disease, β-thalassemia major and hemoglobin H disease are putatively identified. Additionally, at least 1,800 carriers of hemoglobin variants associated with severe conditions in homozygote or compound heterozygote forms are identified yearly. Thus far, approximately 60 patients and 800 healthy sickle cell (HbS) carriers are reported each year among 180,000 newborns. Results are sent to the general practitioner with the recommendation to inform and diagnose both parents of the healthy carriers to exclude genetic risk, while patients and their parents are referred directly to a pediatrician. This study was performed to determine how often parents of identified carriers and affected newborns are seen in genetic centers for counseling. Methods: In this retrospective study, we collected anonymized data from 7 of the 8 Dutch clinical genetic centers from January 1, 2007, until December 31, 2010. Results: After an initial general increase in total counseling intakes, a decline was noticed in the third year, while the requests for prenatal diagnoses remained relatively stable. In 2007 and 2013, genetic counselors were asked for self-reported knowledge. They found hemoglobinopathy counseling complex, but by 2013, they indicated they had acquired sufficient knowledge on most hemoglobinopathy aspects. Conclusion: We could not observe a significant increase in genetic counseling for hemoglobinopathy after its introduction into newborn screening. Although 120 HbS carriers and 60 patients are expected to be born from couples at risk annually, only 33 at risk couples out of 540 families of diagnosed newborns received optimal care and information at a genetics center in 4 years.

Next-generation sequencing is radically changing how DNA diagnostic laboratories operate. What started as a single-gene profession is now developing into gene panel sequencing and whole exome and genome sequencing (WES/WGS) analyses. With further advances in sequencing technology and concomitant price reductions, whole genome sequencing (WGS) will soon become the standard and be routinely offered. Here we focus on the critical steps involved in performing WGS, with a particular emphasis on points where WGS differs from WES, the important variables that should be taken into account, and the quality control measures that can be taken to monitor the process. The points discussed here, combined with recent publications on guidelines for reporting variants, will facilitate the routine implementation of WGS into a diagnostic setting. This article is protected by copyright. All rights reserved. ispartof: Human Mutation vol:38 issue:8 pages:912-921 ispartof: location:United States status: published

Vehicle dynamics development relies on subjective assessments (SA), which is a resource-intensive procedure requiring both expert drivers and vehicles. Furthermore, development projects becoming sh ...

We present, on behalf of EuroGentest and the European Society of Human Genetics, guidelines for the evaluation and validation of next-generation sequencing (NGS) applications for the diagnosis of genetic disorders. The work was performed by a group of laboratory geneticists and bioinformaticians, and discussed with clinical geneticists, industry and patients' representatives, and other stakeholders in the field of human genetics. The statements that were written during the elaboration of the guidelines are presented here. The background document and full guidelines are available as supplementary material. They include many examples to assist the laboratories in the implementation of NGS and accreditation of this service. The work and ideas presented by others in guidelines that have emerged elsewhere in the course of the past few years were also considered and are acknowledged in the full text. Interestingly, a few new insights that have not been cited before have emerged during the preparation of the guidelines. The most important new feature is the presentation of a 'rating system' for NGS-based diagnostic tests. The guidelines and statements have been applauded by the genetic diagnostic community, and thus seem to be valuable for the harmonization and quality assurance of NGS diagnostics in Europe.European Journal of Human Genetics advance online publication, 28 October 2015; doi:10.1038/ejhg.2015.226. ispartof: European Journal of Human Genetics vol:24 issue:1 pages:2-5 ispartof: location:England status: published

Prenatal diagnosis for Duchenne muscular dystrophy (DMD) was introduced in the Netherlands in 1984. We have investigated the impact of 26 years (1984-2009) of prenatal testing. Of the 635 prenatal diagnoses, 51% were males; nearly half (46%) of these were affected or had an increased risk of DMD. As a result 145 male fetuses were aborted and 174 unaffected boys were born. The vast majority (78%) of females, now 16 years or older, who were identified prenatally have not been tested for carrier status. Their average risk of being a carrier is 28%. We compared the incidences of DMD in the periods 1961-1974 and 1993-2002. The incidence of DMD did not decline but the percentage of first affected boys increased from 62 to 88%. We conclude that a high proportion of families with de novo mutations in the DMD gene cannot make use of prenatal diagnosis, partly because the older affected boys are not diagnosed before the age of five. Current policy, widely accepted in the genetic community, dictates that female fetuses are not tested for carrier status. These females remain untested as adults and risk having affected offspring as well as progressive cardiac disease. We see an urgent need for a change in policy to improve the chances of prevention of DMD. The first step would be to introduce neonatal screening of males. The next is to test females for carrier status if requested, prenatally if fetal DNA is available or postnatally even before adulthood. European Journal of Human Genetics (2013) 21, 21-26; doi: 10.1038/ejhg.2012.101; published online 6 June 2012

Objective The aim of this study was to develop a pyrophosphorolysis-activated polymerization (PAP) assay for non-invasive prenatal diagnosis (NIPD) of β-thalassemia major and sickle-cell disease (SCD). PAP is able to detect mutations in free fetal DNA in a highly contaminating environment of maternal plasma DNA. Methods Pyrophosphorolysis-activated polymerization primers were designed for 12 informative SNPs, genotyped by melting curve analysis (MCA) in both parents. The PAP assay was tested in a series of 13 plasma DNA samples collected from pregnant women. A retrospective NIPD was performed in a couple at risk for SCD. Results All PAP reactions were optimized and able to detect 97% wildtype gDNA. In all 13 cases, the paternal allele was detected by PAP in maternal plasma at 10 to 18 weeks of gestation. For the couple at risk, PAP showed presence of the normal paternal SNP allele in maternal plasma, which was confirmed by results of the chorionic villus sampling analysis. Conclusions In contrast to other methods used for NIPD, the combined PAP and MCA analysis detecting the normal paternal allele is also applicable for couples at risk carrying the same mutation, provided that a previously born child is available for testing to determine the linkage to the paternal SNPs. © 2012 John Wiley & Sons, Ltd.

Item does not contain fulltext Implementation of multiplex ligation-dependent probe amplification (MLPA) for thalassemia causing deletions has lead to the detection of new rearrangements. Knowledge of the exact breakpoint sequences should give more insight into the molecular mechanisms underlying these rearrangements, and would facilitate the design of gap-PCRs. We have designed a custom fine-tiling array with oligonucleotides covering the complete globin gene clusters. We hybridized 27 DNA samples containing newly identified deletions and nine positive controls. We designed specific primers to amplify relatively short fragments containing the breakpoint sequence and analyzed these by direct sequencing. Results from nine positive controls showed that array comparative genomic hybridization (aCGH) is suitable to detect small and large rearrangements. We were able to locate all breakpoints to a region of approximately 2 kb. We designed breakpoint primers for 22 cases and amplification was successful in 19 cases. For 12 of these, the exact locations of the breakpoints were determined. Seven of these deletions have not been reported before. aCGH is a valuable tool for high-resolution breakpoint characterization. The combination of MLPA and aCGH has lead to relatively cheap and easy to perform PCR assays, which might be of use for laboratories as an alternative for MLPA in populations where only a limited number of specific deletions occur with high frequency.

Although sequencing of a human genome gradually becomes an option, zooming in on the region of interest remains attractive and cost saving. We performed array-based sequence capture using 385K Roche NimbleGen, Inc. arrays to zoom in on the protein-coding and immediate intron-flanking sequences of 112 genes, potentially involved in mental retardation and congenital malformation. Captured material was sequenced using Illumina technology. A data analysis pipeline was built that detects sequence variants, positions them in relation to the gene, checks for presence in databases (eg, db single-nucleotide polymorphism (SNP)) and predicts the potential consequences at the level of RNA splicing and protein translation. In the samples analyzed, all known variants were reliably detected, including pathogenic variants from control cases and SNPs derived from array experiments. Although overall coverage varied considerably, it was reproducible per region and facilitated the detection of large deletions and duplications (copy number variations), including a partial deletion in the B3GALTL gene from a patient sample. For ultimate diagnostic application, overall results need to be improved. Future arrays should contain probes from both DNA strands, and to obtain a more even coverage, one could add fewer probes from densely and more probes from sparsely covered regions. European Journal of Human Genetics (2011) 19, 50-55; doi:10.1038/ejhg.2010.145; published online 24 November 2010

Multiple osteochondromas (MO) is an autosomal dominant disorder caused by germline mutations in EXT1 and/or EXT2. In contrast, solitary osteochondroma (SO) is nonhereditary. Products of the EXT gene are involved in heparan sulfate (HS) biosynthesis. In this study, we investigated whether osteochondromas arise via either loss of heterozygosity (2 hits) or haploinsufficiency. An in vitro three-dimensional chondrogenic pellet model was used to compare heterozygous bone marrow-derived mesenchymal stem cells (MSCs EXTwt/-) of MO patients with normal MSCs and the corresponding tumor specimens (presumed EXT-/-). We demonstrated a second hit in EXT in five of eight osteochondromas. HS chain length and structure, in vitro chondrogenesis, and EXT expression levels were identical in both EXTwt/- and normal MSCs. Immunohistochemistry for HS, HS proteoglycans, and HS-dependent signaling pathways (eg, TGF-beta/BMP, Wnt, and PTHLH) also showed no differences. The cartilaginous cap of osteochondroma contained a mixture of HS-positive and HS-negative cells. Because a heterozygous EXT mutation does not affect chondrogenesis, EXT, HS, or downstream signaling pathways in MSCs, our results refute the haploinsufficiency theory. We found a second hit in 63% of analyzed osteochondromas, supporting the hypothesis that osteochondromas arise via loss of heterozygosity. The detection of the second hit may depend on the ratio of HS-positive (normal) versus HS-negative (mutated) cells in the cartilaginous cap of the osteochondroma. (Am J Pathol 2010, 177:1946-1957; DOI: 10.2353/ajpath.2010.100296)

High-density single-nucleotide polymorphism (SNP) genotyping technology enables extensive genotyping as well as the detection of increasingly smaller chromosomal aberrations. In this study, we assess molecular karyotyping as first-round analysis of patients with mental retardation and/or multiple congenital abnormalities (MR/MCA). We used different commercially available SNP array platforms, the Affymetrix GeneChip 262K NspI, the Genechip 238K StyI, the Illumina HumanHap 300 and HumanCNV 370 BeadChip, to detect copy number variants (CNVs) in 318 patients with unexplained MR/MCA. We found abnormalities in 22.6% of the patients, including six CNVs that overlap known microdeletion/duplication syndromes, eight CNVs that overlap recently described syndromes, 63 potentially pathogenic CNVs (in 52 patients), four large segments of homozygosity and two mosaic trisomies for an entire chromosome. This study shows that high-density SNP array analysis reveals a much higher diagnostic yield as that of conventional karyotyping. SNP arrays have the potential to detect CNVs, mosaics, uniparental disomies and loss of heterozygosity in one experiment. We, therefore, propose a novel diagnostic approach to all MR/MCA patients by first analyzing every patient with an SNP array instead of conventional karyotyping.

We report on multiple genomic aberrations in a patient with mental retardation. In addition, he had hypogonadism, elevated thyroid hormone levels, hearing loss, delayed speech development and mild dysmorphic features. First, we identified a mosaic karyotype, 45,X/46,X,psu dic(Y). The pseudo-dicentric Y chromosome has three short arm segments. Second, we found a germline mutation (Pro453Thr) of the thyroid hormone receptor beta (THRB) which is associated with resistance to thyroid hormone. Third, he was found to be a carrier of a heterozygous ATP7B mutation (c.2575 + 5G > C), the Wilson disease gene. Even though an array-CGH (with a density of similar to 1 Mb) did not reveal any further genomic gains or losses, we cannot exclude that all contributing factors have been identified. However, this case report shows that with increasing technological possibilities we can find more than one cause for developmental problems in a single patient. The identification of multiple causes in a single patient may complicate explaining the disorder and genetic counseling. (C) 2009 Wiley-Liss, Inc.

A large number of sequence variants identified in BRCA1 and BRCA2 cannot be distinguished as either disease-causing mutations or neutral variants. These so-called unclassified variants (UVs) include variants that are located in the intronic sequences of BRCA1 and BRCA2. The purpose of this study was to assess the use of splice-site prediction programs (SSPPs) to select intronic variants in BRCA1 and BRCA2 that are likely to affect RNA splicing. We performed in vitro molecular characterization of RNA of six intronic variants in BRCA1 and BRCA2. In four cases (BRCA1, c.81-6T>A and c.4986+5G>T; BRCA2, c.7617+2T>G and c.8754+5G>A) a deleterious effect on RNA splicing was seen, whereas the c.135-15_-12del variant in BRCA1 showed no effect on RNA splicing. In the case of the BRCA2 c.68-7T>A variant, RNA analysis was not sufficient to establish the clinical significance. Six SSPPs were used to predict whether an effect on RNA splicing was expected for these six variants as well as for 23 intronic variants in BRCA1 for which the effect on RNA splicing has been published. Out of a total of 174 predictions, 161 (93%) were informative (i.e., the wild-type splice-site was recognized). No false-negative predictions were observed; an effect on RNA splicing was always predicted by these programs. In four cases (2.5%) a false-positive prediction was observed. For DNA diagnostic laboratories, these programs are therefore very useful to select intronic variants that are likely to affect RNA splicing for further analysis.

The presence of a duplication as well as a triplication in one chromosome is a rare rearrangement and not easy to distinguish with routine chromosomal analysis. Recent developments in array technologies, however, not only allow screening of the whole genome at a higher resolution, but also make it possible to characterize complex chromosomal rearrangements in more detail. Here we report a molecular cytogenetic analysis of a 16-year old female with severe mental retardation and an abnormality at the end of the long arm of chromosome 9. Subtelomeric multiplex ligation-dependent probe amplification (MLPA) analysis revealed that the extra material originated from the telomeric end of chromosome 9q. Fine mapping using a high-resolution single nucleotide polymorphism (SNP) array detected a duplication of approximately 400kb upstream of a approximately 2.4Mb triplication followed by a duplication of approximately 130kb of chromosome 9q34.3. This study underscores the value of combining conventional karyotyping with novel array technologies to unravel complex chromosomal alterations in order to study their phenotypic impact.

Contains fulltext : 69186.pdf (Publisher’s version ) (Closed access) We describe a novel heterozygous mutation in exon 3 of the HFE-gene that was co-inherited with Cys282Tyr in two unrelated Dutch men both presenting a classical form of hereditary hemochromatosis. Heterozygosity for this mutation was also found in one out of 100 healthy controls of Dutch descent. This c.548T>C mutation converts a leucine to a proline residue at position 183 in the alpha2-helix of the HFE-protein (Leu183Pro). Standard bioinformatics analysis shows that the mutation is likely to disturb the HFE interaction with TfR1. This disrupting role of the mutation in the iron regulatory pathway is further corroborated by the familial co-occurrence of the observed compound heterozygosity with increased serum iron parameters. Haplotype analysis strongly suggests that this novel mutation arose from a common ancestor in the distant past. These findings may have implications for HFE-testing of iron overloaded heterozygous Cys282Tyr-patients of Northern European origin and their relatives.

Blepharophimosis-Ptosis-Epicanthus inversus syndrome (BPES) is a well-characterized rare syndrome that includes an eyelid malformation associated with (type I) or without premature ovarian failure (type II). Patients with typical BPES have four major characteristics: blepharophimosis, ptosis, epicanthus inversus and telecanthus. Mutations in the FOXL2 gene, encoding a forkhead transcription factor, are responsible for the majority of both types of BPES. However, many patients with BPES-like features, i.e., having at least two major characteristics of BPES, have an unidentified cause. Here, we report on a group of 27 patients with BPES-like features, but without an identified genetic defect in the FOXL2 gene or flanking region. These patients were analyzed with whole-genome high-density arrays in order to identify copy number variants (CNVs) that might explain the BPES-like phenotype. In nine out of 27 patients (33%) CNVs not previously described as polymorphisms were detected. Four of these patients displayed psychomotor retardation as an additional clinical characteristic. In conclusion, we demonstrate that BPES-like phenotypes are frequently caused by CNVs, and we emphasize the importance of whole-genome copy number screening to identify the underlying genetic causes of these phenotypes.

Item does not contain fulltext Here, we report a patient with a novel brachydactyly-syndactyly syndrome and a de novo translocation 46,XY,t(4;6)(q12;p23). We mapped the breakpoint and identified genes in the breakpoint region. One of the genes on chromosome 6, the membrane-associated O-acetyl transferase gene 1 (MBOAT1), was disrupted by the breakpoint. This gene consists of 13 exons and encodes a protein of 495 amino acids. MBOAT1 is predicted to be a transmembrane protein and belongs to the superfamily of membrane-bound O-acyltransferases. These proteins transfer organic compounds, usually fatty acids, onto hydroxyl groups of membrane-embedded targets. Identification of the transferred acyl group and the target may reveal the signaling pathways altered in this novel brachydactyly-syndactyly syndrome.

Background: Recessive mutations in the leptin receptor (LEPR) are a rare cause of hyperphagia and severe early-onset obesity. To date, the phenotype has only been described in 25 obese children, some of whom also had altered immune function, hypogonadotropic hypogonadism, reduced growth hormone secretion, hypothalamic hypothyroidism or reduced adult height. We provide a detailed description of the phenotype of 2 affected girls to add to this knowledge. Methods: Whole-exome sequencing and targeted sequencing were used to detect the LEPR mutations. RNA analysis was performed to assess the effect of splice-site mutations. Results: In 2 unrelated girls with severe obesity, three novel LEPR mutations were detected. Longitudinal growth data show normal childhood growth, and in the older girl, a normal adult height despite hypogonadotropic hypogonadism and the lack of an obvious pubertal growth spurt. Bone age is remarkably advanced in the younger (prepubertal) girl, and bone mineral density (BMD) is high in both girls, which might be directly or indirectly related to leptin resistance. Conclusion: The spectrum of clinical features of LEPR deficiency may be expanded with increased BMD. Future observations in LEPR-deficient subjects should help further unravel the role of leptin in human bone biology.

The challenge in noninvasive prenatal diagnosis for monogenic disorders lies in the detection of low levels of fetal variants in the excess of maternal cell-free plasma DNA. Next-generation sequencing, which is the main method used for noninvasive prenatal testing and diagnosis, can overcome this challenge. However, this method may not be accessible to all genetic laboratories. Moreover, shotgun next-generation sequencing as, for instance, currently applied for noninvasive fetal trisomy screening may not be suitable for the detection of inherited mutations. We have developed a sensitive, mutation-specific, and fast alternative for next-generation sequencing-mediated noninvasive prenatal diagnosis using a PCR-based method. For this proof-of-principle study, noninvasive fetal paternally inherited mutation detection was performed using cell-free DNA from maternal plasma. Preferential amplification of the paternally inherited allele was accomplished through a personalized approach using a blocking probe against maternal sequences in a high-resolution melting curve analysis-based assay. Enhanced detection of the fetal paternally inherited mutation was obtained for both an autosomal dominant and a recessive monogenic disorder by blocking the amplification of maternal sequences in maternal plasma.

Although δ-thalassemia (δ-thal) is not categorized as a severe disease, it is essential to know the molecular spectrum of the δ gene mutations frequently occurring in specific areas, particularly if these areas are characterized by a high rate of β-thalassemia (β-thal) such as Oman. This is because coinherited δ-globin gene defects can interfere with the basic diagnosis of a β-thal carrier when this is based upon the measurement of the Hb A2 only. Because of that, we have investigated 33 patients with low Hb A2 levels, collected from different hospitals in Oman. Some cases had a second Hb A2 fraction, while others had only significantly lower Hb A2 levels. Among these patients, 20 did carry a δ-globin gene mutation, the rest were carriers of α thalassemia (α-thal) defects or could be iron depleted or both. In total, eight different known mutations and two novel δ variants were found. The characterization of the δ-globin gene mutation spectrum will improve carrier diagnostics and genetic counseling in the Omani population screened for β-thal.

Background/Aims: In addition to genome-wide association studies (GWAS), height-associated genes may be uncovered by studying individuals with extreme short or tall stature. Methods: Genome-wide analysis for copy number variants (CNVs), using single nucleotide polymorphism (SNP) arrays, was performed in 49 index cases born small for gestational age with persistent short stature. Segregation analysis was performed, and genes in CNVs were compared with information from GWAS, gene expression in rodents' growth plates, and published information. Results: CNVs were detected in 13 cases. In 5 children a known cause of short stature was found: UPD7, UPD14, a duplication of the SHOX enhancer region, an IGF1R deletion, and a 22q11.21 deletion. In the remaining 8 cases, potential pathogenic CNVs were detected, either de novo (n = 1), segregating (n = 2), or not segregating with short stature (n = 5). Bioinformatic analysis of the de novo and segregating CNVs suggested that HOXD4, AGPS, PDE11A, OSBPL6, PRKRA and PLEKHA3, and possibly DGKB and TNFRSF11B are potential candidate genes. A SERPINA7 or NRK defect may be associated with an X-linked form of short stature. Conclusion: SNP arrays detected 5 known causes of short stature with prenatal onset and suggested several potential candidate genes.

Background: The underlying causes of mental retardation remain unknown in about half the cases. Recent array-CGH studies demonstrated cryptic imbalances in about 25% of patients previously thought to be chromosomally normal. Objective and methods: Array-CGH with approximately 3500 large insert clones spaced at ∼1 Mb intervals was used to investigate DNA copy number changes in 81 mentally impaired individuals. Results: Imbalances never observed in control chromosomes were detected in 20 patients (25%): seven were de novo, nine were inherited, and four could not have their origin determined. Six other alterations detected by array were disregarded because they were shown by FISH either to hybridise to both homologues similarly in a presumptive deletion (one case) or to involve clones that hybridised to multiple sites (five cases). All de novo imbalances were assumed to be causally related to the abnormal phenotypes. Among the others, a causal relation between the rearrangements and an aberrant phenotype could be inferred in six cases, including two imbalances of the X chromosome, where the associated clinical features segregated as X linked recessive traits. Conclusions: In all, 13 of 81 patients (16%) were found to have chromosomal imbalances probably related to their clinical features. The clinical significance of the seven remaining imbalances remains unclear. The limited ability to differentiate between inherited copy number variations which cause abnormal phenotypes and rare variants unrelated to clinical alterations currently constitutes a limitation in the use of CGH-microarray for guiding genetic counselling.

Background: During T4 supplementation of patients with thyroidal (primary) congenital hypothyroidism (CH) TSH concentrations are frequently elevated despite free T4 (FT4) concentrations being well within the reference range. To examine the thyroid’s regulatory system, we analyzed thyroid function determinants in children with congenital and acquired thyroid disorders and in controls. Methods: Retrospectively, plasma FT4, TSH, and T3 concentrations were analyzed in T4-supplemented children aged 0.5–20.0 yr with thyroidal CH, central (secondary or tertiary) CH, or autoimmune thyroid disease and in control children with type 1 diabetes mellitus. Results: When TSH was within the reference range (0.4–4.0 mU/ liter), mean FT4 in thyroidal CH [1.65 ng/dl; 95% confidence interval (CI), 1.62–1.67] was significantly higher than in autoimmune thyroid disease (1.15 ng/dl; 95% CI, 1.11–1.19) and diabetes (1.08 ng/dl; 95% CI,1.06–1.10).IncentralCH,whenTSHwaslessthanorequalto0.02 mU/liter, mean FT4 was 1.27 ng/dl (95% CI, 1.24–1.29). When FT4 was within the reference range (0.78–1.79 ng/dl), 43% of the TSH measurements in thyroidal CH were more than 4.0 mU/liter, compared with 18% in autoimmune thyroid disease and 0% in type 1 diabetesmellitus;incentralCH,95%ofTSHmeasurementswereless than 0.4 mU/liter. Conclusions: In T4-supplemented patients with thyroidal CH, when TSH concentrations are established within the reference range, FT4 concentrations tend to be elevated, and vice versa. Because this phenomenoncouldnotbeobservedinacquiredthyroidalhypothyroidism, we hypothesize that a pre- and/or perinatal hypothyroid state shifts the setpoint of the thyroid’s regulatory system. In central CH, when FT4 concentrations are established within the reference range, the pituitary secretes only minute amounts of TSH. For monitoring T4 supplementation, reference ranges for FT4 and TSH should be adapted to the etiology of hypothyroidism. (J Clin Endocrinol Metab 90: 4094–4100, 2005)

Duchenne and Becker muscular dystrophy (DMD and BMD) are caused by mutations in the dystrophin gene. Large rearrangements in the gene are found in about two,thirds of DMD patients, with similar to60% carrying deletions and 5-10% carrying duplications. Most of the remaining 30-35% of patients are expected to have small nucleotide substitutions, insertions, or deletions. To detect these subtle changes within the coding and splice site determining sequences of the dystrophin gene, we established a semiautomated denaturing gradient gel electrophoresis (DGGE) mutation scanning system. The DGGE scan covers the dystrophin gene with 95 amplicons, PCRed either individually or in a multiplex setup. PCR and pooling were performed semiautomatically, using a pipetting robot and 384-well plates, enabling concurrent amplification of DNA of four patients in one run. Amplification of individual fragments was performed using one PCR program. The products were pooled just before gel loading; DGGE requires only a single gel condition. Validation was performed using DNA samples harboring 39 known DMD variants, all of which could be readily detected. DGGE mutation scanning was applied to analyze 135 DMD/BMD patients and potential DMD carriers without large deletions or duplications. In DNA from 25 out of 44 DMD patients (57%) and from 5 out of 39 BMD patients (13%), we identified clear pathogenic changes. All mutations were different, with the exception of one DMD mutation, which occurred twice. In DNA from 10 out of 44 potential DMD carriers, including four obligate carriers, we detected causative changes, including one pathogenic change in every obligate carrier. In addition to these pathogenic changes, we detected 15 unique unclassified variants, i.e., changes for which a pathogenic nature is uncertain. (C) 2003 Wiley-Liss, Inc.

Risk estimation in breast cancer families is often estimated by use of the Claus tables. We analyzed the family histories of 196 counselees; compared the Claus tables with the Claus, the BRCA1/2, the BRCA1/2/ models; and performed linear regression analysis to extend the Claus tables with characteristics of hereditary breast cancer. Finally, we compared the Claus extended method with the Claus, the BRCA1/2, and the BRCA1/2/u models. We found 47% agreement for Claus table versus Claus model; 39% agreement for Claus table versus BRCA1/2 model; 48% agreement for Claus table versus BRCA1/2/u model; 37% agreement for Claus extended method versus Claus model; 44% agreement for Claus extended model versus BRCA1/2 model; and 66% agreement for Claus extended method versus BRCA1/2/u model. The regression formula (Claus extended method) for the lifetime risk for breast cancer was 0.08 + 0.40 ∗ Claus Table + 0.07 ∗ ovarian cancer + 0.08 ∗ bilateral breast cancer + 0.07 ∗ multiple cases. This new method for risk estimation, which is an extension of the Claus tables, incorporates information on the presence of ovarian cancer, bilateral breast cancer, and whether there are more than two affected relatives with breast cancer. This extension might offer a good alternative for breast cancer risk estimation in clinical practice.

We describe a patient with somatic mosaicism of a point mutation in the dystrophin gene causing benign muscular dystrophy with an unusual asymmetrical distribution of muscle weakness and contractures. To our knowledge this is the first patient with asymmetrical weakness and contractures in an ambulatory patient with a dystrophinopathy. (C) 2003 Elsevier Science B.V. All rights reserved

Item does not contain fulltext OBJECTIVE: Autosomal dominant facioscapulohumeral muscular dystrophy (FSHD) is associated with a contraction of the D4Z4 repeat array on chromosome 4. So far, homozygosity or compound heterozygosity for FSHD alleles has not been described, and it has been debated whether the absence of such subjects is because of the rarity or the lethality of the disorder. METHODS: Two unrelated families in which the probands are compound heterozygous for two FSHD-sized alleles were studied. Clinical examination, pulsed-field gel electrophoresis (PFGE) studies of DNA with probes proximal and distal to D4Z4, and cytogenetic analysis of metaphase chromosomes by FISH were performed. RESULTS: Complementary molecular and cytogenetic approaches confirmed the chromosome 4qA origin of all FSHD-sized repeat arrays that segregate in the families. CONCLUSIONS: Heterozygosity for FSHD-sized alleles is compatible with life in men and women. A possible dosage effect was observed in both probands in whom each 4qA allele contributed to the FSHD phenotype. Because at least one of the FSHD alleles in both families showed an unusual low penetrance, the authors propose that susceptibility for FSHD is partly determined by intrinsic properties of the disease allele other than the residual D4Z4 repeat size alone.