Showing papers in "Clinical Genetics in 2010"

The human phenotype ontology.

Abstract: A standardized, controlled vocabulary allows phenotypic information to be described in an unambiguous fashion in medical publications and databases. The Human Phenotype Ontology (HPO) is being developed in an effort to provide such a vocabulary. The use of an ontology to capture phenotypic information allows the use of computational algorithms that exploit semantic similarity between related phenotypic abnormalities to define phenotypic similarity metrics, which can be used to perform database searches for clinical diagnostics or as a basis for incorporating the human phenome into large-scale computational analysis of gene expression patterns and other cellular phenomena associated with human disease. The HPO is freely available at http://www.human-phenotype-ontology.org.

PALB2 mutations in European familial pancreatic cancer families.

Abstract: Recently, PALB2 was reported to be a new pancreatic cancer susceptibility gene as determined by exomic sequencing, as truncating PALB2 mutations were identified in 3 of 96 American patients with familial pancreatic cancer (FPC). Representing the European Registry of Hereditary Pancreatitis and Familial Pancreatic Cancer (EUROPAC) and the German National Case Collection for Familial Pancreatic Cancer (FaPaCa), we evaluated whether truncating mutations could also be detected in European FPC families. We have directly sequenced the 13 exons of the PALB2 gene in affected index patients of 81 FPC families. An index patient was defined as the first medically identified patient, stimulating investigation of other members of the family to discover a possible genetic factor. None of these patients carried a BRCA2 mutation. We identified three (3.7%) truncating PALB2 mutations, each producing different stop codons: R414X, 508-9delAG and 3116delA. Interestingly, each of these three families also had a history of breast cancer. Therefore, PALB2 mutations might be causative for FPC in a small subset of European families, especially in those with an additional occurrence of breast cancer.

Molecular epidemiological survey of haemoglobinopathies in the Guangxi Zhuang Autonomous Region of southern China

Abstract: Accurate and up-to-date data on the frequency of haemoglobinopathies among the populations of Guangxi Zhuang Autonomous Region, where haemoglobinopathies are most endemic in China, are required. In our study, a total of 5789 samples obtained from members of the Han, Zhang, and Yao ethnic groups in six geographical areas of Guangxi Province were analysed systematically in terms of both haematological and molecular parameters. The results presented that the total heterozygote frequency of thalassaemias and other haemoglobinopathies was 24.51%, of which 17.55% was due to alpha-thalassaemia, 6.43% to beta-thalassaemia, 0.38% to structural haemoglobin variants, and 0.16% to delta-thalassaemia. The mutational spectrum among the local population for each type of disorder was described, including the first report on the true prevalence of three silent alpha thalassemia defects, -alpha(3.7)/(4.78%), -alpha(4.2)/(1.61%) and Hb Westmead (alpha(WS)alpha/) (1.57%) and of delta-thalassemia resulting from five novel and two rare mutations never before identified in Chinese individuals. Comparison of the frequencies of alpha-globin mutations among the ethnic groups showed that there was a statistically significant difference between the Han (15.71%) and Zhuang (20.12%), and between the Han (15.71%) and Yao (20.84%) ethnic groups. In addition, we have performed the first extensive study of haematological parameters of the Hb Westmead mutation using a group of Chinese subjects with compound heterozygosity for this variant and an alpha-thalassaemia deletion. The knowledge gained in this study will enable us to estimate the health burden in this high-risk population and to elucidate the various genetic alterations that underlie haemoglobinopathies.

The role of germline AIP, MEN1, PRKAR1A, CDKN1B and CDKN2C mutations in causing pituitary adenomas in a large cohort of children, adolescents, and patients with genetic syndromes.

Abstract: The prevalence of germline mutations in MEN1, AIP, PRKAR1A, CDKN1B and CDKN2CI is unknown among pediatric patients with pituitary adenomas (PA). In this study, we screened children with PA for mutations in these genes; somatic GNAS mutations were also studied in a limited number of growth hormone (GH) or prolactin (PRL)-secreting PA. We studied 74 and 6 patients with either isolated Cushing disease (CD) or GH- or PRL-secreting PA, respectively. We also screened four pediatric patients with CD, and four with GH/PRL-secreting tumors who had some syndromic features. There was one AIP mutation (p.Lys103Arg) among 74 CD patients. Two MEN1 mutations that occurred in patients with recurrent or difficult-to-treat disease were found among patients with CD. There was one MEN1 and three AIP mutations (p.Gln307ProfsX104, p.Pro114fsX, p.Lys241X) among pediatric patients with isolated GH- or PRL-secreting PA and one additional MEN1 mutation in a patient with positive family history. There were no mutations in the PRKAR1A, CDKN1B, CDKN2C or GNAS genes. Thus, germline AIP or MEN1 gene mutations are frequent among pediatric patients with GH- or PRL-secreting PA but are significantly rarer in pediatric CD; PRKAR1A mutations are not present in PA outside of Carney complex.

Mutation detection rate and spectrum in familial hypercholesterolaemia patients in the UK pilot cascade project

Abstract: Cascade testing using DNA-mutation information is now recommended in the UK for patients with familial hypercholesterolaemia (FH). We compared the detection rate and mutation spectrum in FH patients with a clinical diagnosis of definite (DFH) and possible (PFH) FH. Six hundred and thirty-five probands from six UK centres were tested for 18 low-density lipoprotein receptor gene (LDLR) mutations, APOB p.Arg3527Gln and PCSK9 p.Asp374Tyr using a commercial amplification refractory mutation system (ARMS) kit. Samples with no mutation detected were screened in all exons by single strand conformation polymorphism analysis (SSCP)/denaturing high performance liquid chromatography electrophoresis (dHPLC)/direct-sequencing, followed by multiplex ligation-dependent probe amplification (MLPA) to detect deletions and duplications in LDLR.The detection rate was significantly higher in the 190 DFH patients compared to the 394 PFH patients (56.3% and 28.4%, p > 0.00001). Fifty-one patients had inadequate information to determine PFH/DFH status, and in this group the detection rate was similar to the PFH group (25.5%, p = 0.63 vs PFH). Overall, 232 patients had detected mutations (107 different; 6.9% not previously reported). The ARMS kit detected 100 (44%) and the MLPA kit 11 (4.7%). Twenty-eight (12%) of the patients had the APOB p.Arg3527Gln and four (1.7%) had the PCSK9 p.Asp374Tyr mutation. Of the 296 relatives tested from 100 families, a mutation was identified in 56.1%. In 31 patients of Indian/Asian origin 10 mutations (two previously unreported) were identified. The utility of the ARMS kit was confirmed, but sequencing is still required in a comprehensive diagnostic service for FH. Even in subjects with a low clinical suspicion of FH, and in those of Indian origin, mutation testing has an acceptable detection rate.

Enzyme replacement therapy for mucopolysaccharidosis VI from 8 weeks of age–a sibling control study

Abstract: Mucopolysaccharidosis type VI (MPS VI) is a progressive, multisystem disorder caused by a deficiency of the lysosomal enzyme N-acetylgalactosamine-4-sulphatase (ASB). Enzyme replacement therapy (ERT) has been shown to clinically benefit affected individuals greater than 6 years of age. This case control study of affected siblings assessed the safety, efficacy and benefits of ERT in children less than 5 years of age. Siblings, aged 8 weeks and 3.6 years, were treated weekly with 1 mg/kg recombinant human N-acetylgalactosamine-4-sulphatase (rhASB) with an end-point of 3.6 years. Clinical and biochemical parameters were monitored to assess the benefits of ERT. The treatment was well tolerated by both siblings. In the younger sibling, ERT was associated with the absence of the development of scoliosis and preserved joint movement, cardiac valves and facial morphology. The older sibling had a marked improvement in joint mobility and cardiac valve pathology and scoliosis slowed or stabilized. Corneal clouding and progressive skeletal changes were observed despite treatment. This study demonstrated a clear benefit of early initiation of ERT to slow or prevent the development of significant pathological changes of MPS VI. These results indicate that the earlier ERT is started, the greater the response.

Genetic factors in non-syndromic congenital heart malformations.

Abstract: The genetic defect in most patients with non-syndromic congenital heart malformations (CHM) is unknown, although more than 40 different genes have already been implicated. Only a minority of CHM seems to be due to monogenetic mutations, and the majority occurs sporadically. The multifactorial inheritance hypothesis of common diseases suggesting that the cumulative effect of multiple genetic and environmental risk factors leads to disease, might also apply for CHM. We review here the monogenic disease genes with high-penetrance mutations, susceptibility genes with reduced-penetrance mutations, and somatic mutations implicated in non-syndromic CHM.

Gene copy number variation and common human disease.

Abstract: Variation in gene copy number is increasingly recognized as a common, heritable source of inter-individual differences in genomic sequence. The role of copy number variation is well established in the pathogenesis of rare genomic disorders. More recently, germline and somatic copy number variation have been shown to be important pathogenic factors in a range of common diseases, including infectious, autoimmune and neuropsychiatric diseases and cancer. In this review, we describe the range of methods available for measuring copy number variants (CNVs) in individuals and populations, including the limitations of presently available assays, and highlight some key examples of common diseases in which CNVs have been shown clearly to have a pathogenic role. Although there has been major progress in this field in the last 5 years, understanding the full contribution of CNVs to the genetic basis of common diseases will require further studies, with more accurate CNV assays and larger cohorts than have presently been completed.

Public understandings of genetics and health.

Abstract: Condit CM. Public understandings of genetics and health. This review of adult public understandings of genetics related to health indicates that the public's understandings overlap with those of professionals in some areas, but not others. Specifically, the majority of the world's people who have been studied understand genetics through the lens of heredity, not in terms of the structural and functional nature of genes. Public understandings of hereditary processes are influenced by models of social relationships and by experiential familiarity with particular conditions as much as by academic research results. Most people hold a fairly strong belief that many health conditions are substantially influenced by both genes and other factors. However, they do not have a stable understanding of the nature of gene–environment interactions. People in cultures where science is not a prominent cultural mode are even less likely to hold the belief structures of professional geneticists. In some areas–notably with regard to racialization of genetic medicine and characterizations of genetic variations as ‘mutations’–at least some members of the public strongly reject some geneticists' constructions. Public understanding of details pertinent to genetic testing generally appears to be weak.

A large cohort study of GJB2 mutations in Japanese hearing loss patients.

Abstract: GJB2 is the gene most frequently associated with hereditary hearing loss, and the GJB2 mutation spectrums vary among different ethnic groups In this study, the mutation spectrum as well as clinical features of patients with GJB2 mutations as found in more than 1000 Japanese hearing loss families are summarized The present results show that the frequency of GJB2 mutations in the Japanese population with hearing loss is 142% overall and 252% in patients with congenital hearing loss c235delC was the most frequent allele (498%), was associated with a more severe phenotype, and was mainly found in patients who were diagnosed by the age of 3 In contrast, the second most frequent was pV37I (165%), which has a milder phenotype and was mainly found in patients diagnosed at a higher age Additional clinical features in hearing loss patients with GJB2 mutations in this study were the near absence of tinnitus, vestibular dysfunction and inner ear malformations

Conquering the complex world of human septins: implications for health and disease

Abstract: Septins are highly conserved filamentous proteins first characterized in budding yeast and subsequently identified in must eukaryotes Septins can bind and hydrolyze GTP, which is intrinsically related to their formation of septin hexamers and functional protein interactions The human septin family is composed of 14 loci, SEPT1-SEPT14, which encode dozens of different septin proteins Their central GTPase and polybasic domain regions are highly conserved but they diverge in their N-terminus and/or C-terminus The mechanism by which the different isoforms are generated is not yet well understood, but one can hypothesize that the use of different promoters and/or alternative splicing could give rise to these variants Septins perform diverse cellular functions according to tissue expression and their interacting partners Functions identified to date include cell division, chromosome segregation, protein scaffolding, cellular polarity, motility, membrane dynamics, vesicle trafficking, exocytosis, apoptosis, and DNA damage response Their expression is tightly regulated to maintain proper filament assembly and normal cellular functions Alterations of these proteins, by mutation or expression changes, have been associated with a variety of cancers and neurological diseases The association of septins with cancer results from alterations of expression in solid tumors or translocations in leukemias [mixed lineage leukemia (MLL)] Expression changes in septins have also been associated with neurological conditions such as Alzheimer's and Parkinson's disease, as well as retinopathies, hepatitis C, spermatogenesis and Listeria infection Pathogenic mutations of SEPT9 were identified in the autosomal dominant neurological disorder hereditary neuralgic amyotrophy (HNA) Human septin research over the past decade has established their importance in cell biology and human disease Further functional characterization of septins is crucial to our understanding of their possible diagnostic, prognostic, and therapeutic applications

Clinical and molecular aspects of aniridia

Abstract: Aniridia is a severe, congenital ocular malformation inherited in an autosomal-dominant fashion with high penetrance and variable expression. Eye morphogenesis in humans involves a molecular genetic cascade in which a number of developmental genes interact in a highly organized process during the embryonic period to produce functional ocular structures. Among these genes, paired box gene 6 (PAX6) has an essential role as it encodes a phylogenetically conserved transcription factor almost universally employed for eye formation in animals with bilateral symmetry, despite widely different embryological origins. To direct eye development, PAX6 regulates the tissue-specific expression of diverse molecules, hormones, and structural proteins. In humans, PAX6 is located in chromosome 11p13, and its mutations lead to a variety of hereditary ocular malformations of the anterior and posterior segment, among which aniridia and most probably foveal hypoplasia are the major signs. Aniridia occurs due to decreased dosage of the PAX6 gene and exists in both sporadic and familial forms. The mutations are scattered throughout the gene and the vast majority of those reported so far are nonsense mutations, frameshift mutations, or splicing errors that are predicted to cause pre-mature truncation of the PAX6 protein, causing haploinsufficiency. Here we review the data regarding the mechanisms and the mutations that relate to aniridia.

Delineation of 15q13.3 microdeletions.

Abstract: The increasing use of array-comparative genomic hybridization (array-CGH) to identify copy number variations (CNVs) in patients with developmental delay (DD), mental retardation and/or dysmorphic features has allowed the recent recognition of numerous genomic imbalances, including the 15q13.3 microdeletion. Patients with this microdeletion generally present with relatively consistent breakpoints at BP4 and BP5, which include the CHRNA7 gene. About 100 index cases have been reported since the first publication in 2008. This large number of patients ascertained through highly variable samples has been necessary to describe the full phenotypic spectrum of this microdeletion, ranging from mental retardation with dysmorphic features, epilepsy, neuropsychiatric disturbances with or without cognitive impairment to complete absence of anomalies. Here, we describe a collaborative study reporting a new cohort of 12 index patients and 13 relatives carrying a heterozygous BP4-BP5 microdeletion out of a series of 4625 patients screened by array-CGH for DD. We confirm the clinical expressivity of the disease as well as the incomplete penetrance in seven families. We showed through a review of the literature that males are more likely to be symptomatic. Sequence analysis of CHRNA7 yielded no data to support the unmasking of recessive variants as a cause of phenotypic variability. We also report the first patient carrying a 15q13.3 homozygous microdeletion inherited from both parents. He had severe epileptic encephalopathy with retinopathy, autistic features and choreoathetosis. Besides the classical approximately 1.5 Mb BP4-BP5 microdeletion, we also describe three index patients and two relatives with a smaller 500 kb microdeletion, including the CHRNA7 gene.

Risk-reducing mastectomy and salpingo-oophorectomy in unaffected BRCA mutation carriers: uptake and timing.

Abstract: Once female carriers of a BRCA mutation are identified they have to make decisions on risk management. The aim of this study is to outline the uptake of risk-reducing surgery in the Danish population of BRCA mutation positive women and to search for factors affecting this decision. We analysed data from 306 healthy BRCA carriers with no personal history of ovarian or breast cancer. We found a 10-year uptake of 75% for risk-reducing salpingo-oophorectomy and 50% for risk-reducing mastectomy by time to event analysis. Age and childbirth influenced this decision. The uptake rate has not changed significantly over the last decade. Risk-reducing surgeries are widely acceptable among Danish BRCA mutation positive women and the uptake of prophylactic mastectomy is higher than in most other countries.

Mutational spectrum in the cardiac transcription factor gene NKX2.5 (CSX) associated with congenital heart disease

Abstract: Heterozygous mutations in the human transcription factor gene NKX2.5 are associated with either isolated or combined congenital heart disease (CHD), primarily secundum atrial septal defect-II (ASD-II), ventricular septal defect (VSD) or tetralogy of Fallot (TOF). Thus, NKX2.5 has an important role at different stages of cardiac development. The frequency of NKX2.5 mutations in a broader phenotypic spectrum of CHD is not completely determined. Here, we report the identification of two novel mutations in the NKX2.5 gene in a screening of 121 patients with a broad spectrum of CHDs. However, mutations were only associated with familial ASD-II and in both, patients also showed atrioventricular (AV) block. We found one missense mutation (R190L) in two siblings with ASD-II and a frame-shift mutation (A255fsX38) at the C-terminus in a mother and daughter. In addition, a single patient with hypoplastic left heart syndrome (HLHS) had the reported sequence variant R25C. Importantly, sporadic cases of CHD that share phenotypic aspects of NKX2.5 mutation carriers were negative for genetic analysis. Thus, even important for cardiac development, germline mutations in NKX2.5 are rare in patients with sporadic CHD and genetic and/or pathophysiologic heterogeneity is likely for sporadic forms of CHD.

Direct-to-consumer genetic testing: good, bad or benign?

Abstract: A wide variety of genetic tests are now being marketed and sold in direct-to-consumer (DTC) commercial transactions. However, risk information revealed through many DTC testing services, especially those based on emerging genome wide-association studies, has limited predictive value for consumers. Some commentators contend that tests are being marketed prematurely, while others support rapid translation of genetic research findings to the marketplace. The potential harms and benefits of DTC access to genetic testing are not yet well understood, but some large-scale studies have recently been launched to examine how consumers understand and use genetic risk information. Greater consumer access to genetic tests creates a need for continuing education for health care professionals so they can respond to patients' inquiries about the benefits, risks and limitations of DTC services. Governmental bodies in many jurisdictions are considering options for regulating practices of DTC genetic testing companies, particularly to govern quality of commercial genetic tests and ensure fair and truthful advertising. Intersectoral initiatives involving government regulators, professional bodies and industry are important to facilitate development of standards to govern this rapidly developing area of personalized genomic commerce.

Refining the phenotype associated with MEF2C haploinsufficiency.

Abstract: Recently, submicroscopic deletions of the 5q14.3 region have been described in patients with severe mental retardation (MR), stereotypic movements, epilepsy and cerebral malformations. Further delineation of a critical region of overlap in these patients pointed to MEF2C as the responsible gene. This finding was further reinforced by the identification of a nonsense mutation in a patient with a similar phenotype. In brain, MEF2C is essential for early neurogenesis, neuronal migration and differentiation. Here we present two additional patients with severe MR, autism spectrum disorder and epilepsy, carrying a very small deletion encompassing the MEF2C gene. This finding strengthens the role of this gene in severe MR, and enables further delineation of the clinical phenotype.

microRNAs in diseases: from candidate to modifier genes

Abstract: Until recently, the search for genetic factors predisposing or causing Mendelian diseases focused almost exclusively on protein coding sequences. As essential components of the regulatory system of gene expression, microRNAs (miRNAs) hold great promises into elucidating a number of inherited diseases. The herein review focuses on the genetic variations, whether copy number variation (CNV) or single nucleotide polymorphism (SNP), alternatively at the levels of the miRNA gene itself and of its target genes. We consider miRNA as the candidate gene, or the regulator of a disease-causing gene, or the modifier gene. The best paradigms of the field are presented in both monogenic diseases and complex traits. The computational tools, which are essential into identifying miRNAs and characterizing miRNA targets, are overviewed.

Co-occurring diagnoses among FMR1 premutation allele carriers.

Abstract: Following the discovery of two disorders associated with premutation alleles of the fragile X mental retardation gene (FMR1), primary ovarian insufficiency [fragile X-associated primary ovarian insufficiency (FXPOI)] and a tremor/ataxia syndrome [fragile X-associated tremor/ataxia disorder (FXTAS)], numerous studies have examined other potential co-morbid conditions, including neuropsychological deficits. Here, the frequency of self-reported diagnoses obtained through medical history interviews from FMR1 premutation carriers and non-carriers aged 18-50 were analyzed. Study subjects included 537 women, 334 of whom carry the premutation and 151 men, 37 of whom carry the premutation. Men with the premutation did not report any medical conditions at higher rates compared with non-carriers, controlling for age, ethnicity/race, and household income. Women with the premutation reported mental health disorders [i.e. attention deficit hyperactivity disorder (ADHD), anxiety, depression] significantly more often than non-carriers. However, after adjusting for covariates, these increased rates were not statistically significant. Additional follow-up analyses examined the consequence of ovarian dysfunction as a cause of co-occurring conditions. Women with an indication of ovarian insufficiency (i.e. irregular cycles) reported higher rates of thyroid problems and depression/anxiety. Because only women, not men, reported these conditions more often, the relationship between FXPOI and hormone irregularities in women should be explored for a potential link with the increase in the reported medical conditions.

Surveillance in von Hippel‐Lindau disease (vHL)

Abstract: von Hippel-Lindau disease (vHL) is a hereditary multisystem cancer syndrome requiring lifelong prophylactic surveillance. Current surveillance recommendations rely on best medical judgement and no evidence of effect exists. We aimed to evaluate the capability of surveillance in manifestation detection, before these turn symptomatic, in order to prevent disabling or even fatal outcomes. We focus on surveillance of central nervous system (CNS) hemangioblastomas, retinal hemangiomas and renal cell carcinoma (RCC) as these have the most severe consequences. On the basis of full medical records from 54 living vHL-mutation carriers, risks of intercurrent manifestations in-between surveillance examinations were determined and clinical consequences of surveillance findings evaluated. Current recommendations of annual ophthalmic and abdominal examinations corresponded to acceptably low intercurrent manifestation risks (1.7% and 1.2%, respectively), whereas recommendations of biennial CNS imaging corresponded to a risk of 7.2%. Annual CNS examinations, however, significantly reduces this risk to 2.7%. Furthermore, most CNS manifestations found due to surveillance (71%, 106 of 150) had clinical consequence for the patient. Also, pre-symptomatic surveillance increased cumulative incidence of clinical vHL diagnosis from 46% to 72% and from 89% to 94% by age 30 and 50 years, respectively. The present results promote optimization of surveillance, expectantly improving clinical vHL outcomes.

Claudins: unlocking the code to tight junction function during embryogenesis and in disease

Abstract: Claudins are the structural and molecular building blocks of tight junctions. Individual cells express more than one claudin family member, which suggests that a combinatorial claudin code that imparts flexibility and dynamic regulation of tight junction function could exist. Although we have learned much from manipulating claudin expression and function in cell lines, loss-of-function and gain-of-function experiments in animal model systems are essential for understanding how claudin-based boundaries function in the context of a living embryo and/or tissue. These in vivo manipulations have pointed to roles for claudins in maintaining the epithelial integrity of cell layers, establishing micro-environments and contributing to the overall shape of an embryo or tissue. In addition, loss-of-function mutations in combination with the characterization of mutations in human disease have demonstrated the importance of claudins in regulating paracellular transport of solutes and water during normal physiological states. In this review, we will discuss specific examples of in vivo studies that illustrate the function of claudin family members during development and in disease.

Respiratory disease in Niemann-Pick type C2 is caused by pulmonary alveolar proteinosis

Abstract: Niemann-Pick diseases are hereditary neurovisceral lysosomal lipid storage disorders, of which the rare type C2 almost uniformly presents with respiratory distress in early infancy. In the patient presented here, the NPC2 exon 4 frameshift mutation c.408_409delAA caused reduced NPC2 protein levels in serum and lung lavage fluid and the synthesis of an aberrant, larger sized protein of around 28 kDa. Protein expression was strongly reduced also in alveolar macrophages. The infant developed failure to thrive and tachypnea. Lung lavage, computer tomography, and histology showed typical signs of pulmonary alveolar proteinosis with an abnormal intraalveolar accumulation of surfactant as well as macrophages. An NPC2-hypomorph animal model also showed pulmonary alveolar proteinosis and accumulation of macrophages in the lung, liver, and spleen long before the mice died. Due to the elevation of cholesterol, the surfactant had an abnormal composition and function. Despite the removal of large amounts of surfactant from the lungs by therapeutic lung lavages, this treatment was only temporarily successful and the infant died of respiratory failure. Our data indicate that respiratory distress in NPC2 disease is associated with a loss of normal NPC2 protein expression in alveolar macrophages and the accumulation of functionally inactive surfactant rich in cholesterol.

A novel DFNB1 deletion allele supports the existence of a distant cis-regulatory region that controls GJB2 and GJB6 expression

Abstract: Eleven affected members of a large German-American family segregating recessively inherited, congenital, non-syndromic sensorineural hearing loss (SNHL) were found to be homozygous for the common 35delG mutation of GJB2, the gene encoding the gap junction protein Connexin 26. Surprisingly, four additional family members with bilateral profound SNHL carried only a single 35delG mutation. Previously, we demonstrated reduced expression of both GJB2 and GJB6 mRNA from the allele carried in trans with that bearing the 35delG mutation in these four persons. Using array comparative genome hybridization (array CGH), we have now identified on this allele a deletion of 131.4 kb whose proximal breakpoint lies more than 100 kb upstream of the transcriptional start sites of GJB2 and GJB6. This deletion, del(chr13:19,837,344-19,968,698), segregates as a completely penetrant DFNB1 allele in this family. It is not present in 528 persons with SNHL and monoallelic mutation of GJB2 or GJB6, and we have not identified any other candidate pathogenic copy number variation by arrayCGH in a subset of 10 such persons. Characterization of distant GJB2/GJB6 cis-regulatory regions evidenced by this allele may be required to find the 'missing' DFNB1 mutations that are believed to exist.

A new classification system for primary lymphatic dysplasias based on phenotype.

Abstract: Traditional classification systems for lymphoedema are of limited use for the diagnosis of specific forms of primary lymphoedema. The understanding of primary lymphoedema has been impeded by confusing terminology and a tendency to simply divide patients into three categories based on the age of onset: lymphoedema congenita manifests at or shortly after birth, lymphoedema praecox is apparent before the age of 35 years and lymphoedema tarda manifests thereafter. The clinical presentation in the spectrum of primary lymphoedema disorders is very variable; the phenotypes of primary lymphoedema conditions vary in the age of onset, site of the oedema, inheritance patterns, associated features and genetic causes. Different inheritance patterns are recognised and there are numerous associated anomalies. Some subgroups, such as Milroy disease and Lymphoedema distichiasis, are well characterised, but others are not. A new clinical classification for primary lymphoedema has been developed as a diagnostic algorithm. Its use is demonstrated on 333 probands referred to our lymphoedema clinic. Grouping patients by accurate phenotyping facilitates molecular investigations, understanding of inheritance patterns, and the natural history of different types of primary lymphoedema. Descriptions of the diagnostic categories, some of which have not been previously clearly defined as distinct clinical entities, are illustrated by clinical cases.

Do common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene?

Abstract: Computational methods are used to predict the molecular consequences of amino-acid substitutions on the basis of evolutionary conservation or protein structure, but their utility in clinical diagnosis or prediction of disease outcome has not been well validated. We evaluated three popular computer programs, namely, PANTHER, SIFT and PolyPhen, by comparing the predicted clinical outcomes for a group of known CFTR missense mutations against the diagnosis of cystic fibrosis (CF) and clinical manifestations in cohorts of subjects with CF-disease and CFTR-related disorders carrying these mutations. Owing to poor specificity, none of tools reliably distinguished between individual mutations that confer CF disease from mutations found in subjects with a CFTR-related disorder or no disease. Prediction scores for CFTR mutations derived from PANTHER showed a significant overall statistical correlation with the spectrum of disease severity associated with mutations in the CFTR gene. In contrast, PolyPhen- and SIFT-derived scores only showed significant differences between CF-causing and non-CF variants. Current computational methods are not recommended for establishing or excluding a CF diagnosis, notably as a newborn screening strategy or in patients with equivocal test results.

Chromodomain proteins in development: lessons from CHARGE syndrome

Abstract: In humans, heterozygous mutations in the adenosine triphosphate-dependent chromatin remodeling gene CHD7 cause CHARGE syndrome, a common cause of deaf-blindness, balance disorders, congenital heart malformations, and olfactory dysfunction with an estimated incidence of approximately 1 in 10,000 newborns. The clinical features of CHARGE in humans and mice are highly variable and incompletely penetrant, and most mutations appear to result in haploinsufficiency of functional CHD7 protein. Mice with heterozygous loss of function mutations in Chd7 are a good model for CHARGE syndrome, and analyses of mouse mutant phenotypes have begun to clarify a role for CHD7 during development and into adulthood. Chd7 heterozygous mutant mice have postnatal delayed growth, inner ear malformations, anosmia/hyposmia, and craniofacial defects, and Chd7 homozygous mutants are embryonic lethal. A central question in developmental biology is how chromodomain proteins like CHD7 regulate important developmental processes, and whether they directly activate or repress downstream gene transcription or act more globally to alter chromatin structure and/or function. CHD7 is expressed in a wide variety of tissues during development, suggesting that it has tissue-specific and developmental stage-specific roles. Here, we review recent and ongoing analyses of CHD7 function in mouse models and cell-based systems. These studies explore tissue-specific effects of CHD7 deficiency, known CHD7 interacting proteins, and downstream target sites for CHD7 binding. CHD7 is emerging as a critical regulator of important developmental processes in organs affected by human CHARGE syndrome.

Large normal and reduced penetrance alleles in Huntington disease: instability in families and frequency at the laboratory, at the clinic and in the population

Abstract: Large normal ('intermediate') alleles may produce de novo expansions in Huntington disease; nevertheless, there is very little evidence about their population prevalence and impact in daily practice, and there are conflicting reports about the extent of their instability We estimated the frequency of large normal alleles (27-35 CAGs) and of reduced penetrance alleles (36-39 CAGs), as well as the frequency of genotypes carrying them, in (i) a diagnostic laboratory, (ii) a genetic counselling clinic and (iii) the general population Large normal alleles were present in 6% of a large control sample, 7% of consultands who took pre-symptomatic testing and 7% of samples in the laboratory Reduced penetrance alleles were found in 1 of 1772 control chromosomes (01% of individuals), 5% of 146 pre-symptomatic testees and over 2% of 1214 diagnostic samples (350 families) All 16 alleles sized 27-32 CAGs seemed to be transmitted stably; alleles ≥ 36 repeats were unstable in five families Seven small full penetrance alleles contracted into the reduced penetrance range, but none into the large normal range Evidence showed that large normal alleles are relatively frequent and that those with reduced penetrance are not a rare event, either at the laboratory or the clinic This reinforces the need to understand the genomic context of repeat instability in each family and population

Testing for CHEK2 in the cancer genetics clinic: ready for prime time?

Abstract: The 1100delC mutation of the CHEK2 gene was found to be a cause of breast cancer in 2002. The lifetime risk of breast cancer among women with a mutation and with a family history of breast cancer is approximately 25%. These women are good candidates for screening with MRI and for chemoprevention with tamoxifen. It is reasonable to test for this single mutation when women undergo testing for BRCA1 and BRCA2.

Detailed molecular and clinical characterization of three patients with 21q deletions

Abstract: We have investigated three patients with 21q deletions, two with developmental delay, dysmorphic features and internal organ malformations, and one with cognitive function within the normal range but with some deficits in gross and fine motor development. All aberrations were characterized by array-comparative genomic hybridization (array-CGH). In addition, extensive fluorescence in situ hybridization (FISH) mapping on metaphase chromosomes and mechanically stretched chromosomes was performed on patient 1 who had an extremely complex intrachromosomal rearrangement with 16 breakpoints, four deletions and four duplications. Patients 2 and 3 had interstitial deletions comprising 21q21.1-21q22.11 and 21q11.2-21q21.3, respectively. Partial deletions of 21q are rare and these patients display a highly variable phenotype depending on the size and position of the deletion. A review of the literature identified 38 cases with pure 21q deletions. Twenty-three of these had reliable mapping data. The combined information of present and previous cases suggests that the ITSN1 gene is involved in severe mental retardation in patients with 21q deletion. In addition, a critical region of 0.56 Mb containing four genes, KCNE1, DSCR1, CLIC6 and RUNX1, is associated with severe congenital heart defects, and deletions of the most proximal 15-17 Mb of 21q is associated with mild or no cognitive impairment, but may lead to problems with balance and motor function.

Clinical involvement in daughters of men with fragile X-associated tremor ataxia syndrome.

Abstract: Women with the fragile X mental retardation 1 (FMR1) premutation often have concerns about neurological and medical problems, as they become older and if their fathers experience fragile X-associated tremor/ataxia syndrome (FXTAS). We therefore determined the prevalence of these problems in 110 daughters of men with FXTAS [mean age of 44.8 years (SD 8.2)]. We compared them with 43 female controls with normal FMR1 alleles [mean age of 43.8 years (SD 8.1)] and 36 premutation carrier daughters of parents with the premutation, but without FXTAS [mean age of 43.5 years (SD 7.7)]. Overall, daughters of men with FXTAS have a higher prevalence of neurological symptoms including tremor, balance problems, memory problems, and dizziness, menopausal symptoms, and psychiatric involvement including sleep problems and anxiety when compared with non-carrier female controls. Reported balance problems and menopausal symptoms were significantly higher in daughters of men with FXTAS than in carrier daughters of parents without FXTAS, suggesting the potential influence of background gene effects. Therefore, neurological, psychological and gynecological surveillance should be warranted to better provide appropriate counseling, management and care for daughters of men with FXTAS. Biological markers of additional gene effects that predispose individuals with the premutation to FXTAS need to be developed.