Showing papers in "European Journal of Human Genetics in 2008"
••
[...]
TL;DR: The FMR1 gene product, FMRP, is a selective RNA-binding protein that negatively regulates local protein synthesis in neuronal dendrites that results in reduced synaptic strength due to AMPA receptor trafficking abnormalities that lead to the fragile X phenotype.
Abstract: Fragile X syndrome, an X-linked dominant disorder with reduced penetrance, is associated with intellectual and emotional disabilities ranging from learning problems to mental retardation, and mood instability to autism. It is most often caused by the transcriptional silencing of the FMR1 gene, due to an expansion of a CGG repeat found in the 5'-untranslated region. The FMR1 gene product, FMRP, is a selective RNA-binding protein that negatively regulates local protein synthesis in neuronal dendrites. In its absence, the transcripts normally regulated by FMRP are over translated. The resulting over abundance of certain proteins results in reduced synaptic strength due to AMPA receptor trafficking abnormalities that lead, at least in part, to the fragile X phenotype.
447 citations
••
TL;DR: It is concluded that succinate dehydrogenase deficiency may be the cause of a subgroup of GISTs and this offers a therapeutic target for Gists that may not respond to STI571 and its analogs.
Abstract: Gastrointestinal stromal tumors (GISTs) may be caused by germline mutations of the KIT and platelet-derived growth factor receptor-α (PDGFRA) genes and treated by Imatinib mesylate (STI571) or other protein tyrosine kinase inhibitors. However, not all GISTs harbor these genetic defects and several do not respond to STI571 suggesting that other molecular mechanisms may be implicated in GIST pathogenesis. In a subset of patients with GISTs, the lesions are associated with paragangliomas; the condition is familial and transmitted as an autosomal-dominant trait. We investigated 11 patients with the dyad of ‘paraganglioma and gastric stromal sarcoma’; in eight (from seven unrelated families), the GISTs were caused by germline mutations of the genes encoding subunits B, C, or D (the SDHB, SDHC and SDHD genes, respectively). In this report, we present the molecular effects of these mutations on these genes and the clinical information on the patients. We conclude that succinate dehydrogenase deficiency may be the cause of a subgroup of GISTs and this offers a therapeutic target for GISTs that may not respond to STI571 and its analogs.
426 citations
••
TL;DR: Improved understanding of the biology of PTEN and the PI3K/Akt/mTOR pathway means inhibitors of this pathway are being developed as anticancer agents and could have applications for patients with PHTS, for whom no medical options currently exist.
Abstract: The PTEN hamartoma tumor syndromes (PHTS) are a collection of rare clinical syndromes characterized by germline mutations of the tumor suppressor PTEN. These syndromes are driven by cellular overgrowth, leading to benign hamartomas in virtually any organ. Cowden syndrome (CS), the prototypic PHTS syndrome, is associated with increased susceptibility to breast, thyroid, and endometrial cancer. PTEN is located on chromosome 10q22-23 and negatively regulates the prosurvival PI3K/Akt/mTOR pathway through its lipid phosphatase activity. Loss of PTEN activates this pathway and leads to increased cellular growth, migration, proliferation, and survival. Clinical management of patients with PHTS, particularly those with CS, should include early and frequent screening, surveillance, and preventive care for associated malignancies. Concomitant with improved understanding of the biology of PTEN and the PI3K/Akt/mTOR pathway, inhibitors of this pathway are being developed as anticancer agents. These medications could have applications for patients with PHTS, for whom no medical options currently exist.
286 citations
••
TL;DR: This review discusses the clinical aspects and diagnosis of SLOS, therapeutic interventions and the current understanding of pathophysiological processes involved in SLOS.
Abstract: Smith-Lemli-Opitz syndrome (SLOS) is a malformation syndrome due to a deficiency of 7-dehydrocholesterol reductase (DHCR7). DHCR7 primarily catalyzes the reduction of 7-dehydrocholesterol (7DHC) to cholesterol. In SLOS, this results in decreased cholesterol and increased 7DHC levels, both during embryonic development and after birth. The malformations found in SLOS may result from decreased cholesterol, increased 7DHC or a combination of these two factors. This review discusses the clinical aspects and diagnosis of SLOS, therapeutic interventions and the current understanding of pathophysiological processes involved in SLOS.
261 citations
••
TL;DR: A family with a wide variation in neuropsychiatric illness associated with a deletion of exons 4, 5, and 6 of NLGN4 is described, an autistic boy with a motor tic and his brother has Tourette syndrome and attention deficit hyperactivity disorder.
Abstract: Neuroligin 4 (NLGN4) is a member of a cell adhesion protein family that appears to play a role in the maturation and function of neuronal synapses. Mutations in the X-linked NLGN4 gene are a potential cause of autistic spectrum disorders, and mutations have been reported in several patients with autism, Asperger syndrome, and mental retardation. We describe here a family with a wide variation in neuropsychiatric illness associated with a deletion of exons 4, 5, and 6 of NLGN4. The proband is an autistic boy with a motor tic. His brother has Tourette syndrome and attention deficit hyperactivity disorder. Their mother, a carrier, has a learning disorder, anxiety, and depression. This family demonstrates that NLGN4 mutations can be associated with a wide spectrum of neuropsychiatric conditions and that carriers may be affected with milder symptoms.
253 citations
••
TL;DR: Smith-Magenis syndrome (SMS) is a complex neurobehavioral disorder caused by haploinsufficiency of the retinoic acid-induced 1 (RAI1) gene on chromosome 17p11.2 as discussed by the authors.
Abstract: Smith-Magenis syndrome (SMS) is a complex neurobehavioral disorder caused by haploinsufficiency of the retinoic acid-induced 1 (RAI1) gene on chromosome 17p11.2. Diagnostic strategies include molecular identification of a 17p11.2 microdeletion encompassing RAI1 or a mutation in RAI1. G-banding and fluorescent in situ hybridization (FISH) are the classical methods used to detect the SMS deletions, while multiplex ligation-dependent probe amplification (MLPA) and real-time quantitative PCR are the newer, cost-effective, and high-throughput technologies. Most SMS features are due to RAI1 haploinsufficiency, while the variability and severity of the disorder are modified by other genes in the 17p11.2 region. The functional role for RAI1 is not completely understood, but it is likely involved in transcription, based on homology and preliminary studies. Management of SMS is primarily a multidisciplinary approach and involves treatment for sleep disturbance, speech and occupational therapies, minor medical interventions, and management of behaviors.
209 citations
••
TL;DR: It is suggested that some factor may be interfering with pairing and/or recombination of the sex bivalent at the paternal MI division, and XXY is the only chromosome abnormality known where a substantial proportion (∼50%) arise as the result of non-disjunction at the first paternal meiotic division.
Abstract: The birth prevalence of sex chromosome trisomies (SCT), that is individuals with an XYY, XXY or XXX sex chromosome constitution, is traditionally based on six surveys of unselected newborns carried out in the 1960s and early 1970s. All three SCTs had a prevalence of 1 in 1000 same sex births. We re-examined these prevalences based on additional cytogenetic studies of newborn surveys, spontaneous abortions, perinatal deaths and prenatal diagnoses. The more recent newborn surveys suggest there has been an increase in the prevalence of XXYs, but not of the other two SCTs since the original newborn series. The prevalence of XXYs has risen from 1.09 to 1.72 per 1000 male births (P=0.023). We suggest that such an increase, in the absence of an increase in the prevalence of XXX, is unlikely to be due to increased maternal age. As XXY is the only chromosome abnormality known where a substantial proportion ( approximately 50%) arise as the result of non-disjunction at the first paternal meiotic division, we speculate that some factor may be interfering with pairing and/or recombination of the sex bivalent at the paternal MI division.
200 citations
••
TL;DR: This review discusses methodological issues involved in investigating gene–environment (G × E) interactions in genetic–epidemiological studies of complex diseases and their potential relevance for clinical application and attempts to clarify conceptual differences of the term ‘interaction’ in the statistical and biological sciences.
Abstract: Genetic and environmental risk factors and their interactions contribute to the development of complex diseases In this review, we discuss methodological issues involved in investigating gene-environment (G x E) interactions in genetic-epidemiological studies of complex diseases and their potential relevance for clinical application Although there are some important examples of interactions and applications, the widespread use of the knowledge about G x E interaction for targeted intervention or personalized treatment (pharmacogenetics) is still beyond current means This is due to the fact that convincing evidence and high predictive or discriminative power are necessary conditions for usefulness in clinical practice We attempt to clarify conceptual differences of the term 'interaction' in the statistical and biological sciences, since precise definitions are important for the interpretation of results We argue that the investigation of G x E interactions is more rewarding for the detailed characterization of identified disease genes (ie at advanced stages of genetic research) and the stratified analysis of environmental effects by genotype or vice versa Advantages and disadvantages of different epidemiological study designs are given and sample size requirements are exemplified These issues as well as a critical appraisal of common methodological concerns are finally discussed
181 citations
••
TL;DR: The results indicate that the ACTN3 R577X nonsense allele (X) is under-represented in elite strength athletes, consistent with previous reports indicating that α-actinin-3 deficiency appears to impair muscle performance.
Abstract: Previous reports have shown a lower proportion of the ACTN3 X/X genotype (R577X nonsense polymorphism) in sprint-related athletes compared to the general population, possibly attributed to impairment of muscle function related to α-actinin-3 deficiency. In the present study, we examined the frequency of the X/X genotype in both Black and White elite-level bodybuilders and strength athletes in comparison to the general population. A reference population of 668 Whites (363 men and 305 women) and 208 Blacks (98 men and 110 women) was genotyped for the ACTN3 R577X polymorphism. Strength athletes (52 white and 23 black; 4 women) consisting predominantly of world class and locally competitive bodybuilders, and elite powerlifters were recruited and similarly genotyped. Significantly lower X/X genotype frequencies were observed in the athletes (6.7%) vs controls (16.3%; P = 0.005). The X/X genotype was significantly lower in White athletes (9.7%) vs controls (19.9%; P = 0.018). No black athletes (0%) were observed with the X/X genotype, though this finding only approached statistical significance vs controls (4.8%; P = 0.10). The results indicate that the ACTN3 R577X nonsense allele (X) is under-represented in elite strength athletes, consistent with previous reports indicating that α-actinin-3 deficiency appears to impair muscle performance.
177 citations
••
TL;DR: The large-scale nationwide biological sample collection in Dutch twin families from the Netherlands Twin Register (NTR) and in participants in the Netherlands Study of Depression and Anxiety (NESDA) is described.
Abstract: To identify the genomic regions that confer risk and protection for major depressive disorder (MDD) in humans, large-scale studies are needed. Such studies should collect multiple phenotypes, DNA, and ideally, biological material that allows gene expression analysis, transcriptomic, proteomic, and metabolomic studies. In this paper, we briefly review linkage studies of MDD and then describe the large-scale nationwide biological sample collection in Dutch twin families from the Netherlands Twin Register (NTR) and in participants in the Netherlands Study of Depression and Anxiety (NESDA). Within these studies, 1862 participants with a diagnosis of MDD and 1857 controls at low liability for MDD have been selected for genome-wide genotyping by the US Foundation for the National Institutes of Health Genetic Association Information Network. Stage 1 genome-wide association results are scheduled to be accessible before the end of 2007. Genome-wide association results are open-access and can be viewed at the dbGAP web portal (http://www.ncbi.nlm.nih.gov). Approved users can download the genotype and phenotype data, which have been made available as of 9 October 2007.
174 citations
••
French Alternative Energies and Atomic Energy Commission1, International Agency for Research on Cancer2, Charles University in Prague3, University of Liège4, Palacký University, Olomouc5, Boston Children's Hospital6, Norwegian University of Science and Technology7, National Institutes of Health8, University of Kiel9, Uppsala University10, French Institute of Health and Medical Research11, GlaxoSmithKline12, Council on Education for Public Health13
TL;DR: A method to predict the ethnic origin of samples by comparing the sample genotypes with those from a reference set of samples of known origin is presented, which can be performed using just summary information on the known samples, and individual genotype data are not required.
Abstract: An investigation into fine-scale European population structure was carried out using high-density genetic variation on nearly 6000 individuals originating from across Europe. The individuals were collected as control samples and were genotyped with more than 300 000 SNPs in genome-wide association studies using the Illumina Infinium platform. A major East-West gradient from Russian (Moscow) samples to Spanish samples was identified as the first principal component (PC) of the genetic diversity. The second PC identified a North-South gradient from Norway and Sweden to Romania and Spain. Variation of frequencies at markers in three separate genomic regions, surrounding LCT, HLA and HERC2, were strongly associated with this gradient. The next 18 PCs also accounted for a significant proportion of genetic diversity observed in the sample. We present a method to predict the ethnic origin of samples by comparing the sample genotypes with those from a reference set of samples of known origin. These predictions can be performed using just summary information on the known samples, and individual genotype data are not required. We discuss issues raised by these data and analyses for association studies including the matching of case-only cohorts to appropriate pre-collected control samples for genome-wide association studies.
••
TL;DR: This work lists 215 XLMR conditions, subdivided according to their clinical presentation: 149 with specific clinical findings, including 98 syndromes and 51 neuromuscular conditions, and 66 nonspecific (MRX) forms.
Abstract: X-linked mental retardation (XLMR) is a common cause of inherited intellectual disability with an estimated prevalence of ∼1/1000 males Most XLMR conditions are inherited as X-linked recessive traits, although female carriers may manifest usually milder symptoms We have listed 215 XLMR conditions, subdivided according to their clinical presentation: 149 with specific clinical findings, including 98 syndromes and 51 neuromuscular conditions, and 66 nonspecific (MRX) forms We also present a map of the 82 XLMR genes cloned to date (November 2007) and a map of the 97 conditions that have been positioned by linkage analysis or cytogenetic breakpoints We briefly consider the molecular function of known XLMR proteins and discuss the possible strategies to identify the remaining XLMR genes Final remarks are made on the natural history of XLMR conditions and on diagnostic issues
••
TL;DR: A link between the rare 2 repeat of the 30-bp VNTR in the MAOA gene and much higher levels of self-reported serious and violent delinquency is demonstrated.
Abstract: Genetic studies of delinquent and criminal behavior are rare in spite of the wide recognition that individuals may differ in their propensity for delinquency and criminality. Using 2524 participants in Add Health in the United States, the present study demonstrates a link between the rare 2 repeat of the 30-bp VNTR in the MAOA gene and much higher levels of self-reported serious and violent delinquency. The evidence is based on a statistical association analysis and a functional analysis of MAOA promoter activity using two human brain-derived cell lines: neuroblastoma SH-SY5Y and human glioblastoma 1242-MG. The association analysis shows that men with a 2R report a level of serious delinquency and violent delinquency in adolescence and young adulthood that were about twice (CI: (0.21, 3.24), P=0.025; and CI: (0.37, 2.5), P=0.008 for serious and violent delinquency, respectively) as high as those for participants with the other variants. The results for women are similar, but weaker. In the functional analysis, the 2 repeat exhibits much lower levels of promoter activity than the 3 or 4 repeat.
••
TL;DR: A systematic review of all major health and medical research databases was undertaken using current guidelines to identify original relevant research papers from 1980 to 2007, which explore the issues surrounding parents and their children's communication about inherited genetic risk.
Abstract: In families affected by an inherited genetic condition, parents face a difficult task of having to communicate genetic risk information to their children. A systematic review of all major health and medical research databases was undertaken using current guidelines to identify original relevant research papers from 1980 to 2007, which explore the issues surrounding parents and their children's communication about inherited genetic risk. A total of 9698 abstracts were found of which 158 research papers were reviewed as potentially relevant. A final 17 papers were identified which met predefined inclusion and exclusion criteria. Using a meta-ethnographic approach, all identified studies' findings were analysed as primary data sources by three researchers, who independently identified the key concepts. A high level of congruence emerged between researchers, and agreed concepts were used to examine similarities and differences between papers. The findings informed the development of a narrative framework exploring the issues that related to parents' explanations of inherited genetic risk to their children, the reasons for sharing information, children's understanding of parents' explanations, the emotions evoked for family members and the support and guidance received from health professionals. Providing information, checking understanding, and explaining and managing the emotional feelings that arise were integral to supporting children's coping with genetic risk information. However, many parents struggled with one or more of these components and required more support specific to the child's developmental stage, and family members' transition of readjustment to the impact of the genetic condition.
••
TL;DR: One-year survival of live births with Down syndrome increased, especially in babies with cardiovascular malformations, reaching almost 100%, and there has been no overall change in live birth prevalence.
Abstract: The aims of this study were (1) to determine trends in total prevalence and live birth prevalence of Down syndrome, (2) to analyse trends in factors likely to influence this prevalence and (3) to determine 1-year survival in Down syndrome A retrospective review was made of prospectively collected data on all cases of Down syndrome within a malformation registry born in 1985-2004 Down syndrome affected 1188 pregnancies among 690 215 live births (172 per 1000 total births) The proportion increased over 20 years from 13 to 25 per 1000 total births (P<00001) There were 389 terminations for Down syndrome and 51 stillbirths There were 748 live births with Down syndrome (108 per 1000 live births) The live birth prevalence declined in 1985-1994 and increased in 1995-2004 with no overall change Total live births in the population declined by 20% over 20 years Mothers delivering at 35 years of age or above increased from 6 to 15% The uptake of maternal serum screening increased from zero in 1987 to 35% in 1993 but then plateaued One-year survival of live births with Down syndrome increased, especially in babies with cardiovascular malformations, reaching almost 100% The prevalence of pregnancies affected by Down syndrome has increased significantly, but there has been no overall change in live birth prevalence Increasing maternal age and improved survival of children with Down syndrome have offset the effects of prenatal diagnosis followed by the termination of pregnancy and declining general birth rate
••
TL;DR: Detailed evaluation of SNP chip coverage is conducted, including a map of local coverage – calculated over small consecutive genomic regions and gene Coverage – calculated for each known gene in the genome to reveal the degree of variation of each SNP chip in covering the genome.
Abstract: Genome-wide association (GWA) studies for complex human diseases are now feasible. Many GWA studies rely on commercial SNP chips, for which a common evaluation criterion is global coverage of the genome. Although providing an overall evaluation of an SNP chip, the global coverage does not tell us how the coverage varies across the genome, an important feature that should be taken into consideration, as coverage variation often results in power variation and potentially biased search in subsequent association analysis. To achieve a fuller understanding of SNP chip coverage, we conducted detailed evaluation of coverage, including (1) a map of local coverage - calculated over small consecutive genomic regions and (2) gene coverage - calculated for each known gene in the genome. These evaluations can reveal the degree of variation of each SNP chip in covering the genome and can facilitate SNP chip comparisons at a finer scale.
••
TL;DR: The aims of this review are to provide a timely summary for most of the genome-wide association studies that have been published until June/July 2007 and to evaluate to what extent these results have been validated in subsequent replication studies.
Abstract: The genome-wide association approach has been the most powerful and efficient study design thus far in identifying genetic variants that are associated with complex human diseases. This approach became feasible as the result of several key advancements in genetic knowledge, genotyping technologies, statistical analysis algorithms and the availability of large collections of cases and controls. With all these necessary tools in hand, many genome-wide association studies were recently completed, and many more studies which will explore the genetic basis of various complex diseases and quantitative traits are soon to come. This approach has started to reap the fruits of its labor over the past several months. Publications of genome-wide association studies in several complex diseases such as inflammatory bowel disease, type-2 diabetes, breast cancer and prostate cancer have been abundant in the first half of this year. The aims of this review are firstly, to provide a timely summary for most of the genome-wide association studies that have been published until June/July 2007 and secondly, to evaluate to what extent these results have been validated in subsequent replication studies.
••
TL;DR: A rigorous text-searching and database-mining strategy is applied to extract, as comprehensively as possible, an annotated list of currently known human haploinsufficient genes, including their functions and associated diseases, and a custom-made Java visualization tool is described, HaploGeneMapper, to aid in visualizing the proximity of human haplosufficient genes to SDs and to enable identification of haplo Insufficient genes that are vulnerable to NAHR-mediated deletion.
Abstract: Despite the significance of haploinsufficiency in human disease, no systematic study has been reported into the types of genes that are haploinsufficient in human, or into the mechanisms that commonly lead to their deletion and to the expression of the haploinsufficient phenotype. We have applied a rigorous text-searching and database-mining strategy to extract, as comprehensively as possible, from PubMed and OMIM an annotated list of currently known human haploinsufficient genes, including their functions and associated diseases. Gene-set enrichment analysis shows that genes-encoding transcription factors, and genes that function in development, the cell cycle, and nucleic acid metabolism are overrepresented among haploinsufficient genes in human. Many of the phenotypes associated with loss-of-function or deletion of one copy of a haploinsufficient gene describe mental retardation, developmental or metabolic disorders, or tumourigenesis. We also found that haploinsufficient genes are less likely than the complete set of human genes to be situated between pairs of segmental duplications (SDs) that are in close proximity to each other on the same chromosome. Given that SDs can initiate non-allelic homologous recombination (NAHR) and the deletion of adjacent genomic regions, this suggests that the location of haploinsufficient genes between SD pairs, from whence they may suffer intra-genomic rearrangement and loss, is selectively disadvantageous. We describe a custom-made Java visualization tool, HaploGeneMapper, to aid in visualizing the proximity of human haploinsufficient genes to SDs and to enable identification of haploinsufficient genes that are vulnerable to NAHR-mediated deletion.
••
TL;DR: Findings provide strong evidence that MLH 1 promoter methylation in normal body cells mimics HNPCC and constitutes a pathogenic pre-lesion in MLH1.
Abstract: Germline mutations in mismatch repair (MMR) genes, tumours with high microsatellite instability (MSI-H) and loss of MMR protein expression are the hallmarks of HNPCC (Lynch syndrome). While somatic MLH1 promoter hypermethylation is generally accepted in the tumorigenesis of sporadic tumours, abnormal MLH1 promoter methylation in normal body cells is controversially discussed as a mechanism predisposing patients to HNPCC. In all 94 patients suspected of HNPCC-syndrome with a mean age of onset of 45.5 years, MLH1-deficiency in their tumours but no germline mutation, underwent methylation-specific PCR-screening for MLH1 promoter methylation. In peripheral blood cells of 12 patients an MLH1 promoter methylation, in seven informative cases allele-specific, was found. Normal colonic tissue, buccal mucosa, and tumour tissue available from three patients also presented abnormal methylation in the MLH1 promoter. The heredity of aberrant methylation is questionable. Pro: MLH1 promoter methylation was found in a patient and his mother giving evidence for a familial predisposition for an epimutation in MLH1. Contra: a de novo set-up of methylation in one patient, a mosaic or incomplete methylation pattern in six patients, and no evidence for inheritance of MLH1 promoter methylation in the remaining families. Our findings provide strong evidence that MLH1 promoter methylation in normal body cells mimics HNPCC and constitutes a pathogenic pre-lesion in MLH1. The identification of hypermethylation as an epigenetic defect has important implications for surveillance recommendations, as these patients should be treated like Lynch syndrome patients, whereas the heritability of methylation is still under investigation.
••
TL;DR: High-resolution Y-chromosome analysis of males from the United Arab Emirates, Qatar and Yemen revealed high diversity in their Y-haplogroup substructure possibly a result of gene flow along the coastal crescent-shaped corridor of the Gulf of Oman facilitating human dispersals.
Abstract: Arabia has served as a strategic crossroads for human disseminations, providing a natural connection between the distant populations of China and India in the east to the western civilizations along the Mediterranean. To explore this region's critical role in the migratory episodes leaving Africa to Eurasia and back, high-resolution Y-chromosome analysis of males from the United Arab Emirates (164), Qatar (72) and Yemen (62) was performed. The role of the Levant in the Neolithic dispersal of the E3b1-M35 sublineages is supported by the data, and the distribution and STR-based analyses of J1-M267 representatives points to their spread from the north, most likely during the Neolithic. With the exception of Yemen, southern Arabia, South Iran and South Pakistan display high diversity in their Y-haplogroup substructure possibly a result of gene flow along the coastal crescent-shaped corridor of the Gulf of Oman facilitating human dispersals. Elevated rates of consanguinity may have had an impact in Yemen and Qatar, which experience significant heterozygote deficiencies at various hypervariable autosomal STR loci.
••
TL;DR: Uptake of genetic counselling in hypertrophic cardiomyopathy is comparable to uptake in oncogenetics, and conditional uptake of predictive DNA testing, however, is much higher.
Abstract: Hypertrophic cardiomyopathy is a common autosomal dominant disease, associated with heart failure and arrhythmias predisposing to sudden cardiac death. After the detection of the causal mutation in the proband predictive DNA testing of relatives is possible (cascade screening). Prevention of sudden cardiac death in patients with a high risk by means of an implantable cardioverter defibrillator is effective. In 97 hypertrophic cardiomyopathy families with a sarcomere gene mutation we retrospectively determined uptake of genetic counselling and predictive DNA testing in relatives within 1 year after the detection of the causal mutation in the proband. Uptake of genetic counselling was 39% and did not differ significantly by proband's or relative's gender, nor by young age of the relative (<18 years) or a family history positive for sudden cardiac death. In second-degree relatives, eligible for predictive DNA testing when the first-degree relative had died, uptake was 27.5% (P=0.047). Uptake of predictive genetic testing was 39%; conditional uptake of predictive genetic testing was 99%. Uptake of genetic counselling in hypertrophic cardiomyopathy is comparable to uptake in oncogenetics. Conditional uptake of predictive DNA testing, however, is much higher. Because sudden cardiac death can be prevented uptake of genetic counselling in hypertrophic cardiomyopathy should be as high as possible. To achieve this research into the determinants of uptake is needed.
••
TL;DR: Public health practice has to date concerned itself with environmental or social determinants of health and disease and has paid scant attention to genomic variations within the population, but the advances brought about by genomics are changing these perceptions.
Abstract: Public health practice has to date concerned itself with environmental or social determinants of health and disease and has paid scant attention to genomic variations within the population. The advances brought about by genomics are changing these perceptions. In the long run, this knowledge will enable health promotion messages and disease prevention programmes to be specifically directed at susceptible individuals and families, or at subgroups of the population, based on their genomic risk profile. As the controversial discourse in science and health politics shows, the integration of genomics into public health research, policy and practice is one of the major challenges that our health-care system is currently facing.
•
TL;DR: Liss et al. as mentioned in this paper used Agilent oligonucleotide-based array-CGH to determine the exact breakpoints in 14 patients with partial deletions of this region.
Abstract: Partial deletions of the long arm of chromosome 13 lead to variable phenotypes dependant on the size and position of the deleted region. In order to update the phenotypic map of chromosome 13q21.1‐qter deletions, we applied 244k Agilent oligonucleotide‐based array‐CGH to determine the exact breakpoints in 14 patients with partial deletions of this region. Subsequently, we linked the genotype to the patient's phenotype. Using this approach, we were able to refine the smallest deletion region linked to short stature (13q31.3: 89.5–91.6 Mb), microcephaly (13q33.3–q34), cortical development malformations (13q33.1‐qter), Dandy–Walker malformation (DWM) (13q32.2–q33.1), corpus callosum agenesis (CCA) (13q32.3–q33.1), meningocele/encephalocele (13q31.3‐qter), DWM, CCA, and neural tube defects (NTDs) taken together (13q32.3–q33.1), ano‐/microphthalmia (13q31.3–13qter), cleft lip/palate (13q31.3–13q33.1), lung hypoplasia (13q31.3–13q33.1), and thumb a‐/hypoplasia (13q31.3–q33.1 and 13q33.3–q34). Based on observations of this study and previous reports we suggest a new entity, “distal limb anomalies association,” linked to 13q31.3q33.1 segment. Most of the individuals with deletion of any part of 13q21qter showed surprisingly similar facial dysmorphic features, and thus, a “13q deletion facial appearance” was suggested. Prominent nasal columella was mapped between 13q31.3 and 13q33.3, and micrognathia between 13q21.33 and 13q31.1. The degree of mental delay did not display a particular phenotype–genotype correlation on chromosome 13. In contrast to previous reports of carriers of 13q32 band deletions as the most seriously affected patients, we present two such individuals with long‐term survival, 28 and 2.5 years. © 2009 Wiley‐Liss, Inc.
••
TL;DR: These findings provide the first confirmation that the three 8q24 regions independently influence the risk of prostate cancer and, in particular, advanced disease.
Abstract: Compelling evidence demonstrates chromosome 8q24 as a prostate cancer susceptibility locus. Multiple variants within three adjacent regions at 8q24 have recently been identified to impact the risk of prostate cancer. Yet, the role of these variants in more advanced disease has not been rigorously assessed. To examine the relationship between 8q24 variants and advanced disease, we tested 10 previously associated 8q24 variants in a case-control study of advanced prostate cancer (N=1012). Of these ten 8q24 variants, six were associated with the risk of advanced prostate cancer (P=0.001-0.038). Three of these variants (rs10090154-region 1, rs16901979-region 2, and rs6983267-region 3), each variant residing in one of the three previously reported 8q24 regions, could account for our 8q24 effects on advanced disease. A meta-analysis across 10 studies including our results of four 8q24 variants (rs1442295 and DG8S737-region 1, rs16901979-region 2, and rs6983267-region 3) and prostate cancer risk demonstrated strong associations across a wide array of study designs and populations. Our findings provide the first confirmation that the three 8q24 regions independently influence the risk of prostate cancer and, in particular, advanced disease.
••
TL;DR: It is concluded that the 1858T-allele is a PTPN22 genetic susceptibility factor for autoimmune AD, and other rare variants in PTPn22 do occur, and may also be involved in the pathogenesis.
Abstract: The tyrosine-protein phosphatase non-receptor type 22 (PTPN22) gene was recently identified as an important genetic susceptibility factor in several autoimmune diseases. The increased risk has been broadly explained by the 1858T-allele (rs2476601). As two smaller studies on Addison's disease (AD) have shown diverging results, we aimed to elucidate the predisposing effect of the single-nucleotide polymorphism (SNP) 1858CT in a larger population of AD patients, especially focusing on the AD patients with known autoimmune etiology. We also screened for unknown rare or common variants in the PTPN22 gene that could predispose for AD. The case-control study of Norwegian AD patients (n=332) and controls (n=990) showed a significant association between autoimmune AD (n=302) and the PTPN22 1858T risk allele (P=0.016). The association of AD with 1858T was supported by a meta-analysis combining our genotype data with that of others published previously (P=0.003). The mutation screening of PTPN22 in AD patients (n=332) and controls (n=112) revealed eight missense variants, five of which have not been reported previously. In conclusion, the 1858T-allele is a PTPN22 genetic susceptibility factor for autoimmune AD. Other rare variants in PTPN22 do occur, and may also be involved in the pathogenesis.
••
TL;DR: The ideal of genetic counselling is rather consistent in the guidelines, but there are some contradictions between the requirements of objective information-giving and adapting counselling to counsellee's circumstances.
Abstract: The objective of this article is to review guidelines that address counselling in the context of genetic testing in order to summarise what aspects of counselling they consider most important, and to examine how they construct the ideal of genetic counselling. Guidelines were collected by examining the websites of different international professional, political, ethical and patient organisations, either previously known or found with the help of the Google search engine, and also using references listed in other studies. The most frequently mentioned topics in the collected 56 guidelines were sought, and this was carried out with the software package Qualitative Solutions and Research for Non-numerical Unstructured Data Indexing Searching and Theorizing. Topics related to genetic counselling that were mentioned in at least 30 of 56 collected documents were considered to be the most important aspects of genetic counselling. The ideal of genetic counselling is expressed in the analysed guidelines as being composed of (1) an appropriately trained professional who understands genetics and its ethical implications well; (2) relevant and objective information; (3) assurance of the counsellee's understanding; (4) psychological support; (5) informed consent; (6) confidentiality of genetic information; (7) considering familial implications; (8) appropriate handling of potential discrimination of testing; and (9) assuring autonomous decision-making by the counsellee. The ideal of genetic counselling is rather consistent in the guidelines, but there are some contradictions between the requirements of objective information-giving and adapting counselling to counsellee's circumstances.
••
TL;DR: Two novel germline RUNX1 mutations are reported on: an out-of-frame 8 bp heterozygous deletion (c.442_449del) in an FPD/AML pedigree and a de novo 3.5 Mb deletion in the 21q22.11.12 region encompassing the RunX1 gene in a mentally retarded female patient with short stature and thrombocytopenia.
Abstract: Germline RUNX1 mutations result in a rare autosomal dominant condition characterized by qualitative and quantitative platelet defects and predisposition to the development of myeloid malignancies (familial platelet disorder with propensity to acute myeloid leukaemia, FPD/AML). Only 13 pedigrees have previously been described so far. We report on two novel germline RUNX1 mutations: (1) an out-of-frame 8 bp heterozygous deletion (c.442_449del) in an FPD/AML pedigree and (2) a de novo 3.5 Mb deletion in the 21q22.11.21q22.12 region encompassing the RUNX1 gene in a mentally retarded female patient with short stature and thrombocytopenia. Interestingly, a similar de novo submicroscopic deletion has been recently reported in the literature in a mentally retarded patient. Mental retardation is one of the most common disorders and primary causes of thrombocytopenia are rare. When occurring together, these features should prompt to test for 21q22 deletion for comprehensive genetic counselling and clinical management.
••
TL;DR: PDE8B is another PDE gene linked to iMAD; it is a candidate causative gene for other adrenocortical lesions linked to the cAMP signaling pathway and possibly for tumors in other tissues.
Abstract: Bilateral adrenocortical hyperplasia (BAH) is the second most common cause of corticotropin-independent Cushing syndrome (CS) Genetic forms of BAH have been associated with complex syndromes such as Carney Complex and McCune-Albright syndrome or may present as isolated micronodular adrenocortical disease (iMAD) usually in children and young adults with CS A genome-wide association study identified inactivating phosphodiesterase (PDE) 11A (PDE11A)-sequencing defects as low-penetrance predisposing factors for iMAD and related abnormalities; we also described a mutation (c914A > C/H305P) in cyclic AMP (cAMP)-specific PDE8B, in a patient with iMAD In this study we further characterize this mutation; we also found a novel PDE8B isoform that is highly expressed in the adrenal gland This mutation is shown to significantly affect the ability of the protein to degrade cAMP in vitro Tumor tissues from patients with iMAD and no mutations in the coding PDE8B sequence or any other related genes (PRKAR1A, PDE11A) showed downregulated PDE8B expression (compared to normal adrenal cortex) Pde8b is detectable in the adrenal gland of newborn mice and is widely expressed in other mouse tissues We conclude that PDE8B is another PDE gene linked to iMAD; it is a candidate causative gene for other adrenocortical lesions linked to the cAMP signaling pathway and possibly for tumors in other tissues
••
TL;DR: Epigenetic analysis of the FMR1 gene demonstrated the lack of DNA methylation and a methylation pattern of lysines 4 and 27 on histone H3 similar to that of normal controls, in accordance with normal transcription levels and consistent with a euchromatic configuration.
Abstract: Fragile X syndrome (FXS) is caused by the expansion of a CGG repeat in the 5'UTR of the FMR1 gene and the subsequent methylation of all CpG sites in the promoter region. We recently identified, in unrelated FXS families, two rare males with an unmethylated full mutation, that is, with an expanded CGG repeat (>200 triplets) lacking the typical CpG methylation in the FMR1 promoter. These individuals are not mentally retarded and do not appear to be mosaic for premutation or methylated full mutation alleles. We established lymphoblastoid and fibroblast cell lines that showed essentially normal levels of the FMR1-mRNA but reduced translational efficiency of the corresponding mRNA. Epigenetic analysis of the FMR1 gene demonstrated the lack of DNA methylation and a methylation pattern of lysines 4 and 27 on histone H3 similar to that of normal controls, in accordance with normal transcription levels and consistent with a euchromatic configuration. On the other hand, histone H3/H4 acetylation and lysine 9 methylation on histone H3 were similar to those of typical FXS cell lines, suggesting that these epigenetic changes are not sufficient for FMR1 gene inactivation. These findings demonstrate remarkable consistency and suggest a common genetic mechanism causing this rare FMR1 epigenotype. The discovery of such a mechanism may be important in view of therapeutic attempts to convert methylated into unmethylated full mutations, restoring the expression of the FMR1 gene.
••
TL;DR: In an in vivo assay of flux through this metabolic pathway using dermal fibroblasts obtained from an affected individual, proline and ornithine biosynthetic activity of P5 CS was not affected by the H784Y substitution, suggesting that P5CS may possess additional uncharacterised functions that affect connective tissue and central nervous system function.
Abstract: There are several rare syndromes combining wrinkled, redundant skin and neurological abnormalities. Although phenotypic overlap between conditions has suggested that some might be allelic to one another, the aetiology for many of them remains unknown. A consanguineous New Zealand Maori family has been characterised that segregates an autosomal recessive connective tissue disorder (joint dislocations, lax skin) associated with neurological abnormalities (severe global developmental delay, choreoathetosis) without metabolic abnormalities in four affected children. A genome-screen performed under a hypothesis of homozygosity by descent for an ancestral mutation, identified a locus at 10q23 (Z=3.63). One gene within the candidate interval, ALDH18A1, encoding Δ1-pyrroline-5-carboxylate synthase (P5CS), was considered a plausible disease gene since a missense mutation had previously been shown to cause progressive neurodegeneration, cataracts, skin laxity, joint dislocations and metabolic derangement in a consanguineous Algerian family. A missense mutation, 2350C>T, was identified in ALDH18A1, which predicts the substitution H784Y. H784 is invariant across all phyla and lies within a previously unrecognised, conserved C-terminal motif in P5CS. In an in vivo assay of flux through this metabolic pathway using dermal fibroblasts obtained from an affected individual, proline and ornithine biosynthetic activity of P5CS was not affected by the H784Y substitution. These data suggest that P5CS may possess additional uncharacterised functions that affect connective tissue and central nervous system function.