Loss-of-Function Mutations in PTPN11 Cause Metachondromatosis, but Not Ollier Disease or Maffucci Syndrome.

Metachondromatosis (MC) is a rare, autosomal dominant, incompletely penetrant combined exostosis and enchondromatosis tumor syndrome. MC is clinically distinct from other multiple exostosis or multiple enchondromatosis syndromes and is unlinked to EXT1 and EXT2, the genes responsible for autosomal dominant multiple osteochondromas (MO). To identify a gene for MC, we performed linkage analysis with high-density SNP arrays in a single family, used a targeted array to capture exons and promoter sequences from the linked interval in 16 participants from 11 MC families, and sequenced the captured DNA using high-throughput parallel sequencing technologies. DNA capture and parallel sequencing identified heterozygous putative loss-of-function mutations in PTPN11 in 4 of the 11 families. Sanger sequence analysis of PTPN11 coding regions in a total of 17 MC families identified mutations in 10 of them (5 frameshift, 2 nonsense, and 3 splice-site mutations). Copy number analysis of sequencing reads from a second targeted capture that included the entire PTPN11 gene identified an additional family with a 15 kb deletion spanning exon 7 of PTPN11. Microdissected MC lesions from two patients with PTPN11 mutations demonstrated loss-of-heterozygosity for the wild-type allele. We next sequenced PTPN11 in DNA samples from 54 patients with the multiple enchondromatosis disorders Ollier disease or Maffucci syndrome, but found no coding sequence PTPN11 mutations. We conclude that heterozygous loss-of-function mutations in PTPN11 are a frequent cause of MC, that lesions in patients with MC appear to arise following a "second hit," that MC may be locus heterogeneous since 1 familial and 5 sporadically occurring cases lacked obvious disease-causing PTPN11 mutations, and that PTPN11 mutations are not a common cause of Ollier disease or Maffucci syndrome.

Cancer risk in the Swiss HIV Cohort Study: associations with immunodeficiency, smoking, and highly active antiretroviral therapy.

BACKGROUND: Persons infected with human immunodeficiency virus (HIV) have an increased risk for several cancers, but the influences of behavioral risk factors, such as smoking and intravenous drug use, and highly active antiretroviral therapy (HAART) on cancer risk are not clear. METHODS: Patient records were linked between the Swiss HIV Cohort Study and Swiss cantonal cancer registries. Observed and expected numbers of incident cancers were assessed in 7304 persons infected with HIV followed for 28,836 person-years. Relative risks for cancer compared with those for the general population were determined by estimating cancer registry-, sex-, age-, and period-standardized incidence ratios (SIRs). RESULTS: Highly elevated SIRs were confirmed in persons infected with HIV for Kaposi sarcoma (KS) (SIR = 192, 95% confidence interval [CI] = 170 to 217) and non-Hodgkin lymphoma (SIR = 76.4, 95% CI = 66.5 to 87.4). Statistically significantly elevated SIRs were also observed for anal cancer (SIR = 33.4, 95% CI = 10.5 to 78.6); Hodgkin lymphoma (SIR = 17.3, 95% CI = 10.2 to 27.4); cancers of the cervix (SIR = 8.0, 95% CI = 2.9 to 17.4); liver (SIR = 7.0, 95% CI = 2.2 to 16.5); lip, mouth, and pharynx (SIR = 4.1, 95% CI = 2.1 to 7.4); trachea, lung, and bronchus (SIR = 3.2, 95% CI = 1.7 to 5.4); and skin, nonmelanomatous (SIR = 3.2, 95% CI = 2.2 to 4.5). In HAART users, SIRs for KS (SIR = 25.3, 95% CI = 10.8 to 50.1) and non-Hodgkin lymphoma (SIR = 24.2, 95% CI = 15.0 to 37.1) were lower than those for nonusers (KS SIR = 239, 95% CI = 211 to 270; non-Hodgkin lymphoma SIR = 99.3, 95% CI = 85.8 to 114). Among HAART users, however, the SIR (although not absolute numbers) for Hodgkin lymphoma (SIR = 36.2, 95% CI = 16.4 to 68.9) was comparable to that for KS and non-Hodgkin lymphoma. No clear impact of HAART on SIRs emerged for cervical cancer or non-acquired immunodeficiency syndrome-defining cancers. Cancers of the lung, lip, mouth, or pharynx were not observed among nonsmokers. CONCLUSION: In persons infected with HIV, HAART use may prevent most excess risk of KS and non-Hodgkin lymphoma, but not that of Hodgkin lymphoma and other non-acquired immunodeficiency syndrome-defining cancers. No cancers of the lip, mouth, pharynx, or lung were observed in nonsmokers.

Toll-like receptor 2 (TLR2) polymorphisms are associated with reversal reaction in leprosy.

BACKGROUND: Leprosy is characterized by a spectrum of clinical manifestations that depend on the type of immune response against the pathogen. Patients may undergo immunological changes known as "reactional states" (reversal reaction and erythema nodosum leprosum) that result in major clinical deterioration. The goal of the present study was to assess the effect of Toll-like receptor 2 (TLR2) polymorphisms on susceptibility to and clinical presentation of leprosy. METHODS: Three polymorphisms in TLR2 (597C-->T, 1350T-->C, and a microsatellite marker) were analyzed in 431 Ethiopian patients with leprosy and 187 control subjects. The polymorphism-associated risk of developing leprosy, lepromatous (vs. tuberculoid) leprosy, and leprosy reactions was assessed by multivariate logistic regression models. RESULTS: The microsatellite and the 597C-->T polymorphisms both influenced susceptibility to reversal reaction. Although the 597T allele had a protective effect (odds ratio [OR], 0.34 [95% confidence interval {CI}, 0.17-0.68]; P= .002 under the dominant model), homozygosity for the 280-bp allelic length of the microsatellite strongly increased the risk of reversal reaction (OR, 5.83 [95% CI, 1.98-17.15]; P= .001 under the recessive model). These associations were consistent among 3 different ethnic groups. CONCLUSIONS: These data suggest a significant role for TLR-2 in the occurrence of leprosy reversal reaction and provide new insights into the immunogenetics of the disease.

Association study of 182 candidate genes in anorexia nervosa.

We performed association studies with 5,151 SNPs that were judged as likely candidate genetic variations conferring susceptibility to anorexia nervosa (AN) based on location under reported linkage peaks, previous results in the literature (182 candidate genes), brain expression, biological plausibility, and estrogen responsivity. We employed a case-control design that tested each SNP individually as well as haplotypes derived from these SNPs in 1,085 case individuals with AN diagnoses and 677 control individuals. We also performed separate association analyses using three increasingly restrictive case definitions for AN: all individuals with any subtype of AN (All AN: n = 1,085); individuals with AN with no binge eating behavior (AN with No Binge Eating: n = 687); and individuals with the restricting subtype of AN (Restricting AN: n = 421). After accounting for multiple comparisons, there were no statistically significant associations for any individual SNP or haplotype block with any definition of illness. These results underscore the importance of large samples to yield appropriate power to detect genotypic differences in individuals with AN and also motivate complementary approaches involving Genome-Wide Association (GWA) studies, Copy Number Variation (CNV) analyses, sequencing-based rare variant discovery assays, and pathway-based analysis in order to make up for deficiencies in traditional candidate gene approaches to AN.

Geographic variation in sex-chromosome differentiation in the common frog (Rana temporaria).

In sharp contrast with birds and mammals, sex-determination systems in ectothermic vertebrates are often highly dynamic and sometimes multifactorial. Both environmental and genetic effects have been documented in common frogs (Rana temporaria). One genetic linkage group, mapping to the largest pair of chromosomes and harbouring the candidate sex-determining gene Dmrt1, associates with sex in several populations throughout Europe, but association varies both within and among populations. Here, we show that sex association at this linkage group differs among populations along a 1500-km transect across Sweden. Genetic differentiation between sexes is strongest (FST  = 0.152) in a northern-boreal population, where male-specific alleles and heterozygote excesses (FIS  = -0.418 in males, +0.025 in females) testify to a male-heterogametic system and lack of X-Y recombination. In the southernmost population (nemoral climate), in contrast, sexes share the same alleles at the same frequencies (FST  = 0.007 between sexes), suggesting unrestricted recombination. Other populations show intermediate levels of sex differentiation, with males falling in two categories: some cluster with females, while others display male-specific Y haplotypes. This polymorphism may result from differences between populations in the patterns of X-Y recombination, co-option of an alternative sex-chromosome pair, or a mixed sex-determination system where maleness is controlled either by genes or by environment depending on populations or families. We propose approaches to test among these alternative models, to disentangle the effects of climate and phylogeography on the latitudinal trend, and to sort out how this polymorphism relates to the 'sexual races' described in common frogs in the 1930s.

Neonatal mortality in infants with low birth weigh

Objective To evaluate the factors associated with neonatal mortality in infant born with low birth weight. Method Cross-sectional study that analyzed data from 771 live births with low birth weight (<2500 g) in the city of Cuiabá, MT, in 2010, of whom 54 died in the neonatal period. We obtained data from the Information System on Live Births and Mortality, by integrated linkage. Results In multiple logistic regression, neonatal mortality was associated with: number of prenatal visits less than 7 (OR=3.80;CI:1,66-8,70); gestational age less than 37 weeks (OR=4.77;CI:1.48-15.38), Apgar score less than 7 at the 1st minute (OR=4.25;CI:1.84-9.81) and the 5th minute (OR=5.72,CI:2.24-14.60) and presence of congenital anomaly (OR=14.39;IC:2.72-76.09). Conclusion Neonatal mortality in infants with low birth weight is associated with avoidable factors through adequate attention to prenatal care, childbirth and infants.


Intra-Industry Trade, Multilateral Trade Integration, and Invasive Species Risk, December 2006

We analyze the linkage between protectionism and invasive species (IS) hazard in the context of two-way trade and multilateral trade integration, two major features of real-world agricultural trade. Multilateral integration includes the joint reduction of tariffs and trade costs among trading partners. Multilateral trade integration is more likely to increase damages from IS than predicted by unilateral trade opening under the classic Heckscher-Ohlin-Samuelson (HOS) framework because domestic production (the base susceptible to damages) is likely to increase with expanding export markets. A country integrating its trade with a partner characterized by relatively higher tariff and trade costs is also more likely to experience increased IS damages via expanded domestic production for the same reason. We illustrate our analytical results with a stylized model of the world wheat market.

Allelic proportions of 16 STR loci-including the new European Standard Set (ESS) loci-in a Swiss population sample.

Allele frequencies and forensically relevant population statistics of 16 STR loci, including the new European Standard Set (ESS) loci, were estimated from 668 unrelated individuals of Caucasian appearance living in different parts of Switzerland. The samples were amplified with a combination of the following three kits: AmpFlSTR® NGM SElect?, PowerPlex® ESI17 and PowerPlex® ESX 17. All loci were highly polymorphic and no significant departure from Hardy-Weinberg equilibrium and linkage equilibrium was detected after correction for sampling.

Genetics of essential tremor.

Essential tremor (ET) is a prevalent condition manifesting with progressive action tremor. Although ET was traditionally viewed as a sporadic disease, a significant proportion of cases report a positive family history of tremor. Autosomal dominant inheritance can be demonstrated in many families. Previously, genome-wide linkage studies in families mapped three loci for ET, hereditary essential tremor-1 (ETM1), ETM2 and ETM3. However, no causal mutation has been replicated in candidate genes within these loci, including dopamine D3 receptor (DRD3) and HS1-binding protein 3 (HS1BP3). Recently, the first genome-wide association study in ET followed by replication studies conducted in diverse populations identified a significant association between the leucine-rich repeat and Ig domain containing 1 gene (LINGO1) SNP rs9652490 and risk for ET Although further novel variants were indentified in LINGO1 and its paralog LINGO2 that may be associated with risk for ET, the pathogenic mechanisms involved remain elusive. Given the possibility that ET as a complex trait may be influenced by the combined effects of rare variants, novel high-throughput technologies sequencing all exons across the genome (exome sequencing) or the whole genome (genome sequencing) may become crucial in understanding/deciphering the genetic background of ET.

Analysis of malaria associated genetic traits in Cabo Verde, a melting pot of European and sub Saharan settlers

Malaria has occurred in the Cabo Verde archipelago with epidemic characteristics since its colonization. Nowadays, it occurs in Santiago Island alone and though prophylaxis is not recommended by the World Health Organization, studies have highlight the prospect of malaria becoming a serious public health problem as a result of the presence of antimalarial drug resistance associated with mutations in the parasite populations and underscore the need for tighter surveillance. Despite the presumptive weak immune status of the population, severe symptoms of malaria are not observed and many people present a subclinical course of the disease. No data on the prevalence of sicklecell trait and red cell glucose-6-phosphate dehydrogenase deficiency (two classical genetic factors associated with resistance to severe malaria) were available for the Cabo Verde archipelago and, therefore, we studied the low morbidity from malaria in relation to the particular genetic characteristics of the human host population. We also included the analysis of the pyruvate kinase deficiency associated gene, reported as putatively associated with resistance to the disease. Allelic frequencies of the polymorphisms examined are closer to European than to African populations and no malaria selection signatures were found. No association was found between the analyzed human factors and infection but one result is of high interest: a linkage disequilibrium test revealed an association of distant loci in the PKLR gene and adjacent regions, only in non-infected individuals. This could mean a more conserved gene region selected in association to protection against the infection and/or the disease.

Pulse wave analysis of aortic pressure: diastole should also be considered.

BACKGROUND: : The systolic augmentation index (sAix), calculated from the central aortic pulse wave (reconstructed from the noninvasive recording of the radial pulse with applanation tonometry), is widely used as a simple index of central arterial stiffness, but has the disadvantage of also being influenced by the timing of the reflected with respect to the forward pressure wave, as shown by its inverse dependence on heart rate (HR). During diastole, the central aortic pulse also contains reflected waves, but their relationship to arterial stiffness and HR has not been studied. METHODS: : In 48 men and 45 women, all healthy, with ages ranging from 19 to 70 years, we measured pulse wave velocity (PWV, patients supine), a standard evaluator of arterial stiffness, and carried out radial applanation tonometry (patients sitting and supine). The impact of reflected waves on the diastolic part of the aortic pressure waveform was quantified in the form of a diastolic augmentation index (dAix). RESULTS: : Across ages, sexes, and body position, there was an inverse relationship between the sAix and the dAix. When PWV and HR were added as covariates to a prediction model including age, sex and body position as main factors, the sAix was directly related to PWV (P < 0.0001) and inversely to HR (P < 0.0001). With the same analysis, the dAix was inversely related to PWV (P < 0.0001) and independent of HR (P = 0.52). CONCLUSION: : The dAix has the same degree of linkage to arterial stiffness as the more conventional sAix, while being immune to the confounding effect of HR. The quantification of diastolic aortic pressure augmentation by reflected waves could be a useful adjunct to pulse wave analysis.

Evolution of Y chromosomes : lessons from mammals and amphibians

RÉSUMÉ : Le sexe des individus peut être déterminé par l'environnement ou la génétique. Lorsque la détermination du sexe est génétique, il y a dans le génome, la présence de chromosomes spécifiques qui détermineront le sexe. Dans cette thèse, j'ai étudié l'évolution des chromosomes sexuels et dans quel contexte des marqueurs sur ces chromosomes peuvent être utilisés. Pour explorer la formation du chromosome Y, nous avons étudié les caractéristiques des chromosomes sexuels chez la rainette verte, Hyla arborea. Dans un premier temps, nous avons utilisé un marqueur situé sur les chromosomes sexuels X et Y chez plusieurs espèces appartenant au groupe de la rainette verte. Cela nous a permis de révéler chez toutes ces espèces une hétérogamétie mâle. Dans un deuxième temps, nous avons tiré profit de deux autres marqueurs situés sur les chromosomes sexuels pour montrer que la recombinaison est supprimée chez les mâles mais pas chez les femelles. Pour expliquer la réduction de la variabilité sur le chromosome Y, il n'est pas nécessaire d'invoquer le balayage sélectif ou la sélection d'arrière-plan : le nombre de copies plus petit du chromosome Y dans le génome et l'absence de recombinaison suffisent à l'expliquer. Nous avons également analysé plus en détail la suppression de la recombinaison chez les mâles de H. arborea. Les modèles classiques de l'évolution des chromosomes sexuels supposent que la taille de la région non-recombinante augmente progressivement pendant l'évolution du chromosome Y, due à l'accumulation de changements structuraux. Dans cette étude, nous montrons un modèle différent, à savoir que la recombinaison est supprimée ou diminuée non seulement sur les chromosomes sexuels mais aussi sur les autosomes chez les mâles, dû à l'action de modificateurs généraux. En utilisant des marqueurs localisés sur le chromosome Y, ainsi que sur l'ADN mitochondrial et le chromosome X, nous avons étudié l'histoire évolutive de la musaraigne musette, Crocidura russula. Cette étude illustre que les analyses génétiques avec plusieurs types de marqueurs génétiques peuvent faciliter l'interprétation de l'histoire évolutive des espèces, mais que l'utilisation des marqueurs sur les chromosomes X et Y pour des études phylogéographiques est limitée par le peu de polymorphisme observé sur ces deux types de marqueurs. Le même jeu de données combiné avec des simulations a été employé pour comprendre les facteurs responsables de la faible variabilité sur le chromosome Y qui peut être expliqué, dans notre étude, par la démographie et les traits d'histoire de vie de C. russula. SUMMARY The sex of an individual is determined either by its environment or its genetics. Genetic sex determination relies on the presence of specific chromosomes that will determine the sex of their bearer. In this thesis, I studied the evolution of the sex chromosomes and the context in which markers on this type of chromosomes can be used. To explore the evolution of a Y chromosome, we studied the nascent sex chromosomes in the European tree frog Hyla arborea. First; we amplified a sex specific marker in several related species of European tree frog and found a homogeneous pattern of male heterogamety. Secondly, we used two additional sex-specific markers to show that recombination is suppressed in males but not in females. There is, therefore, no need to invoke background selection or selective sweeps to explain the reduced genetic variability on the Y chromosome, because the lower number of copies of the Y chromosomes per breeding pair and the absence of recombination are sufficient. To further analyze the suppression of recombination in male European. tree frogs, we constructed a microsatellite linkage map for this species. Classical models of sex-chromosome evolution assume that the non-recombining region expands progressively during the long-term evolution of the Y chromosome, owing to the accumulation of structural changes. Here we show a strikingly different pattern: recombination is suppressed or depressed both on sex chromosomes and autosomes in the heterogametic sex, presumably due to the action of general modifiers. We investigated the evolutionary history of the greater white-toothed shrew, Crocidura russula, using markers on both sex chromosomes and mtDNA. This study illustrates that multilocus genetic analyses facilitates the interpretation of a species' evolutionary history. It also demonstrates that phylogeographic inferences from X and Y chromosomal markers are restricted by the low levels of observed polymorphism. Combining this genetic study with simulations, we determined that the demography and the life-history traits of this species can alone be responsible for the low Y diversity. In conclusion, this thesis shows that sex chromosomes, in combination with autosomes or mtDNA, are necessary to understand the evolution of sex chromosomes and to precisely infer the population history of a species.

A missense mutation in myelin oligodendrocyte glycoprotein as a cause of familial narcolepsy with cataplexy.

Narcolepsy is a rare sleep disorder characterized by excessive daytime sleepiness and cataplexy. Familial narcolepsy accounts for less than 10% of all narcolepsy cases. However, documented multiplex families are very rare and causative mutations have not been identified to date. To identify a causative mutation in familial narcolepsy, we performed linkage analysis in the largest ever reported family, which has 12 affected members, and sequenced coding regions of the genome (exome sequencing) of three affected members with narcolepsy and cataplexy. We successfully mapped a candidate locus on chromosomal region 6p22.1 (LOD score ¼ 3.85) by linkage analysis. Exome sequencing identified a missense mutation in the second exon of MOG within the linkage region. A c.398C>G mutation was present in all affected family members but absent in unaffected members and 775 unrelated control subjects. Transient expression of mutant myelin oligodendrocyte glycoprotein (MOG) in mouse oligodendrocytes showed abnormal subcellular localization, suggesting an altered function of the mutant MOG. MOG has recently been linked to various neuropsychiatric disorders and is considered as a key autoantigen in multiple sclerosis and in its animal model, experimental autoimmune encephalitis. Our finding of a pathogenic MOG mutation highlights a major role for myelin and oligodendrocytes in narcolepsy and further emphasizes glial involvement in neurodegeneration and neurobehavioral disorders. [corrected].

Mutations leading to X-linked hypohidrotic ectodermal dysplasia affect three major functional domains in the tumor necrosis factor family member ectodysplasin-A.

Mutations in the epithelial morphogen ectodysplasin-A (EDA), a member of the tumor necrosis factor (TNF) family, are responsible for the human disorder X-linked hypohidrotic ectodermal dysplasia (XLHED) characterized by impaired development of hair, eccrine sweat glands, and teeth. EDA-A1 and EDA-A2 are two splice variants of EDA, which bind distinct EDA-A1 and X-linked EDA-A2 receptors. We identified a series of novel EDA mutations in families with XLHED, allowing the identification of the following three functionally important regions in EDA: a C-terminal TNF homology domain, a collagen domain, and a furin protease recognition sequence. Mutations in the TNF homology domain impair binding of both splice variants to their receptors. Mutations in the collagen domain can inhibit multimerization of the TNF homology region, whereas those in the consensus furin recognition sequence prevent proteolytic cleavage of EDA. Finally, a mutation affecting an intron splice donor site is predicted to eliminate specifically the EDA-A1 but not the EDA-A2 splice variant. Thus a proteolytically processed, oligomeric form of EDA-A1 is required in vivo for proper morphogenesis.

Zapfen-Stäbchen-Dystrophie durch eine neue reinerbige RPE65-Mutation in Leberscher kongenitaler Amaurose Cone-Rod Dystrophy Caused by a Novel Homozygous RPE65 Mutation in Leber Congenital Amaurosis.

Background: The aim of this study was to describe an unexpected phenotype in a family with Leber congenital amaurosis (LCA) due to a retinal pigment epithelium-specific protein 65 kDa (RPE65) homozygous mutation. History and Signs: We analyzed a family from Yemen in which 3 individuals were affected with LCA. Linkage analysis using markers flanking the known LCA genes was done, followed by direct sequencing of RPE65. Therapy and Outcome: Severe visual impairment and night blindness were observed during infancy. We observed photophobia only in the 8-year-old patient. The youngest affected had bilateral hyperopia of + 3.50 and visual acuity of 1/60. The oldest two had visual acuity limited to hand movements in the right eye (OD) and counting fingers in the left eye (OS) for the oldest and of 5/60 OD, 6/60 OS for the other. They showed disc pallor, attenuated vessels, white flecks in the retina mid-periphery and bull's eye maculopathy. ERGs of the oldest child were completely unresponsive. Genomic sequencing identified a novel homozygous missense mutation, IVS2-3C > G, in the second RPE65 intron. Conclusions: We identified a novel LCA-related homozygous RPE65 mutation associated with a severe clinical presentation including an early and severe cone dysfunction. This is in contrast with the presentation associated with other RPE65 mutations predominantly causing rod-cone dystrophy with residual visual function.