Detecting genetic modifiers of spondyloepimetaphyseal dysplasia with joint laxity in the Caucasian Afrikaner community.

Spondyloepimetaphyseal dysplasia with joint laxity (SEMDJL) is an autosomal-recessive skeletal dysplasia. A relatively large number of patients with SEMDJL have been identified in the Caucasian Afrikaans-speaking community in South Africa. We used a combination of Genome-Wide Human Single Nucleotide Polymorphism (SNP) Array 6.0 data and whole exomic data to potentially dissect genetic modifiers associated with SEMDJL in Caucasian Afrikaans-speaking patients. Leveraging the family-based association signal in prioritizing candidate mutations, we identified two potential modifier genes, COL1A2 and MATN1, and replicating previously identified mutation in KIF22. Importantly, our findings of genetic modifier genes and previously identified mutations are layered on the same sub-network implicated in syndromes characterized by skeletal abnormalities and intellectual disability, bone and connective tissue fragility. This study has potentially provided crucial insights in identifying the indirect modifying mutation(s) linked to the true causal mutation associated with SEMDJL. It is a critical lesson that one may use constructively especially when the pace of exomic sequencing of rare disorders continues apace.

Pathogenic gene screening in 91 Chinese patients with short stature of unknown etiology with a targeted next-generation sequencing panel.

BACKGROUND: Dwarfism is a common severe growth disorder, but the etiology is unclear in the majority of cases. Recombinant human growth hormone may be a treatment option, but it has limited efficacy. The currently known laboratory assays do not meet the precision requirements for clinical diagnosis. Here, we have constructed a targeted next-generation sequencing (NGS) panel of selected genes that are suspected to be associated with dwarfism for genetic screening. METHODS: Genetic screening of 91 children with short stature of unknown etiology was performed with the help of the NGS panel. All the coding regions and exon-intron boundaries of 166 genes were included in the panel. To clarify the pathogenicity of these mutations, their clinical data were reviewed and analyzed. RESULTS: The assay identified p.A72G, p.I282V, and p.P491S variants of the PTPN11 gene and a p.I437T variant of the SOS1 gene in 4 cases with Noonan syndrome. A frameshift mutation (p.D2407fs) of the ACAN gene was identified in a case of idiopathic short stature with moderately advanced bone age. A p.R904C variant of the COL2A1 gene was found in a patient, who was accordingly diagnosed with Stickler syndrome. Severe short stature without limb deformity was associated with a p.G11A variant of HOXD13. In addition, we evaluated evidence that a p.D401N variant of the COMP gene may cause multiple epiphyseal dysplasia. CONCLUSIONS: Our findings suggest that syndromes, particularly Noonan syndrome, may be overlooked due to atypical clinical features. This gene panel has been verified to be effective for the rapid screening of genetic etiologies associated with short stature and for guiding precision medicine-based clinical management.

Pseudoacondroplasia en una familia / Pseudoacondroplasya. Presentation of an affected family

Introducción: la pseudoacondroplasia es una displasia esquelética de transmisión autosómica dominante. Por tanto, el progenitor afectado tiene alto riesgo de transmitir el gen mutado a su descendencia. Los enfermos se caracterizan por una baja estatura desproporcionada, afectaciones en los huesos largos, la columna vertebral y las articulaciones. Debido al deficitario crecimiento de las epífisis, los afectados padecen artrosis temprana.Objetivo: presentar una familia afectada de pseudoacondroplasia, de interés debido a los pocos casos documentados en el país.Presentación de caso: familia con baja talla desproporcionada y alteraciones articulares, uno de cuyos miembros -menor de 12 años- asistió por ese motivo, acompañado de su madre, a la consulta de genética clínica. Como antecedentes patológicos familiares se refirieron baja talla del abuelo y los tíos maternos. Durante el examen físico del menor se constató que su talla (por debajo del tercer percentil) y su peso (entre el tercer y décimo percentiles), estaban en desproporción con su edad. Presentó alteraciones en manos y pies, y escoliosis torácica con cifosis. La madre del menor, también de baja talla, presentó deformidades en las articulaciones de los codos y rodillas, asociadas a dolores, y deformidad en el tórax (causada por escoliosis de la columna torácica).Conclusiones: la pseudoacondroplasia es una de las displasias óseas cuyo diagnóstico se dificulta en ocasiones por la expresión variable del fenotipo, que en muchos casos se interpreta como baja talla familiar. Una vez diagnosticada la enfermedad se debe asesorar a las familias afectadas acerca del riesgo de recurrencia en la descendencia(AU)

Introduction: pseudoachondroplasia is a skeletal dysplasia of autosomal dominant transmission. Therefore, the affected parent has a high risk of transmitting the mutated gene to their offspring. The patients are characterized by a disproportionate short stature, affectations in the long bones, the spine and the joints. Due to the deficient growth of the epiphyses, those affected suffer from early joint diseases.Objective: to present a family affected by pseudoachondroplasia, of interest due to the few cases documented in the country.Case presentation: family with disproportionate short stature and joint alterations, one of whose members -child under 12 years old- attended for that reason, accompanied by his mother, to the clinical genetic consultation. As a family pathological background they referred to the short stature of the grandfather and the maternal uncles. During the physical examination of the child it was found that his height (below the third percentile) and his weight (between the third and tenth percentiles), were in disproportion with his age. He presented alterations in the hands and feet, and thoracic scoliosis with kyphosis. The mother of the child, also of low stature, presented deformities in the joints of the elbows and knees, associated with pain, and deformity in the thorax (caused by scoliosis of the thoracic spine).Conclusions: pseudoacondroplasia is one of the bone dysplasias whose diagnosis is sometimes difficult due to the variable expression of the phenotype, which in many cases is interpreted as low family size. Once the disease has been diagnosed, the affected families should be advised about the risk of recurrence in the offspring(AU)

A novel COL10A1 mutation in a Chinese pedigree with Schmid type metaphyseal chondrodysplasia.

BACKGROUND: Schmid type metaphyseal chondrodysplasia (MCDS) is a kind of autosomal inherited epiphyseal dysplasia caused by a mutation of the COL10A1 gene. Clinical expression of this mutation includes a waddling gait, coxa vara, genu varus or genu valgus and shortened lower limbs among others. To date, over 40 kinds of heterozygous mutations have been identified in the collagen domain of COL10A1 but data on family pedigrees for these is lacking. METHODS: Nineteen people without a history of interbreeding were selected for the three generations pedigree of MCDS. The proband is a 13 year-old boy with short limbs, hip varus, and tibial varus. In this group, seven people had MCDS (two men, five women). Blood samples for DNA extraction and mutational analysis were collected to sequence the CLO10A1 gene. RESULTS: Chromas atlas analysis and monoclonal sequencing revealed that 7 of the patients in the family are missing a C nucleotide in the third exon of the COL10A1 gene (c.2005delC). CONCLUSIONS: The COL10A1 gene mutation results in a frameshift mutation from codon 669, the substitution of 7 amino acids, and premature termination of expression (p.his669thrfsX8). In contrast to the other mutations identified, c.2005delC is close to the C-terminus of the protein sequence and may result in genetic heterogeneity of the Chinese population.

A novel splicing mutation in the SEDL gene causes spondyloepiphyseal dysplasia tarda in a large Chinese pedigree.

The X-linked form of spondyloepiphyseal dysplasia tarda (SEDT, OMIM# 313400) is a rare osteochondrodysplasia caused by mutations in the SEDL (TRAPPC2, OMIM# 300202) gene. It is clinically characterized by disproportionate short stature, barrel-shaped chests and early development of degenerative joint disease. We report here a novel mutation in the intron 3 splice-donor site (c. 93+5G>C) segregated in an X-link pattern in a large Chinese family with SEDT. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis revealed that the mutation causes an aberrant splicing of exon 3, resulting in the elimination of 31 codons in the exon and a considerable loss function of the SEDL protein. This mutation was not detected in the 100 healthy controls. This novel mutation adds to the spectrum of previously-identified disease-causing mutations. Pre-symptomatic molecular diagnosis and prenatal diagnosis of the pregnant carriers could be helpful to families with SEDT.

PAPSS2 mutations cause autosomal recessive brachyolmia.

BACKGROUND: Brachyolmia is a heterogeneous group of skeletal dysplasias that primarily affects the spine. Clinical and genetic heterogeneity have been reported; at least three types of brachyolmia are known. TRPV4 mutations have been identified in an autosomal dominant form of brachyolmia; however, disease genes for autosomal recessive (AR) forms remain totally unknown. We conducted a study on a Turkish family with an AR brachyolmia, with the aim of identifying a disease gene for AR brachyolmia. METHODS AND RESULTS: We examined three affected individuals of the family using exon capture followed by next generation sequencing and identified its disease gene, PAPSS2 (phosphoadenosine-phosphosulfate synthetase 2). The patients had a homozygous loss of function mutation, c.337_338insG (p.A113GfsX18). We further examined three patients with similar brachyolmia phenotypes (two Japanese and a Korean) and also identified loss of function mutations in PAPSS2; one patient was homozygous for IVS3+2delT, and the other two were compound heterozygotes for c.616-634del19 (p.V206SfsX9) and c.1309-1310delAG (p.R437GfsX19), and c.480_481insCGTA (p.K161RfsX6) and c.661delA (p.I221SfsX40), respectively. The six patients had short-trunk short stature that became conspicuous during childhood with normal intelligence and facies. Their radiographic features included rectangular vertebral bodies with irregular endplates and narrow intervertebral discs, precocious calcification of rib cartilages, short femoral neck, and mildly shortened metacarpals. Spinal changes were very similar among the six patients; however, epiphyseal and metaphyseal changes of the tubular bones were variable. CONCLUSIONS: We identified PAPSS2 as the disease gene for an AR brachyolmia. PAPSS2 mutations have produced a skeletal dysplasia family, with a gradation of phenotypes ranging from brachyolmia to spondylo-epi-metaphyseal dysplasia.

Revisit of multiple epiphyseal dysplasia: ethnic difference in genotypes and comparison of radiographic features linked to the COMP and MATN3 genes.

Multiple epiphyseal dysplasia (MED) is a genetically heterogeneous group of diseases characterized by variable degrees of epiphyseal abnormality primarily involving the hip and knee joints. The purpose of this study was to investigate the frequency of mutations in individuals with a clinical and radiographic diagnosis of MED and to test the hypothesis that characteristic radiological findings may be helpful in predicting the gene responsible. The radiographs of 74 Korean patients were evaluated by a panel of skeletal dysplasia experts. Six genes known to be associated with MED (COMP, MATN3, COL9A1, COL9A2, COL9A3, and DTDST) were screened by sequencing. Mutations were found in 55 of the 63 patients (87%). MATN3 mutations were found in 30 patients (55%), followed by COMP mutations in 23 (41%), and COL9A2 and DTDST mutations in one patient (2%) each. Comparisons of radiographic findings in patients with COMP and MATN3 mutations showed that albeit marked abnormalities in hip and knee joints were observed in both groups, the degree of involvement and the morphology of dysplastic epiphyses differed markedly. The contour of the pelvic acetabulum, the presence of metaphyseal vertical striations, and/or the brachydactyly of the hand were also found to be highly correlated with the genotypes. The study confirms that MATN3 and COMP are the genes most frequently responsible for MED and that subtle radiographic signs may give precious indications on which gene(s) should be prioritized for mutational screening in a given individual.

Identification of a Gypsy SHOX mutation (p.A170P) in Léri-Weill dyschondrosteosis and Langer mesomelic dysplasia.

We report the clinical and molecular characteristics of 12 Spanish families with multiple members affected with Léri-Weill dyschondrosteosis (LWD) or Langer mesomelic dysplasia (LMD), who present the SHOX (short stature homeobox gene) mutation p.A170P (c.508G>C) in heterozygosity or homozygosity, respectively. In all studied families, the A170P mutation co-segregated with the fully penetrant phenotype of mesomelic limb shortening and Madelung deformity. A shared haplotype around SHOX was observed by microsatellite analysis, confirming the presence of a common ancestor, probably of Gypsy origin, as 11 of the families were of this ethnic group. Mutation screening in 359 Eastern-European Gypsies failed to identify any carriers. For the first time, we have shown SHOX expression in the human growth plate of a 22-week LMD fetus, homozygous for the A170P mutation. Although the mutant SHOX protein was expressed in all zones of the growth plate, the chondrocyte columns in the proliferative zone were disorganized with the chondrocytes occurring in smaller columnal clusters. We have also identified a novel mutation at the same residue, c. 509C>A (p.A170D), in two unrelated Spanish LWD families, which similar to A170P mutation impedes nuclear localization of SHOX. In conclusion, we have identified A170P as the first frequent SHOX mutation in Gypsy LWD and LMD individuals.

PAR1 deletions downstream of SHOX are the most frequent defect in a Spanish cohort of Léri-Weill dyschondrosteosis (LWD) probands.

Léri-Weill dyschondrosteosis (LWD) is a skeletal dysplasia characterized by disproportionate short stature and Madelung deformity. Mutations or deletions of the SHOX gene have been previously identified as the main cause of LWD. We recently identified the existence of a second class of pseudoautosomal region 1 (PAR1) deletions which do not include SHOX, implicated in the etiopathogenesis of LWD. The deletions map at least 30-250 kb downstream of SHOX, are variable in size and clearly cosegregate with the LWD phenotype. In order to determine the frequency of this new type of deletions in the Spanish population we analyzed the distribution of PAR1 defects, including the screening of SHOX deletions, mutations, and PAR1 deletions downstream of SHOX, in a total of 26 LWD probands by a combination of MLPA, microsatellite analysis, SNP genotyping, dHPLC, and DNA sequencing. A molecular defect was identified in 16/26 LWD patients (61.5%): 10 PAR1 deletions downstream of SHOX, four SHOX encompassing deletions, and two SHOX mutations. No apparent phenotypic differences were observed between patients with SHOX defects and those with PAR1 deletions downstream of SHOX. In the examined cohort of Spanish LWD probands, PAR1 deletions downstream of SHOX represent the highest proportion of identified mutations (38%) compared to SHOX deletions (15%) and mutations (8%). As a consequence of our findings, the screening of this region should be included in the routine genetic testing of LWD. Also, LWD patients who tested negative for SHOX defects should be re-evaluated for PAR1 deletions downstream of SHOX.

Uniparental disomy in cartilage-hair hypoplasia.

Cartilage-hair hypoplasia (CHH) is an autosomal recessive disorder that presents with pleiotropic manifestations including impaired skeletal growth and cellular immunity. It is most prevalent among two founder populations, the Old Order Amish in the USA and the Finns. The gene has been localized to 9p13 by linkage analysis and linkage disequilibrium mapping. A statistically significant deficiency of affected members resulting in a lower than expected segregation ratio has been reported in the Amish, but was not found in a previous study in Finnish CHH families. Reduced penetrance was the mechanism suggested in the Amish, but could not be verified by haplotype analyses performed after the assignment of the CHH gene. Here we have carried out segregation analysis of 101 Finnish CHH families, but again, evidence of a significant deficiency of affected members was not found. Nevertheless, among 54 uniplex families, 2 patients with CHH and uniparental disomy (UPD) for chromosome 9 were discovered. UPD might contribute to low segregation ratios by increasing the number of families with only 1 affected individual. These observations show that UPD may occur in an unexpectedly high number of the patients and should be taken into account in the genetic counselling and prenatal diagnostics of CHH families.

Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland.

Linkage disequilibrium mapping in isolated populations provides a powerful tool for fine structure localization of disease genes. Here, Luria and Delbrück's classical methods for analysing bacterial cultures are adapted to the study of human isolated founder populations in order to estimate (i) the recombination fraction between a disease locus and a marker; (ii) the expected degree of allelic homogeneity in a population; and (iii) the mutation rate of marker loci. Using these methods, we report striking linkage disequilibrium for diastrophic dysplasia (DTD) in Finland indicating that the DTD gene should lie within 0.06 centimorgans (or about 60 kilobases) of the CSF1R gene. Predictions about allelic homogeneity in Finland and mutation rates in simple sequence repeats are confirmed by independent observations.

Sedaghatian congenital lethal metaphyseal chondrodysplasia--observations in a second Iranian family and histopathological studies.

In 1980, Sedaghatian described in two brothers and one sister a neonatally lethal disorder associated with slight rhizomelic limb shortness, mild platyspondyly, and severe metaphyseal dysplasia. Here data are presented on another Iranian infant with the Sedaghatian syndrome who died on day 4 and was found to have histologic evidence of severe epimetaphyseal dysplasia. The occurrence in children of both sexes in one instance, born to normal parents who were first cousins, and currently apparent confinement of the disorder to Iranians suggests that the Sedaghatian syndrome is an autosomal recessive trait with high gene frequency in Iranians. This may be a more complexly pleiotropic syndrome than suggested by the roentgenograms, since one of Sedaghatian's patients also had "microphthalmia, asymmetry of ears, depressed nasal bridge, broad nose, short neck, prominent sternum, and short lower extremities."