An optimized DHPLC protocol for molecular testing of the EXT1 and EXT2 genes in hereditary multiple osteochondromas

Hereditary multiple osteochondromas (MO) is an autosomal dominant bone disorder characterized by the presence of bony outgrowths (osteochondromas or exostoses) on the long bones. MO is caused by mutations in the EXT1 or EXT2 genes, which encode glycosyltransferases implicated in heparan sulfate biosynthesis. Standard mutation analysis performed by sequencing analysis of all coding exons of the EXT1 and EXT2 genes reveals a mutation in approximately 80% of the MO patients. We have now optimized and validated a denaturing high-performance liquid chromatography (DHPLC)-based protocol for screening of all EXT1- and EXT2-coding exons in a set of 49 MO patients with an EXT1 or EXT2 mutation. Under the optimized DHPLC conditions, all mutations were detected. These include 20 previously described mutations and 29 new mutations - 20 new EXT1 and nine new EXT2 mutations. The protocol described here, therefore, provides a sensitive and cost-sparing alternative for direct sequencing analysis of the MO-causing genes.     

遗传性多发性骨软骨瘤的基因诊断及产前诊断

目的 研究家族遗传性骨软骨瘤病(hereditary multiple exostoses,HME)的致病基因及产前诊断.方法 应用连锁分析方法对一个HME家系EXT1、EXT2和EXT3基因进行分析.致病基因定位后,用PCR-测序法进行了突变分析.结果 在该家系中EXT2基因第6外显子发生1个新的无义突变(c.1006C>T),该突变导致第336位编码谷氨酰胺的密码子CAA变为终止密码子TAA(Gln336X).根据上述结果配合遗传咨询进行了产前诊断,结果显示胎儿正常.结论 在家族遗传性骨软骨瘤家系中发现一新的EXT2基因突变,并应用于产前诊断.     

山西汉族遗传性多发性骨软骨瘤家系EXT1及EXT2基因突变研究

目的 对山西一个汉族遗传性多发性骨软骨瘤家系的EXT1和EXT2基因的全部外显子序列进行分析,以寻找致病突变.方法 用PCR扩增先证者EXT1和EXT2基因的全部外显子,将PCR产物送直接测序分析.结果 发现EXT1基因2种同义突变(P477P、E587E)、3种内含子突变(c.1537-48A＞G、c.1721 +203 A＞G、c.1722-103 C＞G).EXT2基因共发现5种内含子突变(c.-29-148 A＞T、c.1080-18 T＞A、c.1336-93 C＞T、c.1526-166 C＞T、c.1526-195C＞T).其中,EXT1 P477P、EXT1 E587E和EXT2 c.1080-18 T＞A为多发性骨软骨瘤突变数据库已收录的多态位点,其余7个位点尚未见报道.结论 对该家系EXT1、EXT2基因全部外显子的测序分析未发现明确的致病突变,该家系遗传性多发性骨软骨瘤的发生是否由除EXT1、EXT2外的其它EXT相关基因引起尚需进一步的连锁定位分析.     

Identification of a novel mutation in EXT2 in a fourth‐generation Korean family with multiple osteochondromas and overview of mutation spectrum

Multiple osteochondromas (MOs) or hereditary multiple exostoses is a rare autosomal‐dominant disease characterized by growths of MOs, which are benign cartilage‐capped bone tumors that grow away from the growth plates. Almost 90% of MOs have a molecular explanation and 10% are unexplained. MOs are genetically heterogeneous with two causal genes on 8q24.11 (EXT1) and 11p12 (EXT2), with a higher frequency in EXT1. MO is a very rare genetic disorder, and the genotype–phenotype of MO with EXT2 mutation has not been well investigated in Korea. We present the clinical radiographic and molecular analysis of a four‐generation Korean family with 11 MO‐affected members (seven males and four females). The affected members from the third generation available for molecular analysis and their detailed medical histories showed moderate‐to‐severe phenotypes (clinical classes II–III), including bony deformities and limb misalignment with pain requiring surgical correction. The x‐rays showed MOs in multiple sites. A novel EXT2 frameshift mutation (c.590delC, p.P197Qfs*73) was revealed by targeted exome sequencing in the affected members of this family. In this article, we not only expand the phenotypic–genotypic spectrum of MOs but also highlight the phenotypic heterogeneity in a family with the same mutation. In addition, we compiled the mutation spectrum of EXT2 from a literature review and identified that exon 2 of EXT2 is a mutation hot spot. Early medical attention with diagnosis of MO through careful examination of the clinical manifestations and genetic analysis can provide the opportunity to establish coordinated multispecialty management of the patient.     

A novel EXT2 mutation in a consanguineous family with severe developmental delay,microcephaly, seizures,feeding difficulties,and osteopenia extends the phenotypic spectrum of autosomal recessive EXT2-related syndrome (AREXT2)

We report a consanguineous family where 2 boys presented with developmental delay, hypotonia, microcephaly, seizures, gastro-intestinal abnormalities, osteopenia, and neurological regression. Whole exome sequencing performed in one of the boys revealed the presence of a novel homozygous missense variant in the EXT2 gene: c.11C?>?T (p.Ser4Leu). Segregation analysis by Sanger sequencing confirmed homozygous by descent autosomal recessive transmission of this mutation. Another family was previously reported with homozygous mutations in this gene in four siblings affected with a nearly similar clinical condition (Farhan et al., 2015). We discuss the similarities and differences between the two syndromes and propose AREXT2 as a new acronym for EXT2-related diseases.     

Interstitial deletion of 11 (P11.2p12): A newly described contiguous gene deletion syndrome involving the gene for hereditary multiple exostoses (EXT2)

Individuals with deletions of the proximal portion of the short arm of chromosome 11 share many manifestations including mental retardation, biparietal foramina, minor facial anomalies, and multiple cartilaginous exostoses. The finding of multiple exostoses in these patients is remarkable as the disorder hereditary multiple exostoses, which is inherited in an autosomal dominant manner, has recently been mapped by linkage to three regions, including proximal 11p. We report the clinical and molecular findings in an additional patient with an 11(p11.2p12) deletion. Cytogenetic and molecular analysis demonstrated a de novo, paternally derived deletion for markers which have been shown to be tightly linked to the 11p locus (EXT2). These data support the location of EXT2 within this region and also provide information regarding the ordering of polymorphic markers on 11p. Deletion 11(p11.2p12) is a rare, yet specific, deletion syndrome involving the EXT2 locus, a gene for parietal foramina, and a mental retardation locus, and therefore can be classified as a contiguous gene deletion syndrome. © 1996 Wiley-Liss, Inc.     

Mutation frequencies of EXT1 and EXT2 in 43 Japanese families with hereditary multiple exostoses

Hereditary multiple exostoses (EXT) is an autosomal dominant bone disease characterized by the formation of cartilage‐capped prominences. EXT is genetically heterogeneous with at least four chromosomal loci. Among the four loci, the exostosis type 1 gene (EXT1) and type 2 gene (EXT2) have been cloned. Previous studies have shown that disease‐type‐specific frequency of mutations is different among various ethnic populations. To determine those frequencies in the Japanese, we conducted a large‐scale mutation screening on both genes. In 23 of 43 Japanese families examined, we found 21 different mutations, of which 18 are novel. Seventeen (40%) of the 23 families had a mutation in EXT1 and six (14%) had a mutation in EXT2, suggesting that the former mutations are more frequent than the latter in Japanese EXT families. Of the 17 families with EXT1 mutations, 13 had those causing premature termination of the EXT1 protein and four showed missense mutations, whereas five of the six families with EXT2 mutations had those causing premature termination and one showed missense mutation. Interestingly, all four EXT1 missense mutations occurred in an arginine residue at codon 340 (R340) that is known as a critical site for expression of heparan sulfate glycosaminoglycans, suggesting that the region encompassing the arginine residue may play an important role in the function of the EXT1 protein. These results expand our knowledge of the ethnic difference of EXT and the structure‐function relationship of the EXT genes. © Wiley‐Liss. Inc.     

Novel mutations in the EXT1 gene in two consanguineous families affected with multiple hereditary exostoses (familial osteochondromatosis)

Multiple hereditary exostoses (HME) is an autosomal dominant developmental disorder exhibiting multiple osteocartilaginous bone tumors that generally arise near the ends of growing long bones. Here, we report two large consanguineous families from Pakistan, who display the typical features of HME. Affected individuals also show a previously unreported feature--bilateral overriding of single toes. Analysis using microsatellite markers for each of the known EXT loci, EXT1, EXT2, and EXT3 showed linkage to EXT1. In the first family, mutation analysis of the EXT1 gene revealed that affected individuals were heterozygous for an in-frame G-to-C transversion at the conserved splice donor site in intron 1. This mutation is predicted to disrupt splicing of the first intron and produce a frameshift that leads to a premature termination codon. In the second family, an insertion of an A in exon 8 is predicted to produce a frameshift at codon 555 followed by a premature termination, a further 10 codons downstream. In both families, an increased number of affected male subjects were observed. In affected females in family 2, phenotypic variability and incomplete penetrance were noted.     

Multiple hereditary exostoses (MHE): elucidating the pathogenesis of a rare skeletal disorder through interdisciplinary research

An interdisciplinary and international group of clinicians and scientists gathered in Philadelphia, PA, to attend the fourth International Research Conference on Multiple Hereditary Exostoses (MHE), a rare and severe skeletal disorder. MHE is largely caused by autosomal dominant mutations in EXT1 or EXT2, genes encoding Golgi-associated glycosyltransferases responsible for heparan sulfate (HS) synthesis. HS chains are key constituents of cell surface- and extracellular matrix-associated proteoglycans, which are known regulators of skeletal development. MHE affected individuals are HS-deficient, can display skeletal growth retardation and deformities, and consistently develop benign, cartilage-capped bony outgrowths (termed exostoses or osteochondromas) near the growth plates of many skeletal elements. Nearly 2% of patients will have their exostoses progress to malignancy, becoming peripheral chondrosarcomas. Current treatments are limited to the surgical removal of symptomatic exostoses. No definitive treatments have been established to inhibit further formation and growth of exostoses, prevent transition to malignancy, or address other medical problems experienced by MHE patients, including chronic pain. Thus, the goals of the Conference were to assess our current understanding of MHE pathogenesis, identify key gaps in information, envision future therapeutic strategies and discuss ways to test and implement them. This report provides an assessment of the exciting and promising findings in MHE and related fields presented at the Conference and a discussion of the future MHE research directions. The Conference underlined the critical usefulness of gathering experts in several research fields to forge new alliances and identify cross-fertilization areas to benefit both basic and translational biomedical research on the skeleton.     

Novel HARS2 missense variants identified in individuals with sensorineural hearing impairment and Perrault syndrome

Biallelic variants in HARS2 have been associated with Perrault syndrome, characterized by sensorineural hearing impairment and premature ovarian insufficiency. Here we report three novel families, compound heterozygous for missense variants in HARS2 identified by next-generation sequencing, namely c.172A > G (p.Lys58Glu) and c.448C > T (p.Arg150Cys) identified in two sisters aged 13 and 16 years and their older brother, c.448C > T (p.Arg150Cys) and c.980G > A (p.Arg327Gln) identified in a seven year old girl, and finally c.137T > A (p.Leu46Gln) and c.259C > T (p.Arg87Cys) identified in a 32 year old woman. Clinically, all five individuals presented with early onset, rapidly progressive hearing impairment. Whereas the oldest female fulfilled the criteria of Perrault syndrome, the three younger females, aged 7, 13 and 16, all had apparently normal ovarian function, apart from irregular menstrual periods in the oldest female at age 16. The present report expands the list of HARS2 variants and helps gain further knowledge to the phenotype.     

Hutchinson-Gilford progeria syndrome: report of a Libyan family and evidence of autosomal recessive inheritance

A Libyan family with the Hutchinson-Gilford progeria syndrome affecting three children of two sisters is described. The proband was ascertained because of repeated unhealing fractures. The pattern of inheritance appeared autosomal recessive.     

一个遗传性多发性骨软骨瘤家系的基因突变检测

目的 确定一个遗传性多发性骨软骨瘤(hereditary multiple exostoses,HME)家系的致病基因.方法 应用与EXT1、EXT2紧密连锁的短串联重复序列(short tandem repeat,STR)对该家系进行连锁分析,确定候选基因,然后对候选基因的编码区及外显子与内含子交界处进行PCR-测序法突变分析.结果 该家系致病基因被定位在EXT2基因区,测序发现EXT2基因536G>A无义突变,该突变位于EXT2基因第3外显子,导致编码第180位氨基酸的密码子成为终止密码,突变与疾病共分离,其余外显子未发现突变.另发现1例外显不全.结论 EXT2基因536G>A突变是导致这个家系发生骨软骨瘤的原因.     

Two sisters with clinical diagnosis of Wiskott-Aldrich syndrome: Is the condition in the family autosomal recessive?

We report two sisters in a family representing manifestations of Wiskott-Aldrich syndrome' (WAS), an X-linked immunodeficiency disorder. An elder sister had suffered from recurrent infections, small thrombocy-topenic petechiae, purpura, and eczema for 7 years. The younger sister had the same manifestations as the elder sister's for a 2-year period, and died of intracranial bleeding at age 2 years. All the laboratory data of the two patients were compatible with WAS, although they were females. Sialophorin analysis with the selective radioactive labeling method of this protein revealed that in the elder sister a 115-KD band that should be specific for sialophorin was reduced in quantity, and instead an additional 135-KD fragment was present as a main band. Poly-merase chain reaction (PCR) analysis of the sialophorin gene and single-strand conformation polymorphism (SSCP) analysis of the PCR product demonstrated that there were no detectable size-change nor elec-trophoretic mobility change in the DNA from both patients. The results indicated that their sialophorin gene structure might be normal. Studies on the mother-daughter transmission of X chromosome using a pERT84-MaeIII polymorphic marker mapped at Xp21 and HPRT gene polymorphism at Xq26 suggested that each sister had inherited a different X chromosome from the mother. Two explanations are plausible for the occurrence of the WAS in our patients: the WAS in the patients is attributable to an autosomal gene mutation which may regulate the sialophorin gene expression through the WAS gene, or, alternatively, the condition in this family is an autosomal recessive disorder separated etiologically from the X-linked WAS. © 1995 Wiley-Liss, Inc.     

Autosomal recessive ichthyosis with hypotrichosis syndrome: further delineation of the phenotype

Autosomal recessive ichthyosis with hypotrichosis (ARIH) syndrome, which is characterized by congenital ichthyosis, abnormal hair and corneal involvement, has recently been shown in one consanguineous Israeli Arab family to be caused by a mutation in the ST14 gene, which encodes serine protease matriptase. No other families have so far been described since the original report. In this current report we describe a female patient from a second family with ARIH syndrome who carries a homozygous novel mutation, p.M1I. The patient has congenital ichthyosis, light brown, curly, sparse hair, improving with age, and sparse body hair, eyebrows and eyelashes. She does not suffer from photophobia, but has blepharitis. The phenotype of this patient closely resembles that of the affected individuals in the previously reported family, although she does not have tooth abnormalities and the ichthyosis is milder.     

Expanding the phenotypic spectrum of GABRG2 variants: a recurrent GABRG2 missense variant associated with a severe phenotype

Pathogenic missense and truncating variants in the GABRG2 gene cause a spectrum of epilepsies, from Dravet syndrome to milder simple febrile seizures. In most cases, pathogenic missense variants in the GABRG2 gene segregate with a febrile seizure phenotype. In this case series, we report a recurrent, de novo missense variant (c0.316?G?>?A; p.A106T) in the GABRG2 gene that was identified in five unrelated individuals. These patients were described to have a more severe phenotype than previously reported for GABRG2 missense variants. Common features include variable early-onset seizures, significant motor and speech delays, intellectual disability, hypotonia, movement disorder, dysmorphic features and vision/ocular issues. Our report further explores a recurrent pathogenic missense variant within the GABRG2 variant family and broadens the spectrum of associated phenotypes for GABRG2-associated disorders.     

A novel missense variant in GPT2 causes non-syndromic autosomal recessive intellectual disability in a consanguineous Iranian family

Intellectual disability (ID) affects 1–3% of the general population worldwide. Genetic factors play an undeniable role in the etiology of Non-Syndromic Intellectual disability (NS-ID). Nowadays, whole-exome sequencing (WES) technique is used frequently to identify the causative genes in such heterogeneous diseases. Herein, we subjected four patients with initial diagnostics of NS-ID in a consanguineous Iranian family. To find the possible genetic cause(s), Trio-WES was performed on the proband and his both healthy parents. Sanger sequencing was performed to confirm the identified variant by WES and also investigate whether it co-segregates with the patients’ phenotype in the family. Using several online in-silico predictors, the probable impacts of the variant on structure and function of GPT2 protein were predicted. A novel variant, c.266A>G; p.(Glu89Gly), in exon 3 of GPT2 (NM_133443.3) was identified using Trio-WES. The candidate variant was also verified by Sanger sequencing. All affected members showed the common clinical features suffering from a non-progressive mild-to-severe ID. Also, different clinical observations compared to previously reported cases such as no facial features, no obvious structural malformations, ability to speak but with difficulty, and lack of any morphological defects were noted for the first time in this family. The c.266A>G; p.(Glu89Gly) variant reported here is the sixth variant identified up to now in the GPT2 gene, to be associated with NS-ID. Our data support the potential malfunction of the substituted GPT2 protein resulted from the novel variant, however, we strongly suggest confirming this finding more by doing functional analysis.     

Novel sequence variants in the TMIE gene in families with autosomal recessive nonsyndromic hearing impairment

To date, 37 genes have been identified for nonsyndromic hearing impairment (NSHI). Identifying the functional sequence variants within these genes and knowing their population-specific frequencies is of public health value, in particular for genetic screening for NSHI. To determine putatively functional sequence variants in the transmembrane inner ear (TMIE) gene in Pakistani and Jordanian families with autosomal recessive (AR) NSHI, four Jordanian and 168 Pakistani families with ARNSHI that is not due to GJB2 (CX26) were submitted to a genome scan. Two-point and multipoint parametric linkage analyses were performed, and families with logarithmic odds (LOD) scores of 1.0 or greater within the TMIE region underwent further DNA sequencing. The evolutionary conservation and location in predicted protein domains of amino acid residues where sequence variants occurred were studied to elucidate the possible effects of these sequence variants on function. Of seven families that were screened for TMIE, putatively functional sequence variants were found to segregate with hearing impairment in four families but were not seen in not less than 110 ethnically matched control chromosomes. The previously reported c.241C>T (p.R81C) variant was observed in two Pakistani families. Two novel variants, c.92A>G (p.E31G) and the splice site mutation c.212 −2A>C, were identified in one Pakistani and one Jordanian family, respectively. The c.92A>G (p.E31G) variant occurred at a residue that is conserved in the mouse and is predicted to be extracellular. Conservation and potential functionality of previously published mutations were also examined. The prevalence of functional TMIE variants in Pakistani families is 1.7% [95% confidence interval (CI) 0.3–4.8]. Further studies on the spectrum, prevalence rates, and functional effect of sequence variants in the TMIE gene in other populations should demonstrate the true importance of this gene as a cause of hearing impairment.     

Steinfeld syndrome: Report of a second family and further delineation of a rare autosomal dominant disorder

We report on a fetus with alobar holoprosencephaly, microphthalmia, midline cleft lip and palate, absent nose, dysplastic ears, radial defects, pentalogy of Fallot, unilateral renal aplasia, absent gallbladder, vertebral anomalies, and absence of ribs. The father had a cleft palate, bilateral colobomas of the iris and retina, a bifid uvula, vertebral anomalies, and unilateral congential hearing loss. His sister had a cleft lip. On the basis of this family and the family reported by Steinfeld [1982], this malformation syndrome can be defined as a rare autosomal dominant syndrome whose main component manifestations are holoprosencephaly, predominantly radial limb deficiency, heart defects, kidney malformations, absence of gallbladder, and vertebral anomalies. © 1993 Wiley-Liss, Inc.     

Novel variants in CDH2 are associated with a new syndrome including Peters anomaly

Peters anomaly (PA) is a congenital corneal opacity associated with corneo-lenticular attachments. PA can be isolated or part of a syndrome with most cases remaining genetically unsolved. Exome sequencing of a trio with syndromic PA and 145 additional unexplained probands with developmental ocular conditions identified a de novo splicing and three novel missense heterozygous CDH2 variants affecting the extracellular cadherin domains in four individuals with PA. Syndromic anomalies were seen in three individuals and included left-sided cardiac lesions, dysmorphic facial features, and decreasing height percentiles; brain magnetic resonance imaging identified agenesis of the corpus callosum and hypoplasia of the inferior cerebellar vermis. CDH2 encodes for N-cadherin, a transmembrane protein that mediates cell-cell adhesion in multiple tissues. Immunostaining in mouse embryonic eyes confirmed N-cadherin is present in the lens stalk at the time of separation from the future cornea and in the developing lens and corneal endothelium at later stages, supporting a possible role in PA. Previous studies in animal models have noted the importance of Cdh2/cdh2 in the development of the eye, heart, brain, and skeletal structures, also consistent with the patient features presented here. Examination of CDH2 in additional patients with PA is indicated to confirm this association.