NGS and phenotypic ontology-based approaches increase the diagnostic yield in syndromic retinal diseases.

Syndromic retinal diseases (SRDs) are a group of complex inherited systemic disorders, with challenging molecular underpinnings and clinical management. Our main goal is to improve clinical and molecular SRDs diagnosis, by applying a structured phenotypic ontology and next-generation sequencing (NGS)-based pipelines. A prospective and retrospective cohort study was performed on 100 probands with an a priori diagnosis of non-Usher SRDs, using available clinical data, including Human Phenotype Ontology annotation, and further classification into seven clinical categories (ciliopathies, specific syndromes and five others). Retrospective molecular diagnosis was assessed using different molecular and bioinformatic methods depending on availability. Subsequently, uncharacterized probands were prospectively screened using other NGS approaches to extend the number of analyzed genes. After phenotypic classification, ciliopathies were the most common SRD (35%). A global characterization rate of 52% was obtained, with six cases incompletely characterized for a gene that partially explained the phenotype. An improved characterization rate was achieved addressing prospective cases (83%) and well-recognizable syndrome (62%) subgroups. The 27% of the fully characterized cases were reclassified into a different clinical category after identification of the disease-causing gene. Clinical-exome sequencing is the most appropriate first-tier approach for prospective cases, whereas whole-exome sequencing and bioinformatic reanalysis increases the diagnosis of uncharacterized retrospective cases to 45%, mostly those with unspecific symptoms. Our study describes a comprehensive approach to SRDs in daily clinical practice and the importance of thorough clinical assessment and selection of the most appropriate molecular test to be used to solve these complex cases and elucidate novel associations.

Azathioprine hypersensitivity syndrome: report of two cases with cutaneous manifestations.

Azathioprine is an immunosuppressant drug used in many dermatological and nondermatological pathologies. Azathioprine hypersensitivity syndrome (AHS) is a rare idiosyncratic reaction that is not related to dose or thiopurine methyltransferase activity. Up to half of cases of AHS can present with variable cutaneous manifestations besides fever, malaise and other systemic symptoms. It is important to be aware of AHS, as continuance or reintroduction of the drug can led to multiorgan failure and cardiovascular collapse.

Five years' experience of the clinical exome sequencing in a Spanish single center.

Nowadays, exome sequencing is a robust and cost-efficient genetic diagnostic tool already implemented in many clinical laboratories. Despite it has undoubtedly improved our diagnostic capacity and has allowed the discovery of many new Mendelian-disease genes, it only provides a molecular diagnosis in up to 25-30% of cases. Here, we comprehensively evaluate the results of a large sample set of 4974 clinical exomes performed in our laboratory over a period of 5 years, showing a global diagnostic rate of 24.62% (1391/4974). For the evaluation we establish different groups of diseases and demonstrate how the diagnostic rate is not only dependent on the analyzed group of diseases (43.12% in ophthalmological cases vs 16.61% in neurological cases) but on the specific disorder (47.49% in retinal dystrophies vs 24.02% in optic atrophy; 18.88% in neuropathies/paraparesias vs 11.43% in dementias). We also detail the most frequent mutated genes within each group of disorders and discuss, on our experience, further investigations and directions needed for the benefit of patients.

Prenatal diagnosis of skeletal dysplasia due to FGFR3 gene mutations: a 9-year experience : prenatal diagnosis in FGFR3 gene.

PURPOSE: Prenatal diagnosis with ultrasound findings compatible with skeletal dysplasia due to FGFR3 mutations over a 9 year period in pregnancies and abortuses. METHODS: 54 samples were studied. Aneuploidy studies were carried out on all samples. By sequencing analysis, we determined mutations for achondroplasia (ACH), hypochondroplasia (HCH), and type I and type II tanathophoric dysplasia (TD). RESULTS: 2 chorionic villi samples had a G380R mutation due to a mother with ACH; 4 amniotic fluid samples with TDs in which the foetuses had micromelia plus hypoplastic thoraces; 5 samples from abortuses with TDs. Neither ACH nor HCH occurred in sporadic cases. CONCLUSIONS: Molecular studies in ongoing pregnancies are indicated in cases with an affected parent, a family history with positive molecular studies (maternal anxiety), and when the US finding demonstrates micromelia with a hypoplastic thorax. A protocol for tissues of abortuses should include an X-ray, pathologic anatomy, and genetic studies.

Two non-contiguous duplications in the DMD gene in a Spanish family.

DMD and BMD are X-linked myopathy diseases in most cases caused by intragenic deletions, but duplications also appear in a significant number of cases. We present a complex duplication pattern detected by MLPA, a recently formulated method applied here to amplify the 79 exons of the DMD gene. We found a double-duplication in two DMD-affected brothers and in their carrier mother, which consist of two non-contiguous duplications encompassing exons 2 to 7 and exons 50 to 55. Different models are presented to explain formation of this genetic variant.

A small and active ring X chromosome in a female with features of Kabuki syndrome.

A ring X chromosome is found in about 6% of patients with Turner syndrome (TS), often with mosaicism for a 45,X cell line. Patients with this karyotype are reported to have a higher incidence of a more severe phenotype including mental retardation. In fact, some studies have shown a correlation between this severity and the presence or absence of an intact and functional X inactivation center (XIST). However, the phenotype of the individuals with r(X) cannot be entirely defined in terms of their X-inactivation patterns. Nevertheless, a small group of these patients have been described to manifest clinical features reminiscent of the Kabuki syndrome. Here we present a female patient with clinical features resembling Kabuki syndrome and a mos 45,X/46,X,r(X) karyotype. Methylation analyses of polymorphic alleles of the androgen receptor gene showed that both alleles were unmethylated suggesting an active ring chromosome. A specific X chromosome array CGH was performed estimating the size of the ring to be 17 Mb, lacking the XIST gene, and including some genes with possible implications in the phenotype of the patient.

Partial paternal uniparental disomy (UPD) of chromosome 1 in a patient with Stargardt disease.

PURPOSE: Stargardt disease (STGD) is the most common juvenile macular dystrophy, characterized by central visual impairment. All recessively inherited cases are thought to be due to mutations in the ABCA4 gene, mapped to 1p21-p13. METHODS: To describe a form of non-mendelian inheritance in a patient with STGD identified through the course of a conventional mutational screening performed on 77 STGD families. DNA from the patient and relatives was analyzed for variants in all 50 exons of the ABCA4 gene by screening on the ABCR400 microarray; results were confirmed by direct sequencing. Haplotype analyses, standard and high-resolution (HR) karyotypes, and multiplex ligation-dependent probe amplification (MLPA) were also performed. RESULTS: A patient with STGD caused by the homozygous p.Arg1129Leu mutation in the ABCA4 gene was found to be the daughter of a noncarrier mother and a father who was heterozygous for this change. Haplotype analysis suggested that no maternal ABCA4 allele was transmitted to the patient. Microsatellite markers spanning the entire chromosome 1 identified a homozygous region of at least 4.4 Mb, involving the ABCA4 gene. The cytogenetic study revealed normal female karyotype. Further evaluation with MLPA showed the patient had a normal dosage for both copies of the ABCA4 gene, thus suggesting partial paternal isodisomy but not a maternal microdeletion. CONCLUSIONS: We report that recessive STGD can rarely be inherited from only one unaffected carrier parent in a non-mendelian manner. This study also demonstrates that genomic alterations contribute to only a small fraction of disease-associated alleles for ABCA4.

Increased parental ages and uniparental disomy 15: a paternal age effect?

Parental ages associated with both maternal and paternal uniparental disomy (UPD) of chromosome 15 are highly elevated in comparison to Zurich population-based controls, with mean maternal and paternal ages of 35.6 and 38.1, respectively for UPD patients (diagnosed in Zurich) and 28.0 and 31.0, in controls. The parental ages are also significantly higher than observed for trisomies of other chromosomes diagnosed in Zurich. The higher age of UPD cases may be due to the fact that two errors, both a gain and a loss of a chromosome 15, are necessary. We suggest that gamete complementation, zygote formation from two gametes one of which is nullisomic and the other disomic for the same chromosome, may be a major mechanism of UPD formation, as well as secondary loss of a chromosome in a trisomic conception, and that there is an association between increased paternal age and nondisjunction.

Molecular study of 45,X conceptuses: correlation with clinical findings.

The parental origin of the single X in 45 cases (40 liveborns and 5 fetuses) with a 45,X karyotype was studied using polymorphic DNA probes. The single X was paternal in origin (Xp) in 10 cases (22.2%) and maternal (Xm) in 35 cases (77.8%). Y chromosome material was detected in 1 out of the 35 cases with a 45,Xm constitution. Analysis of parental ages and clinical data of the patients with respect to the origin of the single X revealed no significant differences between the origins.

Cryptic 6q subtelomeric deletion associated with a paracentric inversion in a mildly retarded child.

We report on a girl with minor anomalies and developmental delay carrying an apparently balanced paracentric inversion of chromosome 6q (q22qter). Fluorescent in situ hybridization analysis demonstrated a deletion of the subtelomeric region of 6q. This illustrates the use of specific subtelomeric fluorescent in situ hybridization probes to detect cryptic deletions as an important cause of mental retardation in seemingly balanced chromosome rearrangements.

Distal deletion of chromosome 13 in a child with the "opitz" GBBB syndrome.

We describe a patient who had craniofacial and genitourinary abnormalities, swallowing difficulties, esophageal dysfunction, hypotonia and moderate developmental delay, and who also had a terminal deletion of chromosome 13 (q32.3qter). This MCA pattern strongly suggests the Opitz GBBB syndrome. The deletion of chromosome 13 was interpreted as terminal with a breakpoint at 12q32.3. Coagulation factors VII and X located in 13q34, were markedly reduced in the propositus. Although there is some clinical overlap between patients with terminal deletion of 13q and those with the Opitz GBBB syndrome, our patient manifests a whole pattern of abnormalities characteristics of the latter disorder. The concurrence of the Opitz GBBB syndrome and the chromosome abnormality in our patient could be due to chance or, be because a gene for the Opitz GBBB syndrome is located at the tip of 13q.

Proximal partial 5p trisomy resulting from a maternal (19;5) insertion.

We present a case with a partial duplication 5p11-->5p13.3 resulting from a maternal ins (19,5)(p11;p11-p13.3). The diagnosis was confirmed by FISH and complement component determinations. The clinical picture was similar to those described in patients with complete duplication of the short arm and in some patients with partial 5p duplications, affecting at least band 5p13. A special significance of band 5p13 in the clinical severity of 5p duplications is discussed.

Tetrasomy 5p mosaicism due to an extra i(5p) in a severely affected girl.

We present a case of mosaic 5p tetrasomy. The mosaicism 46,XX/47,XX,+i(5p) was found at different ratios in blood lymphocytes, skin fibroblasts, and chondrocytes. The origin of the extra isochromosome was confirmed by FISH. The clinical picture corresponds to that described in trisomy 5p patients, although it was more severe than the two previously reported cases of mosaic 5p tetrasomy. No correlation between clinical severity and proportion of tetrasomic cells in blood or fibroblasts was found in these cases.

Ser186Pro mutation of RHO gene in a Spanish autosomal dominant retinitis pigmentosa (ADRP) family.

A Spanish family affected with autosomal dominant retinitis pigmentosa (ADRP) with a diffuse phenotype showed a mutation in the rhodopsin gene. The mutation was the transition T-->C in codon 186, which has been reported once before in an American patient (Dryja et al., Proc Natl Acad Sci USA 1991;88:9370-9374). This change replaces a serine by a proline in the second intradiscal loop of the protein, generating a molecule that is probably folding- and transport-defective.

Retinitis pigmentosa, mental retardation, marked short stature, and brachydactyly in two sibs.

We present two siblings with retinitis pigmentosa, mental retardation, markedly short stature, and brachydactyly. This association of clinical findings appears to be distinct from previously described syndromes and seems to represent the pleiotropic effects of a single autosomal recessive gene.

Choroideremia, sensorineural deafness, and primary ovarian failure in a woman with a balanced X-4 translocation.

We present clinical and cytogenetic studies of a female patient affected with choroideremia, mild sensorineural deafness, and primary amenorrhea showing a balanced translocation between chromosomes X and 4. The breakpoint was precisely defined applying FISH techniques: 46,X,t(X;4)(q21.2;p16.3).ish t(X;4)(D4S96+, D4F26+; wcpX+). The X-chromosomal breakpoint was located within a region where both the choroideremia locus and a deafness locus (DFN3/POU3F4) have been mapped. The presence of X-linked disorders in this balanced carrier of X-autosomal translocations (XAT) can be explained either by the disruption of the structural coding or regulatory sequences of the gene(s) or by the submicroscopic deletion of this region leading to a contiguous gene deletion syndrome. The primary ovarian failure (POF) found in the present case has been already observed in XAT when the breakpoint is within a previously defined critical region (Xq13-26). A position effect is postulated as a possible explanation.

A maternal inherited translocation t(1;22)(q11;p11) in two infertile brothers.

We report two infertile brothers presenting with azoospermia and oligozoospermia. Cytogenetic studies using G-banding and FISH analysis on lymphocyte cultures revealed an autosomal balanced reciprocal translocation t(1;22)(q11;p11) in both males. The same translocation was found in their mother, but not in a third fertile brother and maternal uncle suggesting that this translocation might compromise the male but not the female gametogenesis in this family.

A MELAS phenotype and a paternal inherited inversion of chromosome 10 in a female patient.

A MELAS phenotype and a paternal inherited inversion of chromosome 10 in a female patient: We describe a patient suffering from encephalomyopathy with overlapping symptoms, including MELAS and Kearn-Sayre syndrome features. Mutations in tRNA LEU (UUR) were not found in mtDNA of blood cells, suggesting a different genetic defect. Cytogenetic studies revealed a paternal inherited pericentric inversion of chromosome 10 (p13;q22) pat. Although the presence of the same inversion in the father and in the apparently asymptomatic sister does rather suggest that the concurrence of the mitochondrial disease in the patient was due to chance, some alternative explanations to associate both events might be proposed.

Aniridia as part of a WAGR syndrome in a girl whose brother presented hypospadias.

Aniridia can arise as part of the WAGR syndrome (Wilms tumour. aniridia, genitourinary anomalies, and mental retardation), due to a deletion or chromosomal region 11p13. We report a girl with a complete WAGR syndrome, whose brother presented hypospadias. Cytogenetic, FISH and molecular studies showed a deletion in one chromosome 11 of the patient. No cytogenetic rearrangement or deletion affecting the genes included in this region (PAX6 and WT1) were observed in her brother and parents. This excludes a higher risk than that of the general population for developing Wilms tumour in the brother and supports that the presence of WAGR syndrome in the patient and hypospadias in her brother is a chance association. We conclude that the identification and definition of the deletions in the WAGR region, which include the WT1 locus are important in order to identify a high tumour risk in infant patients with aniridia including those without other WAGR anomalies.

[Achondroplasia: molecular study of 28 patients]. / Acondroplasia: estudio molecular de 28 pacientes.

BACKGROUND: The main goal of the study is to investigate in the Spanish population the value of searching for the Gly380Arg mutation in the transmembrane domain of fibroblast growth factor receptor-3 (FGFR3#) as the basis for the molecular diagnosis of achondroplasia. PATIENTS AND METHODS: Twenty eight achondroplastic patients were studied. Genomic DNA obtained from blood was used to amplify using PCR a 164 bp segment of FGFR3 encompassing the transmembrane domain. The occurrence of the G-->A transition and of the G-->C transversion at the first base of codon 380 were investigated by digestion with the restriction enzymes Sfcl and Mspl followed by electrophoretic analysis of the products. RESULTS: All achondroplastic patients were found to be heterozygous for the Gly380Arg mutation, as a consequence of the G-->A transition in 27 cases and of the G-->C transversion in the remaining patient. None of these changes were found in control subjects including a hypochondroplastic patient. CONCLUSIONS: The identification of the Gly380Arg mutation can be used in Spain for conclusive diagnosis of achondroplasia. The guanine at the first position of codon 380 of FGFR3 exhibits similarly increased frequency of mutation than in other populations, an thus it is unlikely that the genetic background of the population determines the mutation potential of this guanine.