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.

Los defectos en las extremidades, una facies peculiar y el fallo de medro no siempre constituyen un síndrome de Cornelia de Lange / Limbs defects, peculiar face and failure to thrive is not always Cornelia de Lange Syndrome

Las malformaciones de las extremidades son raras y su etiología, variable. Existen síndromes genéticos que combinan estas malformaciones con discapacidad intelectual y otras malformaciones graves, como el síndrome de Cornelia de Lange. Presentamos el caso de una paciente con malformaciones severas en las 4 extremidades, discapacidad intelectual y características faciales peculiares que llevaron al diagnóstico presuntivo de síndrome de Cornelia de Lange. Presentamos el caso de una niña de 4 años de edad, padres consanguíneos y etnia gitana, con antecedentes de retraso del crecimiento intrauterino, bajo peso al nacer, microcefalia y múltiples malformaciones en ambas manos y pies, incluida la mano derecha hendida, con diagnóstico presuntivo de síndrome de Cornelia de Lange. Durante el primer año de vida se realizaron varios estudios con los siguientes resultados: cariotipo 46, XX; estudio de deleciones subteloméricas (técnica MLPA) normal; ecocardiograma y electrocardiograma sin hallazgos; evaluación oftalmológica y auditiva normales; ultrasonido abdominal y transfontanelar normales. A los 4 años se le aplicó una técnica de array de hibridación genómica comparada (comparative genomic hybridization) (array-CGH) con resolución de 180 kb, que detectó una deleción causal de 8,4 Mb en la citobanda 2q31.1q31.2. La deleción de 2q31 está asociada a la malformación de mano/pie hendido, y la correlación genotipo-fenotipo indica que las deleciones intersticiales de la región 2q31.1 muestran malformaciones en los miembros si incluyen una región crítica de 2,5 Mb, que incluye el cluster de HOXD y las regiones adyacentes en sentido 5’ y 3’. Concluimos que ante un paciente con malformaciones graves y signos y síntomas superpuestos de varios síndromes, es aconsejable comenzar el plan de trabajo con array-CGH, y si esta técnica no está disponible, realizar un cariotipo de alta resolución con la intención de descartar reordenamientos cromosómicos (AU)

Severe limbs deformities are rare and its etiology is variable. There are known genetic syndromes that combine limbs deformities, mental disability and other mayor malformations, such as Cornelia de Lange syndrome. We present the case of a patient with severe deformities in 4 limbs, mental disability and minor facial features that lead to the presumptive diagnosis of Cornelia de Lange syndrome. Four years old female her parents are consanguineous and from gipsy ethnicity. History of intrauterine growth retardation, low birth weight, microcephaly and multiple deformities in both hands and both feet including split-hand deformity of the right hand. Presumptive diagnosis of Cornelia de Lange syndrome, during the first year of life these studies were performed: kariotype 46, XX, subtelomeric deletion study (MLPA technique): normal, echocardiogram and EKG without abnormalities, oftalmologic and audition evaluation: normal and cranial and abdominal ultrasound also normal. At four years old array comparative genomic hybridization 180 kb was performed and it showed a causal deletion of 8.4 Mb at cytoband 2q31.1q31.2. 2q31 deletion is associated with the split hand/foot malformation, the genotype-phenotype correlation of interstitial deletions of the 2q31.1 region shows that limbs malformation are associated to a critical 2.5 Mb deletion containing the HOXD cluster and surrounding 5’ and 3’ regions. We conclude that when a patient presents major malformations and overlapping signs and symptoms of various syndromes it is wise to begin the workup with high resolution karyotype and/or, where available, array-CGH in order to rule out cytogenetic rearrangements (AU)

Could a patient with SMC1A duplication be classified as a human cohesinopathy?

The disorders caused by mutations in genes encoding subunits and accessory proteins of cohesin complex are collectively termed as cohesinopathies. The best known cohesinopathy is Cornelia de Lange Syndrome (CdLS), which is a multisystem developmental disorder characterized by facial dysmorphism, limb malformations, growth and cognitive impairment. Mutations in five genes, encoding subunits of the cohesin complex (SMC1A, SMC3, RAD21) and its regulators (NIPBL, HDAC8), are responsible for ∼ 70% of CdLS cases. We describe a 16-year-old boy with facial dysmorphism, growth retardation, intellectual disability, hirsutism and small hands, who has a small Supernumerary Marker Chromosome (sSMC) present in mosaic form. sSMC is composed of two duplicated segments encompassing 17 genes including SMC1A gene, at the regions Xp11.22 and Xp11.21q11.1. Clinical comparison between our patient with a previously reported individual with a SMC1A duplication and four male carriers of similar sSMC reported in databases, suggest that they all share clinical features related to cohesinopathies. Although our patient does not have the classical CdLS craniofacial phenotype, he has pre and postnatal growth retardation, intellectual disability and mild musculoskeletal anomalies, features commonly seen in patients with cohesinopathies.

Prenatal diagnosis of Huntington disease in maternal plasma: direct and indirect study.

BACKGROUND AND PURPOSE: The presence of cell-free fetal DNA in maternal plasma could allow performing a non-invasive prenatal diagnosis of Huntington disease (HD). The great advantage of this diagnosis is the absence of risk of fetal loss that it entails. METHODS: Maternal plasma from four pregnant women in their first trimester of gestation with a fetus at-risk was studied. In all the four cases, the father was affected. RESULTS: The diagnosis was performed both by a direct study of the mutation and an indirect haplotype study. By the direct analysis, three out of the four fetuses could be correctly diagnosed whilst the indirect analysis was only conclusive in one case. CONCLUSIONS: Non-invasive prenatal diagnosis of HD is possible by the analysis of fetal DNA in maternal plasma. Direct analysis of the mutation has shown higher accuracy than the haplotype analysis except for long expansions. Haplotype analysis would need to be improved for the study of Juvenile-onset HD. This diagnostic method would be limited to those couples with an affected male however this situation represents 80-90% of the pregnancies at-risk of HD. Moreover, it could be used as a confirmation test of healthy embryos transferred on pre-implantation genetic studies of HD.

Improvement in strategies for the non-invasive prenatal diagnosis of Huntington disease.

PURPOSE: We focused on the improvements of prenatal diagnosis by the analysis of DNA from maternal plasma, using Huntington disease as a model of disease. METHODS: We studied plasma from a pregnancy at risk of having a fetus affected with Huntington disease by the use of two direct analysis of the mutation and polymorphic STRs. RESULTS: Direct methods were not informative. Analysis with STRs revealed the presence of the allele that does not co-segregate with the disease, thus the fetus was healthy. CONCLUSIONS: This strategy is very useful to face complex cases when the direct study is not informative not only for Huntington disease but also for many other disorders.

Foetal sex determination in maternal blood from the seventh week of gestation and its role in diagnosing haemophilia in the foetuses of female carriers.

The existence of foetal DNA in maternal blood, discovered in 1997, opened new possibilities for noninvasive prenatal diagnosis. This includes foetal sex assessment by the detection of specific Y chromosome sequences in maternal blood, particularly important when a foetus may be affected by an X-linked disorder such as haemophilia. This study aims to validate this sex assessment method and to test its clinical utility in the diagnosis of 15 potentially affected pregnancies in female carriers of haemophilia. In the validation study, 316 maternal blood samples from 196 pregnant women at gestations ranging from 5 weeks to 12 weeks were analysed. In the clinical study, 15 pregnancies at risk of having a haemophilic foetus were tested. All pregnancies in the validation study were correctly diagnosed. The accuracy and specificity of the methodology from the seventh week of gestation was 100%. The sex of all 15 pregnancies identified as being at risk of bearing a haemophilic foetus was correctly diagnosed. Foetal sex assessment by detecting specific Y chromosome sequences in maternal blood is now routinely used in our hospital because of its high accuracy from the seventh week of gestation. Reliable foetal gender determination from maternal blood of pregnant women carriers of haemophilia in the first trimester of gestation can avoid more conventional, invasive methods of prenatal diagnosis.

Diagnóstico prenatal no invasivo en células fetales obtenidas de sangre periférica materna / Non-invasive prenatal diagnosis on fetal cells from maternal blood

El aislamiento de los eritroblastos fetales presentes en la sangre materna para su posterior estudio representa un prometedor método de diagnóstico prenatal no invasivo.En nuestro laboratorio hemos realizado un estudio poblacional con el que se pretendía realizar una valoración práctica de las técnicas desarrolladas para un diagnóstico prenatal no invasivo. Para el enriquecimiento de las muestras en eritroblastos fetales se empleó el método que se consideró más adecuado para la rutina del laboratorio y para su posterior estudio mediante técnica de FISH. El estudio permitió determinar que la mayor sensibilidad diagnóstica se obtenía en la semana 15 de gestación (76 por ciento), observándose una clara diferencia entre la sensibilidad obtenida en el primer (25 por ciento) y segundo (61,5 por ciento) trimestre de gestación. Distintos grupos están trabajando para modificar las técnicas actuales y así obtener mejores resultados. Sin embargo, desde el punto de vista de una unidad de diagnóstico prenatal existen todavía aspectos que han de resolverse: - No hay un consenso acerca de la mejor semana para realizar el estudio.- Las técnicas son laboriosas y no recuperan un número suficiente de células para el estudio.- La sensibilidad alcanzada no es óptima. - E I coste es muy caro. Por todo ello esta técnica no puede aplicarse todavía a la rutina del diagnóstico prenatal. En el presente artículo, además de presentar nuestros resultados, se discute sobre el estado actual del tema, así como las perspectivas futuras (AU)

ADN fetal en plasma de gestante: aplicaciones en el diagnóstico prenatal / Fetal DNA in maternal plasma: applications in prenatal diagnosis

La presencia de ADN fetal en el suero y el plasma de gestante está llevando al desarrollo de diferentes estrategias para realizar diagnóstico prenatal no invasivo. Hasta el momento diversos autores han publicado principalmente resultados en la detección de sexo fetal y factor RhD. Estos datos han motivado que nuestro grupo evalúe esta metodología para su posible aplicación diagnóstica. Hemos obtenido resultados satisfactorios en la determinación de sexo fetal, enfermedades mendelianas de origen paterno (como fibrosis quistica y corea de Huntington), así como en la determinación del factor RhD fetal (AU)

Huntington disease-unaffected fetus diagnosed from maternal plasma using QF-PCR.

The discovery of fetal DNA in maternal plasma from early pregnancies has led to new opportunities for clinical application. In the last few years there have been numerous reported applications, mainly fetal gender and RhD genotyping. The prenatal diagnosis of some inherited genetic diseases such as Huntington disease is also very frequently required in the prenatal diagnosis routine. We have successfully diagnosed, with a non-invasive procedure, an unaffected HD fetus at the 13th week of gestation using fetal DNA from maternal plasma and the quantitative fluorescent PCR method, which is one of the most sensitive ways to detect fetal DNA in maternal plasma at such an early time of gestation.

Prenatal detection of a cystic fibrosis mutation in fetal DNA from maternal plasma.

OBJECTIVES: Maternal plasma and serum are being used to detect fetal DNA by PCR in order to determine certain conditions such as fetal gender and RhD without invasive procedures. Because of the presence of maternal DNA in plasma, these approaches are limited to paternally inherited disorders or those de novo present in the fetus. We have assessed the possibility of performing the detection of a single-gene disorder such as a fetal paternally inherited Cystic Fibrosis mutation (Q890X) in maternal plasma. METHODS: The analysis was performed at 13 weeks of gestation using DNA extracted from maternal plasma. We used a PCR amplification of the Q890X mutation and a posterior restriction analysis of the PCR product. RESULTS: We were able to detect the presence of the mutation and thus the fetal condition of being a carrier of the paternal mutation. CONCLUSIONS: We have made evident the possibility of detecting an inherited paternal mutation in a non-invasive way at the 13t(hr) weeks of pregnancy. This methodology could be very useful in cases of paternally inherited dominant disorders. The technical improvements in fetal DNA detection and analysis might lead to the development of new applications in the non-invasive prenatal diagnosis field.

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.

Aplicaciones prácticas de la técnica de FISH

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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.

Prenatal diagnosis on fetal cells from maternal blood: practical comparative evaluation of the first and second trimesters.

Objectives- Several attempts have been made to determine the gestational period in which the maximum number of fetal cells can be found in maternal blood and consequently which is the best week in which to perform a reliable non-invasive prenatal diagnosis. Most studies conclude that the number of nucleated red blood cells (NRBC) increases in line with gestation, but the number of cells that are fetal in origin (FNRBC) decreases in the third trimester. The aim of the present study was to make a practical comparative evaluation of the first and second trimesters to ascertain the period in which a greater number of FNRBC can be found of the total number of NRBC identified. Methods- Double density gradient and a posterior positive selection (CD71) by magnetic activated cell sorting (MACS) were employed. In the final fraction, erythroblasts were identified using Kleihauer staining and were studied using the fluorescence in situ hybridization (FISH) interphasic technique. Results- There was a significant difference (p<0.05) between the mean number of FNRBC found in the first and second trimesters. Conclusions- The number of FNRBC increases from the first to the second trimester. It appears that the optimum week in which to perform a reliable non-invasive prenatal diagnosis is around the 15th week.

Chromosomal mosaicism for isochromosome 11q confined to CVS direct preparations.

OBJECTIVE: To analyse the discrepancy between the karyotype in direct preparations of chorionic villus sampling (CVS) and the fetal karyotype and its possible fetal phenotypic repercussion. METHODS: The karyotype was obtained from direct and cultured preparations of CVS. FISH was performed in direct CVS preparations and in four different areas of term placenta. RESULTS: Karyotype and FISH analysis in CVS revealed a 46,XX/47,XX,+i(11q) cell line. Cultured CVS preparations showed a 46,XX karyotype. Cytogenetic studies in term placenta did not reveal the abnormal cell line. Molecular studies did not detect uniparental disomy for chromosome 11 in the fetus. CONCLUSION: The fetus, at birth, had no phenotypic abnormalities. IUGR was not present during gestation, in accordance with the low proportion of aneuploid cells in term placenta, and UPD for chromosome 11 was not observed.

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.

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.

Rapid identification of a small dicentric supernumerary marker derived from chromosome 16 with a modified FISH technique on amniotic fluid.

Small supernumerary marker chromosomes are seldom found in prenatal diagnosis and the majority of them are difficult to identify. The only possibility to give a more precise prognosis is by establishing its origin. FISH is the best technique to identify the chromosomal origin, but in the majority of cases large amounts of chromosomal material are needed and this is time consuming. We have used a modification of the FISH technique that allows the hybridization of several probes on one slide. Using this method, we have identified the first de novo mosaic dicentric supernumerary marker derived from chromosome 16 (smaller than chromosome 21) in amniotic fluid. The gestation and the follow-up of the baby were normal.