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.

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.

Recomendaciones de buenas prácticas para el diagnóstico genético de abortos espontáneos e interrupciones voluntarias del embarazo por presentar defectos congénitos / Good practice recommendations in the molecular diagnosis of miscarriage and abortion due to multiple congenital malformations

Objetivos: La aparición de defectos congénitos produce una gran ansiedad en la familia y una enorme demanda asistencial. El objetivo principal radica en la redacción de las recomendaciones de buenas prácticas que sirvan de guía a los profesionales sanitarios para el diagnóstico clínico-genético de defectos congénitos. Metodología: El protocolo que proponemos contempla un modelo de actuación óptimo que incluye, la recogida de la información clínica inicial, la obtención de las muestras biológicas y los protocolos de actuación. Resultado: Se ha elaborado un modelo de historia clínica que ayude a la recogida de la información clínica pertinente. En la obtención de las muestras biológicas se aconseja la obtención de muestras fetales (de las 3 capas embrionarias) y muestras de los progenitores que serán procesarán teniendo en cuenta el algoritmo de actuación propuesto para el correcto diagnóstico genético del defecto congénito correspondiente. Conclusión: Esta guía recoge por primera vez, las recomendaciones de buenas prácticas para el diagnóstico genético de abortos con defectos congénitos

Aims: Congenital anomalies can cause anxiety within a family and high healthcare demand. The aim of this study was to write good practice recommendations to guide health professionals in the clinical-genetic diagnosis of congenital defects. Methods: The proposed protocol focuses on an optimal case scenario that includes collection of initial clinical data, biological sampling, and diagnostic algorithms. Results: A model of the optimal clinical history form was created to facilitate the collection of initial clinical data. For sampling, it is recommended to obtain at least one fetal sample (of the three embryonic germ layers). Moreover, samples from both parents should be taken to exclude mosaicism, following the diagnostic algorithm proposed for the correct genetic diagnosis of the corresponding congenital defect. Conclusion: This document is the first to gather good practice recommendations for the pre- and post-natal genetic diagnosis of miscarriages and abortions due to congenital defects

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)

Guidelines for genetic study of aniridia.

INTRODUCTION: Aniridia is a panocular disorder which occurs in 1/50,000 to 1/100,000 live births and can appear either in isolated form or in the context of a syndrome. Isolated aniridia is inherited as an autosomal dominant condition and is caused by mutations of the PAX6 gene. A variety of techniques and methodologies within molecular genetics and cytogenetics are used to study these mutations. OBJECTIVE: To identify the different aspects of this disease and to provide a guide for proper genetic diagnosis leading to improved clinical management of the disease. DEVELOPMENT: Aniridia is an autosomal dominant disease that primarily affects the iris, though it can impact most of the ocular structures. The disease is mainly caused by mutations in the PAX6 gene located on chromosome 11p13 which encodes a transcription factor that is involved in the development of the eye. Genetic analysis of aniridia is complex and requires the use of both molecular genetics and cytogenetics techniques. These procedures are indicated in all cases of aniridia. It is important bear certain clinical and technical aspects in mind prior to starting analysis or providing genetic counseling for patients and their families. CONCLUSIONS: The use of molecular genetic techniques in the genetic diagnosis of aniridia enables patients and their families to receive better clinical management.

Guía para el estudio genético de la aniridia / Guidelines for genetic study of aniridia

Introducción: La aniridia es una enfermedad panocular con una incidencia de entre 1/50.000 a 1/100.000 nacidos vivos, que puede presentarse de forma aislada o en el contexto de un síndrome. Presenta una herencia autosómica dominante y en la mayoría de los casos está causada por mutaciones en el gen PAX6, para cuyo estudio de mutaciones se emplea una gran variedad de técnicas y metodologías de genética molecular y citogenéticas. Objetivo: Recoger los distintos aspectos de esta enfermedad y ofrecer una guía para el adecuado diagnóstico genético que ayude a un mejor manejo clínico de la misma. Desarrollo: La aniridia es una enfermedad autosómica dominante que afecta fundamentalmente al iris, pero también puede afectar a la mayoría de las estructuras oculares. Está causada principalmente por mutaciones en el gen PAX6, ubicado en la región cromosómica 11p13, que codifica para una proteína reguladora de la transcripción imprescindible en el desarrollo del ojo. El análisis genético de la aniridia es complejo y requiere tanto de técnicas de genética molecular (secuenciación, CGH-array o MLPA) como citogenéticas (cariotipo y FISH). Este estudio está indicado en todos los casos de aniridia y es importante tener en cuenta ciertas consideraciones tanto clínicas como técnicas antes de abordar su análisis y el asesoramiento genético de los pacientes y familias afectados por esta enfermedad. Conclusiones: La aplicación de técnicas de genética molecular al diagnóstico genético de la aniridia permite un mejor manejo clínico tanto de los afectados como de sus familiares(AU)

Introduction: Aniridia is a panocular disorder which occurs in 1/50,000 to 1/100,000 live births and can appear either in isolated form or in the context of a syndrome. Isolated aniridia is inherited as an autosomal dominant condition and is caused by mutations of the PAX6 gene. A variety of techniques and methodologies within molecular genetics and cytogenetics are used to study these mutations. Objective: To identify the different aspects of this disease and to provide a guide for proper genetic diagnosis leading to improved clinical management of the disease. Development: Aniridia is an autosomal dominant disease that primarily affects the iris, though it can impact most of the ocular structures. The disease is mainly caused by mutations in the PAX6 gene located on chromosome 11p13 which encodes a transcription factor that is involved in the development of the eye. Genetic analysis of aniridia is complex and requires the use of both molecular genetics and cytogenetics techniques. These procedures are indicated in all cases of aniridia. It is important bear certain clinical and technical aspects in mind prior to starting analysis or providing genetic counseling for patients and their families. Conclusions: The use of molecular genetic techniques in the genetic diagnosis of aniridia enables patients and their families to receive better clinical management(AU)

Estudio colaborativo de abortos espontáneos: empleo de técnicas moleculares en muestras cuyo resultado citogenético no puede ser establecido / Colaborative study of spontaneus abortion: use of molecular techniques in failure culture samples

Introducción. El conocimiento de la causa de abortopermite ofrecer un adecuado consejo genético, además dereducir el estrés psicológico y el sentimiento de culpabilidadgenerado en la mujer tras sufrir un aborto. En la actualidadel estudio de abortos se realiza mediante técnicas citogenéticas,aunque muchas veces no es posible ofrecer un diagnósticodebido al fracaso de cultivo que acontece entre el5-42 % de los casos. En este trabajo se pretende evaluar lasensibilidad de las técnicas moleculares para el estudio dealteraciones cromosómicas en aquellos casos cuyo resultadocitogenético no puede ser establecido.Metodología. Se han estudiado 70 muestras de abortosdel primer y segundo trimestre de gestación mediante citogenéticay genética molecular (Quantitative FluorescentPolymerase chain Reaction [QF-PCR] y Multiplex ligationdependentProbe Amplification [MLPA]).Resultados. No se pudo establecer un resultado citogenéticoen el 37,2 % de las muestras. 44 fueron cariotipadas,obteniéndose 37 cariotipos normales y 7 anómalos. El estudiomolecular permitió establecer una dotación cromosómicaen el 100% de los casos, se encontraron alteraciones en10, de los cuales 3 carecían de resultado citogenético.Conclusiones. Se propone incluir en el protocolo de estudiode abortos el empleo de las técnicas citadas en casode fracaso del cultivo celular. La colaboración entre laboratoriosde citogenética y genética molecular especializados,permitiría ofrecer un resultado a la mayoría de las pacientes,esencial a la hora de poder establecer un adecuado consejogenético(AU)

Introduction. The knowledge of miscarriage causepermits offering an appropriate genetic counselling andmoreover, reduces psychological distress and self blamefeelings in women with a miscarriage. Nowadays, chromosomalstudy of abortions is mostly performed usingcytogenetic techniques. In few cases, no diagnosis can beestablished due to the high rate of culture failure (5-42%). Here, we try to evaluate the usefulness of moleculartechniques for the chromosomal study of those casesin which a cytogenetic result can not be established.Methods. A total of 70 miscarriage samples from thefirst and second trimesters of gestation have been studiedby karyotyping and molecular techniques (QF-PCRy MLPA).Results. The karyotype could not be established in37.2% of cases. Karyotype could be obtained in 44 samples,being 37 normal and 7 chromosomally abnormal.Molecular studies permitted to obtain a result in 100% ofthe cases, finding abnormalities in 10 of them, including3 in which the karyotype had not been established.Conclusions. We propose the use of molecular techniquesin those cases in which the culture fails. The collaborationbetween cytogenetic and molecular laboratorieswould permit to establish a result in the majority ofcases, which would represent an improvement for the offeringof an appropriate genetic counselling(AU)

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.

Protocolo recomendado para el estudio cromosómico de abortos espontáneos: abordaje citogenético y molecular / Recommended protocol for the chromosomal study of spontaneous miscarriages: cytogenetic and molecular approach

Las alteraciones cromosómicas son responsables de más del 60 % de las pérdidas embrionarias que acontecen durante el primer trimestre de gestación. El diagnóstico de la causa del aborto reduce significativamente tanto el estrés psicológico a largo plazo como el sentimiento de culpabilidad generado en la mujer tras sufrir un aborto y permite ofrecer un adecuado consejo genético a estas parejas de cara a futuros embarazos. Tradicionalmente, el estudio cromosómico de los abortos espontáneos se ha abordado mediante el cultivo celular de los restos fetales para su posterior cariotipado. Sin embargo, el estudio citogenético de los restos abortivos en particular presenta determinadas limitaciones, como la elevada tasa de fracaso del cultivo celular o el sobrecrecimiento de células de origen materno en el cultivo. El empleo de técnicas moleculares como la QF-PCR y MLPA permite obtener información acerca de la constitución cromosómica del aborto solventando tales limitaciones. En el presente trabajo se propone el protocolo óptimo para el estudio cromosómico de los restos abortivos incluyendo un abordaje citogenético y molecular

Chromosomal abnormalities account for at least 60 % offirst trimester fetal losses. Identification of the cause of fetal loss significantly reduces long-term psychological distress and self-blame feelings in women with a miscarriage and enables offering an improved genetic counselling to these couples in future pregnancies. Routine cytogenetic study of miscarriagesentails high rates of culture failure or misdiagnosis due to maternal cell contamination. On the other hand, molecular techniques such as QF-PCR and MLPA have been proved to be reliable methods to obtain information about chromosomal constitution of miscarriages, solving culture related limitations. In the present manuscript, we propose the optimal protocol for the chromosomal study of spontaneous abortions from a combined cytogenetic and molecular approach

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.

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.

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.

Prenatal diagnosis of 46, XX male fetus.

Prenatal diagnosis of sex differentiation disorders is extremely rare and is estimated in 1/2500 analyzed gestations. A group of this disorders are the 46, XX males and its incidence is estimated in 1/20000 male neonates. We report a male XX fetus in which the diagnosis of sex determination was requested at 20 gestation weeks to clarify the real gender of the fetus. Discrepancy between cytogenetic and ultrasonographic was detected.

New approach for the refinement of the location of the X-chromosome breakpoint in a previously described female patient with choroideremia carrying a X;4 translocation.

Choroideremia (CHM) is an X-linked recessive ophthalmic disease characterized by a progressive degeneration of the choroid and the pigmented epithelium of the retina. We present the genetic characterization of a female patient affected with CHM who has been previously studied cytogenetically and showed a balanced translocation between chromosomes X and 4 [46,X,t(X;4)(q21;p16)]. The breakpoint in the X chromosome lies in the locus of CHM gene and for this reason, we have elucidated whether or not CHM was disrupted in the X chromosome involved in the translocation using different techniques. FISH showed that the 3'UTR and the last exons of the CHM were on the der(X) chromosome, and the 5'UTR and first exons of this gene were on the der(4) chromosome. Expression level analysis revealed that the breakpoint in the der(X) was located between exons 8 and 9 of the CHM gene because the expression level decreased from this point onwards. Based on this result the expression level analysis proved to be a valid method to pinpoint the location of breakpoints when the gene being expressed in peripheral blood is disrupted. Our results confirmed that the CHM gene was indeed disrupted in the X chromosome involved in the translocation. Besides, the nonrandom inactivation of the normal X chromosome observed using a methylation-specific polymerase chain reaction (M-PCR) technique explained the CHM in the female patient.