[Current perspectives on genome-based diagnostic tests in Pediatrics]. / Perspectivas actuales sobre el diagnóstico genómico en pediatría.

Etiological diagnosis is essential in the clinical management of individual patients. Some children with complex medical conditions are subjected to numerous testing, known as "diagnostic odyssey", which often gives no conclusive results. In recent years, a revolution in genomic medicine is underway with the use of technologies that promise to increase the ability to make a diagnosis and reduce the time involved. The main advantages and limitations of genomic diagnosis, as opposed to usual methodologies are reviewed with an emphasis on Pediatrics.

Diagnostic yield of genetic testing in adults with sensorineural hearing loss.

INTRODUCTION: The contribution of genetic causes to sensorineural hearing loss (SNHL) in adults is less clear than in children, and genetic diagnosis is still not standardized in adults. In this study we present the genetic results obtained in a cohort of adult patients with SNHL. MATERIALS AND METHODS: We included 63 adults with SNHL that received genetic testing between 2019 and 2022. Whole exome sequencing was performed and variants in genes related to hearing loss (virtual panel with 244 genes) were prioritised and analysed. RESULTS: 24% (15/63) of patients were genetically diagnosed: 87% (13/15) of patients had non-syndromic hearing loss and 13% (2/15) had syndromic hearing loss. We identified pathogenic and likely pathogenic variants in 11 different genes. CONCLUSIONS: Our results show that a significant proportion of adults with SNHL have a genetic origin, and that implementation of genetic testing improves diagnostic accuracy and allows personalized management of these patients.

The KDM6B mutation: Phenotype and clinical characteristics-Report of a case.

INTRODUCTION: Alterations in the genes of lysine methylation as Lysine-specific demethylase 6B (KDM6B) have been associated with multiple neurodevelopmental disorders. Until now, there are few cases in the literature attributed to KDM6B mutations. This gap may be due to the fact that the exome sequencing technique is still being implemented in routine clinical practice. MATERIAL AND METHODS: A case is presented with its clinical and phenotypic characteristics. The sequence exome analysis was done with the Nimblegen SeqCap EZ MedExome capture kit+mtDNA 47Mb. The psychopathological approach from mental health was carried out through individual and family interviews, the Conner's questionnaires, ADHD rating scale, as well as the psychometry. RESULTS: A frameshift variant in the KDM6B gene related to neurodevelopmental disorders with facial and body dysmorphia was obtained. The case was oriented as a neurodevelopmental disorder secondary to a genetic alteration and a comorbid Attention Deficit Hyperactivity Disorder (ADHD). CONCLUSIONS: The clinical peculiarities shared by patients identified with the KDM6B mutation, raises the need to recognize it as a particular entity. The possibility of applying the exome sequencing technique to patients with syndromic phenotype and developmental impairment may clarify its etiopathogenesis. It is highly probable that the complexity of these cases requires an approach by a multidisciplinary team that includes genetics, neurology and psychiatry, among other specialties. The coordinated approach is essential to have a comprehensive vision of the case.

Diagnostic yield of clinical exome sequencing in congenital hypogonadotropic hypogonadism considering the degree of olfactory impairment.

INTRODUCTION: Congenital hypogonadotropic hypogonadism (CHH) can present alone or in association with anosmia or other congenital malformations. More than 30 genes have been identified as being involved in the pathogenesis of CHH with different patterns of inheritance, and the increasing availability of next generation sequencing (NGS) has increased the diagnostic yield. METHODS: We analysed the diagnostic yield of NGS in patients with CHH using the clinical exome filtered with virtual panels. We also assessed whether designing panels based on the presence/absence of microsmia increased the diagnostic yield. RESULTS: The use of a 34-gene virtual panel confirmed the diagnosis of CHH in 5 out of 9 patients (55%) patients. In 2 out of 9 (22%), the findings were inconclusive. Applying the presence/absence of microsmia criterion to choose genes for analysis did not improve the diagnostic yield. CONCLUSIONS: The approach to the genetic study of patients with CHH varies depending on the resources of each healthcare facility, so the sensitivity of testing may vary substantially depending on whether panels, clinical exome sequencing or whole exome sequencing (WES) are used. The analysis of all genes related to CHH regardless of the presence/absence of microsmia seems to be the best approach.

Variant rs4149584 (R92Q) of the TNFRSF1A gene in patients with familial multiple sclerosis.

INTRODUCTION: Genomic studies have identified numerous genetic variants associated with susceptibility to multiple sclerosis (MS); however, each one explains only a small percentage of the risk of developing the disease. These variants are located in genes involved in specific pathways, which supports the hypothesis that the risk of developing MS may be linked to alterations in these pathways, rather than in specific genes. We analyzed the role of the TNFRSF1A gene, which encodes one of the TNF-α receptors involved in a signaling pathway previously linked to autoimmune disease. METHODS: We included 138 individuals from 23 families including at least 2 members with MS, and analyzed the presence of exonic variants of TNFRSF1A through whole-exome sequencing. We also conducted a functional study to analyze the pathogenic mechanism of variant rs4149584 (-g.6442643C > G, NM_001065.4:c.362 G > A, R92Q) by plasmid transfection into human oligodendroglioma (HOG) cells, which behave like oligodendrocyte lineage cells; protein labeling was used to locate the protein within cells. We also analyzed the ability of transfected HOG cells to proliferate and differentiate into oligodendrocytes. RESULTS: Variant rs4149584 was found in 2 patients with MS (3.85%), one patient with another autoimmune disease (7.6%), and in 5 unaffected individuals (7.46%). The 2 patients with MS and variant rs4149584 were homozygous carriers and belonged to the same family, whereas the remaining individuals presented the variant in heterozygosis. The study of HOG cells transfected with the mutation showed that the protein does not reach the cell membrane, but rather accumulates in the cytoplasm, particularly in the endoplasmic reticulum and near the nucleus; this suggests that, in the cells presenting the mutation, TNFRSF1 does not act as a transmembrane protein, which may alter its signaling pathway. The study of cell proliferation and differentiation found that transfected cells continue to be able to differentiate into oligodendrocytes and are probably still capable of producing myelin, although they present a lower rate of proliferation than wild-type cells. CONCLUSIONS: Variant rs4149584 is associated with risk of developing MS. We analyzed its functional role in oligodendrocyte lineage cells and found an association with MS in homozygous carriers. However, the associated molecular alterations do not influence the differentiation into oligodendrocytes; we were therefore unable to confirm whether this variant alone is pathogenic in MS, at least in heterozygosis.

Exonic variants of the P2RX7 gene in familial multiple sclerosis.

INTRODUCTION: Several studies have analysed the presence of P2RX7 variants in patients with MS, reporting diverging results. METHODS: Our study analyses P2RX7 variants detected through whole-exome sequencing (WES). RESULTS: We analysed P2RX7, P2RX4, and CAMKK2 gene variants detected by whole-exome sequencing in all living members (n = 127) of 21 families including at least 2 individuals with multiple sclerosis. P2RX7 gene polymorphisms previously associated with autoimmune disease. Although no differences were observed between individuals with and without multiple sclerosis, we found greater polymorphism of gain-of-function variants of P2RX7 in families with individuals with multiple sclerosis than in the general population. Copresence of gain-of-function and loss-of-function variants was not observed to reduce the risk of presenting the disease. Three families displayed heterozygous gain-of-function SNPs in patients with multiple sclerosis but not in healthy individuals. We were unable to determine the impact of copresence of P2RX4 and CAMKK2 variants with P2RX7 variants, or the potential effect of the different haplotypes described in the gene. No clinical correlations with other autoimmune diseases were observed in our cohort. CONCLUSIONS: Our results support the hypothesis that the disease is polygenic and point to a previously unknown mechanism of genetic predisposition to familial forms of multiple sclerosis. P2RX7 gene activity can be modified, which suggests the possibility of preventive pharmacological treatments for families including patients with familial multiple sclerosis.

[Diagnostic yield of clinical exome sequencing in congenital hypogonadotropic hypogonadism considering the degree of olfactory impairment]. / Análisis del rendimiento de la secuenciación del exoma clínico en hipogonadismo hipogonadotropo congénito teniendo en cuenta el grado de alteración del olfato.

INTRODUCTION: Congenital hypogonadotropic hypogonadism (CHH) can present alone or in association with anosmia or other congenital malformations. More than 30 genes have been identified as being involved in the pathogenesis of CHH with different patterns of inheritance, and the increasing availability of next generation sequencing (NGS) has increased the diagnostic yield. METHODS: We analysed the diagnostic yield of NGS in patients with CHH using the clinical exome filtered with virtual panels. We also assessed whether designing panels based on the presence/absence of microsmia increased the diagnostic yield. RESULTS: The use of a 34-gene virtual panel confirmed the diagnosis of CHH in 5 out of 9 patients (55%). In 2 out of 9 (22%), the findings were inconclusive. Applying the presence/absence of microsmia criterion to choose genes for analysis did not improve the diagnostic yield. CONCLUSIONS: The approach to the genetic study of patients with CHH varies depending on the resources of each healthcare facility, so the sensitivity of testing may vary substantially depending on whether panels, clinical exome sequencing or whole exome sequencing (WES) are used. The analysis of every genes related to CHH regardless of the presence/absence of microsmia seems to be the best approach.

The KDM6B mutation: Phenotype and clinical characteristics-Report of a case.

INTRODUCTION: Alterations in the genes of lysine methylation as Lysine-specific demethylase 6B (KDM6B) have been associated with multiple neurodevelopmental disorders. Until now, there are few cases in the literature attributed to KDM6B mutations. This gap may be due to the fact that the exome sequencing technique is still being implemented in routine clinical practice. MATERIAL AND METHODS: A case is presented with its clinical and phenotypic characteristics. The sequence exome analysis was done with the Nimblegen SeqCap EZ MedExome capture kit+mtDNA 47Mb. The psychopathological approach from mental health was carried out through individual and family interviews, the Conner's questionnaires, ADHD rating scale, as well as the psychometry. RESULTS: A frameshift variant in the KDM6B gene related to neurodevelopmental disorders with facial and body dysmorphia was obtained. The case was oriented as a neurodevelopmental disorder secondary to a genetic alteration and a comorbid Attention Deficit Hyperactivity Disorder (ADHD). CONCLUSIONS: The clinical peculiarities shared by patients identified with the KDM6B mutation, raises the need to recognize it as a particular entity. The possibility of applying the exome sequencing technique to patients with syndromic phenotype and developmental impairment may clarify its etiopathogenesis. It is highly probable that the complexity of these cases requires an approach by a multidisciplinary team that includes genetics, neurology and psychiatry, among other specialties. The coordinated approach is essential to have a comprehensive vision of the case.

Importancia de la genómica en el diagnóstico de nuevas variantes asociadas a trastornos del tejido conectivo con solapamiento fenotípico

La Aracnodactilia Contractural Congénita  (ACC) es una enfermedad del tejido conectivo de herencia autosómica dominante, causada por variantes en el gen FBN2 que codifica la fibrilina-2. Tiene características específicas como contracturas congénitas, oreja con hélice superior arrugada, camptodactilia, pectus carinatum y complicaciones como escoliosis y la cifoescoliosis. Publicamos el caso de una paciente femenina de 19 años con historia de delgadez, velocidad de crecimiento acelerada, talla alta, pérdida de peso, contracturas articulares, hipotonía congénita, pubertad precoz, hábito marfanoide, pectus carinatum y leve aracnodactilia. Se sospecha de enfermedad del colágeno y se solicita secuenciación del exoma completo mediante NGS  (del inglés Next Generation Sequencing) + CNVs  (del inglés Copy Number Variations) genes relacionados con colagenopatías; se identificó una variante en el gen FBN2  (NM_001999.4): c.4394G>A; p.Cys1465Tyr; estado heterocigoto de significancia clínica probablemente patogénica. La ACC es fenotípicamente similar al síndrome de Marfán y se caracteriza por aracnodactilia, dolicostenomelia, escoliosis, contracturas congénitas múltiples y anomalías de los oídos externos. A diferencia del síndrome de Marfán; no tiene compromiso ocular ni afecta la raíz aórtica. Cuenta con variabilidad fenotípica que le dan la heterogeneidad que pueden interferir y retrasar el proceso diagnóstico y terapéutico específico al solaparse con otras condiciones médicas. Los avances en la medicina y la genómica con la utilización de nuevos métodos diagnósticos han permitido que cada día nos acerquemos más a la medicina 6P  (precisión, predicción, prevención, personalizada, participativa con enfoque poblacional) que impacta en el diagnóstico, tratamiento específico, seguimiento, pronóstico y adecuado asesoramiento genético de las enfermedades. (provisto por Infomedic International)

Contractural arachnodactyly congenita  (CCA) is an autosomal dominantly inherited connective tissue disease caused by variants in the FBN2 gene encoding fibrillin-2. It has specific features such as congenital contractures, wrinkled upper helix ear, camptodactyly, pectus carinatum and complications such as scoliosis and kyphoscoliosis. We publish the case of a 19-year-old female patient with a history of thinness, accelerated growth velocity, tall stature, weight loss, joint contractures, congenital hypotonia, precocious puberty, marfanoid habitus, pectus carinatum and mild arachnodactyly. Collagen disease was suspected and whole exome sequencing by NGS  (Next Generation Sequencing) + CNVs  (Copy Number Variations) genes related to collagenopathies was requested; a variant was identified in the FBN2 gene  (NM_001999.4): c.4394G>A; p.Cys1465Tyr; heterozygous state of probably pathogenic clinical significance. CCA is phenotypically similar to Marfan syndrome and is characterized by arachnodactyly, dolichostenomelia, scoliosis, multiple congenital contractures, and external ear anomalies. Unlike Marfan syndrome, it has no ocular involvement and does not affect the aortic root. It has phenotypic variability that gives it heterogeneity that can interfere and delay the specific diagnostic and therapeutic process by overlapping with other medical conditions. Advances in medicine and genomics with the use of new diagnostic methods have allowed us to get closer to 6P medicine  (precision, prediction, prevention, personalized, participatory with a population approach) that impacts on the diagnosis, specific treatment, follow-up, prognosis and adequate genetic counseling of diseases. (provided by Infomedic International)

Variantes genómicas asociadas a errores congénitos en el metabolismo de los carbohidratos en el suroccidente colombiano

Introducción: Los Errores Innatos del Metabolismo (EIM) de carbohidratos son el resultado de la interrupción de las vías catabólicas o anabólicas de diferentes carbohidratos, siendo la fructosa, la galactosa y el glucógeno los más comunes y pertenecen a un grupo heterogéneo de trastornos que pueden ser hereditarios o pueden ocurrir como resultado de variantes genéticas espontáneas. En los EIM, están las vías de los carbohidratos alteradas, tanto las vías catabólicas como las anabólicas, incluyendo el metabolismo de la fructosa, galactosa y glucógeno, dando lugar a un grupo heterogéneo de trastornos. Sin embargo, los datos sobre estas patologías en Colombia son escasos. Nuestro estudio tuvo como objetivo identificar variantes genómicas asociadas a EIM por carbohidratos en población del suroccidente colombiano carente de diagnóstico clínico. Resultados: Realizamos un estudio transversal, secuenciando 320 exomas y clasificando las variantes de acuerdo a guías estándar. Identificamos 286 variantes, incluyendo 206 nuevas y 73 variantes benignas o probablemente benignas. En particular, seis variantes en genes como GALT, GAK1, ALDOB, GAA y SLC2A1 tenían un significado incierto, y una variante patogénica en el gen GALT se asoció con la galactosemia clásica. Curiosamente, el 18% eran intrónicas, el 5% con sentido erroneo, el 10% sinónimas y el 67% variantes no notificadas. Conclusiones: Estos hallazgos ponen de relieve la necesidad de programas de diagnóstico precoz para aplicar tratamientos específicos, incluido el manejo transdisciplinar para minimizar la morbilidad y la mortalidad. El consejo genético y la educación sobre el riesgo son cruciales, facilitando enfoques de medicina anticipatoria y preventiva, avanzando así en la medicina de precisión.   (provisto por Infomedic International)

Introduction: Carbohydrate Inborn Errors of Metabolism (IEMs) result from disruption of the catabolic or anabolic pathways of different carbohydrates, fructose, galactose and glycogen being the most common and belong to a heterogeneous group of disorders that may be inherited or may occur as a result of spontaneous genetic variants. In IEM, there are altered carbohydrate pathways, both catabolic and anabolic pathways, including fructose, galactose and glycogen metabolism, resulting in a heterogeneous group of disorders. However, data on these pathologies in Colombia are scarce. The aim of our study was to identify genomic variants associated with carbohydrate IEM in the southwestern Colombian population lacking clinical diagnosis. Results: We performed a cross-sectional study, sequencing 320 exomes and classifying variants according to standard guidelines. We identified 286 variants, including 206 new variants and 73 benign or probably benign variants. Notably, six variants in genes such as GALT, GAK1, ALDOB, GAA and SLC2A1 were of uncertain significance, and one pathogenic variant in the GALT gene was associated with classic galactosemia. Interestingly, 18% were intronic, 5% missense, 10% synonymous, and 67% unreported variants. Conclusions: These findings highlight the need for early diagnostic programs to implement targeted treatments, including transdisciplinary management to minimize morbidity and mortality. Genetic counseling and risk education are crucial, facilitating anticipatory and preventive medicine approaches, thus advancing precision medicine. (provided by Infomedic International)

Actuales retos diagnósticos genómicos en los Síndromes Hemofagocíticos en pediatría: reporte de caso

Introducción: La linfohistiocitosis hemofagocítica familiar (FHL) es una enfermedad del sistema autoinmune que se presenta con un síndrome inflamatorio excesivo causado por linfocitos T activados e histiocitosis. Cursa con herencia autosómica recesiva ligada al cromosoma X. Aproximadamente el 90% de los niños diagnosticados son menores de 2 años y la incidencia es de aproximadamente 0.12 por 100.000. Se puede dividir en cinco subtipos según la variante genética causante. Las variantes patogénicas más involucradas son en los genes de la perforina 1 (PRF1) y homólogo D de la proteína UNC-13 (UNC13D). Caso clínico: Se presenta el caso de un preadolescente de 11 años, con antecedente de infecciones recurrentes, quien cursa con síndrome convulsivo asociado a fiebre, peso y talla bajas para la edad, hepatomegalia y discapacidad cognitiva. En el abordaje inicial se descartan enfermedades infecciosas, inmunológicas, hematológicas, metabólicas y oncológicas. El exoma clínico para inmunodeficiencias primarias muestra una variante patogénica p.A91V homocigota en el gen de la PRF1 de herencia autosómica recesiva, resultado relacionado con linfohistiocitosis hemofagocítica familiar tipo 2 (FHL2). Discusión y conclusión: El cambio conformacional del PRF1 alterado reduce la actividad citotóxica de la proteína y provoca la enfermedad. Los pacientes portadores de defectos en el gen PRF1 son vulnerables a infecciones, enfermedades autoinmunes y tumores malignos. Con un diagnóstico definido y preciso es posible orientar las acciones en salud, pautas de seguimiento, evaluación de riesgo de heredabilidad a través de un caso índice para así encontrar otros posibles portadores, realizar un asesoramiento genético completo, implementar e iniciar tratamientos dirigidos que aminoren la morbilidad y mortalidad asociada a esta patología. Actualmente se cuenta con varios estudios en diferentes fases de investigación sobre moléculas que pueden intervenir en la historia natural de la enfermedad. (provisto por Infomedic International)

Introduction: Familial hemophagocytic lymphohistiocytosis (FHL) is a disease of the autoimmune system that presents with an excessive inflammatory syndrome caused by activated T lymphocytes and histiocytosis. It occurs with autosomal recessive inheritance linked to the chromosome X. Approximately 90% of diagnosed children are under 2 years of age and the incidence is approximately 0.12 per 100,000. It can be divided into five subtypes depending on the causative genetic variant. The most involved pathogenic variants are in the perforin 1 (PRF1) and UNC-13 protein homolog D (UNC13D) genes. Clinical case: The case of an 11-year-old preadolescent is presented, with a history of recurrent infections, who presents with convulsive syndrome associated with fever, low weight and height for age, hepatomegaly and cognitive disability. In the initial approach, infectious, immunological, hematological, metabolic and oncological diseases are ruled out. The clinical exome for primary immunodeficiencies shows a homozygous pathogenic variant p.A91V in the PRF1 gene of autosomal recessive inheritance, a result related to familial hemophagocytic lymphohistiocytosis type 2 (FHL2). Discussion and conclusion: The altered PRF1 conformational change reduces the cytotoxic activity of the protein and causes disease. Patients carrying defects in the PRF1 gene are vulnerable to infections, autoimmune diseases and malignant tumors. With a defined and precise diagnosis, it is possible to guide health actions, follow-up guidelines, evaluation of heritability risk through an index case in order to find other possible carriers, carry out complete genetic counseling, implement and initiate targeted treatments that reduce the morbidity and mortality associated with this pathology. Currently, there are several studies in different phases of research on molecules that may intervene in the natural history of the disease. (provided by Infomedic International)

Novel Pathogenic Mutation Mapping of ASPM Gene in Consanguineous Pakistani Families with Primary Microcephaly / Novo mapeamento de mutações patogênicas do gene ASPM em famílias consanguíneas com microcefalia primária do Paquistão

Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental disorder characterized by a congenitally reduced head circumference (-3 to -5 SD) and non-progressive intellectual disability. The objective of the study was to evaluate pathogenic mutations in the ASPM gene to understand etiology and molecular mechanism of primary microcephaly. Blood samples were collected from various families across different remote areas of Pakistan from February 2017 to May 2019 who were identified to be affected with primary microcephaly. DNA extraction was performed using the salting-out method; the quality and quantity of DNA were evaluated using spectrophotometry and 1% agarose gel electrophoresis, respectively in University of the Punjab. Mutation analysis was performed by whole exome sequencing from the Cologne Center for Genomics, University of Cologne. Sanger sequencing was done in University of the Punjab to confirm the pathogenic nature of mutation. A novel 4-bp deletion mutation c.3877_3880delGAGA was detected in exon 17 of the ASPM gene in two primary microcephaly affected families (A and B), which resulted in a frame shift mutation in the gene followed by truncated protein synthesis (p.Glu1293Lysfs*10), as well as the loss of the calmodulin-binding IQ domain and the Armadillo-like domain in the ASPM protein. Using the in-silico tools Mutation Taster, PROVEAN, and PolyPhen, the pathogenic effect of this novel mutation was tested; it was predicted to be "disease causing", with high pathogenicity scores. One previously reported mutation in exon 24 (c.9730C>T) of the ASPM gene resulting in protein truncation (p.Arg3244*) was also observed in family C. Mutations in the ASPM gene are the most common cause of MCPH in most cases. Therefore, enrolling additional affected families from remote areas of Pakistan would help in identifying or mapping novel mutations in the ASPM gene of primary microcephaly.

Microcefalia primária autossômica recessiva (MCPH) é um distúrbio do neurodesenvolvimento caracterizado por uma redução congênita do perímetro cefálico (-3 a -5 DP) e deficiência intelectual não progressiva. O objetivo do estudo foi avaliar mutações patogênicas no gene ASPM a fim de compreender a etiologia e o mecanismo molecular da microcefalia primária. Amostras de sangue foram coletadas de várias famílias em diferentes áreas remotas do Paquistão de fevereiro de 2017 a maio de 2019, que foram identificadas como afetadas com microcefalia primária. A extração do DNA foi realizada pelo método salting-out; a qualidade e a quantidade de DNA foram avaliadas por espectrofotometria e eletroforese em gel de agarose a 1%, respectivamente, na Universidade de Punjab. A análise de mutação foi realizada por sequenciamento completo do exoma do Cologne Center for Genomics, University of Cologne. O sequenciamento de Sanger foi feito na Universidade do Punjab para confirmar a natureza patogênica da mutação. Uma nova mutação de deleção de 4 bp c.3877_3880delGAGA foi detectada no exon 17 do gene ASPM em duas famílias afetadas por microcefalia primária (A e B), que resultou em uma mutação de frame shift no gene seguida por síntese de proteína truncada (pGlu1293Lysfs * 10), bem como a perda do domínio IQ de ligação à calmodulina e o domínio do tipo Armadillo na proteína ASPM. Usando as ferramentas in-silico Mutation Taster, PROVEAN e PolyPhen, o efeito patogênico dessa nova mutação foi testado; foi previsto ser "causador de doenças", com altos escores de patogenicidade. Uma mutação relatada anteriormente no exon 24 (c.9730C > T) do gene ASPM, resultando em truncamento de proteína (p.Arg3244 *) também foi observada na família C. Mutações no gene ASPM são a causa mais comum de MCPH na maioria dos casos . Portanto, a inscrição de famílias afetadas adicionais de áreas remotas do Paquistão ajudaria a identificar ou mapear novas mutações no gene ASPM da microcefalia primária.

Novel Pathogenic Mutation Mapping of ASPM Gene in Consanguineous Pakistani Families with Primary Microcephaly

Abstract Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental disorder characterized by a congenitally reduced head circumference (-3 to -5 SD) and non-progressive intellectual disability. The objective of the study was to evaluate pathogenic mutations in the ASPM gene to understand etiology and molecular mechanism of primary microcephaly. Blood samples were collected from various families across different remote areas of Pakistan from February 2017 to May 2019 who were identified to be affected with primary microcephaly. DNA extraction was performed using the salting-out method; the quality and quantity of DNA were evaluated using spectrophotometry and 1% agarose gel electrophoresis, respectively in University of the Punjab. Mutation analysis was performed by whole exome sequencing from the Cologne Center for Genomics, University of Cologne. Sanger sequencing was done in University of the Punjab to confirm the pathogenic nature of mutation. A novel 4-bp deletion mutation c.3877_3880delGAGA was detected in exon 17 of the ASPM gene in two primary microcephaly affected families (A and B), which resulted in a frame shift mutation in the gene followed by truncated protein synthesis (p.Glu1293Lysfs*10), as well as the loss of the calmodulin-binding IQ domain and the Armadillo-like domain in the ASPM protein. Using the in-silico tools Mutation Taster, PROVEAN, and PolyPhen, the pathogenic effect of this novel mutation was tested; it was predicted to be disease causing, with high pathogenicity scores. One previously reported mutation in exon 24 (c.9730C>T) of the ASPM gene resulting in protein truncation (p.Arg3244*) was also observed in family C. Mutations in the ASPM gene are the most common cause of MCPH in most cases. Therefore, enrolling additional affected families from remote areas of Pakistan would help in identifying or mapping novel mutations in the ASPM gene of primary microcephaly.

Resumo Microcefalia primária autossômica recessiva (MCPH) é um distúrbio do neurodesenvolvimento caracterizado por uma redução congênita do perímetro cefálico (-3 a -5 DP) e deficiência intelectual não progressiva. O objetivo do estudo foi avaliar mutações patogênicas no gene ASPM a fim de compreender a etiologia e o mecanismo molecular da microcefalia primária. Amostras de sangue foram coletadas de várias famílias em diferentes áreas remotas do Paquistão de fevereiro de 2017 a maio de 2019, que foram identificadas como afetadas com microcefalia primária. A extração do DNA foi realizada pelo método salting-out; a qualidade e a quantidade de DNA foram avaliadas por espectrofotometria e eletroforese em gel de agarose a 1%, respectivamente, na Universidade de Punjab. A análise de mutação foi realizada por sequenciamento completo do exoma do Cologne Center for Genomics, University of Cologne. O sequenciamento de Sanger foi feito na Universidade do Punjab para confirmar a natureza patogênica da mutação. Uma nova mutação de deleção de 4 bp c.3877_3880delGAGA foi detectada no exon 17 do gene ASPM em duas famílias afetadas por microcefalia primária (A e B), que resultou em uma mutação de frame shift no gene seguida por síntese de proteína truncada (pGlu1293Lysfs * 10), bem como a perda do domínio IQ de ligação à calmodulina e o domínio do tipo Armadillo na proteína ASPM. Usando as ferramentas in-silico Mutation Taster, PROVEAN e PolyPhen, o efeito patogênico dessa nova mutação foi testado; foi previsto ser causador de doenças, com altos escores de patogenicidade. Uma mutação relatada anteriormente no exon 24 (c.9730C > T) do gene ASPM, resultando em truncamento de proteína (p.Arg3244 *) também foi observada na família C. Mutações no gene ASPM são a causa mais comum de MCPH na maioria dos casos . Portanto, a inscrição de famílias afetadas adicionais de áreas remotas do Paquistão ajudaria a identificar ou mapear novas mutações no gene ASPM da microcefalia primária.

Diagnóstico prenatal, síndrome Freeman-Sheldon mediante ultrasonido y estudio genético. Reporte de caso / Prenatal diagnosis of Freeman-Sheldon syndrome using ultrasound and genetic testing. Case report

Objetivos: Describir un caso de diagnóstico prenatal de síndrome de Freeman-Sheldon mediante hallazgos ecográficos y secuenciación completa del exoma fetal. Materiales y métodos: Mujer de 33 años, con antecedentes de hipotiroidismo en tratamiento, a quien en semana 19 se realizó ecografía de detalle anatómico, en la cual se observaron deformidades en el feto en más de dos áreas corporales (extremidades superiores e inferiores), sugiriendo el diagnóstico de artrogriposis. Posteriormente, se brindó asesoría genética y se realizó amniocentesis en semana 20 de gestación, con análisis de la hibridación in situ por fluorescencia, seguido de secuenciación completa del exoma fetal. Este último examen permitió identificar una variante patogénica heterocigota en el gen MYH3, la cual se asocia con la artrogriposis distal tipo 2A. Conclusiones: La realización de la secuenciación completa de exoma fetal es un factor clave para identificar la mutación del gen MYH3, y confirma que las deformidades evidenciadas por ultrasonido estaban relacionadas con la artrogriposis distal tipo 2A. Es importante hacer la secuenciación de exoma fetal en fetos que muestren hallazgos de malformaciones articulares en el ultrasonido prenatal.

Objectives: To describe a case of prenatal diagnosis of Freeman-Sheldon syndrome based on ultrasound findings and complete fetal exome sequencing. Materials and methods: A 33-year-old woman currently on treatment for hypothyroidism in whom a 19-week detailed anatomical ultrasound scan showed fetal deformities in more than two body areas (upper and lower limbs), suggesting a diagnosis of arthrogryposis. Genetic counseling was provided and amniocentesis was performed at 20 weeks for fluorescence in situ hybridization (FISH) analysis and complete fetal exome sequencing, with the latter allowing the identification of a heterozygous pathogenic variant of the MYH3 gene which is associated with type 2A distal arthrogryposis. Conclusions: Complete fetal exome sequencing was a key factor in identifying the MYH3 gene mutation and confirmed that the deformities seen on ultrasound were associated with type 2A distal arthrogryposis. It is important to perform complete fetal exome sequencing in cases of joint malformations seen on prenatal ultrasound.

Novel Pathogenic Mutation Mapping of ASPM Gene in Consanguineous Pakistani Families with Primary Microcephaly / Novo mapeamento de mutações patogênicas do gene ASPM em famílias consanguíneas com microcefalia primária do Paquistão

Abstract Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental disorder characterized by a congenitally reduced head circumference (-3 to -5 SD) and non-progressive intellectual disability. The objective of the study was to evaluate pathogenic mutations in the ASPM gene to understand etiology and molecular mechanism of primary microcephaly. Blood samples were collected from various families across different remote areas of Pakistan from February 2017 to May 2019 who were identified to be affected with primary microcephaly. DNA extraction was performed using the salting-out method; the quality and quantity of DNA were evaluated using spectrophotometry and 1% agarose gel electrophoresis, respectively in University of the Punjab. Mutation analysis was performed by whole exome sequencing from the Cologne Center for Genomics, University of Cologne. Sanger sequencing was done in University of the Punjab to confirm the pathogenic nature of mutation. A novel 4-bp deletion mutation c.3877_3880delGAGA was detected in exon 17 of the ASPM gene in two primary microcephaly affected families (A and B), which resulted in a frame shift mutation in the gene followed by truncated protein synthesis (p.Glu1293Lysfs*10), as well as the loss of the calmodulin-binding IQ domain and the Armadillo-like domain in the ASPM protein. Using the in-silico tools Mutation Taster, PROVEAN, and PolyPhen, the pathogenic effect of this novel mutation was tested; it was predicted to be "disease causing," with high pathogenicity scores. One previously reported mutation in exon 24 (c.9730C>T) of the ASPM gene resulting in protein truncation (p.Arg3244*) was also observed in family C. Mutations in the ASPM gene are the most common cause of MCPH in most cases. Therefore, enrolling additional affected families from remote areas of Pakistan would help in identifying or mapping novel mutations in the ASPM gene of primary microcephaly.

Resumo Microcefalia primária autossômica recessiva (MCPH) é um distúrbio do neurodesenvolvimento caracterizado por uma redução congênita do perímetro cefálico (-3 a -5 DP) e deficiência intelectual não progressiva. O objetivo do estudo foi avaliar mutações patogênicas no gene ASPM a fim de compreender a etiologia e o mecanismo molecular da microcefalia primária. Amostras de sangue foram coletadas de várias famílias em diferentes áreas remotas do Paquistão de fevereiro de 2017 a maio de 2019, que foram identificadas como afetadas com microcefalia primária. A extração do DNA foi realizada pelo método salting-out; a qualidade e a quantidade de DNA foram avaliadas por espectrofotometria e eletroforese em gel de agarose a 1%, respectivamente, na Universidade de Punjab. A análise de mutação foi realizada por sequenciamento completo do exoma do Cologne Center for Genomics, University of Cologne. O sequenciamento de Sanger foi feito na Universidade do Punjab para confirmar a natureza patogênica da mutação. Uma nova mutação de deleção de 4 bp c.3877_3880delGAGA foi detectada no exon 17 do gene ASPM em duas famílias afetadas por microcefalia primária (A e B), que resultou em uma mutação de frame shift no gene seguida por síntese de proteína truncada (pGlu1293Lysfs * 10), bem como a perda do domínio IQ de ligação à calmodulina e o domínio do tipo Armadillo na proteína ASPM. Usando as ferramentas in-silico Mutation Taster, PROVEAN e PolyPhen, o efeito patogênico dessa nova mutação foi testado; foi previsto ser "causador de doenças", com altos escores de patogenicidade. Uma mutação relatada anteriormente no exon 24 (c.9730C > T) do gene ASPM, resultando em truncamento de proteína (p.Arg3244 *) também foi observada na família C. Mutações no gene ASPM são a causa mais comum de MCPH na maioria dos casos . Portanto, a inscrição de famílias afetadas adicionais de áreas remotas do Paquistão ajudaria a identificar ou mapear novas mutações no gene ASPM da microcefalia primária.

Introducción al filtrado, análisis y curación de variantes genéticas en pacientes con Discapacidad Intelectual / Introduction to filtering, analysis and curation of genetic variants in patients with Intellectual Disability

Resumen Actualmente la secuenciación del exoma completo (WES; Whole-exome sequencing) mediante la técnica NGS (Next-generation sequencing) es uno de los estudios genéticos más solicitados dentro del abordaje de pacientes con Discapacidad Intelectual con o sin otras anomalías. Al igual que con otros proce dimientos y estudios clínicos, es conveniente que los médicos prescriptores tengan una comprensión clara de los alcances y limitaciones del uso de WES, del proceso de análisis de las variantes genéticas identificadas, así como de aspectos a evaluar acerca de la calidad y estructura de los informes de los estudios de NGS, con el objetivo de que puedan interpretar mejor los resultados de un estudio y plantear de la mejor manera la correlación de los mismos con la clínica observada.

Abstract Currently, Whole exome sequencing (WES) using NGS (Next-generation sequencing) technology is one of the most requested genetic studies within the approach of patients with intellectual disability with or without other anomalies. As with other procedures and clinical studies, it is convenient for prescribing physicians to have a clear understanding of the scope and limitations of the use of WES, the analysis process of the genetic variants identified, as well as aspects to be evaluated regarding quality and structure of the reports of the NGS studies, with the aim that they can better interpret the results of a study, evaluate its quality, and propose in the best way the correlation of the same with the observed phenotype.

Intervention of next-generation sequencing in diagnosis of Alzheimer's disease: challenges and future prospects / Intervenção do sequenciamento de nova geração no diagnóstico da doença de Alzheimer: desafios e perspectivas futuras

ABSTRACT Clinical diagnosis of several neurodegenerative disorders based on clinical phenotype is challenging due to its heterogeneous nature and overlapping disease manifestations. Therefore, the identification of underlying genetic mechanisms is of paramount importance for better diagnosis and therapeutic regimens. With the emergence of next-generation sequencing, it becomes easier to identify all gene variants in the genome simultaneously, with a system-wide and unbiased approach. Presently various bioinformatics databases are maintained on discovered gene variants and phenotypic indications are available online. Since individuals are unique in their genome, evaluation based on their genetic makeup helps evolve the diagnosis, counselling, and treatment process at the personal level. This article aims to briefly summarize the utilization of next-generation sequencing in deciphering the genetic causes of Alzheimer's disease and address the limitations of whole genome and exome sequencing.

RESUMO O diagnóstico clínico de vários distúrbios neurodegenerativos com base no fenótipo clínico é difícil devido à sua natureza heterogênea e às manifestações da doença que se sobrepõem. Portanto, a identificação dos mecanismos genéticos subjacentes é de suma importância para um melhor diagnóstico e regimes terapêuticos. Com o surgimento do sequenciamento de próxima geração, o diagnóstico se tornou mais acessível com uma abordagem imparcial em todo o sistema para identificar simultaneamente todas as variantes de genes no genoma. Atualmente, vários bancos de dados de bioinformática sobre variantes genéticas descobertas e indicações fenotípicas estão disponíveis online. Uma vez que os indivíduos são únicos em seu genoma, a avaliação com base em sua composição genética ajudou na evolução do processo de diagnóstico, aconselhamento e tratamento em nível pessoal. Este artigo teve como objetivo resumir brevemente a utilização do sequenciamento de próxima geração para decifrar as causas genéticas da doença de Alzheimer (DA) e abordar as limitações do sequenciamento completo do genoma e do exoma.

The KDM6B mutation: Phenotype and clinical characteristics—Report of a case / La mutación KDM6B: fenotipo y características clínicas—Informe de un caso

Introduction: Alterations in the genes of lysine methylation as Lysine-specific demethylase 6B (KDM6B) have been associated with multiple neurodevelopmental disorders. Until now, there are few cases in the literature attributed to KDM6B mutations. This gap may be due to the fact that the exome sequencing technique is still being implemented in routine clinical practice.Material and methods: A case is presented with its clinical and phenotypic characteristics. The sequence exome analysis was done with the Nimblegen SeqCap EZ MedExome capture kit+mtDNA 47Mb. The psychopathological approach from mental health was carried out through individual and family interviews, the Conner's questionnaires, ADHD rating scale, as well as the psychometry.Results: A frameshift variant in the KDM6B gene related to neurodevelopmental disorders with facial and body dysmorphia was obtained. The case was oriented as a neurodevelopmental disorder secondary to a genetic alteration and a comorbid Attention Deficit Hyperactivity Disorder (ADHD).Conclusions: The clinical peculiarities shared by patients identified with the KDM6B mutation, raises the need to recognize it as a particular entity. The possibility of applying the exome sequencing technique to patients with syndromic phenotype and developmental impairment may clarify its etiopathogenesis. It is highly probable that the complexity of these cases requires an approach by a multidisciplinary team that includes genetics, neurology and psychiatry, among other specialties. The coordinated approach is essential to have a comprehensive vision of the case. (AU)

Introducción: Las alteraciones en los genes de metilación de lisina como la desmetilasa 6B de lisina (KDM6B) se han asociado con múltiples trastornos del neurodesarrollo. Hasta ahora, existen pocos casos en la literatura atribuidos a mutaciones del gen KDM6B. Esta brecha puede deberse al hecho de que la técnica de secuenciación del exoma aún está en fase de implementación en la práctica clínica habitual.Material y métodos: Se presenta un caso con características clínicas y fenotípicas. El análisis de secuenciación exómica se realizó con el kit de captura Nimblegen SeqCap EZ MedExome + mtDNA 47Mb. La aproximación psicopatológica desde salud mental se realizó a través de entrevistas individuales, familiares, los cuestionarios Conners, ADHD rating scale, así como la psicometría.Resultados: Se obtuvo una variante de cambio en el gen KDM6B que ha sido relacionado con trastornos del neurodesarrollo con dismorfias faciales y corporales. El caso fue orientado como un trastorno del neurodesarrollo secundario a una alteración genética, un trastorno por déficit de atención e hiperactividad (TDAH).Conclusiones: Las peculiaridades clínicas que comparten los pacientes identificados con la mutación KDM6B, plantea la necesidad de reconocerla como una entidad particular. La posibilidad de aplicar la técnica de secuenciación del exoma a pacientes con fenotipo sindrómico y retraso generalizado en el desarrollo puede aclarar su etiopatogenia. Es muy probable que la complejidad de estos casos requiera el abordaje de un equipo multidisciplinar que incluya genetistas, neurólogos y psiquiatras, entre otras especialidades. El enfoque coordinado es fundamental para obtener una visión integral del caso. (AU)

Análisis del rendimiento de la secuenciación del exoma clínico en hipogonadismo hipogonadotropo congénito teniendo en cuenta el grado de alteración del olfato / Diagnostic yield of clinical exome sequencing in congenital hypogonadotropic hypogonadism considering the degree of olfactory impairment

Introducción: El hipogonadismo hipogonadotropo congénito (HHC) puede presentarse de manera aislada o acompañado de anosmia o de malformaciones congénitas. Más de 30 genes han sido implicados en la patogénesis de HHC; además, se han descrito varios patrones de herencia asociados a esta entidad. La creciente disponibilidad de técnicas de secuenciación masiva (NGS) ha permitido que aumente el rendimiento diagnóstico del estudio de esta patología. Pacientes y métodos: Evaluamos el rendimiento diagnóstico del estudio mediante NGS de pacientes con HHC, usando la secuenciación del exoma clínico filtrado por paneles virtuales. Además, se analizó si el diseño de estos paneles, basándose en la presencia/ausencia de microsmia/anosmia aumentaban este rendimiento diagnóstico. Resultados: Usando un panel virtual compuesto de 34 genes pudimos confirmar el diagnóstico de HHC en cinco de nueve pacientes (55%). En dos de nueve individuos (22%) estudiados se obtuvieron resultados no concluyentes. La ausencia/presencia de microsmia para la elección de genes a estudiar no mejora el rendimiento diagnóstico. Conclusiones: El abordaje del estudio genético de pacientes con HHC puede variar en función de las técnicas disponibles en cada centro, por lo que la sensibilidad del test utilizado variará, dependiendo si se utiliza secuenciación de paneles, exoma clínico o exoma completo. El análisis de todos los genes relacionados con HHC independientemente de la presencia/ausencia de microsmia pareciera el abordaje con mejor rendimiento. (AU)

Introduction: Congenital hypogonadotropic hypogonadism (CHH) can present alone or in association with anosmia or other congenital malformations. More than 30 genes have been identified as being involved in the pathogenesis of CHH with different patterns of inheritance, and the increasing availability of next generation sequencing (NGS) has increased the diagnostic yield. Methods: We analysed the diagnostic yield of NGS in patients with CHH using the clinical exome filtered with virtual panels. We also assessed whether designing panels based on the presence/absence of microsmia increased the diagnostic yield. Results: The use of a 34-gene virtual panel confirmed the diagnosis of CHH in 5 out of 9 patients (55%). In 2 out of 9 (22%), the findings were inconclusive. Applying the presence/absence of microsmia criterion to choose genes for analysis did not improve the diagnostic yield. Conclusions: The approach to the genetic study of patients with CHH varies depending on the resources of each healthcare facility, so the sensitivity of testing may vary substantially depending on whether panels, clinical exome sequencing or whole exome sequencing (WES) are used. The analysis of every genes related to CHH regardless of the presence/absence of microsmia seems to be the best approach. (AU)

Elevated IgA and IL-10 levels in very-early-onset inflammatory bowel disease secondary to IL-10 receptor deficiency / Níveis elevados de IgA e IL-10 na doença inflamatória intestinal de início muito precoce secundária à deficiência do receptor de IL-10

ABSTRACT Objective: To report two patients with very-early-onset inflammatory bowel disease (VEOIBD) secondary to interleukin-10 receptor (IL-10R) mutations, explore immunophenotyping data and plasma cytokine profile on these cases compared to healthy controls, and describe the phenotype of IL-10/IL-10R mutations based on a literature review. Case description: We report on two female infants referred to our tertiary center at the age of ten months, with severe colonic and perianal disease, as well as significant malnutrition, who had shown limited response to usual inflammatory bowel disease (IBD) therapy agents. In the first case, whole-exome sequencing (WES) revealed a homozygous (c.537G>A/p.T179T) mutation in exon 4 of the IL-10RA gene, while in the second patient, compound heterozygosity was identified, also in the IL-10RA gene (chr11:117.859.199 variant A>G/p.Tyr57Cys and chr11: 117.860.335 variant G>T/p.Val123Leu). Both patients underwent hematopoietic cell transplantation (HCT). Immunological work-up of these patients revealed increased IL-10 plasma levels and increased IgA. Comments: Our case reports disclose novel findings on plasma cytokine profile in IL-10R deficiency, and we describe the severe phenotype of IL-10/IL-10R deficiency that should be recognized by physicians.

RESUMO Objetivo: Relatar os casos de duas pacientes com doença inflamatória intestinal de início muito precoce (em inglês VEOIBD) secundária a mutações do receptor de interleucina 10 (IL-10R), explorar dados de imunofenotipagem e perfil de citocinas plasmáticas nesses casos em comparação com indivíduos saudáveis e descrever o fenótipo de mutações IL-10/IL-10R com base em uma revisão da literatura. Descrição do caso: Duas lactentes do sexo feminino foram encaminhadas ao nosso centro terciário, ambas com dez meses no momento do encaminhamento, com doença colônica e perianal grave, bem como desnutrição significativa, tendo uma resposta limitada aos agentes de terapia usuais de doença inflamatória intestinal (DII). No primeiro caso, o sequenciamento completo do exoma revelou mutação homozigótica (c. 537G>A/p.T179T) no exon 4 do gene IL-10RA, enquanto no segundo caso heterozigosidade composta foi identificada também no gene IL-10RA [chr11: 117.859.199 - variante A>G/p.Tyr57Cys e chr11: 117.860.335 - variante G>T/ p.Val123Leu]. Ambas as pacientes foram submetidas a Transplante de Células-Tronco Hematopoiéticas. A investigação imunológica das pacientes revelou aumento dos níveis plasmáticos de IL-10 e aumento da IgA. Comentários: Nossos relatos de casos descrevem novos achados no perfil de citocinas plasmáticas na deficiência de IL-10R, e relatamos o fenótipo grave da deficiência de IL-10/IL-10R que deve ser reconhecido pelos médicos.