Next-generation sequencing-based genetic testing and phenotype correlation in retinitis pigmentosa patients from India

Purpose: Inherited retinal dystrophies (IRD) are a heterogeneous group of retinal diseases leading to progressive loss of photoreceptors through apoptosis. Retinitis pigmentosa (RP) is considered the most common form of IRD. Panel?based testing in RP has proven effective in identifying the causative genetic mutations in 70% and 80% of the patients. This is a retrospective, observational, single?center study of 107 RP patients who had undergone next?generation sequencing?based targeted gene panel testing for IRD genes. These patients were inspected for common phenotypic features to arrive at meaningful genotype–phenotype correlation. Methods: Patients underwent complete ophthalmic examination, and blood was collected from the proband for DNA extraction after documenting the pedigree. Targeted Next Generation Sequencing (NGS) was done by panel?based testing for IRD genes followed by co?segregation analysis wherever applicable. Results: Of the 107 patients, 72 patients had pathogenic mutations. The mean age of onset of symptoms was 14 ± 12 years (range: 5–55). Mean (Best Corrected Visual Acuity) BCVA was 6/48 (0.9 logMAR) (range 0.0–3.0). At presentation, over one?third of eyes had BCVA worse than 6/60 (<1 logMAR). Phenotype analysis with the gene defects showed overlapping features, such as peripheral well?defined chorioretinal atrophic patches in patients with CERKL, PROM1, and RPE65 gene mutations and large macular lesions in patients with RDH12 and CRX gene mutations, respectively. Nummular or clump?like pigmentation was noted in CRB1, TTC8, PDE6A, and PDE6B. Conclusion: NGS?based genetic testing can help clinicians to diagnose RP more accurately, and phenotypic correlations can also help in better patient counselling with respect to prognosis and guidance regarding ongoing newer gene?based therapies.

Cellular consequences of small supernumerary marker chromosome derived from chromosome 12: mosaicism in daughter and father

Constitutional genomic imbalances are known to cause malformations, disabilities, neurodevelopmental delay, and dysmorphia and can lead to dysfunctions in the cell cycle. In extremely rare genetic conditions such as small supernumerary marker chromosomes (sSMC), it is important to understand the cellular consequences of this extra marker, as well the factors that contribute to their maintenance or elimination through successive cell cycles and phenotypic impact. The study of chromosomal mosaicism provides a natural model to characterize the effect of aneuploidy on genome stability and compare cells with the same genetic background and environment exposure, but differing in the presence of sSMC. Here, we report the functional characterization of different cell lines from two familial patients with mosaic sSMC derived from chromosome 12. We performed studies of proliferation dynamics, stability, and variability of these cells using fluorescent in situ hybridization (FISH), sister chromatid exchanges (SCE), and conventional staining. We also quantified the telomere-related genomic instability of sSMC cells using 3D telomeric profile analysis by quantitative-FISH. sSMC cells exhibited differences in the cell cycle dynamics compared to normal cells. First, the sSMC cells exhibited lower proliferation index and higher frequency of SCE than normal cells, associated with a higher level of chromosomal instability. Second, sSMC cells exhibited more telomeric-related genomic instability. Lastly, the differences of sSMC cells distribution among tissues could explain different phenotypic repercussions observed in patients. These results will help in our understanding of the sSMC stability, maintenance during cell cycle, and the cell cycle variables involved in the different phenotypic manifestations.

Clinical, Pathological and Genetic Analysis of Alport Syndrome in Children / 罕见病研究

  Objective  To explore the phenotype-genotype correlation of Alport syndrome in children.  Methods  Retrospectively analyze the clinical and pathological features of 55 patients with Alport syndrome with COL4A mutations detected by second-generation sequencing, who were treated at Beijing Children's Hospital from January 2016 to December 2020.  Results  A total of 55 children with Alport syndrome were included. All cases had hematuria, including 31 cases (56.4%) with gross hematuria and 24 cases (43.6%) with microscopic hematuria. A total of 39 (70.9%) patients also had proteinuria. Extrarenal manifestations were pres- ent in 12 patients (21.8%). 36(65.4%) patients had a family history of Alport syndrome. 32 patients underwent pathological examination and 23 of them had the specific pathological changes of Alport syndrome. In 55 cases, 36 (65.4%) were diagnosed as X-linked Alport syndrome, 5(9.1%) were diagnosed as autosomal recessive Alport syndrome, 10(18.2%) were diagnosed as autosomal dominate Alport syndrome, and 4(7.3%) were diagnosed as digenic Alport syndrome. Missense mutations in COL4A genes accounted for 62.5%, 67.5% of missense mutations resulted in glycine substitution. There were statistical significances in proteinuria degree and hearing loss between male and female patients with XLAS (P < 0.05) as well as statistical significance in the degree of proteinuria between autosomal recessive Alport syndrome and autosomal dominate Alport syndrome (P=0.044), and there was critical statistical significance in the age of onset. There was statistical significance in hearing loss between children with renal impairment and children with normal renal function (P=0.001).  Conclusions  Most of the pathogenic variants in COL4A genes that cause Alport syndrome result in glycine substitutions. The degree of proteinuria and hearing loss of males with XLAS were greater than those of females. The degree of proteinuria in autosomal recessive Alport syndrome was greater than that of children with autosomal dominate Alport syndrome, and the age of onset was earlier than that of autosomal dominate Alport syndrome. Renal manifestation was more severe in children with hearing loss. The early clinical manifestations of Alport syndrome are diverse and pathological manifestations may be atypical. The application of next-generation sequencing can reduce misdiagnosises of Alport syndrome.

Síndrome de Silver-Russell. Aspectos clínicos y etiopatológicos de una entidad ejemplo de impronta genómica / Silver-Russell syndrome. Clinical and etiopathological aspects of a model genomic imprinting entity

El síndrome de Silver-Russell se caracteriza por retraso del crecimiento intrauterino asimétrico, con circunferencia craneal normal, barbilla pequeña y puntiaguda, que proporciona un aspecto de rostro triangular. Puede, además, presentar asimetría corporal, entre otros. Tiene una incidencia mundial estimada de 1 en 30 000-100 000 nacimientos, aunque este número es, probablemente, subestimado. En alrededor del 60 % de los casos, se puede identificar una causa molecular y la principal es la hipometilación del alelo paterno en la región de control de impresión 1 localizado en 11p15.5-p15.4. Realizar el diagnóstico de esta entidad, excluir los diagnósticos diferenciales y conocer las correlaciones (epi)genotipo-fenotipo son necesarios para realizar el adecuado seguimiento, brindar las opciones terapéuticas disponibles y el oportuno asesoramiento genético familiar. El objetivo del presente artículo es mostrar el estado actual del síndrome de Silver-Russell, un ejemplo de trastorno de impronta genómica.

Silver-Russell syndrome is characterized by asymmetrical intrauterine growth retardation, with normal head circumference and small, pointed chin, which results in a triangular face. It can also include body asymmetry, among other characteristics. Its global incidence is estimated at 1 in 30 000-100 000 births, even though this figure may be underestimated. In approximately 60 % of cases, a molecular cause can be identified, and the main one is hypomethylation of the paternal allele at the imprinting control region 1 located at 11p15.5-p15.4. It is necessary to make the diagnosis of this entity, exclude differential diagnoses, and know (epi)genotype-phenotype correlations in order to ensure an adequate follow-up, provide available therapeutic options, and offer a timely family genetic counseling. The objective of this article is to describe the current status of the Silver-Russell syndrome, a model of genomic imprinting disorder.

Primary Hyperoxaluria in Korean Pediatric Patients

BACKGROUND: Primary hyperoxaluria (PH), a rare inborn error of glyoxylate meta bolism causing overproduction of oxalate, is classified into three genetic subgroups: type 1–3 (PH1–PH3) caused by AGXT, GRHPR , and HOGA1 gene mutations, respectively. We performed a retrospective case series study of Korean pediatric patients with PH.METHODS: In total, 11 unrelated pediatric patients were recruited and their phenotypes and genotypes were analyzed by a retrospective review of their medical records.RESULTS: Mutational analyses revealed biallelic AGXT mutations (PH1) in nine patients and a single heterozygous GRHPR and HOGA1 mutation in one patient each. The c.33dupC was the most common AGXT mutation with an allelic frequency of 44%. The median age of onset was 3 months (range, 2 months-3 years), and eight patients with PH1 presented with end stage renal disease (ESRD). Patients with two truncating mutations showed an earlier age of onset and more frequent retinal involvement than patients with one truncating mutation. Among eight PH1 patients presenting with ESRD, five patients were treated with intensive dialysis followed by liver transplantation (n=5) with/without subsequent kidney transplantation (n=3).CONCLUSION: Most patients presented with severe infantile forms of PH. Patients with two truncating mutations displayed more severe phenotypes than those of patients with one truncating mutation. Sequential liver and kidney transplantation was adopted for PH1 patients presenting with ESRD. A larger nation-wide multicenter study is needed to confirm the genotype-phenotype correlations and outcomes of organ transplantation.

Special AT-rich binding protein 2-associated syndrome: a case report and literature review / 中华神经科杂志

Objective@#To retrospectively analyse the genetic characteristics, diagnosis, treatment and prognosis of special AT-rich binding protein 2 (SATB2)-associated syndrome.@*Methods@#Clinical data of one case of SATB2-associated syndrome diagnosed in Children′s Hospital Affiliated to Zhengzhou University in January 2018, were collected including clinical test, treatment plan, follow-up outcomes. The clinical characteristics of SATB2-associated syndrome were analyzed, and literature review was conducted.@*Results@#The female proband, eight-year-old, were admitted with the clinical manifestations including epilepsy seizures, delayed language development, sparse hair, long face, prominent forehead, long nose, lower eyelid cleft oblique, low ear, smooth philtrum, small mandible, sparse teeth arrangement, and lack of some teeth. The intelligence quotient score was 49. The brain magnetic resonance imaging showed myelinated dysplasia. Long-range video-electroencephalography showed spike-wave activity, slow spike-wave discharges in the bilateral middle and posterior temporal regions. The trio whole exome sequencing (trio WES) test showed that the proband carried a heterozygous nonsense mutation c.1300 C>T (p.Gln434Ter) in the SATB2 gene, and the muation was de novo comfirmed by pedigree analysis. Thirty-seven literatures relevant to SATB2-associated syndrome, from January 1989 to June 2019, were retrieved. Threre were 23 overseas literatures and one domestic report, including a total number of 158 cases. There were 49 missense mutations, 38 nonsense mutations, 32 frameshift mutations, seven splicing-site mutations, six translocation mutations, one insertion mutation, 22 gene-deletions and three gene-duplications. Among the 158 reported cases, 90 were male and 62 female, sex was not described in six cases. One hundred and fifty-eight (100.0%) patients had mental retardation, 44 (30.6%) with growth retardation, 107 (84.3%) with facial deformities, 70 (45.5%) with cleft palate, 135 (98.5%) with dental abnormalities, 66 (43.4%) with language retardation, 29 (20.0%) with epileptic seizures, and 50 (46.3%) with neuroimaging abnormalities.@*Conclusions@#The main clinical manifestations of SATB2-related syndromes are severe developmental retardation, low intelligence, delayed language development, language deficiency, high palatal arch and cleft palate, rare epilepsy seizures, dental anomalies and scant hair. The study identified a novel nonsense mutation c. 1300 C>T (p. Gln434Ter) in the SATB2 gene, which is responsible for the development of SATB2-associated syndrome.

Nueva mutación del gen TSC2 en un paciente pediátrico con diagnóstico clínico de esclerosis tuberosa / Novel mutation in TSC2 gene in pediatric patient with clinical diagnosis of tuberous sclerosis

El complejo de esclerosis tuberosa es un desorden neurocutáneo autosómico dominante causado por mutaciones en los genes TSC1 o TSC2. El diagnóstico se basa en criterios clínicos o el criterio genético. La presentación clínica es altamente variable y las manifestaciones de la enfermedad pueden desarrollarse durante toda la vida. Se reporta el caso de un niño que cumple criterios clínicos para el diagnóstico de esclerosis tuberosa y cuyo estudio molecular identificó una variante nueva del gen TSC2. Se trata de una mutación sin sentido, esporádica, no reportada previamente (c.583_586dupATCG) localizada en el exón 6, que provoca un codón de parada temprano y altera la estructura de la proteína. Puede considerarse una variante patogénica por el tipo de mutación y permite ampliar el espectro de variantes del gen TSC2 como causa del complejo de esclerosis tuberosa.

Tuberous sclerosis complex (TSC) is a neurocutaneous autosomal dominant disorder that results from mutations within either the TSC1 gene or the TSC2 gene. Diagnosis is based on well-established clinical criteria or genetic criteria. Clinical features are highly variable and could be developing over the life. We present a case of TSC with a molecular test that identified a novel variant in TSC2 gene. It is a sporadic missense mutation which has not been previously reported in the literature. It is caused by premature termination of protein translation and results in the production of truncated and non-functional proteins. This mutation is considered as a pathogenic variant and allows to broaden the spectrum of variants of TSC2 gene as a cause of TSC.

The Challenge of Diagnosis and Indication for Treatment in Fabry Disease

Abstract Fabry disease, caused by deficient alpha-galactosidase A lysosomal enzyme activity, remains challenging to health-care professionals. Laboratory diagnosis in males is carried out by determination of alpha-galactosidase A activity; for females, enzymatic activity determination fails to detect the disease in about two-thirds of the patients, and only the identification of a pathogenic mutation in the GLA gene allows for a definite diagnosis. The hurdle to be overcome in this field is to determine whether a mutation that has never been described determines a ''classic'' or ''nonclassic'' phenotype, because this will have an impact on the decision-making for treatment initiation. Besides the enzymatic determination and GLA gene mutation determination, researchers are still searching for a good biomarker, and it seems that plasma lyso-Gb3 is a useful tool that correlates to the degree of substrate storage in organs. The ideal time for treatment initiation for children and nonclassic phenotype remains unclear.

Clinical Characteristics and Genotype-Phenotype Correlation of Korean Patients with Spinal and Bulbar Muscular Atrophy

PURPOSE: Spinal and bulbar muscular atrophy (SBMA) is an X-linked motor neuron disease characterized by proximal muscle weakness, muscle atrophy, and fasciculation. Although SBMA is not uncommon in Korea, there is only one study reporting clinical characteristics and genotype-phenotype correlation in Korean patients. MATERIALS AND METHODS: In this study, age at the onset of symptoms, the score of severity assessed by impairment of activities of daily living milestones, and rate of disease progression, and their correlations with the number of CAG repeats in the androgen receptor (AR) gene, as well as possible correlations among clinical characteristics, were analyzed in 40 SBMA patients. RESULTS: The median ages at onset and at diagnosis were 44.5 and 52.5 years, respectively, and median interval between onset and diagnosis and median rate of disease progression were 5.0 years and 0.23 score/year, respectively. The median number of CAG repeats in the AR gene was 44 and the number of CAG repeats showed a significant inverse correlation with the age at onset of symptoms (r=-0.407, p=0.009). In addition, patients with early symptom onset had slower rate of disease progression. CONCLUSION: As a report with the largest and recent Korean cohort, this study demonstrates clinical features of Korean patients with SBMA and reaffirms the inverse correlation between the age at disease onset and the number of CAG repeats. Interestingly, this study shows a possibility that the rate of disease progression may be influenced by the age at onset of symptoms.

A Missing Correlation between the Number and Type of MEFV Mutations and Severity of Clinical Manifestations in Egyptian Pediatric FMF Patients.

Aims: Previous researches identified the gene for Familial Mediterranean Fever (FMF) and found several different gene mutations that cause this inherited rheumatic disease. The aim of this work is to investigate the correlation between severity of symptoms of FMF and the number and type of MEFV variants, as well as to shed light on the correlation between the genotype and phenotype of Egyptian pediatric FMF patients. Study Design: Retrospective study. Place and Duration of Study: Department of Pediatrics, Kasr El Aini Hospital, Cairo University Medical School, Cairo, Egypt, between January 2012 and February 2013. Methodology: This study involved 35 childhood cases of Egyptian ethnic origin suspected to suffer from FMF. They include 19 males and 16 females of age range between 1-17 years. MEFV mutations in each patient were determined by performing DNA isolation and purification, in vitro amplification (PCR), and reverse hybridization using an FMF StripAssay. Results: Our results revealed 14% homozygous, 34% single heterozygous, 35% compound heterozygous-bi, and 17% compound heterozygous-tri patients. Twelve MEFV mutations were covered where all mutations were concentrated on exons 10 and 2. Severity of clinical manifestations and severity score did not linearly correlate with the number of variants, nor with the type of variant. Conclusion: Our results question the strength of genotype-phenotype correlation in FMF and indicate that MEFV genotypes express much more variable phenotypes than previously suggested. Our results also revealed no association between the number of mutations and severity of clinical manifestations.

Variable clinical expression in patients with a germline MEN1 disease gene mutation: clues to a genotype-phenotype correlation

Multiple endocrine neoplasia type 1 is an inherited endocrine tumor syndrome, predominantly characterized by tumors of the parathyroid glands, gastroenteropancreatic tumors, pituitary adenomas, adrenal adenomas, and neuroendocrine tumors of the thymus, lungs or stomach. Multiple endocrine neoplasia type 1 is caused by germline mutations of the multiple endocrine neoplasia type 1 tumor suppressor gene. The initial germline mutation, loss of the wild-type allele, and modifying genetic and possibly epigenetic and environmental events eventually result in multiple endocrine neoplasia type 1 tumors. Our understanding of the function of the multiple endocrine neoplasia type 1 gene product, menin, has increased significantly over the years. However, to date, no clear genotype-phenotype correlation has been established. In this review we discuss reports on exceptional clinical presentations of multiple endocrine neoplasia type 1, which may provide more insight into the pathogenesis of this disorder and offer clues for a possible genotype-phenotype correlation.

La trisomía 21: 50 años después de lejeune / the 21-trisomy: 50 years after lejeune

El síndrome de Down, es la causa más frecuente de discapacidad intelectual, fue descrito por primera vez en el año 1886, durante una era de grandes cambios en el conocimiento de la genética y la evolución. Ocurre con una frecuencia de 1 por cada 700 nacidos vivos. En muchos casos la historia de la investigación en el síndrome de Down cursa paralela a la historia de la genética humana y ha sido fuente de grandes progresos en esta ciencia. En esta revisión se describe la interrelación entre los avances del conocimiento de la genética y el conocimiento del síndrome de Down tomando en consideración el impacto del descubrimiento de su etiología realizado en 1959 por Jerone Lejeune. Con motivo de la celebración de los 50 años de este acontecimiento, se escogió este descubrimiento como marcador de división cronológica de las etapas de producción del conocimiento sobre el síndrome, obteniéndose la era pre y pos-Lejeune, desde su descripción inicial al presente y sobre la base de esta perspectiva histórica se especula brevemente acerca del futuro de la investigación en el síndrome de Down

Down syndrome, is the most common cause of intellectual disabilities, it was first described in 1866, during an era of great change in understanding of genetics and evolution. It occurs in about I of every 700 newborns. In many instances, The history of research on Down syndrome courses parallels with the history of human genetics and it has inspired progress in human genetics. In this revision, it is described the interplay between advances in the understandins of genetics and the understanding of the Down syndrome and it was considered the finding of its etiology by Jerone Lejeune in 1959, as the index, Fifty years the discovery of the origin of the Down syndrome, it has been utilized for the division of two eras in the generation of knowledge in Down syndrome, the pre and the post-Lejeune era, from its initial description to the present, and on the basis of this historical perspective, speculate briefly about the future of research on Down syndrome

Genotype-phenotype correlation in Brazillian Rett syndrome patients / Correlação genótipo-fenótipo em pacientes brasileiras com síndrome de Rett

BACKGROUND: Rett syndrome (RS) is a severe neurodevelopmental X-linked dominant disorder caused by mutations in the MECP2 gene. PURPOSE: To search for point mutations on the MECP2 gene and to establish a correlation between the main point mutations found and the phenotype. METHOD: Clinical evaluation of 105 patients, following a standard protocol. Detection of point mutations on the MECP2 gene was performed on peripheral blood DNA by sequencing the coding region of the gene. RESULTS: Classical RS was seen in 68 percent of the patients. Pathogenic point mutations were found in 64.1 percent of all patients and in 70.42 percent of those with the classical phenotype. Four new sequence variations were found, and their nature suggests patogenicity. Genotype-phenotype correlations were performed. CONCLUSION: Detailed clinical descriptions and identification of the underlying genetic alterations of this Brazilian RS population add to our knowledge of genotype/phenotype correlations, guiding the implementation of mutation searching programs.

INTRODUÇÃO: A síndrome de Rett é uma grave doença do neurodesenvolvimento ligada ao X dominante, causada por mutações no gene MECP2. OBJETIVOS: Identificar mutações de ponto no gene MECP2 e estabelecer uma correlação entre as principais mutações encontradas e o fenótipo. MÉTODO: Avaliação clínica de 105 pacientes, seguindo um protocolo estabelecido. A identificação de mutações de ponto foi realizada em DNA de sangue periférico por sequenciamento da região codificante do gene amplificada por PCR. RESULTADOS: Em 68 por cento dos pacientes observou-se o quadro clássico da síndrome. Mutações de ponto patogênicas foram encontradas em 64,1 por cento dos pacientes e em 70,42 por cento das pacientes com o quadro clássico. Quatro novas variações de seqüência foram identificadas e sua natureza sugere patogenicidade. Correlações genótipo-fenótipo foram estabelecidas. CONCLUSÃO: Descrições clínicas detalhadas desta população brasileira de pacientes acrescenta conhecimento às correlações genótipo-fenótipo nesta grave condição, que podem auxiliar na implantação de programas de triagem de mutações.

The spectrum of 5p deletion in Korean 20 patients with Cri du chat syndrome

PURPOSE: Cri-du-Chat syndrome (CdCs) is a rare but clinically recongnizable condition with an estimated incidence of 1:50,000 live births. The clinical characteristics of the syndrome include severe psychomotor and mental retardation, microcephaly, hypertelorism, hypotonia, and slow growth. Also the size of the chromosome 5p deletion ranges were known from the region 5p13 to the terminal region. In this study, we report the spectrum of 5p deletion in Korean 20 pts. with CdCs and genotype-phenotype associations in CdCs. METHODS: In order to delineate genotype-phenotype correlation, molecular cytogenetic studies including GTG banding and clinical characterization were performed on Korean 20 pts with CdCs including parents. CGH array and Fluorescence in situ hybridization (FISH) analysis were used to confirm a terminal deletion karyotype and map more precisely the location of the deletion breakpoint. RESULTS: Molecular analysis of the spectrum of 5p deletion revealed 9 pts (45%) with a del (5)(p14), 7 pts. (35%) a del (5)(p13), 3 pts. (15%) a del (5)(p15.1) and 1 pt. (5%) a del (5)(p15.2) in 20 pts with CdCs. 4(20%)pts were identified to have additional chromosome abnormalites of deficiency and duplication involving chromosomes of 6, 8, 18, & 22. Parental study identified 3 familial case (2 paternal and 1 maternal origin) showing parents being a balanced translocation carrier. And the comparison study of the deletion break points among these 20 pts. with their phenotype has showed the varying clinical pheno-types in the CdCs critical region. CONCLUSION: The characterization of 5p deletion including parental study may help to delineate the genotypephenotype correlation in CdCs. Also these molecular cytogenetic analyses will be able to offer better information for accurate genetic diagnosis in CdCs and further make possible useful genetic counseling in pts. and family.