Clinical exome sequencing findings in 1589 patients.

Clinical exome sequencing (CES) is important for the diagnosis of Mendelian diseases, which are clinically and etiologically heterogeneous. Sharing of large amounts of CES data associated with clinical findings will increase the accuracy of variant interpretation. We performed a retrospective study to state the diagnostic yield of CES in 1589 patients with a wide phenotypic spectrum. CES was performed using the Sophia Clinical Exome Sequencing Kit with 4493 genes, followed by sequencing on a NextSeq 500 system. The diagnosis rate was 36.8% when only pathogenic and likely pathogenic variants were included. Consanguineous unions and positive family history were associated with a high diagnostic yield. The neurological disease group had the highest number of patients. The groups with high diagnosis rates were ear, eye, and muscle disease groups. Seven candidate genes (EFHC2, HSPB3, FAAH2, ITGB1, GYG2, CD177, and CSTF2T) that are not yet associated with human diseases were identified. Owing to the high diagnostic yield of CES compared with that of other genetic tests, it can be used as a standard diagnostic test in patients with rare genetic disorders that require a wide differential diagnosis, especially in laboratories with limited resources.

ATP7B Gene Variant Profile Identified by NGS in Wilson's Disease.

Background: Wilson's disease (WD) is a copper metabolism disorder caused by ATP7B gene mutations and shows an autosomal recessive pattern of inheritance. We aimed to contribute to the mutation profile of ATP7B and show demographic and phenotypic differences in this study. Materials and methods: The clinical and demographic characteristics of patients who underwent ATP7B gene sequence analysis using next-generation sequencing were evaluated to improve genotype-phenotype correlation in WD. Results: An uncertain significance (D563N) and seven likely pathogenic (Y532D, Y715Y, T977K, K1028*, E1086K, A1227Pfs*103, and E1242K) variants were identified as associated with WD. Uniparental disomy was detected in one case. Conclusion: Our work expanded the ATP7B variant spectrum and pointed to clinical heterogeneity in ATP7B variants among patients with WD. All symptomatic patients had hepatic involvement and were clinically and/or genetically diagnosed with WD in the pediatric period. T977K, A1003V, H1069Q, E1086K, and N1270S variants were associated with hepatic failure.

Acquired Thrombotic Thrombocytopenic Purpura in a 5-Year-old Child With Wiskott-Aldrich Syndrome.

Thrombocytopenia is often seen as a laboratory finding during childhood. A supposed idiopathic thrombocytopenic purpura patient who was later diagnosed as Wiskott-Aldrich syndrome (WAS) and developed acquired thrombotic thrombocytopenic purpura (aTTP). Although autoimmune manifestations in WAS described, aTTP was reported just once. Five-year-old-boy was initially brought with cough, bloody stool (diarrhea), oral mucosal bleeding at 12th months of age. Following diagnosed with idiopathic thrombocytopenic purpura and receiving intravenous immunoglobulin, platelet count raised from 20,000 to 50,000/µL. One year after WAS diagnosis by mutation analysis, he presented with complaints of resistant fever, epistaxis, and melena. Hemoglobin decreased from 10 to 5.9 g/dL. Schistocytes in peripheral blood smear and high anti-ADAMTS-13 antibody level indicated development of aTTP.

Coexistence of Three Different Mutations in a Male Infant: neurofibromatosis Type 1, Progressive Familial Intrahepatic Cholestasis Type 2 and LPIN3.

IntroductionThe coexistence of progressive familial intrahepatic cholestasis type 2, failure to thrive due to an LPIN3 mutation, and stigmata of neonatal neurofibromatosis represents a complex diagnostic challenge. Case report: We present a child with cholestasis requiring hepatic transplantation, explained by the progressive familial intrahepatic cholestasis type 2, failure to thrive could be contributed to by the LPIN3 mutation, and skin findings along with the family history of the patient was due to neurofibromatosis type 1. Conclusion: Our case illustrates the complexities of multiple genetic mutations in a child.

Patients with cerebrotendinous xanthomatosis diagnosed with diverse multisystem involvement.

Cerebrotendinous xanthomatosis (CTX) is a lipid storage disease caused by deficiency of sterol 27-hydroxylase enzyme encoded by CYP27A1 gene. This multicenter, cross-sectional descriptive study aimed to document clinical characteristics of CTX patients of different ages, clinical presentations of early-diagnosed patients, and responses to short-term chenodeoxycholic acid (CDCA) treatment. Seven of 11 CTX patients were diagnosed in childhood. Three patients (27%) had neonatal cholestasis, seven (63%) patients had a history of frequent watery defecation started in infantile period, and eight (72.7%) patients had juvenile cataract. Four patients in the adult age group had pyramidal signs and parkinsonism symptoms. The mean Mignarri score at diagnosis was significantly lower in the pediatric patients (267.8 ± 51.4) than in the adult patients (450.0 ± 64.0, p = 0.001). No significant difference was determined between pediatric patients and adult patients regarding plasma cholestanol concentration at diagnosis (p = 0.482). The frequency of defecation decreased with treatment in six children, who had diarrhea at admission. Compared to pretreatment values, patients' body weight and standardized body mass index significantly increased at the 12th month of treatment. In conclusion, Mignarri scores are lower in the pediatric patients than in adult patients since the most determinative signs of the CTX disease are not apparent yet in the childhood. The disease is frequently overlooked in routine practice as the disease presents itself with different clinical combinations both in adults and in children. CTX is potentially a treatable disease; thereby, enhanced awareness is critically important for early diagnosis particularly in children.

A Novel Homozygous Mutation in CYP11A1 Gene is Associated with Severe Adrenal Insufficiency in 46, XX Patient.

BACKGROUND: One of the causes of congenital adrenal insufficiency, a genetically heterogeneous disorder is a mutation in the CYP11A1 gene, which is responsible for the initiation of steriodogenesis by converting cholesterol to pregnenolone. Case: In a now 3 years and 3 months-old girl, adrenal insufficiency was diagnosed in the neonatal period. Clinical exome sequencing for primary adrenal insufficiency revealed a homozygous p.Thr330Met (c.989C>T) variant in the CYP11A1 (NM_000781) gene. Conclusion: Different types of inheritance patterns have been observed in CYP11A1-related adrenal insufficiency cases. We consider our case is an due to an autosomal recessive inheritance.

A Novel Nonsense FMN2 Mutation in Nonsyndromic Autosomal Recessive Intellectual Disability Syndrome.

Introduction Genetic causes of the intellectual disability Nonsyndromic Autosomal-Recessive Intellectual Disability Syndrome (MRT47, MIM 616193) are mutations in the recently described FMN2 (formin 2 gene). Case report: A boy with intellectual disability had a novel homozygous nonsense mutation (c.2245C > T/p.Gln749*) leading to a premature stop codon in exon 6 of the FMN2 (NM_001305424) gene detected by Clinical Exome Sequencing (CES). Conclusion: Clinical features of a patient with a novel nonsense FMN2 mutation is presented. We urge the change in the OMIM nomenclature from Mental Retardation, Autosomal Recessive 47 (MRT47, MIM 616193) to 'Nonsyndromic Autosomal-Recessive Intellectual Disability Syndrome'.

A Very Rare Congenital Dyserythropoietic Anemia Variant-Type IV in a Patient With a Novel Mutation in the KLF1 Gene: A Case Report and Review of the Literature.

Congenital dyserythropoietic anemias comprise a group of very rare hereditary disorders characterized by ineffective erythropoiesis and distinct morphologic abnormalities of the erythroblasts in the bone marrow. The wide variety of phenotypes observed in these patients makes the diagnosis difficult; identification of the genetic variants is crucial in differential diagnosis and clinical management. We report the nineth case with congenital dyserythropoietic anemia type IV, with a novel mutation that has not been reported before.

Glutathione synthetase deficiency: a novel mutation with femur agenesis.

Introduction: Glutathione synthetase (GSS) deficiency is an autosomal recessive disorder (frequency < 1/1,000,000) with different varyingly severe clinical manifestations that include metabolic acidosis, hemolytic anemia, hyperbilirubinemia, neurological disorders and sepsis. Case report: This infant was small for gestational age, had hemolytic anemia, metabolic acidosis, bilateral subependymal pseudocysts and increased echogenicity of the basal ganglia. GSS deficiency was confirmed by genetic analysis. The patient also had unilateral right femur agenesis. Conclusion: By using next generation sequencing analysis, we identified a novel homozygous variant c.800G > A, p.Arg267Gln in the GSS gene of this patient. Femur agenesis had not previously been associated with GSS.

The relationship between CRP gene polymorphism (rs2794521, rs3091244), ASDAS-CRP and ASDAS-ESR in ankylosing spondylitis.

Background: We aimed to investigate the haplotypes and alleles of two variants (rs2794521 and rs3091244) in AS patients and to examine their relationship with ASDAS-CRP and ASDAS-ESR values.Methods: We evaluated 160 AS patients diagnosed according to the ASAS criteria. ASDAS-CRP and ASDAS-ESR values were calculated. ESR and CRP were examined. The restriction fragment length polymorphism (RFLP) method was used for detecting the rs2794521 and rs3091244 regions on the CRP gene.Results: As a result of the evaluation of rs2794521 gene polymorphism using PCR, TT, TC and CC genotypes were observed in 90, 81 and 9 individuals, respectively. As a result of the evaluation of rs3091244 gene polymorphism, CC, AC and TT genotypes were observed in 104, 51 and 5 individuals, respectively. T allele and C allele were found in rs2794521 gene by 75% and 25%, respectively. In addition, T allele, C allele and A allele were found in rs3091244 gene by 80%, 17% and 3%, respectively. With the help of regression equation, ASDAS-CRP level was 0.34 units higher in cases with rs3091244 C allele than cases without rs3091244 C alleles.Conclusion: CRP rs3091244 C allele may be associated with the increased relative risk for ASDAS-CRP.

Novel PLVAP Mutation in Protein Losing Enteropathy.

Introduction: A genetic cause of the protein-losing enteropathy (PLE) disease Diarrhea 10 (DIAR10) are mutations in the recently described PLVAP (plasmalemma vesicle protein). Case report: An infant with fatal PLE had a novel homozygous frameshift mutation (c.339dupT; p.Ala114Cysfs*9) leading to a premature stop codon in exon 1 of the PLVAP (NM_031310) gene detected by Whole Exome Sequencing (WES). Conclusion: The frameshift mutation (PLVAP; c.339dupT; p.Ala114Cysfs*9) we have described in our patient has not been previously reported. This is the fifth case reported with a mutation in PLVAP associated with PLE and DIAR10.

Delayed Puberty and Gonadal Failure in Patients with HAX1 Mutation.

PURPOSE: Homozygous mutations in the HAX1 gene cause an autosomal recessive form of severe congenital neutropenia (SCN). There are limited data on cases of gonadal insufficiency that involve the HAX1 gene mutation. We aimed to evaluate the pubertal development and gonadal functions of our patients with a p.Trp44X mutation in the HAX1 gene. METHOD: Pubertal development, physical and laboratory findings of one male and seven female patients with HAX1 deficiency were evaluated. RESULTS: The age of the patients was between 13 and 25 years. All female patients were diagnosed with primary ovarian insufficiency (POI) based on amenorrhea and elevated gonadotropins. The ovary volumes in female patients were determined to be smaller than normal for their age through sonographic studies. Short stature associated with gonadal insufficiency was also observed in three patients. CONCLUSION: The HAX1 gene is important for ovarian development, in which a p.Trp44X mutation may cause POI in female patients. It is crucial to follow up and evaluate the gonadal functions of female patients in such cases.

Association of GSTM1, GSTT1, GSTP1-ILE105VAL and ACE I/D polymorphisms with ankylosing spondylitis.

Ankylosing spondylitis (AS) is a chronic inflammatory disease of unknown origin. The aim of this study is to clarify the relationships between susceptibility and severity of AS and GST-mu1 (GSTM1), GST-theta1 (GSTT1), GST-pi1 (GSTP1)-Ile105Val and angiotensin-converting enzyme (ACE) I/D polymorphisms in AS patients. One hundred thirty-eight AS patients and seventy-one healthy controls were enrolled in this study. Erythrocyte sedimentation rate and C-reactive protein (CRP) levels of the AS patients were recorded. The scores of the numeric rating scale (NRS) pain, the Bath Ankylosing Spondylitis Activity Index, the Bath Ankylosing Spondylitis Metrology Index and the Bath Ankylosing Spondylitis Functional Index were calculated. The genotypes distributions and allele frequencies of GSTM1, GSTT1, GSTP1-Ile105Val and ACE I/D polymorphisms were compared between patients and healthy controls. The Multiplex polymerase chain reaction (PCR) and the PCR-restriction fragment length polymorphism methods were used to detect the polymorphisms of ACE I/D, the GSTT1 and GSTM1 genes and the GSTP1-Ile105Val polymorphism, respectively. There were significantly higher levels of the GSTT1 null and the ACE II genotypes in AS patients compared to those in healthy controls (p = 0.002 and 0.005, respectively). We found significantly higher levels of CRP and the NRS pain scores in the patients with ACE ID or DD genotypes compared to those in the patients with ACE II genotypes (p = 0.005 and 0.035, respectively). The present results showed that genes involved in protection from oxidative stress and ACE gene may influence disease development and course in AS.

NOTCH3 Variants in Patients with Suspected CADASIL.

Background: Cerebral autosomal dominant arteriopathy with subcortical infarctions and leukoencephalopathy (CADASIL) is the most common hereditary form of cerebral small vessel disease. It is clinically, radiologically, and genetically heterogeneous and is caused by NOTCH3 mutations. Methods: In this study, we analyzed NOTCH3 in 368 patients with suspected CADASIL using next-generation sequencing. The significant variants detected were reported along with the clinical and radiological features of the patients. Results: Heterozygous NOTCH3 changes, mostly missense mutations, were detected in 44 of the 368 patients (~12%). Conclusions: In this single-center study conducted on a large patient group, 30 different variants were detected, 17 of which were novel. CADASIL, which can result in mortality, has a heterogeneous phenotype among individuals in terms of clinical, demographic, and radiological findings regardless of the NOTCH3 variant.

Evaluation of the JAK2-V617F gene mutation in Turkish patients with essential thrombocythemia and polycythemia vera.

An activating mutation of Janus kinase 2 (JAK2-V617F) was previously described in chronic myeloproliferative disorders (MPD). In previously published studies, the frequency of the JAK2-V617F mutation was determined to be 80-90 % for patients with polycythemia vera (PV) and 40-70 % for essential thrombocythemia (ET). In this study, we analyzed the relationship between the JAK2-V617F mutation and clinical-hematological parameters in Turkish patients with MPD and compared these findings with published studies from other geographic regions. A total of 148 patients were studied; of which, 70 were diagnosed with PV and 78 with ET. The mutation status of JAK2 was determined using a tetra-primer polymerase chain reaction. We found that 80 % of the PV group and 42 % of the ET group were positive for the JAK2-V617F mutation. When all patients were analyzed, the levels of white blood cells, hemoglobin and splenomegaly were significantly different in patients with the JAK2-V617F mutation (p < 0.05). To our knowledge, this study is the first to evaluate the relationship between MPD and JAK2-V617F in Turkish patients. The JAK2-V617F mutation is frequently detected in the Turkish patients with MPD, and especially in patients with PV. Hence, it would be useful to include JAK2 mutation screening in the initial evaluation of patients suspected to have MPD.

Newly defined peroxisomal disease with novel ACBD5 mutation.

Peroxisomal disorders are a heterogeneous group of diseases caused by mutations in a large number of genes. One of the genetic disorders known to cause this situation is ACBD5 (Acyl-CoA binding-domain-containing-5) gene mutations that have been described in recent years. Here, we report two siblings with a novel homozygous nonsense variation (c.1297C>T, p.Arg433*) in ACBD5 (NM_145698.4) gene using Clinical Exome Sequencing (Sophia Genetics).