Targeted gene panel testing in pediatric epilepsy: Diagnostic outcomes and expanding genetic insights.

Purpose: We aimed to evaluate the diagnostic yield of epilepsy gene panel testing in epilepsy patients whose seizures began within the first year after birth. We included 112 patients with seizure onset before 12 months and no known etiology.Methods: Deep targeted sequencing with a custom-designed capture probe was performed to ensure the detection of germline or mosaic sequence variants and copy number variations (CNVs).Results: We identified pathogenic or likely pathogenic variants in 53 patients (47.3%, 53/112), including five with pathogenic CNVs. Two putative pathogenic mosaic variants in SCN8A and KCNQ2 were also detected and validated. Those with neonatal onset (61.5%, 16/26) or early infantile onset (50.0%, 29/58) showed higher diagnostic rates than those with late infantile onset (28.5%, 8/28). The diagnostic rate was similar between patients with a specific syndrome (51.9%, 27/52) and those with no recognizable syndrome (43.3%, 26/60).Conclusion: Epilepsy gene panel testing identified a genetic cause in nearly half of the infantile onset epilepsy patients. Since the phenotypic spectrum is expanding and characterizing it at seizure onset is difficult, this group should be prioritized for epilepsy gene panel testing.

Evaluating clinical factors for improved utilization of targeted gene panel testing for inborn errors of immunity in a U.S. tertiary care pediatric hospital

NGS-based multiple gene panel resequencing in combination with a high resolution CGH-array was used to identify genetic risk factors for hereditary breast and/or ovarian cancer in 237 high risk patients who were previously tested negative for pathogenic BRCA1/2 variants. All patients were screened for pathogenic variants in 94 different cancer predisposing genes. We identified 32 pathogenic variants in 14 different genes (ATM, BLM, BRCA1, CDH1, CHEK2, FANCG, FANCM, FH, HRAS, PALB2, PMS2, PTEN, RAD51C and NBN) in 30 patients (12.7%). Two pathogenic BRCA1 variants that were previously undetected due to less comprehensive and sensitive methods were found. Five pathogenic variants are novel, three of which occur in genes yet unrelated to hereditary breast and/or ovarian cancer (FANCG, FH and HRAS). In our cohort we discovered a remarkably high frequency of truncating variants in FANCM (2.1%), which has recently been suggested as a susceptibility gene for hereditary breast cancer. Two patients of our cohort carried two different pathogenic variants each and 10 other patients in whom a pathogenic variant was confirmed also harbored a variant of unknown significance in a breast and ovarian cancer susceptibility gene. We were able to identify pathogenic variants predisposing for tumor formation in 12.3% of BRCA1/2 negative breast and/or ovarian cancer patients.

Dissecting the phenotypic and genetic spectrum of early childhood-onset generalized epilepsies

BackgroundAlthough there is relatively much information about the status of cystic fibrosis disease in different countries of the world, limited data are available on this disease among Syrian children. Therefore, we did a retrospective study that included 173 children diagnosed with cystic fibrosis according to the diagnostic criteria. This study was conducted to determine the diagnostic, clinical, and genetic characteristics of patients with cystic fibrosis in Syria and to assess the relationship between the genotype and the phenotype of disease in these patients.ResultsAs a result of the early classical manifestations, CF diagnosis was established in the present study by the age of 1 year in 78.6%; the mortality rate was 23.1% (82.5% of them were in the first year of life). The prevalence of respiratory and gastrointestinal symptoms was 81.5% and 78.6%, respectively with an average age of 7.8 and 3.4 months. Consanguinity was reported in 75.7% of the families. The most common pathogenic variant in the sample was F508del (36%) followed by W1282X (17%). There was a statistical correlation between incidence of steatorrhea and the presence of class I pathogenic variants. A relationship between the mortality rate and the presence of class II pathogenic variants (pathogenic deletion variants) was also observed. There was no statistical relationship between other clinical manifestation and pathogenic variant classes. However, the incidence of most CF-related conditions was a little higher in the presence of classes I, II, and III pathogenic variants compared to their incidence in the presence of classes IV and V pathogenic variants.ConclusionsThe number of cases diagnosed with cystic fibrosis in Syria is less than the number of real cases, and there is a need to perform CFTR gene sequencing on large sample sizes, to determine all CFTR pathogenic variants that could exist in Syrian patients and to make a better evaluation of the relationship between genotype and phenotype of the disease.

The identification of pathogenic variants in developmental epileptic encephalopathy (DEE) genes can be vital for counseling and individualized treatment. Penetrance is usually considered to be high or full, although this has never been studied in population cohorts. Recent evidence shows that common polygenic risk factors (polygenic risk score [PRS]) are increased in DEE cases, suggesting they might modify risk. We calculated the penetrance of autosomal dominant epilepsy variants that have previously been classified as (likely) pathogenic in ClinVar, in two large cohorts (n = 42 863 and n = 386 306) using whole genome sequencing data. Next, we calculated PRS to assess whether common variants could modify epilepsy risk among people carrying pathogenic variants. Most people carrying pathogenic DEE variants did not have epilepsy. Penetrance estimates suggested that the probability of epilepsy in pathogenic variant carriers ranges between 4.1% and 9.8%. Among people carrying epilepsy variants, PRS was predictive of an epilepsy diagnosis. A high PRS was associated with increased risk of severe epilepsy, whereas a low PRS seems protective in people carrying a pathogenic variant. Our results suggest that average variant penetrance is lower than expected and modified by PRS. A high PRS combined with a pathogenic variant may be necessary to develop a severe epilepsy phenotype like DEE. Reconsidering penetrance assumptions could improve variant classification and diagnostic yield. Our findings may enhance genetic counseling by refining risk estimates and could extend to other diseases.

This study aimed to evaluate the clinical utility of whole-exome sequencing in a group of infantile-onset epilepsy patients who tested negative for epilepsy using a gene panel test. Whole-exome sequencing was performed on 59 patients who tested negative on customized epilepsy gene panel testing. We identified eight pathogenic or likely pathogenic sequence variants in eight different genes (FARS2, YWHAG, KCNC1, DYRK1A, SMC1A, PIGA, OGT, and FGF12), one pathogenic structural variant (8.6 Mb-sized deletion on chromosome X [140 994 419-149 630 805]), and three putative low-frequency mosaic variants from three different genes (GABBR2, MTOR, and CUX1). Subsequent whole-exome sequencing revealed an additional 8% of diagnostic yield with genetic confirmation of epilepsy in 55.4% (62/112) of our cohort. Three genes (YWHAG, KCNC1, and FGF12) were identified as epilepsy-causing genes after the original gene panel was designed. The others were initially linked with mitochondrial encephalopathy or different neurodevelopmental disorders, although an epilepsy phenotype was listed as one of the clinical features. Application of whole-exome sequencing following epilepsy gene panel testing provided 8% of additional diagnostic yield in an infantile-onset epilepsy cohort. Whole-exome sequencing could provide an opportunity to reanalyze newly recognized epilepsy-linked genes without updating the gene panel design.

540 Background: The reported frequency of germline pathogenic variants (PVs) in patients with pancreatic cancer is 8-10%. Depending on the setting, pancreatic cancer-associated germline PVs in the BRCA and CDKN2A genes are the most commonly detected. The mismatch repair genes (MMR; Lynch syndrome) , TP53, STK11, ATM and PALB2 are also associated with an increased risk of pancreatic cancer . The identification of PVs in patients with pancreatic cancer is important as there may be a benefit of targeted therapies, such as PARP inhibitors for cases with defective double strand break repair or response to immunotherapy with defective MMR and high tumor mutational burden. Additionally, identification of predisposing PVs can enable screening and prevention for other family members through cascade testing. According to international guidelines, all patients diagnosed with exocrine pancreatic cancer are candidates for genetic testing. However, there is an underrepresentation of ethnic/ racial minorities, including Hispanic patients, in genetic studies. Methods: Between April 2017 and May 2020, patients with diagnosis of pancreatic adenocarcinoma who were treated at the Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán and enrolled in the international Clinical Cancer Genomics Community Research Network registry were included in this analysis. Genetic testing was performed by full sequencing of the following genes: BRCA1, BRCA2, TP53, NF1, ATM, CHEK2, PALB2, CDKN2A, BRIP1, RAD50, RAD51C, RAD51D, MLH1, MSH2, MSH6, PMS2 and EPCAM, as well as multiplex ligation-dependent probe amplification for selected genes and BRCA1 ex9-12del (Mexican founder mutation) screening with a three-primer polymerase chain reaction. Pedigrees, clinical and demographic data were obtained from the clinical records. Results: Forty-two patients with a diagnosis of pancreatic adenocarcinoma were included, with a median age at diagnosis of 57 years (range, 43-79), and 23/42 (55%) were women. The proportion of cases with operable, unresectable and metastatic disease at diagnosis was similar (33.3% for each group). The frequency of PVs was 11.9% ( ATM n =2, TP53 n =1, PALB2 n =1 and CHEK2 n =1). With a median follow-up 20 months 29/42 patients had died at the time of analysis (69%), the median overall survival was 16 months (range 3-84 months). No PVs were detected in the 4/42 patients who met the definition of familial pancreatic cancer (9.5%). Conclusions: Our results confirm the presence of PVs in cancer susceptibility genes in Mexican patients with pancreatic cancer, which is similar to that reported in other populations. However, it is notable that no BRCA PVs were identified in this small sample, as they are the most common PV found in other populations. Given to the heterogeneity of the PVs identified, our study supports the use of multi- gene panel testing in Hispanic patients with pancreatic cancer.

PurposeThis study aimed to define the genotypic and phenotypic spectrum of reversible acute liver failure (ALF) of infancy resulting from biallelic pathogenic TRMU variants and determine the role of cysteine supplementation in its treatment. MethodsIndividuals with biallelic (likely) pathogenic variants in TRMU were studied within an international retrospective collection of de-identified patient data. ResultsIn 62 individuals, including 30 previously unreported cases, we described 47 (likely) pathogenic TRMU variants, of which 17 were novel, and 1 intragenic deletion. Of these 62 individuals, 42 were alive at a median age of 6.8 (0.6-22) years after a median follow-up of 3.6 (0.1-22) years. The most frequent finding, occurring in all but 2 individuals, was liver involvement. ALF occurred only in the first year of life and was reported in 43 of 62 individuals; 11 of whom received liver transplantation. Loss-of-function TRMU variants were associated with poor survival. Supplementation with at least 1 cysteine source, typically N-acetylcysteine, improved survival significantly. Neurodevelopmental delay was observed in 11 individuals and persisted in 4 of the survivors, but we were unable to determine whether this was a primary or a secondary consequence of TRMU deficiency. ConclusionIn most patients, TRMU-associated ALF was a transient, reversible disease and cysteine supplementation improved survival.

Pitfalls of clinical exome and gene panel testing: alternative transcripts

Mutations in the ATP1A3 gene are known to cause alternating hemiplegia of childhood (AHC) and rapid-onset dystonia parkinsonism (RDP). Both conditions are childhood-onset neurological disorders with distinct symptoms and different times of onset. ATP1A3 has also been associated with CAPOS syndrome (cerebellar ataxia, areflexia, pes cavus, optic atrophy, and sensorineural hearing loss). Within the various ATP1A3-related neurological syndromes, a specific genotype-phenotype correlation is starting to emerge. Several mutations such as the relatively common p.E815K pathogenic variant have been shown to strongly correlate with AHC, while others may cause both AHC and RDP. A significant subset of patients with AHC and RDP are reported to have epileptic seizures. Even though detailed clinical descriptions of seizures in childhood are rare, seizures involving apneic events seem to be frequent in ATP1A3-related neurological disorders. Here, we describe two children with unexplained severe apnea beginning around the first year of life and pathogenic variants in ATP1A3. We hypothesize that the symptoms are early-onset autonomic seizures related to the underlying pathogenic ATP1A3 variants.

Hereditary cataracts are characterized by significant clinical and genetic heterogeneity, which can pose challenges for early DNA diagnosis. To comprehensively address this problem, it is essential to investigate the epidemiology of the disease, perform population studies to determine the spectrum and frequencies of mutations in the responsible genes, and examine clinical and genetic correlations. Based on modern concepts, non-syndromic hereditary cataracts are predominantly caused by genetic disease forms associated with mutations in crystallin and connexin genes. Therefore, a comprehensive approach to studying hereditary cataracts is necessary for early diagnosis and improved treatment outcomes. The crystallin (CRYAA, CRYAB, CRYGC, CRYGD, and CRYBA1) and connexin (GJA8, GJA3) genes were analyzed in 45 unrelated families from the Volga–Ural Region (VUR) with hereditary congenital cataracts. Pathogenic and probably pathogenic nucleotide variants were identified in ten unrelated families, nine of which had cataracts in an autosomal dominant pattern of inheritance. Two previously undescribed likely pathogenic missense variants were identified in the CRYAA gene: c.253C > T (p.L85F) in one family and c.291C > G (p.H97Q) in two families. The known mutation c.272_274delGAG (p.G91del) was found in the CRYBA1 gene in one family, while no pathogenic variants were found in the CRYAB, CRYGC, or CRYGD genes in the examined patients. In the GJA8 gene, the known mutation c.68G > C (p.R23T) was found in two families, and previously undescribed variants were identified in two other families: a c.133_142del deletion (p.W45Sfs*72) and a missense variant, c.179G > A (p.G60D). In one patient with a recessive form of cataract, two compound-heterozygous variants were identified—a previously undescribed likely pathogenic missense variant, c.143A > G (p.E48G), and a known variant with uncertain pathogenetic significance, c.741T > G (p.I24M). Additionally, a previously undescribed deletion, c.del1126_1139 (p.D376Qfs*69), was identified in the GJA3 gene in one family. In all families where mutations were identified, cataracts were diagnosed either immediately after birth or during the first year of life. The clinical presentation of the cataracts varied depending on the type of lens opacity, resulting in various clinical forms. This information emphasizes the importance of early diagnosis and genetic testing for hereditary congenital cataracts to guide appropriate management and improve outcomes.

Pathogenic variants in SCN3A, encoding the voltage-gated sodium channel subunit Nav1.3, cause severe childhood onset epilepsy and malformation of cortical development. Here, we define the spectrum of clinical, genetic, and neuroimaging features of SCN3A-related neurodevelopmental disorder. Patients were ascertained via an international collaborative network. We compared sodium channels containing wild-type versus variant Nav1.3 subunits coexpressed with β1 and β2 subunits using whole-cell voltage clamp electrophysiological recordings in a heterologous mammalian system (HEK-293T cells). Of 22 patients with pathogenic SCN3A variants, most had treatment-resistant epilepsy beginning in the first year of life (16/21, 76%; median onset, 2 weeks), with severe or profound developmental delay (15/20, 75%). Many, but not all (15/19, 79%), exhibited malformations of cortical development. Pathogenic variants clustered in transmembrane segments 4 to 6 of domains II to IV. Most pathogenic missense variants tested (10/11, 91%) displayed gain of channel function, with increased persistent current and/or a leftward shift in the voltage dependence of activation, and all variants associated with malformation of cortical development exhibited gain of channel function. One variant (p.Ile1468Arg) exhibited mixed effects, with gain and partial loss of function. Two variants demonstrated loss of channel function. Our study defines SCN3A-related neurodevelopmental disorder along a spectrum of severity, but typically including epilepsy and severe or profound developmental delay/intellectual disability. Malformations of cortical development are a characteristic feature of this unusual channelopathy syndrome, present in >75% of affected individuals. Gain of function at the channel level in developing neurons is likely an important mechanism of disease pathogenesis. ANN NEUROL 2020;88:348-362.

BackgroundInherited peripheral neuropathy (IPN) is a clinically and genetically heterogeneous group of disorders with more than 90 genes associated with the different subtypes. Sequential gene screening is gradually being replaced by next generation sequencing (NGS) applications.MethodsWe designed and validated a targeted NGS panel assay including 56 genes associated with known causes of IPN. We report our findings following NGS panel testing of 448 patients with different types of clinically-suspected IPN.ResultsGenetic diagnosis was achieved in 137 patients (31 %) and involved 195 pathogenic variants in 31 genes. 93 patients had pathogenic variants in genes where a resulting phenotype follows dominant inheritance, 32 in genes where this would follow recessive inheritance, and 12 presented with X-linked disease.Almost half of the diagnosed patients (64) had a pathogenic variant either in genes not previously available for routine diagnostic testing in a UK laboratory (50 patients) or in genes whose primary clinical association was not IPN (14).Seven patients had a pathogenic variant in a gene not hitherto indicated from their phenotype and three patients had more than one pathogenic variant, explaining their complex phenotype and providing information essential for accurate prediction of recurrence risks.ConclusionsOur results demonstrate that targeted gene panel testing is an unbiased approach which overcomes the limitations imposed by limited existing knowledge for rare genes, reveals high heterogeneity, and provides high diagnostic yield. It is therefore a highly efficient and cost effective tool for achieving a genetic diagnosis for IPN.Electronic supplementary materialThe online version of this article (doi:10.1186/s12881-015-0224-8) contains supplementary material, which is available to authorized users.

Objective To test the hypothesis that consuming Mediterranean diet and using olive oil for cooking/dressing salads during pregnancy might be associated with less wheezing during the first year of the offspring's life. Methods A study was conducted in 1,409 infants (mean age, 16.6 ± 2.5 months) attending healthy infant clinics in Spain. Dietary data of mothers' intake during pregnancy was collected by means of a parental food frequency questionnaire. Demographic information and data on wheezing during the first year of the offspring's life were also recorded. Infants were stratified according to any wheezing (42.2%) during the first year of life. Results In the univariate analysis, adherence to a Mediterranean diet and using olive oil for cooking/dressing salads during pregnancy were both significantly associated with less wheezing during the first year of life. However, after multivariate analysis, only olive oil consumption during pregnancy remained associated with less wheezing in the studied period (aOR = 0.57 [95% CI = 0.4–0.9]); whereas male gender (1.8 [1.4–2.3]), day care attendance (2.15 [1.5–3.1]), maternal asthma (2.16 [1.3–3.6]), maternal smoking during pregnancy (1.83 [1.3–2.2]), infant eczema (1.95 [1.3–2.9]), and mould stains on the household walls (1.72 [1.2–2.5]) remained associated with wheezing. Conclusion Our findings suggest a protective effect (primary prevention) of olive oil use during pregnancy on wheezing during the first year of the offspring's life. Pediatr Pulmonol. 2010; 45:395–402. © 2010 Wiley-Liss, Inc.