Next generation sequencing panel as an effective approach to genetic testing in patients with a highly variable phenotype of neuromuscular disorders

Neuromuscular disorders (NMDs) include a wide range of diseases affecting the peripheral nervous system. The genetic diagnoses are increasingly obtained with using the next generation sequencing (NGS). We applied the custom-design targeted NGS panel including 89 genes, together with genotyping and multiplex ligation-dependent probe amplification (MLPA) to identify a genetic spectrum of NMDs in 52 Polish patients. As a result, the genetic diagnosis was determined by NGS panel in 29 patients so its diagnostic utility is estimated at 55.8%. The most pathogenic variants were found in CLCN1, followed by CAPN3, SCN4A, and SGCA genes. Genotyping of myotonic dystrophy type 1 and 2 (DM1 and DM2) as a secondary approach has been performed. The co-occurrence of CAPN3 and CNBP mutations in one patient as well as DYSF and CNBP mutations in another suggests possibly more complex inheritance as well as expression of a phenotype. In 7 individuals with single nucleotide variant found in NGS testing, the MLPA of the CAPN3 gene was performed detecting the deletion encompassing exons 2-8 in the CAPN3 gene in one patient, confirming recessive limb-girdle muscular dystrophy type 1 (LGMDR1). Thirty patients obtained a genetic diagnosis (57.7%) after using NGS testing, genotyping and MLPA analysis. The study allowed for the identification of 27 known and 4 novel pathogenic/likely pathogenic variants and variants of uncertain significance (VUS) associated with NMDs.In conclusion, the diagnostic approach with diverse molecular techniques enables to broaden the mutational spectrum and maximizes the diagnostic yield. Furthermore, the co-occurrence of DM2 and LGMD has been detected in 2 individuals.

Next-generation sequencing of 500 POI patients identified novel responsible monogenic and oligogenic variants

BACKGROUND

Premature ovarian insufficiency refers to the loss of ovarian function before 40 years of age. The etiology is heterogeneous, and genetic factors account for 20-25% of cases. However, how to transform genetic findings to clinical molecular diagnose remains a challenge. To identify potential causative variations for POI, a next generation sequencing panel with 28 known causative genes of POI was designed, and a large cohort of 500 Chinese Han patients was screened directly. Pathogenic evaluation of the identified variants and the phenotype analysis were performed according to monogenic or oligogenic variants.

RESULTS

A total of 14.4% (72/500) of the patients carried 61 pathogenic or likely pathogenic variants in 19 of the genes in the panel. Interestingly, 58 variants (95.1%, 58/61) were firstly identified in patients with POI. FOXL2 harbored the highest occurrence frequency (3.2%, 16/500), among whom presented with isolated ovarian insufficiency instead of blepharophimosis-ptosis-epicanthus inversus syndrome. Moreover, luciferase reporter assay confirmed variant p.R349G, which account for 2.6% of POI cases, impaired the transcriptional repressive effect of FOXL2 on CYP17A1. The novel compound heterozygous variants in NOBOX and MSH4 were confirmed by pedigree haplotype analysis, and digenic heterozygous variants in MSH4 and MSH5 were firstly identified. Furthermore, nine patients (1.8%, 9/500) with digenic or multigenic pathogenic variants presented with delayed menarche, early onset of POI and high prevalence of primary amenorrhea compared with those with monogenic variation(s).

CONCLUSIONS

The genetic architecture of POI has been enriched through the targeted gene panel in a large cohort of patients with POI. Specific variants in pleiotropic genes may result in isolated POI rather than syndromic POI, whereas oligogenic defects might have cumulative deleterious effects on the severity of POI phenotype.

Novel ACTN2 missense variant is associated with idiopathic ventricular fibrillation: a case report

BACKGROUND

Idiopathic ventricular fibrillation (VF) is a diagnosis of exclusion made in patients who experience VF without an attributable cause. Pathogenic variants of the ACTN2 gene encoding the sarcomeric protein alpha-actinin-2 are known to cause hypertrophic and dilated cardiomyopathy. We show that ACTN2 variants may also be associated with malignant arrhythmias in the absence of overt structural heart disease.

CASE SUMMARY

A 48-year-old female presented with cardiac arrest due to VF without any history of cardiovascular disease or family history of sudden cardiac death. Troponin I was elevated at 0.698 ng/mL, but coronary angiography showed no significant coronary artery disease. Substance abuse testing showed elevated benzodiazepine and sertraline levels, which she was taking for anxiety. Electrocardiogram showed normal QRS complexes without prolonged PR or QTc intervals. She underwent therapeutic hypothermia. Cardiac magnetic resonance imaging at 2 weeks showed normal biventricular function without structural abnormalities, fibrosis, or evidence of myocardial infarction. A targeted gene panel revealed a heterozygous missense variant of unknown significance (VUS) in exon 18 of the ACTN2 gene (c.2162G > A/p.R721H).

DISCUSSION

The identified VUS is located in a highly conserved residue of a spectrin-like repeat domain of alpha-actinin-2. Spectrin-like domains of alpha-actinin-2 bind and regulate the ion channels Na_v1.5, K_v1.4, and K_v1.5, which contribute to the myocardial action potential. The VUS was predicted as pathogenic by MutationTaster, Polymorphism Phenotyping v2, and Sorting Intolerant From Tolerant in silico missense prediction tools. The c.2162G > A/p.R721H alpha-actinin-2 variant may result in dysregulation of cardiac ion channels, leading to arrhythmias.

Study of ten causal genes in Turkish patients with clinically suspected maturity-onset diabetes of the young (MODY) using a targeted next-generation sequencing panel

BACKGROUND

Maturity-onset diabetes of the young (MODY), which is the most common cause of monogenic diabetes, has an autosomal dominant pattern of inheritance and exhibits marked clinical and genetic heterogeneity. The aim of the current study was to investigate molecular defects in patients with clinically suspected MODY using a next-generation sequencing (NGS)-based targeted gene panel.

METHODS

Candidate patients with clinical suspicion of MODY and their parents were included in the study. Molecular genetic analyses were performed on genomic DNA by using NGS. A panel of ten MODY-causal genes involving GCK, HNF1A, HNF1B, HNF4A, ABCC8, CEL, INS, KCNJ11, NEUROD1, PDX1 was designed and subsequently implemented to screen 40 patients for genetic variants.

RESULTS

Ten different pathogenic or likely pathogenic variants were identified in MODY-suspected patients, with a diagnostic rate of 25%. Three variants of uncertain significance were also detected in the same screen. A novel pathogenic variant in the gene HNF1A (c.505_506delAA [p.Lys169AlafsTer18]) was described for the first time in this report. Intriguingly, we were able to detect variants associated with rare forms of MODY in our study population.

CONCLUSIONS

Our results suggest that in heterogenous diseases such as MODY, NGS analysis enables accurate identification of underlying molecular defects in a timely and cost-effective manner. Although MODY accounts for 2-5% of all diabetic cases, molecular genetic diagnosis of MODY is necessary for optimal long-term treatment and prognosis as well as for effective genetic counseling.

Very Early-Onset Inflammatory Bowel Disease: A Challenging Field for Pediatric Gastroenterologists

With the increasing number of children with inflammatory bowel disease (IBD), very early-onset IBD (VEO-IBD), defined as IBD that is diagnosed or that develops before 6 years of age, has become a field of innovation among pediatric gastroenterologists. Advances in genetic testing have enabled the diagnosis of IBD caused by gene mutations, also known as monogenic or Mendelian disorder-associated IBD (MD-IBD), with approximately 60 causative genes reported to date. The diagnosis of VEO-IBD requires endoscopic and histological evaluations. However, satisfactory small bowel imaging studies may not be feasible in this small population. Both genetic and immunological approaches are necessary for the diagnosis of MD-IBD, which can differ among countries according to the available resources. As a result of the use of targeted gene panels covered by the national health insurance and the nationwide research project investigating inborn errors of immunity, an efficient approach for the diagnosis of MD-IBD has been developed in Japan. Proper management of VEO-IBD by pediatric gastroenterologists constitutes a challenge. Some MD-IBDs can be curable by allogenic hematopoietic stem cell transplantation. With an understanding of the affected gene functions, targeted therapies are being developed. Social and psychological support systems for both children and their families should also be provided to improve their quality of life. Multidisciplinary team care would contribute to early diagnosis, proper therapeutic interventions, and improved quality of life in patients and their families.

Clinical and genetic features of congenital dyserythropoietic anemia (CDA)

INTRODUCTION

Congenital dyserythropoietic anemias (CDA) are characterized by hyporegenerative anemia with inadequate reticulocyte values, ineffective erythropoiesis, and hemolysis. Distinctive morphology of bone marrow erythroblasts and identification of causative genes allow classification into 4 types caused by variants in CDAN1, c15orf41, SEC23B, KIF23, and KLF1 genes.

OBJECTIVE

Identify pathogenic variants in CDA patients.

METHODS

Massive parallel sequencing with a targeted gene panel, Sanger sequencing, Comparative Genome Hybridization (CGH), and in silico predictive analysis of pathogenicity.

RESULTS

Pathogenic variants were found in 21 of 53 patients studied from 44 unrelated families. Six variants were found in CDAN1: two reported, p.Arg714Trp and p.Arg725Trp and, four novel, p.Arg623Trp, p.Arg946Trp, p.Phe1125Ser and p.Ser1227Gly. Twelve variants were found in SEC23B: seven reported, p.Arg14Trp, p.Glu109Lys, p.Arg217Ter, c.835-2A>G, p.Arg535Ter, p.Arg550Ter and p.Arg718Ter and, five novel, p.Val164Leu, p.Arg190Gln, p.Gln521Ter, p.Arg546Trp, and p.Arg611Gln. The variant p.Glu325Lys in KLF1 was found in one patient and p.Tyr365Cys in ALAS2 in an other. Moreover, we identified genomic rearrangements by CGH in some SEC23B-monoallelic patients.

CONCLUSIONS

New technologies for genetic studies will help to find variants in other genes, in addition to those known, that contribute to or modulate the CDA phenotype or support the correct diagnosis.

GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data

BACKGROUND

NGS technology represents a powerful alternative to the standard Sanger sequencing in the context of clinical setting. The proprietary software that are generally used for variant calling often depend on preset parameters that may not fit in a satisfactory manner for different genes. GATK, which is widely used in the academic world, is rich in parameters for variant calling. However the self-adjusting parameter calibration of GATK requires data from a large number of exomes. When these are not available, which is the standard condition of a diagnostic laboratory, the parameters must be set by the operator (hard filtering). The aim of the present paper was to set up a procedure to assess the best parameters to be used in the hard filtering of GATK. This was pursued by using classification trees on true and false variants from simulated sequences of a real dataset data.

RESULTS

We simulated two datasets, with different coverages, including all the sequence alterations identified in a real dataset according to their observed frequencies. Simulated sequences were aligned with standard protocols and then regression trees were built up to identify the most reliable parameters and cutoff values to discriminate true and false variant calls. Moreover, we analyzed flanking sequences of region presenting a high rate of false positive calls observing that such sequences present a low complexity make up.

CONCLUSIONS

Our results showed that GATK hard filtering parameter values can be tailored through a simulation study based-on the DNA region of interest to ameliorate the accuracy of the variant calling.

Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort

Background

Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients receive an accurate clinical genetic diagnosis. To address this we have developed a massively parallel sequencing targeted DSD gene panel which allows us to sequence all 64 known diagnostic DSD genes and candidate genes simultaneously.

Results

We analyzed DNA from the largest reported international cohort of patients with DSD (278 patients with 46,XY DSD and 48 with 46,XX DSD). Our targeted gene panel compares favorably with other sequencing platforms. We found a total of 28 diagnostic genes that are implicated in DSD, highlighting the genetic spectrum of this disorder. Sequencing revealed 93 previously unreported DSD gene variants. Overall, we identified a likely genetic diagnosis in 43% of patients with 46,XY DSD. In patients with 46,XY disorders of androgen synthesis and action the genetic diagnosis rate reached 60%. Surprisingly, little difference in diagnostic rate was observed between singletons and trios. In many cases our findings are informative as to the likely cause of the DSD, which will facilitate clinical management.

Conclusions

Our massively parallel sequencing targeted DSD gene panel represents an economical means of improving the genetic diagnostic capability for patients affected by DSD. Implementation of this panel in a large cohort of patients has expanded our understanding of the underlying genetic etiology of DSD. The inclusion of research candidate genes also provides an invaluable resource for future identification of novel genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1105-y) contains supplementary material, which is available to authorized users.