scholarly journals A Case Report of Genetic Cascade Screening in Dilated Cardio-myopathy: A Perspective for Preventive Cardiology

2021 ◽  
Author(s):  
Zeinab Barati ◽  
Dariush Farhoud ◽  
Uwe Nixdorff ◽  
Mohammadreza Mohammadhasani ◽  
Maryam Eslami ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genetic Disorders ◽  
Clinical Manifestations ◽  
Cascade Screening ◽  
Preventive Cardiology ◽  
Treatment And Prevention ◽  
Whole Exome ◽  
Diagnostic Role ◽  
Predictive Risk ◽  
Next Generation Sequencing Ngs

Cardiomyopathies are heterogeneous and critical disorders of cardiovascular diseases. One of the most common inherited cardiomyopathies is DCM (dilated cardiomyopathy). Genetic disorders are found in approximately 50% of DCM cases. We aimed to describe a case of DCM in a 42-year-old woman in 2018 at Farhud Genetic Clinic, Tehran, Iran. To detect genetic involvement, Next-generation sequencing (NGS) was performed and the data were evaluated carefully. Variations in different genes coding crucial proteins in cardiac muscle structure (i.e. Titin, Obscurin, MYH6, and LAMA4) and proteins involved in channels (i.e. CAVNA1C, SCN1B and SCN5A) were detected by whole-exome sequencing (WES). In agreement with the clinical manifestations and molecular analysis, DCM was confirmed. This study provides further evidence on the diagnostic role of NGS in borderline DCM cases. It also shows the recently developed high throughput sequencing can provide clinicians with this approach to diagnosis, treatment, and prevention of such hard-to-diagnose disorders. Furthermore, this study highlights the basis of personalized medicine, namely detection of high-risk individuals by revealing some genetic variants as predictive risk factors, and initial prevention of DCM.

scholarly journals Case Report: Application of whole exome sequencing for accurate diagnosis of rare syndromes of mineralocorticoid excess

F1000Research ◽  
2017 ◽  
Vol 5 ◽  
pp. 1592 ◽  
Author(s):  
Ranjit Narayanan ◽  
Shamsudheen Karuthedath Vellarikkal ◽  
Rijith Jayarajan ◽  
Ankit Verma ◽  
Vishal Dixit ◽  
...  
Keyword(s):  
Case Report ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Disease Surveillance ◽  
Genetic Disorders ◽  
Clinical Manifestations ◽  
Accurate Diagnosis ◽  
South Indian ◽  
Whole Exome ◽  
Apparent Mineralocorticoid Excess

Syndromes of mineralocorticoid excess (SME) are closely related clinical manifestations occurring within a specific set of diseases. Overlapping clinical manifestations of such syndromes often create a dilemma in accurate diagnosis, which is crucial for disease surveillance and management especially in rare genetic disorders. Here we demonstrate the use of whole exome sequencing (WES) for accurate diagnosis of rare SME and report that p.R337C variation in the HSD11B2 gene causes progressive apparent mineralocorticoid excess (AME) syndrome in a South Indian family of Mappila origin.

scholarly journals High-Throughput Sequencing to Identify Mutations Associated with Retinal Dystrophies

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1269
Author(s):  
Fei Song ◽  
Marta Owczarek-Lipska ◽  
Tim Ahmels ◽  
Marius Book ◽  
Sabine Aisenbrey ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genetic Diagnosis ◽  
Clinical Manifestations ◽  
Sequence Variants ◽  
Pathogenic Variants ◽  
Retinal Dystrophies ◽  
Whole Exome ◽  
Uncertain Significance ◽  
Disease Associated Genes ◽  
Intronic Variants

Retinal dystrophies (RD) are clinically and genetically heterogenous disorders showing mutations in over 270 disease-associated genes. Several millions of people worldwide are affected with different types of RD. Studying the relevance of disease-associated sequence alterations will assist in understanding disorders and may lead to the development of therapeutic approaches. Here, we established a whole exome sequencing (WES) pipeline to rapidly identify disease-associated mutations in patients. Sanger sequencing was applied to identify deep-intronic variants and to verify the co-segregation of WES results within families. We analyzed 26 unrelated patients with different syndromic and non-syndromic clinical manifestations of RD. All patients underwent ophthalmic examinations. We identified nine novel disease-associated sequence variants among 37 variants identified in total. The sequence variants located to 17 different genes. Interestingly, two cases presenting with Stargardt disease carried deep-intronic variants in ABCA4. We have classified 21 variants as pathogenic variants, 4 as benign/likely benign variants, and 12 as variants of uncertain significance. This study highlights the importance of WES-based mutation analyses in RD patients supporting clinical decisions, broadly based genetic diagnosis and support genetic counselling. It is essential for any genetic therapy to expand the mutation spectrum, understand the genes’ function, and correlate phenotypes with genotypes.

scholarly journals Case Report: Application of whole exome sequencing for accurate diagnosis of rare syndromes of mineralocorticoid excess

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1592 ◽  
Author(s):  
Ranjit Narayanan ◽  
Shamsudheen Karuthedath Vellarikkal ◽  
Rijith Jayarajan ◽  
Ankit Verma ◽  
Vishal Dixit ◽  
...  
Keyword(s):  
Case Report ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Disease Surveillance ◽  
Genetic Disorders ◽  
Clinical Manifestations ◽  
Accurate Diagnosis ◽  
South Indian ◽  
Whole Exome ◽  
Apparent Mineralocorticoid Excess

Syndromes of mineralocorticoid excess (SME) are closely related clinical manifestations occurring within a specific set of diseases. Overlapping clinical manifestations of such syndromes often create a dilemma in accurate diagnosis, which is crucial for disease surveillance and management especially in rare genetic disorders. Here we demonstrate the use of whole exome sequencing (WES) for accurate diagnosis of rare SME and report that p.R337C variation in the HSD11B2 gene causes progressive apparent mineralocorticoid excess (AME) syndrome in a South Indian family of Mappila origin.

Singapore Undiagnosed Disease Program: Genomic Analysis aids Diagnosis and Clinical Management

2020 ◽  
Vol 106 (1) ◽  
pp. 31-37 ◽  
Author(s):  
Neha S Bhatia ◽  
Jiin Ying Lim ◽  
Carine Bonnard ◽  
Jyn-Ling Kuan ◽  
Maggie Brett ◽  
...  
Keyword(s):  
Diagnostic Yield ◽  
Genetic Disorders ◽  
Genomic Analysis ◽  
Chromosomal Microarray ◽  
Diagnostic Study ◽  
Undiagnosed Disease ◽  
Whole Exome ◽  
Time To Diagnosis ◽  
Aids Diagnosis ◽  
Next Generation Sequencing Ngs

ObjectiveUse next-generation sequencing (NGS) technology to improve our diagnostic yield in patients with suspected genetic disorders in the Asian setting.DesignA diagnostic study conducted between 2014 and 2019 (and ongoing) under the Singapore Undiagnosed Disease Program. Date of last analysis was 1 July 2019.SettingInpatient and outpatient genetics service at two large academic centres in Singapore.PatientsInclusion criteria: patients suspected of genetic disorders, based on abnormal antenatal ultrasound, multiple congenital anomalies and developmental delay. Exclusion criteria: patients with known genetic disorders, either after clinical assessment or investigations (such as karyotype or chromosomal microarray).InterventionsUse of NGS technology—whole exome sequencing (WES) or whole genome sequencing (WGS).Main outcome measures(1) Diagnostic yield by sequencing type, (2) diagnostic yield by phenotypical categories, (3) reduction in time to diagnosis and (4) change in clinical outcomes and management.ResultsWe demonstrate a 37.8% diagnostic yield for WES (n=172) and a 33.3% yield for WGS (n=24). The yield was higher when sequencing was conducted on trios (40.2%), as well as for certain phenotypes (neuromuscular, 54%, and skeletal dysplasia, 50%). In addition to aiding genetic counselling in 100% of the families, a positive result led to a change in treatment in 27% of patients.ConclusionGenomic sequencing is an effective method for diagnosing rare disease or previous ‘undiagnosed’ disease. The clinical utility of WES/WGS is seen in the shortened time to diagnosis and the discovery of novel variants. Additionally, reaching a diagnosis significantly impacts families and leads to alteration in management of these patients.

scholarly journals Transcriptome Profile Alterations with Carbon Nanotubes, Quantum Dots, and Silver Nanoparticles: A Review

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 794
Author(s):  
Cullen Horstmann ◽  
Victoria Davenport ◽  
Min Zhang ◽  
Alyse Peters ◽  
Kyoungtae Kim
Keyword(s):  
Carbon Nanotubes ◽  
Quantum Dots ◽  
High Throughput Sequencing ◽  
The Body ◽  
Rna Seq ◽  
Mechanisms Of Toxicity ◽  
Promising Tool ◽  
Engineered Nanomaterial ◽  
Next Generation Sequencing Ngs ◽  
Transcriptomic Changes

Next-generation sequencing (NGS) technology has revolutionized sequence-based research. In recent years, high-throughput sequencing has become the method of choice in studying the toxicity of chemical agents through observing and measuring changes in transcript levels. Engineered nanomaterial (ENM)-toxicity has become a major field of research and has adopted microarray and newer RNA-Seq methods. Recently, nanotechnology has become a promising tool in the diagnosis and treatment of several diseases in humans. However, due to their high stability, they are likely capable of remaining in the body and environment for long periods of time. Their mechanisms of toxicity and long-lasting effects on our health is still poorly understood. This review explores the effects of three ENMs including carbon nanotubes (CNTs), quantum dots (QDs), and Ag nanoparticles (AgNPs) by cross examining publications on transcriptomic changes induced by these nanomaterials.

scholarly journals Phenocopy of a heterozygous carrier of X-linked retinitis pigmentosa due to mosaicism for a RHO variant

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ine Strubbe ◽  
Caroline Van Cauwenbergh ◽  
Julie De Zaeytijd ◽  
Sarah De Jaegere ◽  
Marieke De Bruyne ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Somatic Mosaicism ◽  
Retinal Disease ◽  
Hair Follicles ◽  
Disease Genes ◽  
Female Carrier ◽  
Autofluorescence Imaging ◽  
Targeted Next Generation Sequencing ◽  
Whole Exome ◽  
Next Generation Sequencing Ngs

AbstractWe describe both phenotype and pathogenesis in two male siblings with typical retinitis pigmentosa (RP) and the potentially X-linked RP (XLRP) carrier phenotype in their mother. Two affected sons, two unaffected daughters, and their mother underwent detailed ophthalmological assessments including Goldmann perimetry, color vision testing, multimodal imaging and ISCEV-standard electroretinography. Genetic testing consisted of targeted next-generation sequencing (NGS) of known XLRP genes and whole exome sequencing (WES) of known inherited retinal disease genes (RetNet-WES). Variant validation and segregation analysis were performed by Sanger sequencing. The mutational load of the RHO variant in the mother was assessed in DNA from leucocytes, buccal cells and hair follicles using targeted NGS. Both affected sons showed signs of classical RP, while the mother displayed patches of hyperautofluorescence on blue light autofluorescence imaging and regional, intraretinal, spicular pigmentation, reminiscent of a carrier phenotype of XLRP. XLRP testing was negative. RetNet-WES testing revealed RHO variant c.404G > C p.(Arg135Pro) in a mosaic state (21% of the reads) in the mother and in a heterozygous state in both sons. Targeted NGQSS of the RHO variant in different maternal tissues showed a mutation load between 25.06% and 41.72%. We report for the first time that somatic mosaicism of RHO variant c.404G > C p.(Arg135Pro) mimics the phenotype of a female carrier of XLRP, in combination with heterozygosity for the variant in the two affected sons.

scholarly journals Facial cleft? The first case of manitoba‐oculo‐tricho‐anal syndrome with novel mutations in China: a case report

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shuchen Gu ◽  
Yimin Khoong ◽  
Xin Huang ◽  
Tao Zan
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clinical Manifestations ◽  
Sporadic Case ◽  
Facial Cleft ◽  
Ocular Manifestations ◽  
First Case ◽  
Whole Exome ◽  
Chinese Girl ◽  
Low Prevalence

Abstract Background Manitoba-oculo-tricho-anal (MOTA) syndrome is a rare syndrome with only 27 cases reported worldwide so far, but none was reported in the population of Eastern Asia. Such extremely low prevalence might be contributed by misdiagnosis due to its similarities in ocular manifestations with facial cleft. In our study, we discovered the first case of MOTA syndrome in the population of China, with 2 novel FRAS1 related extracellular matrix 1 (FREM1) gene stop-gain mutations confirmed by whole exome sequencing. Case presentation A 12-year-old Chinese girl presented with facial cleft-like deformities including aberrant hairline, blepharon-coloboma and broad bifid nose since birth. Whole exome sequencing resulted in the identification of 2 novel stop-gain mutations in the FREM1 gene. Diagnosis of MOTA syndrome was then established. Conclusions We discovered the first sporadic case of MOTA syndrome according to clinical manifestations and genetic etiology in the Chinese population. We have identified 2 novel stop-gain mutations in FREM1 gene which further expands the spectrum of mutational seen in the MOTA syndrome. Further research should be conducted for better understanding of its mechanism, establishment of an accurate diagnosis, and eventually the exploitation of a more effective and comprehensive therapeutic intervention for MOTA syndrome.

scholarly journals HERVs establish a distinct molecular subtype in stage II/III colorectal cancer with poor outcome

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Mahdi Golkaram ◽  
Michael L. Salmans ◽  
Shannon Kaplan ◽  
Raakhee Vijayaraghavan ◽  
Marta Martins ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Molecular Subtype ◽  
Endogenous Retroviruses ◽  
Stage Ii ◽  
Clinicopathological Factors ◽  
Whole Exome ◽  
Potential Biomarker ◽  
Whole Transcriptome Sequencing ◽  
Next Generation Sequencing Ngs ◽  
Herv Expression

AbstractColorectal cancer (CRC) is one of the most lethal malignancies. The extreme heterogeneity in survival rate is driving the need for new prognostic biomarkers. Human endogenous retroviruses (hERVs) have been suggested to influence tumor progression, oncogenesis and elicit an immune response. We examined multiple next-generation sequencing (NGS)-derived biomarkers in 114 CRC patients with paired whole-exome and whole-transcriptome sequencing (WES and WTS, respectively). First, we demonstrate that the median expression of hERVs can serve as a potential biomarker for prognosis, relapse, and resistance to chemotherapy in stage II and III CRC. We show that hERV expression and CD8+ tumor-infiltrating T-lymphocytes (TILs) synergistically stratify overall and relapse-free survival (OS and RFS): the median OS of the CD8-/hERV+ subgroup was 29.8 months compared with 37.5 months for other subgroups (HR = 4.4, log-rank P < 0.001). Combing NGS-based biomarkers (hERV/CD8 status) with clinicopathological factors provided a better prediction of patient survival compared to clinicopathological factors alone. Moreover, we explored the association between genomic and transcriptomic features of tumors with high hERV expression and establish this subtype as distinct from previously described consensus molecular subtypes of CRC. Overall, our results underscore a previously unknown role for hERVs in leading to a more aggressive subtype of CRC.

scholarly journals Primary immune deficiencies with defects in neutrophil function

Hematology ◽  
2016 ◽  
Vol 2016 (1) ◽  
pp. 43-50 ◽  
Author(s):  
Mary C. Dinauer
Keyword(s):  
Fungal Infections ◽  
Leukocyte Adhesion ◽  
Genetic Disorders ◽  
Clinical Manifestations ◽  
Treatment Strategies ◽  
Adaptor Protein ◽  
Invasive Fungal Disease ◽  
Neutrophil Function ◽  
Microbial Pathogens ◽  
Immune Deficiencies

Abstract Immune deficiencies resulting from inherited defects in neutrophil function have revealed important features of the innate immune response. Although sharing an increased susceptibility to bacterial and fungal infections, these disorders each have distinctive features in their clinical manifestations and characteristic microbial pathogens. This review provides an update on several genetic disorders with impaired neutrophil function, their pathogenesis, and treatment strategies. These include chronic granulomatous disease, which results from inactivating mutations in the superoxide-generating nicotinamide dinucleotide phosphate oxidase. Superoxide-derived oxidants play an important role in the control of certain bacterial and fungal species, and also contribute to the regulation of inflammation. Also briefly summarized are updates on leukocyte adhesion deficiency, including the severe periodontal disease characteristic of this disorder, and a new immune deficiency associated with defects in caspase recruitment domain–containing protein 9, an adaptor protein that regulates signaling in neutrophils and other myeloid cells, leading to invasive fungal disease.

Identification of novel exonic variants responsible for hereditary breast and ovarian cancer in West Indian population

2021 ◽  
Author(s):  
Bhargav N. Waghela ◽  
Ramesh J. Pandit ◽  
Apurvasinh Puvar ◽  
Franky D. Shah ◽  
Prabhudas S. Patel ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Early Diagnosis ◽  
West Indian ◽  
Disease Association ◽  
Dna Integrity ◽  
Degree Relative ◽  
Mortality And Morbidity ◽  
Whole Exome ◽  
Novel Variants ◽  
Next Generation Sequencing Ngs

Abstract Background Breast and ovarian cancers are the most common cancer types in females in India which pertain to higher mortality and morbidity due to late diagnosis and poor prognosis. Early diagnosis for better prognosis improve the patient’s treatment and survival. The next-generation sequencing (NGS)-based screening has accelerated molecular diagnosis of various cancers. Methods We performed whole exome sequencing (WES) of 30 patients who had a first or second degree relative with breast or ovarian cancer. Further, all these patients are tested negative for BRCA1/2 or other high and moderate risk genes reported for HBOC. WES data from 30 patients were analyzed and variants were called using bcftools. Functional annotation of variants and variant prioritization was performed by Exomiser. The clinical significance of variants was determined by Varsome tool. The functional analysis of genes was determined by STRING analysis and disease association was determined by open target tool. Results We examined the variants based on the prevalence of variants among 30 patients i.e. frequency and disease association determined by the phenotype score of exomiser. From both the approaches, we found novel variants and novel gene candidates associated with HBOC conditions. The variants in HYDIN, AVIL, IWS1, PLA2G6, PRDM4, ST3GAL2, and ZNF717 were predicted highly oncogenic. Moreover, we also found 59 genes having higher phenotype score (phenotype score >0.75) and which are associated with various biological processes such as DNA integrity maintenance, transcriptional regulation, cell cycle and apoptosis. Conclusion The gene variants associated with HBOC condition in West Indian cohort have been revisited. Our findings provide novel as well as highly prevalent variants in the population which could be further studied in detail for their use in early diagnosis and better prognosis of HBOC patients.

Sign in / Sign up

Export Citation Format

Share Document