Exome Sequencing and Epigenetic Analysis of Twins Who Are Discordant for Congenital Cataract

2015 ◽  
Vol 18 (4) ◽  
pp. 393-398 ◽  
Author(s):  
Tanwei Wei ◽  
Hui Sun ◽  
Bo Hu ◽  
Jie Yang ◽  
Chen Qiao ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Candidate Genes ◽  
Sanger Sequencing ◽  
Congenital Cataract ◽  
Genetic Factors ◽  
Twin Pair ◽  
Mutation Screening ◽  
Sequencing Analysis ◽  
Twin Sister ◽  
Epigenetic Events

Purpose: To further understand genetic factors that contribute to congenital cataracts, we sought to identify early post-twinning mutational and epigenetic events that may account for the discordant phenotypes of a twin pair. Methods: A patient with a congenital cataract and her twin sister were assessed for genetic factors that might contribute to their discordant phenotypes by mutation screening of 11 candidate genes (CRYGC, CRYGD, CRYAA, CRYAB, CRYBA1, CRYBB1, CRYBB2, MIP, HSF4, GJA3, and GJA8), exome analysis followed by Sanger sequencing of 10 additional candidate genes (PLEKHO2, FRYL, RBP3, P2RX2, GSR, TRAM1, VEGFA, NARS2, CADPS, and TEKT4), and promoter methylation analysis of five representative genes (TRAM1, CRYAA, HSF4, VEGFA, GJA3, DCT) plus one additional candidate gene (FTL). Results: Mutation screening revealed no gene mutation differences between the patient and her twin sister for the 11 candidate genes. Exome sequencing analysis revealed variations between the twins in 442 genes, 10 of which are expressed in the eye. However, these differential variants could not be confirmed by Sanger sequencing. Furthermore, epigenetic discordance was not detected in the twin pair. Conclusions: The genomic DNA mutational and epigenetic events assessed in this study could not explain the discordance in the development of phenotypic differences between the twin pair, suggesting the possible involvement of somatic mutations or environmental factors. Identification of possible causes requires further research.

scholarly journals NAPG mutation in family members with hereditary hemorrhagic telangiectasia in China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yu Xu ◽  
Yong-Biao Zhang ◽  
Li-Jun Liang ◽  
Jia-Li Tian ◽  
Jin-Ming Lin ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Hereditary Hemorrhagic Telangiectasia ◽  
Sanger Sequencing ◽  
Conformational Stability ◽  
Sequencing Analysis ◽  
Large Pedigree ◽  
Whole Exome ◽  
Variant Filtering ◽  
Genetic Contributions

Abstract Background Hereditary hemorrhagic telangiectasia (HHT) is a disease characterized by arteriovenous malformations in the skin and mucous membranes. We enrolled a large pedigree comprising 32 living members, and screened for mutations responsible for HHT. Methods We performed whole-exome sequencing to identify novel mutations in the pedigree after excluding three previously reported HHT-related genes using Sanger sequencing. We then performed in silico functional analysis of candidate mutations that were obtained using a variant filtering strategy to identify mutations responsible for HHT. Results After screening the HHT-related genes, activin A receptor-like type 1 (ACVRL1), endoglin (ENG), and SMAD family member 4 (SMAD4), we did not detect any co-segregated mutations in this pedigree. Whole-exome sequencing analysis of 7 members and Sanger sequencing analysis of 16 additional members identified a mutation (c.784A > G) in the NSF attachment protein gamma (NAPG) gene that co-segregated with the disease. Functional prediction showed that the mutation was deleterious and might change the conformational stability of the NAPG protein. Conclusions NAPG c.784A > G may potentially lead to HHT. These results expand the current understanding of the genetic contributions to HHT pathogenesis.

scholarly journals Next Generation Exome Sequencing of paediatric Asthma Identifies Rare and Novel Variants in Candidate Genes

2020 ◽  
Author(s):  
Neda Bogari ◽  
Amr A Amin ◽  
Husni H Rayes ◽  
Ahmed Abdelmotelb ◽  
Mohiuddin M Taher ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Candidate Genes ◽  
Association Studies ◽  
Reference Sequence ◽  
Exome Capture ◽  
Sequencing Analysis ◽  
Genetic Determinants ◽  
Paediatric Asthma ◽  
Novel Variants ◽  
The Impact

Abstract Background: Multiple genes have been implicated to have a role in asthma predisposition by association studies. Paediatric patients often manifest more extensive disease and a particularly severe disease course. It is likely that genetic predisposition could play a more substantial role in this group. This study aims to identify the spectrum of rare and novel variation in known paediatric asthma susceptibility genes using whole exome sequencing-analysis in nine individual cases of childhood onset allergic asthma. Data were processed through an analytical pipeline to align sequence reads, conduct quality checks, identify and annotate variants where patient sequence differed from the reference sequence. Results: DNA samples from the nine children with a history of bronchial asthma diagnosis underwent targeted exome capture and sequencing. For each patient, the entire complement of rare variation within strongly associated candidate genes was catalogued. The analysis showed 21 variants in the subjects, 13 had been previously identified and 8 were novel. Also, amongst of which, nineteen were non-synonymous and 2 were nonsense. With regard to the novel variants, the 2 non-synonymous variants in the PRKG1 gene (PRKG1: p.C519W and PRKG1: p.G520W) were presented in 4 cases, and a non-synonymous variant in the MAVS gene (MAVS: p.A45V) was identified in 3 cases. The variants we found in this study will enrich the variants spectrum and build up the database in the Saudi population. Novel eight variants were identified in the study which provides more evidence in the genetic susceptibility in asthma among Saudi children.Conclusion: Screening a cohort of Saudi children for molecular identification of polymorphisms associated with allergic asthmatic response. These, together with the clinical phenotypes, revealed genetic determinants for paediatric asthma and also we compared to the similar previous reports. Providing a genetic screening map for the molecular genetic determinants of allergic disease in Saudi children, with the goal of reducing the impact of chronic diseases on the health and the economy. We belief that the advanced specified statistical filtration/annotation programs used in this study succeeded to release such results in preliminary study, exploring the genetic map of that disease in Saudi children.

scholarly journals O2-10-02: WHOLE EXOME SEQUENCING ANALYSIS IN EARLY ONSET ALZHEIMER REVEALS NOVEL CANDIDATE GENES

2019 ◽  
Vol 15 ◽  
pp. P564-P564
Author(s):  
Victoria Fernandez ◽  
Dalton Huey ◽  
John P. Budde ◽  
Fabiana H.G. Farias ◽  
Oscar Harari ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Candidate Genes ◽  
Whole Exome Sequencing ◽  
Early Onset ◽  
Sequencing Analysis ◽  
Whole Exome

COL4A1 and COL4A2 Mutations Analyses with Perinatal Arterial İschemic Stroke

2020 ◽  
Author(s):  
Ozan Koçak ◽  
Kursat Bora Carman Bora Carman ◽  
Coskun Yarar ◽  
Hirofumi Kodera ◽  
Hirotomo Saitsu ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Small Vessel Disease ◽  
Mutation Screening ◽  
Laboratory Data ◽  
Sequencing Analysis ◽  
Arterial Ischemic Stroke ◽  
Whole Exome ◽  
Perinatal Arterial Ischemic Stroke

Perinatal arterial ischemic stroke (PAIS) is one of the frequent causes of mortality and morbidity, but its etiology remains unclear. COL4A1 and COL4A2 mutations are monogenetic causes of weakness of the basement vascular membranes resulting in cerebral small-vessel disease, cerebral hemorrhage, and porencephaly. We hypothesized that variations in the COL4A1 and COL4A2 genes cause PAIS and performed mutation screening of these genes in 17 PAIS patients by whole-exome sequencing. Clinical, demographic, and laboratory data of the 17 PAIS patients were obtained by evaluating hospital files retrospectively. Patients included in the study were invited to the clinic for COL4A1 and COL4A2 mutation analysis. Results: The patient group consisted of 13 females (76.5%) and four males (23.5%) with a mean age of 107.4 ± 11.5 months. Maternal/fetal and prothrombotic risk factors identified in 52.9% and 94.1% of the patients, respectively. Whole-exome sequencing analysis did not reveal COL4A1 and COL4A2 pathological mutations in any of the patients.  Although we did not find an association between PAIS and COL4A1 and COL4A2 variations, we believe that new studies with larger patient populations may reveal such a relationship.

scholarly journals Association of Mutations in SLC12A1 Encoding the NKCC2 Cotransporter With Neonatal Primary Hyperparathyroidism

2016 ◽  
Vol 101 (5) ◽  
pp. 2196-2200 ◽  
Author(s):  
Dong Li ◽  
Lifeng Tian ◽  
Cuiping Hou ◽  
Cecilia E. Kim ◽  
Hakon Hakonarson ◽  
...  
Keyword(s):  
Primary Hyperparathyroidism ◽  
Exome Sequencing ◽  
Sanger Sequencing ◽  
Bartter Syndrome ◽  
Multiple Organ ◽  
Sequencing Analysis ◽  
Sodium Potassium ◽  
Slc12a1 Gene ◽  
Gland Function

Abstract Context: Primary hyperparathyroidism with hypercalciuria has not been described in the newborn period. Objective: Our objectives are to identify the genetic basis for neonatal primary hyperparathyroidism in a family with 2 affected children. Subjects: An African American boy presenting with mild neonatal primary hyperparathyroidism and hypercalciuria was evaluated at The Children's Hospital of Philadelphia. His older brother with neonatal primary hyperparathyroidism had died in infancy of multiple organ failure. Methods: We collected clinical and biochemical data and performed exome sequencing analysis on DNA from the patient and his unaffected mother after negative genetic testing for known causes of primary hyperparathyroidism. Results: Exome sequencing followed by Sanger sequencing disclosed 2 heterozygous mutations, c.1883C>A, p.(A628D) and c.2786_2787insC, p.(T931fsX10), in the SLC12A1 gene, which was previously implicated in antenatal type 1 Bartter syndrome. Sanger sequencing confirmed the 2 mutations in the proband and his deceased brother; both parents were heterozygous for different mutations and an unaffected sister was homozygous for wild-type alleles. Conclusions: These results demonstrate a previously unrecognized association between neonatal primary hyperparathyroidism and mutation of SLC12A1, the cause of antenatal Bartter syndrome type 1, and suggest that the loss of sodium-potassium-chloride cotransporter-2 cotransporter activity influences parathyroid gland function.

O-026 Exome Sequencing Analysis of Candidate Genes in Very Early Onset Inflammatory Bowel Disease

2013 ◽  
Vol 19 ◽  
pp. S15-S16
Author(s):  
Judith Kelsen ◽  
Christopher Moran ◽  
Kernika Gupta ◽  
Helen Pauly-Hubbard ◽  
Samantha Fish ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Exome Sequencing ◽  
Candidate Genes ◽  
Bowel Disease ◽  
Early Onset ◽  
Sequencing Analysis ◽  
Inflammatory Bowel

scholarly journals Exome sequencing reveals novel causes as well as new candidate genes for human globozoospermia

2020 ◽  
Vol 35 (1) ◽  
pp. 240-252 ◽  
Author(s):  
M S Oud ◽  
Ö Okutman ◽  
L A J Hendricks ◽  
P F de Vries ◽  
B J Houston ◽  
...  
Keyword(s):  
Male Infertility ◽  
Exome Sequencing ◽  
Candidate Genes ◽  
Sanger Sequencing ◽  
Scientific Research ◽  
National Council ◽  
Pathogenic Variants ◽  
New Genes ◽  
Phenotypic Characterisation ◽  
The Impact

Abstract STUDY QUESTION Can exome sequencing identify new genetic causes of globozoospermia? SUMMARY ANSWER Exome sequencing in 15 cases of unexplained globozoospermia revealed deleterious mutations in seven new genes, of which two have been validated as causing globozoospermia when knocked out in mouse models. WHAT IS KNOWN ALREADY Globozoospermia is a rare form of male infertility characterised by round-headed sperm and malformation of the acrosome. Although pathogenic variants in DPY19L2 and SPATA16 are known causes of globozoospermia and explain up to 70% of all cases, genetic causality remains unexplained in the remaining patients. STUDY DESIGN, SIZE, DURATION After pre-screening 16 men for mutations in known globozoospermia genes DPY19L2 and SPATA16, exome sequencing was performed in 15 males with globozoospermia or acrosomal hypoplasia of unknown aetiology. PARTICIPANTS/MATERIALS, SETTING, METHOD Targeted next-generation sequencing and Sanger sequencing was performed for all 16 patients to screen for single-nucleotide variants and copy number variations in DPY19L2 and SPATA16. After exclusion of one patient with DPY19L2 mutations, we performed exome sequencing for the 15 remaining subjects. We prioritised recessive and X-linked protein-altering variants with an allele frequency of <0.5% in the population database GnomAD in genes with an enhanced expression in the testis. All identified candidate variants were confirmed in patients and, where possible, in family members using Sanger sequencing. Ultrastructural examination of semen from one of the patients allowed for a precise phenotypic characterisation of abnormal spermatozoa. MAIN RESULTS AND ROLE OF CHANCE After prioritisation and validation, we identified possibly causative variants in eight of 15 patients investigated by exome sequencing. The analysis revealed homozygous nonsense mutations in ZPBP and CCDC62 in two unrelated patients, as well as rare missense mutations in C2CD6 (also known as ALS2CR11), CCIN, C7orf61 and DHNA17 and a frameshift mutation in GGN in six other patients. All variants identified through exome sequencing, except for the variants in DNAH17, were located in a region of homozygosity. Familial segregation of the nonsense variant in ZPBP revealed two fertile brothers and the patient’s mother to be heterozygous carriers. Paternal DNA was unavailable. Immunohistochemistry confirmed that ZPBP localises to the acrosome in human spermatozoa. Ultrastructural analysis of spermatozoa in the patient with the C7orf61 mutation revealed a mixture of round heads with no acrosomes (globozoospermia) and ovoid or irregular heads with small acrosomes frequently detached from the sperm head (acrosomal hypoplasia). LIMITATIONS, REASONS FOR CAUTION Stringent filtering criteria were used in the exome data analysis which could result in possible pathogenic variants remaining undetected. Additionally, functional follow-up is needed for several candidate genes to confirm the impact of these mutations on normal spermatogenesis. WIDER IMPLICATIONS OF THE FINDINGS Our study revealed an important role for mutations in ZPBP and CCDC62 in human globozoospermia as well as five new candidate genes. These findings provide a more comprehensive understanding of the genetics of male infertility and bring us closer to a complete molecular diagnosis for globozoospermia patients which would help to predict the success of reproductive treatments. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by The Netherlands Organisation for Scientific Research (918–15-667); National Health and Medical Research Council of Australia (APP1120356) and the National Council for Scientific Research (CONICET), Argentina, PIP grant 11220120100279CO. The authors have nothing to disclose.

scholarly journals Next Generation Exome Sequencing of Pediatric Asthma Identifies Rare and Novel Variants in Candidate Genes

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Neda M. Bogari ◽  
Amr A. Amin ◽  
Husni H. Rayes ◽  
Ahmed Abdelmotelb ◽  
Mohiuddin M. Taher ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Candidate Genes ◽  
Whole Exome Sequencing ◽  
Association Studies ◽  
Severe Disease ◽  
Pediatric Asthma ◽  
Sequencing Analysis ◽  
Whole Exome ◽  
Novel Variants ◽  
The Impact

Multiple genes have been implicated to have a role in asthma predisposition by association studies. Pediatric patients often manifest a more extensive form of this disease and a particularly severe disease course. It is likely that genetic predisposition could play a more substantial role in this group. This study is aimed at identifying the spectrum of rare and novel variation in known pediatric asthma susceptibility genes using whole exome sequencing analysis in nine individual cases of childhood onset allergic asthma. DNA samples from the nine children with a history of bronchial asthma diagnosis underwent whole exome sequencing on Ion Proton. For each patient, the entire complement of rare variation within strongly associated candidate genes was catalogued. The analysis showed 21 variants in the subjects, 13 had been previously identified, and 8 were novel. Also, among of which, nineteen were nonsynonymous and 2 were nonsense. With regard to the novel variants, the 2 nonsynonymous variants in the PRKG1 gene (PRKG1: p.C519W and PRKG1: p.G520W) were presented in 4 cases, and a nonsynonymous variant in the MAVS gene (MAVS: p.A45V) was identified in 3 cases. The variants we found in this study will enrich the variant spectrum and build up the database in the Saudi population. Novel eight variants were identified in the study which provides more evidence in the genetic susceptibility in asthma among Saudi children, providing a genetic screening map for the molecular genetic determinants of allergic disease in Saudi children, with the goal of reducing the impact of chronic diseases on the health and the economy. We believe that the advanced specified statistical filtration/annotation programs used in this study succeeded to release such results in a preliminary study, exploring the genetic map of that disease in Saudi children.

scholarly journals Molecular Etiology of Isolated Congenital Cataract Using Next-Generation Sequencing: Single Center Exome Sequencing Data from Turkey

2020 ◽  
Vol 11 (5-6) ◽  
pp. 302-308
Author(s):  
Hande Taylan Sekeroglu ◽  
Beren Karaosmanoglu ◽  
Ekim Z. Taskiran ◽  
Pelin O. Simsek Kiper ◽  
Mehmet Alikasifoglu ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Sanger Sequencing ◽  
Congenital Cataract ◽  
Family Members ◽  
First Year ◽  
Ophthalmological Examination ◽  
Sequencing Data ◽  
Molecular Etiology ◽  
Bilateral Congenital Cataract ◽  
First Year Of Life

Congenital cataract, which refers to lenticular opacity diagnosed at birth or more commonly during the first year of life, is one of the leading causes of childhood blindness. Molecular understanding of the disease pathogenesis has evolved thanks to many studies based on modern technologies. In this study, we aimed to identify and discuss the molecular etiology of nonsyndromic or nonmetabolic bilateral congenital cataract by whole-exome sequencing (WES). Patients with bilateral congenital cataract presumed to be isolated after metabolic and genetic evaluation were enrolled in the study. All patients underwent detailed ophthalmological examination and bilateral cataract surgery. DNA samples of the probands, parents, and available affected family members were analyzed by WES. Variants were validated and confirmed by Sanger sequencing in all probands and in available affected family members. A total of 4 patients (3 girls and 1 boy) were recruited. Two patients had nuclear, 1 patient had total, and 1 patient had combined lamellar and sutural cataract. One family had consanguinity. A heterozygous c.215+1G&#x3e;A mutation in <i>CRYBA1</i>, heterozygous c.432C&#x3e;G (p.Tyr144Ter) mutation in <i>CRYGC</i>, heterozygous c.70A&#x3e;C (p.Pro24Thr) mutation in <i>CRYGD</i>, and a heterozygous c.466G&#x3e;A (p.Gly156Arg) mutation in <i>CRYBB3</i> were detected. All these mutations were confirmed by Sanger sequencing in selected affected individuals. The current study identified all causative mutations of congenital cataract in the crystalline genes. The results confirmed that WES is a very useful tool in the investigation of the diseases with heterogeneous genetic background.

scholarly journals Novel SOX2 Mutation in Autosomal Dominant Cataract-Microcornea Syndrome

2021 ◽  
Author(s):  
Zhi-Bo Lin ◽  
Jin Li ◽  
Hai-Sen Sun ◽  
A-Yong Yu ◽  
Shi-Hao Chen ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Missense Mutation ◽  
Whole Exome Sequencing ◽  
Sanger Sequencing ◽  
Congenital Cataract ◽  
Autosomal Dominant ◽  
Family Members ◽  
High Mobility ◽  
Chinese Family ◽  
Whole Exome

Abstract Background: Congenital cataract-microcornea syndrome (CCMC) is characterized by the association of congenital cataract and microcornea without any other systemic anomaly or dysmorphism. Although several causative genes have been reported in patients with CCMC, the genetic etiology of CCMC is yet to be clearly understood. Purpose: To unravel the genetic cause of autosomal dominant family with CCMC.Methods: All patients and available family members underwent a comprehensive ophthalmologic clinical examination in the hospital by expert ophthalmologists and carried out to clinically diagnosis. All the patients were screened by whole-exome sequencing and then validated using co-segregation by Sanger sequencing. Results: Four CCMC patients from a Chinese family, and five unaffected family members were enrolled in this study. Using whole-exome sequencing, missense mutation c.295G>T (p.a99s, NM_003106.4) in the SOX2 gene was identified and validated by segregation analysis. In addition, this missense mutation was predicted to be damaging by multiple predictive tools. Variant p.Ala99Ser was located in a conservation high mobility group (HMG)-box domain in SOX2 protein, with a potential pathogenic impact of p.Ala99Ser on protein level.Conclusions: A novel missense mutation (c.295G>T, p.Ala99Ser) in the SOX2 gene was found in this Han Chinese family with congenital cataract and microcornea. Our study firstly determined that mutations in SOX2 were associated with CCMC, warranting further investigations on the pathogenesis of this disorder. This result expands the mutation spectrum of SOX2 and provides useful information to study the molecular pathogenesis of CCMC.

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