scholarly journals Novel variants in helicase for meiosis 1 lead to male infertility due to non-obstructive azoospermia

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Dongdong Tang ◽  
Mingrong Lv ◽  
Yang Gao ◽  
Huiru Cheng ◽  
Kuokuo Li ◽  
...  
Keyword(s):  
Male Infertility ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Factors ◽  
Testicular Biopsy ◽  
Severe Form ◽  
Testicular Sperm Extraction ◽  
Obstructive Azoospermia ◽  
Sperm Retrieval ◽  
Whole Exome

Abstract Background Non-obstructive azoospermia (NOA) is the most severe form of male infertility; more than half of the NOA patients are idiopathic. Although many NOA risk genes have been detected, the genetic factors for NOA in majority of the patients are unknown. In addition, it is difficult to retrieve sperm from these patients despite using the microsurgical testicular sperm extraction (microTESE) method. Therefore, we conducted this genetic study to identify the potential genetic factors responsible for NOA and investigate the sperm retrieval rate of microTESE for genetically deficient NOA patients. Methods Semen analyses, sex hormone testing, and testicular biopsy were performed to categorize the patients with NOA. The chromosome karyotypes and Y chromosome microdeletion analyses were used to exclude general genetic factors. Whole exome sequencing and Sanger sequencing were performed to identify potential genetic variants in 51 patients with NOA. Hematoxylin and eosin staining (H&E) and anti-phosphorylated H2AX were used to assess the histopathology of spermatogenesis. Quantitative real time-polymerase chain reaction, western blotting, and immunofluorescence were performed to verify the effects of gene variation on expression. Results We performed whole exome sequencing in 51 NOA patients and identified homozygous helicase for meiosis 1(HFM1) variants (NM_001017975: c.3490C > T: p.Q1164X; c.3470G > A: p.C1157Y) in two patients (3.9%, 2/51). Histopathology of the testis showed that spermatogenesis was completely blocked at metaphase in these two patients carrying the HFM1 homozygous variants. In comparison with unaffected controls, we found a significant reduction in the levels of HFM1 mRNA and protein expression in the testicular tissues from these two patients. The patients were also subjected to microTESE treatment, but the sperms could not be retrieved. Conclusions This study identified novel homozygous variants of HFM1 that are responsible for spermatogenic failure and NOA, and microTESE did not aid in retrieving sperms from these patients.

scholarly journals Novel Variants in HFM1 Lead to Male Infertility Due to Non-obstructive Azoospermia

2021 ◽  
Author(s):  
Dongdong Tang ◽  
Mingrong Lv ◽  
Yang Gao ◽  
Huiru Cheng ◽  
Kuokuo Li ◽  
...  
Keyword(s):  
Male Infertility ◽  
Y Chromosome ◽  
Testicular Biopsy ◽  
Severe Form ◽  
Testicular Sperm Extraction ◽  
Obstructive Azoospermia ◽  
Sperm Retrieval ◽  
Gene Variation ◽  
Y Chromosome Microdeletions ◽  
Whole Exome

Abstract Background Non-obstructive azoospermia (NOA) is the most severe form of male infertility. More than half of the NOA patients were idiopathic for their etiology, in whom it’s difficult to retrieve sperm despite the application of microsurgical testicular sperm extraction (microTESE). Therefore, we conducted to this study to identify the potential genetic factors responsible for NOA, and investigate the sperm retrieval rate of microTESE for the genetic defected NOA.Methods One NOA patient from a consanguineous family (F1-II-1) and fifty NOA patients from non-consanguineous families were included in the study. Semen analyses, chromosome karyotypes, screening of Y chromosome microdeletions, sex hormone testing, and subsequent testicular biopsy were performed to categorize NOA or obstructive azoospermia. Potentialgenetic variants were identified by whole exome sequencing (WES),and confirmed by Sanger sequencing in F1 II-1. The candidate genes were screened in the other fifty NOA patients. Further experiments including quantitative real time-polymerase chain reaction and western blotting were performed to verify the effects of gene variation on gene expression.Results Normal somatic karyotypes and Y chromosome microdeletions were examined in all patients. Hematoxylin and eosin staining (H&E) of the testicular tissues suggested meiotic arrest, and a novel homozygous HFM1 variant (c.3490C>T: p.Q1164X) was identified in F1 II-1. Furthermore, another homozygous HFM1 variant (c.3470G>A: p.C1157Y) was also verified in F2 II-1 from the fifty NOA patients. Significantly decreased expression levels of HFM1 mRNA and protein were observed in the testicular tissues of these two mutants compared with controls. MicroTESE was performed in these two patients, while no sperm were retrieved. Conclusions Our study identified two novel homozygous variants of HFM1 that are responsible for spermatogenic failure and NOA, even microTESE can not contribute to retrieve sperm in these patients.

scholarly journals Azoospermia and reciprocal translocations: should whole-exome sequencing be recommended?

2021 ◽  
Vol 31 (1) ◽  
Author(s):  
Farah Ghieh ◽  
Anne-Laure Barbotin ◽  
Julie Prasivoravong ◽  
Sophie Ferlicot ◽  
Béatrice Mandon-Pepin ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Y Chromosome ◽  
Whole Exome Sequencing ◽  
Chromosome Rearrangements ◽  
Testicular Sperm Extraction ◽  
Comparative Genome Hybridization ◽  
Obstructive Azoospermia ◽  
Meiotic Arrest ◽  
Whole Exome ◽  
Gene Defects

Abstract Background Although chromosome rearrangements are responsible for spermatogenesis failure, their impact depends greatly on the chromosomes involved. At present, karyotyping and Y chromosome microdeletion screening are the first-line genetic tests for patients with non-obstructive azoospermia. Although it is generally acknowledged that X or Y chromosome rearrangements lead to meiotic arrest and thus rule out any chance of sperm retrieval after a testicular biopsy, we currently lack markers for the likelihood of testicular sperm extraction (TESE) in patients with other chromosome rearrangements. Results We investigated the use of a single nucleotide polymorphism comparative genome hybridization array (SNP-CGH) and whole-exome sequencing (WES) for two patients with non-obstructive azoospermia and testicular meiotic arrest, a reciprocal translocation: t(X;21) and t(20;22), and an unsuccessful TESE. No additional gene defects were identified for the t(X;21) carrier - suggesting that t(X;21) alone damages spermatogenesis. In contrast, the highly consanguineous t(20;22) carrier had two deleterious homozygous variants in the TMPRSS9 gene; these might have contributed to testicular meiotic arrest. Genetic defect was confirmed with Sanger sequencing and immunohistochemical assessments on testicular tissue sections. Conclusions Firstly, TMPRSS9 gene defects might impact spermatogenesis. Secondly, as a function of the chromosome breakpoints for azoospermic patients with chromosome rearrangements, provision of the best possible genetic counselling means that genetic testing should not be limited to karyotyping. Given the risks associated with TESE, it is essential to perform WES - especially for consanguineous patients.

DMC1 mutation that causes human non-obstructive azoospermia and premature ovarian insufficiency identified by whole-exome sequencing

2018 ◽  
Vol 55 (3) ◽  
pp. 198-204 ◽  
Author(s):  
Wen-Bin He ◽  
Chao-Feng Tu ◽  
Qiang Liu ◽  
Lan-Lan Meng ◽  
Shi-Min Yuan ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Missense Mutation ◽  
Whole Exome Sequencing ◽  
Male Patient ◽  
Histological Analysis ◽  
Pedigree Analysis ◽  
Obstructive Azoospermia ◽  
Ovarian Insufficiency ◽  
Causative Gene ◽  
Whole Exome

BackgroundThe genetic causes of the majority of male and female infertility caused by human non-obstructive azoospermia (NOA) and premature ovarian insufficiency (POI) with meiotic arrest are unknown.ObjectiveTo identify the genetic cause of NOA and POI in two affected members from a consanguineous Chinese family.MethodsWe performed whole-exome sequencing of DNA from both affected patients. The identified candidate causative gene was further verified by Sanger sequencing for pedigree analysis in this family. In silico analysis was performed to functionally characterise the mutation, and histological analysis was performed using the biopsied testicle sample from the male patient with NOA.ResultsWe identified a novel homozygous missense mutation (NM_007068.3: c.106G>A, p.Asp36Asn) in DMC1, which cosegregated with NOA and POI phenotypes in this family. The identified missense mutation resulted in the substitution of a conserved aspartic residue with asparaginate in the modified H3TH motif of DMC1. This substitution results in protein misfolding. Histological analysis demonstrated a lack of spermatozoa in the male patient’s seminiferous tubules. Immunohistochemistry using a testis biopsy sample from the male patient showed that spermatogenesis was blocked at the zygotene stage during meiotic prophase I.ConclusionsTo the best of our knowledge, this is the first report identifying DMC1 as the causative gene for human NOA and POI. Furthermore, our pedigree analysis shows an autosomal recessive mode of inheritance for NOA and POI caused by DMC1 in this family.

scholarly journals Point-of-care whole-exome sequencing of idiopathic male infertility

2018 ◽  
Vol 20 (11) ◽  
pp. 1365-1373 ◽  
Author(s):  
Khalid A Fakhro ◽  
Haitham Elbardisi ◽  
Mohamed Arafa ◽  
Amal Robay ◽  
Juan L Rodriguez-Flores ◽  
...  
Keyword(s):  
Male Infertility ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Point Of Care ◽  
Idiopathic Male Infertility ◽  
Whole Exome

scholarly journals Strategies for whole-exome sequencing analysis in a case series study of familial male infertility

2020 ◽  
Author(s):  
Masomeh Askari ◽  
Dor Mohammad Kordi Tamandani ◽  
Navid Almadani ◽  
Mehdi Totonchi
Keyword(s):  
Male Infertility ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Case Series ◽  
Sequencing Analysis ◽  
Data Generation ◽  
Male Factor ◽  
Whole Exome ◽  
Case Series Study ◽  
Key Words Male Infertility

Background: Infertility is one of the common health issues around the world. The prevalence of male factor infertility among infertile couples is approximately 30%- 35%, of which genetic factors account for 15%. The family-based whole-exome sequencing (WES) approach can accurately detect novel variants. However, selecting an appropriate sample for data generation using WES has proven to be challenging in familial male infertility studies. The aim of this study was to identify types of pathogenic male infertility in cases of familial asthenozoospermia. Case: Two families with multiple cases were recruited for the purpose of WES. The study population included two affected cases in pedigree I and three affected cases in pedigree II. Two different variant callers (SAMtools and GATK) with a single-sample calling strategy (SSCS) and a multiple-sample calling strategy (MSCS), were applied to identify variant sites. Conclusion: In this study, we represented the results for variant prioritization of WES data without sequencing fertile siblings in the same pedigree by applying two different pipelines (homozygosity and linkage-based strategy). Using the aforementioned strategies, we prioritized annotated variants and generated a logical shortlist of private variants for each pedigree. Key words: Male infertility, Whole-exome sequencing, GATK, SAMtools.

Whole-Exome Sequencing in Evaluation of Thrombophilia: Characterization of Novel Genetic Variants

2019 ◽  
Vol 152 (Supplement_1) ◽  
pp. S35-S35
Author(s):  
Sean Gu ◽  
Lauren Shevell ◽  
Christopher Tormey ◽  
Henry Rinder ◽  
Alfred Lee
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Conformational Changes ◽  
Protein C ◽  
Genetic Factors ◽  
Clinical Laboratory ◽  
Factor V Leiden ◽  
Protein C Deficiency ◽  
Multiple Sequence ◽  
Whole Exome

Abstract Venous thromboembolism (VTE), defined as deep venous thrombosis and pulmonary embolism, is a cause of significant morbidity and mortality worldwide, with an overall incidence of about 10,000,000 cases per year. The majority of VTE is attributable to genetic factors, yet the five major heritable thrombophilias of factor V Leiden, prothrombin gene mutation, antithrombin deficiency, protein C deficiency, and protein S deficiency comprise only a minority of VTE cases, suggesting that further genetic factors must contribute to VTE risk. We performed whole-exome sequencing (WES) in 106 patients with VTE, focusing our analysis on a 55-gene extended thrombophilia panel comprising genes previously reported in next-generation sequencing studies to be associated with VTE. In our cohort, we identified a probable disease-causing genetic variant or variant of unknown significance (VUS) in approximately 60% of study patients. We then selected several novel VUS involving genes with known roles in hemostasis for further characterization to determine their biological and pathological significance in thrombophilia. Multiple sequence alignment analysis showed that several nonsynonymous variants produced amino acid substitutions in highly conserved regions of proteins relevant to hemostasis and thrombosis, including thrombomodulin (TM), heparin cofactor II, ADAMTS13, and von Willebrand factor (vWF). To evaluate the theoretical effects of selected VUS on thrombosis susceptibility, we visualized proteins using PyMol and performed in silico mutagenesis modeling to evaluate for structural alterations that can predict functional and physiological consequences. Our analyses showed that several variants caused conformational changes predicted to either result in a deleterious effect on enzymatic activity or prevent substrate binding to the active site. For example, variants in TM (P401L and V454A) are predicted to decrease thrombin binding and protein C activation, whereas a C668R variant in the spacer domain of ADAMTS13 is predicted to prevent binding to vWF, resulting in ultra-large vWF multimers. We plan to use these results in combination with clinical laboratory-based coagulation testing and family studies to determine pathogenicity of specific variants in thrombosis and thrombophilia. Overall, these findings indicate that WES is a potentially useful tool for inherited thrombophilia and can provide insight into the genetic factors contributing to VTE.

scholarly journals Whole Exome Sequencing Identifies Novel De Novo Variants Interacting with Six Gene Networks in Autism Spectrum Disorder

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 1
Author(s):  
Namshin Kim ◽  
Kyoung Hyoun Kim ◽  
Won-Jun Lim ◽  
Jiwoong Kim ◽  
Soon Ae Kim ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Factors ◽  
De Novo ◽  
Genetic Network ◽  
Autism Spectrum ◽  
Network Analyses ◽  
Functional Relationships ◽  
Whole Exome

Autism spectrum disorder (ASD) is a highly heritable condition caused by a combination of environmental and genetic factors such as de novo and inherited variants, as well as rare or common variants among hundreds of related genes. Previous genome-wide association studies have identified susceptibility genes; however, most ASD-associated genes remain undiscovered. This study aimed to examine rare de novo variants to identify genetic risk factors of ASD using whole exome sequencing (WES), functional characterization, and genetic network analyses of identified variants using Korean familial dataset. We recruited children with ASD and their biological parents. The clinical best estimate diagnosis of ASD was made according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5TM), using comprehensive diagnostic instruments. The final analyses included a total of 151 individuals from 51 families. Variants were identified and filtered using the GATK Best Practices for bioinformatics analysis, followed by genome alignments and annotation to the reference genome assembly GRCh37 (liftover to GRCh38), and further annotated using dbSNP 154 build databases. To evaluate allele frequencies of de novo variants, we used the dbSNP, gnomAD exome v2.1.1, and genome v3.0. We used Ingenuity Pathway Analysis (IPA, Qiagen) software to construct networks using all identified de novo variants with known autism-related genes to find probable relationships. We identified 36 de novo variants with potential relations to ASD; 27 missense, two silent, one nonsense, one splice region, one splice site, one 5′ UTR, and one intronic SNV and two frameshift deletions. We identified six networks with functional relationships. Among the interactions between de novo variants, the IPA assay found that the NF-κB signaling pathway and its interacting genes were commonly observed at two networks. The relatively small cohort size may affect the results of novel ASD genes with de novo variants described in our findings. We did not conduct functional experiments in this study. Because of the diversity and heterogeneity of ASD, the primary purpose of this study was to investigate probable causative relationships between novel de novo variants and known autism genes. Additionally, we based functional relationships with known genes on network analysis rather than on statistical analysis. We identified new variants that may underlie genetic factors contributing to ASD in Korean families using WES and genetic network analyses. We observed novel de novo variants that might be functionally linked to ASD, of which the variants interact with six genetic networks.

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