Next-generation sequencing: toward an increase in the diagnostic yield in patients with apparently idiopathic spermatogenic failure

BackgroundInfertility affects about 7% of the general male population. The underlying cause of male infertility is undefined in about 50% of cases (idiopathic infertility). The number of genes involved in human spermatogenesis is over two thousand. Therefore, it is essential to analyze a large number of genes that may be involved in male infertility. This study aimed to test idiopathic male infertile patients negative for a validated panel of “diagnostic” genes, for a wide panel of genes that we have defined as “pre-diagnostic.”MethodsWe developed a next-generation sequencing (NGS) gene panel including 65 pre-diagnostic genes that were used in 12 patients who were negative to a diagnostic genetic test for male infertility disorders, including primary spermatogenic failure and central hypogonadism, consisting of 110 genes.ResultsAfter NGS sequencing, variants in pre-diagnostic genes were identified in 10/12 patients who were negative to a diagnostic test for primary spermatogenic failure (n = 9) or central hypogonadism (n = 1) due to mutations of single genes. Two pathogenic variants of DNAH5 and CFTR genes and three uncertain significance variants of DNAI1, DNAH11, and CCDC40 genes were found. Moreover, three variants with high impact were found in AMELY, CATSPER 2, and ADCY10 genes.ConclusionThis study suggests that searching for pre-diagnostic genes may be of relevance to find the cause of infertility in patients with apparently idiopathic primary spermatogenic failure due to mutations of single genes and central hypogonadism.

Download Full-text

Next-Generation Sequencing Gene Panels and “Solo” Clinical Exome Sequencing Applied in Structurally Abnormal Fetuses

Fetal Diagnosis and Therapy ◽

10.1159/000519701 ◽

2021 ◽

pp. 1-11

Author(s):

Montse Pauta ◽

Berta Campos ◽

Maria Segura-Puimedon ◽

Gemma Arca ◽

Alfons Nadal ◽

...

Keyword(s):

Next Generation Sequencing ◽

Exome Sequencing ◽

Diagnostic Yield ◽

Monogenic Disease ◽

Chromosomal Microarray Analysis ◽

Next Generation ◽

Clinical Exome Sequencing ◽

Gene Panels ◽

Generation Sequencing ◽

Structural Anomalies

Objective: The aim of the study was to assess the diagnostic yield of 2 different next-generation sequencing (NGS) approaches: gene panel and “solo” clinical exome sequencing (solo-CES), in fetuses with structural anomalies and normal chromosomal microarray analysis (CMA), in the absence of a known familial mutation. Methodology: Gene panels encompassing from 2 to 140 genes, were applied mainly in persistent nuchal fold/fetal hydrops and in large hyperechogenic kidneys. Solo-CES, which entails sequencing the fetus alone and only interpreting the Online Mendelian Inheritance in Man genes, was performed in multisystem or recurrent structural anomalies. Results: During the study period (2015–2020), 153 NGS studies were performed in 148 structurally abnormal fetuses with a normal CMA. The overall diagnostic yield accounted for 35% (53/153) of samples and 36% (53/148) of the fetuses. Diagnostic yield with the gene panels was 31% (15/49), similar to 37% (38/104) in solo-CES. Conclusions: A monogenic disease was established as the underlying cause in 35% of selected fetal structural anomalies by gene panels and solo-CES.

Download Full-text

Diagnostic yield of targeted next generation sequencing in various cancer types: An information-theoretic approach

Cancer Genetics ◽

10.1016/j.cancergen.2015.05.030 ◽

2015 ◽

Vol 208 (9) ◽

pp. 441-447 ◽

Cited By ~ 7

Author(s):

Ian S. Hagemann ◽

Patrick K. O'Neill ◽

Ivan Erill ◽

John D. Pfeifer

Keyword(s):

Next Generation Sequencing ◽

Diagnostic Yield ◽

Theoretic Approach ◽

Next Generation ◽

Information Theoretic ◽

Targeted Next Generation Sequencing ◽

Cancer Types ◽

Information Theoretic Approach ◽

Generation Sequencing

Download Full-text

Targeted next generation sequencing identifies a genetic spectrum of DNA variants in patients with hemiplegic migraine

Cephalalgia Reports ◽

10.1177/2515816319881630 ◽

2019 ◽

Vol 2 ◽

pp. 251581631988163 ◽

Cited By ~ 2

Author(s):

Neven Maksemous ◽

Robert A Smith ◽

Heidi G Sutherland ◽

Bridget H Maher ◽

Omar Ibrahim ◽

...

Keyword(s):

Next Generation Sequencing ◽

Diagnostic Yield ◽

Next Generation ◽

Hemiplegic Migraine ◽

Targeted Next Generation Sequencing ◽

Variants Of Unknown Significance ◽

High Mutation Frequency ◽

Unknown Significance ◽

Atp1a2 Gene ◽

Generation Sequencing

Objective: Hemiplegic migraine in both familial (FHM) and sporadic (SHM) forms is a rare subtype of migraine with aura that can be traced to mutations in the CACNA1A, ATP1A2 and SCN1A genes. It is characterised by severe attacks of typical migraine accompanied by hemiparesis, as well as episodes of complex aura that vary significantly between individuals. Methods: Using a targeted next generation sequencing (NGS) multigene panel, we have sequenced the genomic DNA of 172 suspected hemiplegic migraine cases, in whom no mutation had previously been found by Sanger sequencing (SS) of a limited number of exons with high mutation frequency in FHM genes. Results: Genetic screening identified 29 variants, 10 of which were novel, in 35 cases in the three FHM genes ( CACNA1A, ATP1A2 and SCN1A). Interestingly, in this suspected HM cohort, the ATP1A2 gene harboured the highest number of variants with 24/35 cases (68.6%), while CACNA1A ranked the second gene, with 5 variants identified in 7/35 cases (20%). All detected variants were confirmed by SS and were absent in 100 non-migraine healthy control individuals. Assessment of variants with the American College of Medical Genetics and Genomics guidelines classified 8 variants as pathogenic, 3 as likely pathogenic and 18 as variants of unknown significance. Targeted NGS gene panel increased the diagnostic yield by fourfold over iterative SS in our diagnostics facility. Conclusion: We have identified 29 potentially causative variants in an Australian and New Zealand cohort of suspected HM cases and found that the ATP1A2 gene was the most commonly mutated gene. Our results suggest that screening using NGS multigene panels to investigate ATP1A2 alongside CACNA1A and SCN1A is a clinically useful and efficient method.

Download Full-text

Corrigendum to: Diagnostic Yield of Next-Generation Sequencing in Very Early-Onset Inflammatory Bowel Diseases: A Multicenter Study

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjaa164 ◽

2020 ◽

Author(s):

Fabienne Charbit-Henrion ◽

Marianna Parlato ◽

Sylvain Hanein ◽

Rémi Duclaux-Loras ◽

Jan Nowak ◽

...

Keyword(s):

Next Generation Sequencing ◽

Multicenter Study ◽

Inflammatory Bowel Diseases ◽

Early Onset ◽

Diagnostic Yield ◽

Next Generation ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Generation Sequencing

Download Full-text

Next-generation sequencing (NGS) is a powerful tool to improve diagnostic yield in intellectual disability

European Journal of Paediatric Neurology ◽

10.1016/j.ejpn.2017.04.896 ◽

2017 ◽

Vol 21 ◽

pp. e52

Author(s):

A. Labalme ◽

N. Chatron ◽

M. Till ◽

M.P. Cordier ◽

M. Rossi ◽

...

Keyword(s):

Intellectual Disability ◽

Next Generation Sequencing ◽

Diagnostic Yield ◽

Next Generation ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Download Full-text

Assessment of the incorporation of CNV surveillance into gene panel next-generation sequencing testing for inherited retinal diseases

Journal of Medical Genetics ◽

10.1136/jmedgenet-2017-104791 ◽

2017 ◽

Vol 55 (2) ◽

pp. 114-121 ◽

Cited By ~ 23

Author(s):

Jamie M Ellingford ◽

Bradley Horn ◽

Christopher Campbell ◽

Gavin Arno ◽

Stephanie Barton ◽

...

Keyword(s):

Next Generation Sequencing ◽

Diagnostic Yield ◽

Diagnostic Testing ◽

Read Depth ◽

Gene Panel ◽

Genomic Variation ◽

Next Generation ◽

Diagnostic Laboratory ◽

Inherited Retinal Dystrophies ◽

Generation Sequencing

BackgroundDiagnostic use of gene panel next-generation sequencing (NGS) techniques is commonplace for individuals with inherited retinal dystrophies (IRDs), a highly genetically heterogeneous group of disorders. However, these techniques have often failed to capture the complete spectrum of genomic variation causing IRD, including CNVs. This study assessed the applicability of introducing CNV surveillance into first-tier diagnostic gene panel NGS services for IRD.MethodsThree read-depth algorithms were applied to gene panel NGS data sets for 550 referred individuals, and informatics strategies used for quality assurance and CNV filtering. CNV events were confirmed and reported to referring clinicians through an accredited diagnostic laboratory.ResultsWe confirmed the presence of 33 deletions and 11 duplications, determining these findings to contribute to the confirmed or provisional molecular diagnosis of IRD for 25 individuals. We show that at least 7% of individuals referred for diagnostic testing for IRD have a CNV within genes relevant to their clinical diagnosis, and determined a positive predictive value of 79% for the employed CNV filtering techniques.ConclusionIncorporation of CNV analysis increases diagnostic yield of gene panel NGS diagnostic tests for IRD, increases clarity in diagnostic reporting and expands the spectrum of known disease-causing mutations.

Download Full-text