First custom next-generation sequencing infertility panel in Latin America: design and first results

Abstract

Objective: To present the development of the first custom gene panel for the diagnosis of male and female infertility in Latin America.Methods: We developed a next-generation sequencing (NGS) panel that assesses genes associated with infertility. The panel targeted exons and their flanking regions. Selected introns in the CFTR gene were also included. The FMR1 gene and Y chromosome microdeletions were analyzed with other recommended methodologies. An inhouse developed bioinformatic pipeline was applied for the interpretation of the results. Clear infertility phenotypes, idiopathic infertility, and samples with known pathogenic variants were evaluated.Results: A total of 75 genes were selected based on female (primary ovarian insufficiency, risk of ovarian hyperstimulation syndrome, recurrent pregnancy loss, oocyte maturation defects, and embryo development arrest) and male conditions (azoospermia, severe oligospermia, asthenozoospermia, and teratozoospermia). The panel designed was used to assess 25 DNA samples. Two of the variants found were classified as pathogenic and enable the diagnosis of a woman with secondary amenorrhea and a man with oligoasthenoteratozoospermia. Targeted NGS assay metrics resulted in a mean of 180X coverage, with more than 98% of the bases covered ≥20X. Conclusion:Our custom gene sequencing panel designed for the diagnosis of male and female infertility caused by genetic defects revealed the underlying genetic cause of some cases of infertility. The panel will allow us to develop more precise approaches in assisted reproduction.

Male Infertility Diagnosis: Improvement of Genetic Analysis Performance by the Introduction of Pre-Diagnostic Genes in a Next-Generation Sequencing Custom-Made Panel

“…The elevated number of candidate genes makes it hard to find a genetic cause of infertility in the majority of the cases (22)(23)(24). Anyway, a multi-disease gene panel can improve the identification of the etiology of male infertility (3,25,26). In several cases, idiopathic infertility has a genetic origin, therefore a correct phenotyping and medical history of the infertile patient may represent an initial basis for the genetic interpretation of the disorder (27), especially for the genetic variants of uncertain Severe oligozoospermia was defined for total sperm count <1.0 million; mild oligozoospermia was defined for total sperm count enclosed between 1.0 and 5.0 million; oligozoospermia for total sperm count enclosed between 5.0 and 39.0 million (21).…”

Pharmacogenomic Biomarkers of Follicle-Stimulating Hormone Receptor Malfunction in Females with Impaired Ovarian Response—A Genetic Survey

“…Some examples also have been illustrated in the development of infertility NGS panel for targeted exons and their flanking regions in 75 infertility related genes, including FSHR as one of the diagnostic genes which have proven associations with infertility, in order to assess the genetic variations of infertile patients with a custom bioinformatic pipeline for data analysis. By applying the MiSeq platform of Illumina, investigators revealed the underlying genetic cause of infertility in their 25 samples properly [ 56 ]. França et al also reviewed the ability of NGS methods in the discovery of heterogeneity of some FSHR and other infertility gene-related disorders and concluded the widespread usage of such technologies in the near future for the detection of new players in female reproduction diseases would be recommended [ 57 ].…”

Rare genetic variants suggest dysregulation of signaling pathways in low- and high-risk patients developing severe ovarian hyperstimulation syndrome

“…To investigate if rare variants potentially involved in the development of OHSS were present, variants called in the 12 cases with OHSS were filtered using a predefined in silico gene panel including 76 genes predisposing to OHSS (Online Resource 2). The genes included in the gene panel were selected based on an extensive literature search in PubMed and Online Mendelian Inheritance in Man (OMIM) and were implicated in controlled ovarian stimulation response, associated with OHSS or regulation of gonadotropin action and/or ovarian angiogenesis [3,14,[16][17][18][19][20][21][22][23][24]. The gene panel included both known disease-associated genes related to OHSS and candidate genes which association with OHSS needs further study.…”