Ethical concerns regarding genetic testing for Y chromosome presence in athletes: A position statement of the American College of Medical Genetics and Genomics (ACMG).
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Athletes↗
Biomedical subjects
Mahmoud Aarabi
Publications and source records attributed to Mahmoud Aarabi.
Comprehensive evaluation of ACMG/AMP-based variant classification tools.
MOTIVATION: The American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines represent the gold standard for clinical variant interpretation. Despite the widespread adoption of ACMG/AMP guidelines, a comprehensive comparison of the software tools designed to implement them has been lacking. This represents a significant gap, as clinicians require evidence-based guidance on which tools to use in their practice. RESULTS: We benchmarked four ACMG/AMP-based tools (Franklin, InterVar, TAPES, Genebe) selected from 22 tools, and compared their performance with LIRICAL, a top-performing phenotype-driven tool, using 151 expert-curated datasets from Mendelian disorders. Selection criteria included free availability, VCF compatibility, operational reliability, and not being disease-specific. Our evaluation framework assessed top-N accuracy (N = 1, 5, 10, 20, 50), retention rates, precision, recall, F1 scores, and area under the curve (AUC). Statistical validation employed bootstrap confidence intervals (n = 1000) and Friedman tests. LIRICAL (68.21%) and Franklin (61.59%) demonstrated superior top-10 variant prioritization accuracy in Mendelian disorders, significantly outperforming other tools (P = .0000). Results demonstrate that tools with advanced phenotypic integration significantly outperform those relying primarily on genomic features. AVAILABILITY AND IMPLEMENTATION: All data and source code required to reproduce the findings of this study are openly available in the Code Ocean repository at https://doi.org/10.24433/CO.6562438.v1.
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Testicular expression of synaptonemal complex protein 3 (SYCP3) messenger ribonucleic acid in 110 patients with nonobstructive azoospermia.
OBJECTIVE: To determine the expression of the synaptonemal complex protein-3 (SYCP3) gene in men with nonobstructive azoospermia. DESIGN: Cross-sectional case study. SETTING: Avesina Infertility Clinic, Tehran, Iran. PATIENT(S): One hundred and ten consecutive infertile men presenting nonobstructive azoospermia. INTERVENTION(S): Testicular biopsies for histopathological assessment and analyses of SYCP3 expression level by semiquantitative nested reverse transcription-polymerase chain reaction (RT-PCR). The SYCP3 levels were normalized to expression of the housekeeping phosphoglucomutase 1 gene. MAIN OUTCOME MEASURE(S): Expression of SYCP3 messenger ribonucleic acid (mRNA). Correlation of the histopathological findings with SYCP3 expression levels. RESULTS(S): Testicular SYCP3 mRNA expression was observed in 67/110 (60.9%) patients. The expression level correlated with the degree of spermatogenic failure. Although it was expressed in patients with spermatogenesis and maturation arrest, a lack of expression was seen in all of those men with spermatogonial arrest, Sertoli cell-only syndrome, and testicular atrophy. CONCLUSION(S): These data indicate that SYCP3 is expressed in human testis and is restricted to germ cells. Our findings, in association with those obtained in experimental animals, shows that lack of SYCP3 expression in human testis may have a negative effect on spermatogenesis and male fertility.
Adult↗
Thrombophilic mutations in Iranian patients with infertility and recurrent spontaneous abortion.
Factor V Leiden (FVL) G1691A, methylenetetrahydrofolate reductase (MTHFR) C677T, and factor II (FII) G20210A mutations are three important causes of thrombophilia, the condition that might be related to infertility and recurrent spontaneous abortion (RSA). In this study we evaluated the presence of these three mutations in 36 female patients with unexplained infertility, 65 female patients with unexplained RSA, and 62 healthy fertile women as control group. DNA was extracted from peripheral blood samples and PCR-RFLP was performed for the molecular diagnosis of each mutation. In addition, activated protein C resistance (APC-R) was also evaluated. The frequencies of FVL, MTHFR, and FII mutations (heterozygous and homozygous) in the control group were 0.0%, 38.7%, and 3.2%, respectively. The frequency of FVL mutation in patients with infertility (30.6%) or RSA (20.0%) was significantly higher than that of the control group. A significantly higher MTHFR mutation rate was also observed in patients with RSA (63.1%) as compared to controls. However, the mutation rate of MTHFR in patients with infertility (50.0%) was not statistically different from that in controls. No significant difference was observed in the frequencies of FII mutations between the patients and controls. Decreased levels of APC-R were observed in 25.0% of infertile patients and 18.9% of patients with RSA. In conclusion, our results show a skew towards higher mutation frequencies of FVL and MTHFR in patients that may necessitate detection of such mutations in these Iranian patients.
Abortion, Habitual↗