Purpose: To determine if an explainable artificial intelligence (XAI) model enhances the accuracy and transparency of predicting embryo ploidy status based on embryonic characteristics and clinical data.
Methods: This retrospective study utilized a dataset of 1908 blastocyst embryos. The dataset includes ploidy status, morphokinetic features, morphology grades, and 11 clinical variables. Six machine learning (ML) models including Random Forest (RF), Linear Discriminant Analysis (LDA), Logistic Regression (LR), Support Vector Machine (SVM), AdaBoost (ADA), and Light Gradient-Boosting Machine (LGBM) were trained to predict ploidy status probabilities across three distinct datasets: high-grade embryos (HGE, n = 1107), low-grade embryos (LGE, n = 364), and all-grade embryos (AGE, n = 1471). The model's performance was interpreted using XAI, including SHapley Additive exPlanations (SHAP) and Local Interpretable Model-agnostic Explanations (LIME) techniques.
Results: The mean maternal age was 38.5 ± 3.85 years. The Random Forest (RF) model exhibited superior performance compared to the other five ML models, achieving an accuracy of 0.749 and an AUC of 0.808 for AGE. In the external test set, the RF model achieved an accuracy of 0.714 and an AUC of 0.750 (95% CI, 0.702-0.796). SHAP's feature impact analysis highlighted that maternal age, paternal age, time to blastocyst (tB), and day 5 morphology grade significantly impacted the predictive model. In addition, LIME offered specific case-ploidy prediction probabilities, revealing the model's assigned values for each variable within a finite range.
Conclusion: The model highlights the potential of using XAI algorithms to enhance ploidy prediction, optimize embryo selection as patient-centric consultation, and provides reliability and transparent insights into the decision-making process.
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http://dx.doi.org/10.1007/s10815-024-03178-7 | DOI Listing |
N Engl J Med
December 2024
From the Prenatal Genomics and Therapy Section, Center for Precision Health Research (A.E.T., D.W.B.), and the Section on Social Network Methods, Social and Behavioral Research Branch (J.L.), National Human Genome Research Institute, the Women's Malignancies Branch (C.M.A., I.S.G., P.S.R.) and the Cancer Data Science Laboratory (P.S.R.), Center for Cancer Research, National Cancer Institute, Radiology and Imaging Sciences, Clinical Center (A.A.M., B.R.), and the Office of the Director, Eunice Kennedy Shriver National Institute of Child Health and Human Development (D.W.B.), National Institutes of Health, Bethesda, and Leidos Biomedical Research, Frederick (M.P.) - both in Maryland.
Background: Cell-free DNA (cfDNA) sequence analysis to screen for fetal aneuploidy can incidentally detect maternal cancer. Additional data are needed to identify DNA-sequencing patterns and other biomarkers that can identify pregnant persons who are most likely to have cancer and to determine the best approach for follow-up.
Methods: In this ongoing study we performed cancer screening in pregnant or postpartum persons who did not perceive signs or symptoms of cancer but received unusual clinical cfDNA-sequencing results or results that were nonreportable (i.
Genes (Basel)
December 2024
DA VINCI Polyclinic, Petrovaradinska ulica 110, 10000 Zagreb, Croatia.
Background: Chromosomal numerical and structural alterations are significant causes of various developmental disorders in foetuses. Non-invasive prenatal testing (NIPT) has emerged as an effective screening tool for detecting common aneuploidies, aiding in the identification of individuals who may require further diagnostic work-up.
Methods: This retrospective, monocentric observational study evaluates the usage patterns, test choices, turnaround times (TAT), and outcomes of NIPT between 2013 and 2023 on a sample of 2431 pregnant women at a special hospital offering outpatient services and comprehensive gynaecological/obstetric inpatient care.
BMC Pregnancy Childbirth
December 2024
Reproductive Medical Center, Henan Province Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, No. 1 East Jianshe Road, Erqi District, Zhengzhou, China.
Research Question: Is it possible to predict blastocyst quality, embryo chromosomal ploidy, and clinical pregnancy outcome after single embryo transfer from embryo developmental morphokinetic parameters?
Design: The morphokinetic parameters of 1011 blastocysts from 227 patients undergoing preimplantation genetic testing were examined. Correlations between the morphokinetic parameters and the quality of blastocysts, chromosomal ploidy, and clinical pregnancy outcomes following the transfer of single blastocysts were retrospectively analyzed.
Results: The morphokinetic parameters of embryos in the high-quality blastocyst group were significantly shorter than those in the low-quality blastocyst group (p < 0.
Nat Commun
December 2024
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
Although epigenetic modification has long been recognized as a vital force influencing gene regulation in plants, the dynamics of chromatin structure implicated in the intertwined transcriptional regulation of duplicated genes in polyploids have yet to be understood. Here, we document the dynamic organization of chromatin structure in two subgenomes of allotetraploid cotton (Gossypium hirsutum) by generating 3D genomic, epigenomic and transcriptomic datasets from 12 major tissues/developmental stages covering the life cycle. We systematically identify a subset of genes that are closely associated with specific tissue functions.
View Article and Find Full Text PDFDev Biol
December 2024
Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA. Electronic address:
The Drosophila Ejaculatory duct (ED) is a secretory tissue of the somatic male reproductive system. The ED is involved in the secretion of seminal fluid components and ED-specific antimicrobial peptides that aid in fertility and the female post-mating response. The ED is composed of secretory epithelial cells surrounded by a layer of innervated contractile muscle.
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