Abstract：
OBJECTIVE: To evaluate the technical accuracy, inheritance, and pathogenicity of small copy number variants (CNVs) detected by a targeted next-generation sequencing-based preimplantation genetic testing for aneuploidy (PGT-A) platform.
METHODS: Retrospective observational study performed between 2020 and 2022.
METHODS: Clinic.
METHODS: A total of 12,157 patients who underwent clinical PGT-A performed by targeted next-generation sequencing for whole chromosome and large segmental aneuploidies.
METHODS: An incidental finding was reported when a CNV gain/loss of at least 3 consecutive amplicons appeared in at least 2 embryos from the same in vitro fertilization cycle.
METHODS: The primary outcome measures were the specificity, incidence, inheritance, and pathogenicity of small CNVs detected by the PGT-A platform. Accuracy of the PGT-A platform CNV calls was assessed via concordance with the CNV calls (size and genomic location) on chromosomal microarray of the gamete provider(s). Parental origin of the CNV and pathogenicity classifications were also reported.
RESULTS: An incidental finding that met reporting criteria was identified in 75 (0.62%; 95% confidence interval, 0.5%-0.8%) of 12,157 unique PGT-A patients. Chromosomal microarray follow-up was requested for all cases, and results were received for 1 or both members of 65 reproductive couples. In all cases, 1 of the gamete providers was confirmed to have the CNV identified in the embryos (100.0%, N = 65/65; 95% confidence interval, 94.5-100). The identified CNV was of maternal origin in 34 cases (52.3%) and of paternal origin in 31 cases (47.7%). A significant correlation was identified between PGT-A-predicted CNV sizes and chromosomal microarray detected sizes (r = 0.81) and genomic coordinates on parental deoxyribonucleic acid. Twenty-six (40%) of the CNVs were classified as benign/likely benign, 30 (46.2%) as a variant of uncertain significance, and 9 (13.8%) as pathogenic/likely pathogenic.
CONCLUSIONS: Certain PGT-A platforms may enable the detection of inherited, small CNVs with extremely high specificity without prior knowledge of parental status. Most CNVs in this data set were confirmed to be benign/likely benign or a variant of uncertain significance. Pathogenic/likely pathogenic CNVs associated with a broad range of phenotypic features may also be detected, although a reliable negative predictive value for small CNVs with current PGT-A technologies is unknown because of the many technical challenges.
METHODS: Retrospective observational study performed between 2020 and 2022.
METHODS: Clinic.
METHODS: A total of 12,157 patients who underwent clinical PGT-A performed by targeted next-generation sequencing for whole chromosome and large segmental aneuploidies.
METHODS: An incidental finding was reported when a CNV gain/loss of at least 3 consecutive amplicons appeared in at least 2 embryos from the same in vitro fertilization cycle.
METHODS: The primary outcome measures were the specificity, incidence, inheritance, and pathogenicity of small CNVs detected by the PGT-A platform. Accuracy of the PGT-A platform CNV calls was assessed via concordance with the CNV calls (size and genomic location) on chromosomal microarray of the gamete provider(s). Parental origin of the CNV and pathogenicity classifications were also reported.
RESULTS: An incidental finding that met reporting criteria was identified in 75 (0.62%; 95% confidence interval, 0.5%-0.8%) of 12,157 unique PGT-A patients. Chromosomal microarray follow-up was requested for all cases, and results were received for 1 or both members of 65 reproductive couples. In all cases, 1 of the gamete providers was confirmed to have the CNV identified in the embryos (100.0%, N = 65/65; 95% confidence interval, 94.5-100). The identified CNV was of maternal origin in 34 cases (52.3%) and of paternal origin in 31 cases (47.7%). A significant correlation was identified between PGT-A-predicted CNV sizes and chromosomal microarray detected sizes (r = 0.81) and genomic coordinates on parental deoxyribonucleic acid. Twenty-six (40%) of the CNVs were classified as benign/likely benign, 30 (46.2%) as a variant of uncertain significance, and 9 (13.8%) as pathogenic/likely pathogenic.
CONCLUSIONS: Certain PGT-A platforms may enable the detection of inherited, small CNVs with extremely high specificity without prior knowledge of parental status. Most CNVs in this data set were confirmed to be benign/likely benign or a variant of uncertain significance. Pathogenic/likely pathogenic CNVs associated with a broad range of phenotypic features may also be detected, although a reliable negative predictive value for small CNVs with current PGT-A technologies is unknown because of the many technical challenges.
摘要：
目的：为了评估技术准确性，继承,以及通过基于靶向下一代测序（NGS）的PGT-A平台检测到的小拷贝数变体（CNV）的致病性。
方法：2020-2022年进行回顾性观察性研究。
方法：12,157例接受全染色体和大段非整倍体靶向NGS临床PGT-A治疗的患者。
方法：报道了一个偶然发现，即在同一IVF周期的至少两个胚胎中出现至少三个连续扩增子的CNV增加/丢失。
方法：主要结局指标是特异性，发病率,继承,PGT-A平台检测到的小CNV的致病性。通过与配子提供者的染色体微阵列上的CNV调用(大小和基因组位置)的一致性来评估PGT-A平台CNV调用的准确性。还报道了CNV的亲本起源和致病性分类。
结果：在12,157例独特的PGT-A患者中，有75例（0.62％；95CI：0.5-0.8％），确定了符合报告标准的偶然发现.要求对所有病例进行染色体微阵列随访，并收到65对生殖夫妇中的一个或两个成员的结果。在所有情况下,其中一个配子提供者被证实在胚胎中鉴定出CNV(100.0%:N=65/6595CI:94.5-100).经鉴定的CNV有34例（52.3％）为母体来源，有31例（47.7％）为父系来源。在PGT-A预测的CNV大小与染色体微阵列检测到的大小(r=0.81)和亲本DNA上的基因组坐标之间鉴定出显著的相关性。26（40％）的CNV被分类为良性/可能良性，30(46.2%)作为不确定意义(VUS)的变体，9（13.8%）为致病性/可能致病性。
结论：某些PGT-A平台可以检测遗传，具有极高特异性的小CNV，无需父母身份的先验知识。此数据集中的大多数CNV被证实为良性/可能是良性或VUS;然而,也可以检测到与广泛的表型特征相关的致病性/可能的致病性CNV，尽管由于许多技术挑战，目前PGT-A技术对小CNV的可靠阴性预测值尚不清楚。
方法：2020-2022年进行回顾性观察性研究。
方法：12,157例接受全染色体和大段非整倍体靶向NGS临床PGT-A治疗的患者。
方法：报道了一个偶然发现，即在同一IVF周期的至少两个胚胎中出现至少三个连续扩增子的CNV增加/丢失。
方法：主要结局指标是特异性，发病率,继承,PGT-A平台检测到的小CNV的致病性。通过与配子提供者的染色体微阵列上的CNV调用(大小和基因组位置)的一致性来评估PGT-A平台CNV调用的准确性。还报道了CNV的亲本起源和致病性分类。
结果：在12,157例独特的PGT-A患者中，有75例（0.62％；95CI：0.5-0.8％），确定了符合报告标准的偶然发现.要求对所有病例进行染色体微阵列随访，并收到65对生殖夫妇中的一个或两个成员的结果。在所有情况下,其中一个配子提供者被证实在胚胎中鉴定出CNV(100.0%:N=65/6595CI:94.5-100).经鉴定的CNV有34例（52.3％）为母体来源，有31例（47.7％）为父系来源。在PGT-A预测的CNV大小与染色体微阵列检测到的大小(r=0.81)和亲本DNA上的基因组坐标之间鉴定出显著的相关性。26（40％）的CNV被分类为良性/可能良性，30(46.2%)作为不确定意义(VUS)的变体，9（13.8%）为致病性/可能致病性。
结论：某些PGT-A平台可以检测遗传，具有极高特异性的小CNV，无需父母身份的先验知识。此数据集中的大多数CNV被证实为良性/可能是良性或VUS;然而,也可以检测到与广泛的表型特征相关的致病性/可能的致病性CNV，尽管由于许多技术挑战，目前PGT-A技术对小CNV的可靠阴性预测值尚不清楚。
