Mazzonetto Patricia C, Villela Darine, da Costa Silvia Souza, Krepischi Ana C V, Milanezi Fernanda, Migliavacca Michele P, Pierry Paulo M, Bonaldi Adriano, Almeida Luiz Gustavo D, De Souza Camila Alves, Kroll José Eduardo, Paula Marcelo G, Guarischi-Sousa Rodrigo, Scapulatempo-Neto Cristovam, Rosenberg Carla
The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil.
Diagnósticos da América S.A., DASA, São Paulo, Brazil.
Ann Hum Genet. 2024 Mar;88(2):113-125. doi: 10.1111/ahg.12532. Epub 2023 Oct 9.
Next generation sequencing technology has greatly reduced the cost and time required for sequencing a genome. An approach that is rapidly being adopted as an alternative method for CNV analysis is the low-pass whole genome sequencing (LP-WGS). Here, we evaluated the performance of LP-WGS to detect copy number variants (CNVs) in clinical cytogenetics.
DNA samples with known CNVs detected by chromosomal microarray analyses (CMA) were selected for comparison and used as positive controls; our panel included 44 DNA samples (12 prenatal and 32 postnatal), comprising a total of 55 chromosome imbalances. The selected cases were chosen to provide a wide range of clinically relevant CNVs, the vast majority being associated with intellectual disability or recognizable syndromes. The chromosome imbalances ranged in size from 75 kb to 90.3 Mb, including aneuploidies and two cases of mosaicism.
All CNVs were successfully detected by LP-WGS, showing a high level of consistency and robust performance of the sequencing method. Notably, the size of chromosome imbalances detected by CMA and LP-WGS were compatible between the two different platforms, which indicates that the resolution and sensitivity of the LP-WGS approach are at least similar to those provided by CMA.
Our data show the potential use of LP-WGS to detect CNVs in clinical diagnosis and confirm the method as an alternative for chromosome imbalances detection. The diagnostic effectiveness and feasibility of LP-WGS, in this technical validation study, were evidenced by a clinically representative dataset of CNVs that allowed a systematic assessment of the detection power and the accuracy of the sequencing approach. Further, since the software used in this study is commercially available, the method can easily be tested and implemented in a routine diagnostic setting.
新一代测序技术已大幅降低了基因组测序所需的成本和时间。低覆盖度全基因组测序（LP-WGS）作为一种拷贝数变异（CNV）分析的替代方法正在迅速被采用。在此，我们评估了LP-WGS在临床细胞遗传学中检测拷贝数变异（CNV）的性能。
选择通过染色体微阵列分析（CMA）检测到具有已知CNV的DNA样本进行比较，并用作阳性对照；我们的样本组包括44个DNA样本（12个产前样本和32个产后样本），共包含55个染色体失衡。选择这些病例以提供广泛的临床相关CNV，绝大多数与智力残疾或可识别的综合征相关。染色体失衡的大小范围从75 kb到90.3 Mb，包括非整倍体和两例嵌合体。
LP-WGS成功检测到所有CNV，显示出该测序方法具有高度的一致性和强大的性能。值得注意的是，CMA和LP-WGS检测到的染色体失衡大小在两个不同平台之间是相符的，这表明LP-WGS方法的分辨率和灵敏度至少与CMA提供的相当。
我们的数据显示了LP-WGS在临床诊断中检测CNV的潜在用途，并确认该方法可作为染色体失衡检测的替代方法。在这项技术验证研究中，LP-WGS的诊断有效性和可行性通过一个具有临床代表性的CNV数据集得到了证明，该数据集允许对测序方法的检测能力和准确性进行系统评估。此外，由于本研究中使用的软件是商业可用的，该方法可以很容易地在常规诊断环境中进行测试和实施。
