低通滤波器全基因组测序作为中低收入国家染色体微阵列分析的一种经济有效的替代方法。

IF 1.7 4区 生物学 Q3 GENETICS & HEREDITY
Patricia C. Mazzonetto, Darine Villela, Ana C. V. Krepischi, Paulo M. Pierry, Adriano Bonaldi, Luiz Gustavo D. Almeida, Marcelo G. Paula, Matheus Carvalho Bürger, Ana Gabriela de Oliveira, Gustavo G. G. Fonseca, Roberto Giugliani, Mariluce Riegel-Giugliani, Débora Bertola, Guilherme Lopes Yamamoto, Maria Rita Passos-Bueno, Gabriele da Silva Campos, Ana Claudia Dantas Machado, Juliana F. Mazzeu, Eduardo Perrone, Roseli M. Zechi-Ceide, Nancy M. Kokitsu-Nakata, Társis Paiva Vieira, Carlos Eduardo Steiner, Vera Lúcia Gil-da-Silva-Lopes, Daniela Koeller Rodrigues Vieira, Raquel Boy, João Monteiro de Pina-Neto, Cristovam Scapulatempo-Neto, Fernanda Milanezi, Carla Rosenberg
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引用次数: 0

摘要

低通滤波全基因组测序(LP-WGS)已被用作临床检测拷贝数变异(CNV)的替代方法。与染色体微阵列分析(CMA)相比,基于测序的方法能以更低的成本提供相似的 CNV 检测分辨率。在本研究中,我们评估了 LP-WGS 作为 CMA 更经济实惠的替代方法的效率和可靠性。研究共招募了 1363 名不明原因的神经发育迟缓/智力障碍、自闭症谱系障碍和/或多发性先天性异常患者。这些患者来自巴西不同州的 15 家非营利组织和大学中心。对 1 倍覆盖率(>50kb)的 LP-WGS 分析显示,22% 的病例(304/1363)检测结果呈阳性,其中 219 和 85 例分别对应致病/可能致病(P/LP)CNV 和意义不确定变异(VUS)。我们队列中观察到的 16% 的诊断率(219/1363)与文献中报道的 15%-20% 的 CMA 诊断率相当。如本研究所示,商业软件的使用简化了检验在临床环境中的实施。特别是在巴西这样的国家,CMA 的费用对大多数人来说是一个巨大的障碍,LP-WGS 成为了研究细胞遗传学中拷贝数变化的一种经济有效的替代方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Low-pass whole genome sequencing as a cost-effective alternative to chromosomal microarray analysis for low- and middle-income countries

Low-pass whole genome sequencing (LP-WGS) has been applied as alternative method to detect copy number variants (CNVs) in the clinical setting. Compared with chromosomal microarray analysis (CMA), the sequencing-based approach provides a similar resolution of CNV detection at a lower cost. In this study, we assessed the efficiency and reliability of LP-WGS as a more affordable alternative to CMA. A total of 1363 patients with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies were enrolled. Those patients were referred from 15 nonprofit organizations and university centers located in different states in Brazil. The analysis of LP-WGS at 1x coverage (>50kb) revealed a positive testing result in 22% of the cases (304/1363), in which 219 and 85 correspond to pathogenic/likely pathogenic (P/LP) CNVs and variants of uncertain significance (VUS), respectively. The 16% (219/1363) diagnostic yield observed in our cohort is comparable to the 15%–20% reported for CMA in the literature. The use of commercial software, as demonstrated in this study, simplifies the implementation of the test in clinical settings. Particularly for countries like Brazil, where the cost of CMA presents a substantial barrier to most of the population, LP-WGS emerges as a cost-effective alternative for investigating copy number changes in cytogenetics.

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来源期刊
CiteScore
3.50
自引率
5.00%
发文量
432
审稿时长
2-4 weeks
期刊介绍: The American Journal of Medical Genetics - Part A (AJMG) gives you continuous coverage of all biological and medical aspects of genetic disorders and birth defects, as well as in-depth documentation of phenotype analysis within the current context of genotype/phenotype correlations. In addition to Part A , AJMG also publishes two other parts: Part B: Neuropsychiatric Genetics , covering experimental and clinical investigations of the genetic mechanisms underlying neurologic and psychiatric disorders. Part C: Seminars in Medical Genetics , guest-edited collections of thematic reviews of topical interest to the readership of AJMG .
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