Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland.
Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Health Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands.
Am J Hum Genet. 2021 Aug 5;108(8):1409-1422. doi: 10.1016/j.ajhg.2021.05.012. Epub 2021 Jul 7.
Chromosomal aberrations including structural variations (SVs) are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard cytogenetics. Drawbacks of these tests are a very low resolution (karyotyping) and the inability to detect balanced SVs or indicate the genomic localization and orientation of duplicated segments or insertions (copy number variant [CNV] microarrays). Here, we investigated the ability of optical genome mapping (OGM) to detect known constitutional chromosomal aberrations. Ultra-high-molecular-weight DNA was isolated from 85 blood or cultured cells and processed via OGM. A de novo genome assembly was performed followed by structural variant and CNV calling and annotation, and results were compared to known aberrations from standard-of-care tests (karyotype, FISH, and/or CNV microarray). In total, we analyzed 99 chromosomal aberrations, including seven aneuploidies, 19 deletions, 20 duplications, 34 translocations, six inversions, two insertions, six isochromosomes, one ring chromosome, and four complex rearrangements. Several of these variants encompass complex regions of the human genome involved in repeat-mediated microdeletion/microduplication syndromes. High-resolution OGM reached 100% concordance compared to standard assays for all aberrations with non-centromeric breakpoints. This proof-of-principle study demonstrates the ability of OGM to detect nearly all types of chromosomal aberrations. We also suggest suited filtering strategies to prioritize clinically relevant aberrations and discuss future improvements. These results highlight the potential for OGM to provide a cost-effective and easy-to-use alternative that would allow comprehensive detection of chromosomal aberrations and structural variants, which could give rise to an era of "next-generation cytogenetics."
染色体异常包括结构变异（SVs）是人类遗传疾病的主要原因。它们在临床常规中的检测仍然依赖于标准细胞遗传学。这些测试的缺点是分辨率非常低（核型分析），并且无法检测平衡的 SVs 或指示重复片段或插入物的基因组定位和方向（拷贝数变异[CNV]微阵列）。在这里，我们研究了光学基因组图谱（OGM）检测已知的先天性染色体异常的能力。从 85 个血液或培养细胞中分离出超高分子量 DNA，并通过 OGM 进行处理。然后进行从头基因组组装，随后进行结构变体和 CNV 调用和注释，并将结果与标准护理测试（核型分析，FISH 和/或 CNV 微阵列）中的已知异常进行比较。总共分析了 99 种染色体异常，包括七种非整倍体，19 种缺失，20 种重复，34 种易位，六种倒位，两种插入，六种等臂染色体，一种环状染色体和四种复杂重排。其中一些变体包含涉及重复介导的微缺失/微重复综合征的人类基因组的复杂区域。与非着丝粒断点的标准检测相比，高分辨率 OGM 达到了所有异常的 100％一致性。这项原理验证研究表明，OGM 能够检测几乎所有类型的染色体异常。我们还建议采用合适的过滤策略来优先考虑临床相关的异常，并讨论未来的改进。这些结果强调了 OGM 提供具有成本效益且易于使用的替代方案的潜力，该方案可以全面检测染色体异常和结构变体，从而引发“下一代细胞遗传学”时代。
