Kaplun Ludmila, Krautz-Peterson Greice, Neerman Nir, Stanley Christine, Hussey Shane, Folwick Margo, McGarry Ava, Weiss Shirel, Kaplun Alexander
Variantyx Inc, Framingham, MA, United States.
Front Genet. 2023 Apr 21;14:1145285. doi: 10.3389/fgene.2023.1145285. eCollection 2023.
Technological advances in Next-Generation Sequencing dramatically increased clinical efficiency of genetic testing, allowing detection of a wide variety of variants, from single nucleotide events to large structural aberrations. Whole Genome Sequencing (WGS) has allowed exploration of areas of the genome that might not have been targeted by other approaches, such as intergenic regions. A single technique detecting all genetic variants at once is intended to expedite the diagnostic process while making it more comprehensive and efficient. Nevertheless, there are still several shortcomings that cannot be effectively addressed by short read sequencing, such as determination of the precise size of short tandem repeat (STR) expansions, phasing of potentially compound recessive variants, resolution of some structural variants and exact determination of their boundaries, Therefore, in some cases variants can only be tentatively detected by short reads sequencing and require orthogonal confirmation, particularly for clinical reporting purposes. Moreover, certain regulatory authorities, for example, New York state CLIA, require orthogonal confirmation of every reportable variant. Such orthogonal confirmations often involve numerous different techniques, not necessarily available in the same laboratory and not always performed in an expedited manner, thus negating the advantages of "one-technique-for-all" approach, and making the process lengthy, prone to logistical and analytical faults, and financially inefficient. Fortunately, those weak spots of short read sequencing can be compensated by long read technology that have comparable or better detection of some types of variants while lacking the mentioned above limitations of short read sequencing. At Variantyx we have developed an integrated clinical genetic testing approach, augmenting short read WGS-based variant detection with Oxford Nanopore Technologies (ONT) long read sequencing, providing simultaneous orthogonal confirmation of all types of variants with the additional benefit of improved identification of exact size and position of the detected aberrations. The validation study of this augmented test has demonstrated that Oxford Nanopore Technologies sequencing can efficiently verify multiple types of reportable variants, thus ensuring highly reliable detection and a quick turnaround time for WGS-based clinical genetic testing.
下一代测序技术的进步极大地提高了基因检测的临床效率，能够检测从单核苷酸事件到大型结构畸变等各种各样的变异。全基因组测序（WGS）使得人们能够探索基因组中其他方法可能未靶向的区域，如基因间区域。一种能一次性检测所有基因变异的技术旨在加快诊断过程，同时使其更全面、高效。然而，短读长测序仍存在一些无法有效解决的缺点，比如确定短串联重复序列（STR）扩增的精确大小、潜在复合隐性变异的定相、一些结构变异的解析以及其边界的精确确定。因此，在某些情况下，短读长测序只能初步检测到变异，需要进行正交确认，尤其是出于临床报告目的。此外，某些监管机构，例如纽约州临床实验室改进修正案（CLIA），要求对每个可报告变异进行正交确认。这种正交确认通常涉及许多不同技术，同一实验室不一定都具备，而且也并非总是能快速完成，从而抵消了“一技术通用”方法的优势，使得整个过程冗长，容易出现后勤和分析错误，且在经济上效率低下。幸运的是，短读长测序的这些弱点可以通过长读长技术来弥补，长读长技术对某些类型变异的检测能力相当甚至更好，同时不存在上述短读长测序的局限性。在Variantyx公司，我们开发了一种综合临床基因检测方法，用牛津纳米孔技术（ONT）长读长测序增强基于短读长WGS的变异检测，能同时对所有类型变异进行正交确认，还能额外更好地确定检测到的畸变的精确大小和位置。这种增强检测的验证研究表明，牛津纳米孔技术测序能够有效地验证多种类型的可报告变异，从而确保基于WGS的临床基因检测具有高度可靠的检测结果和快速周转时间。
