Sanford Kobayashi Erica, Batalov Serge, Wenger Aaron M, Lambert Christine, Dhillon Harsharan, Hall Richard J, Baybayan Primo, Ding Yan, Rego Seema, Wigby Kristen, Friedman Jennifer, Hobbs Charlotte, Bainbridge Matthew N
Rady Institute for Genomic Medicine, San Diego, CA, USA.
Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Sci Rep. 2022 Oct 9;12(1):16945. doi: 10.1038/s41598-022-20113-x.
Over the past decade, advances in genetic testing, particularly the advent of next-generation sequencing, have led to a paradigm shift in the diagnosis of molecular diseases and disorders. Despite our present collective ability to interrogate more than 90% of the human genome, portions of the genome have eluded us, resulting in stagnation of diagnostic yield with existing methodologies. Here we show how application of a new technology, long-read sequencing, has the potential to improve molecular diagnostic rates. Whole genome sequencing by long reads was able to cover 98% of next-generation sequencing dead zones, which are areas of the genome that are not interpretable by conventional industry-standard short-read sequencing. Through the ability of long-read sequencing to unambiguously call variants in these regions, we discovered an immunodeficiency due to a variant in IKBKG in a subject who had previously received a negative genome sequencing result. Additionally, we demonstrate the ability of long-read sequencing to detect small variants on par with short-read sequencing, its superior performance in identifying structural variants, and thirdly, its capacity to determine genomic methylation defects in native DNA. Though the latter technical abilities have been demonstrated, we demonstrate the clinical application of this technology to successfully identify multiple types of variants using a single test.
在过去十年中，基因检测技术取得了显著进展，尤其是新一代测序技术的出现，引发了分子疾病和紊乱诊断领域的范式转变。尽管目前我们有能力对超过90%的人类基因组进行检测，但基因组的某些部分仍未被我们所了解，导致现有方法的诊断效率停滞不前。在此，我们展示了一种新技术——长读长测序的应用如何有潜力提高分子诊断率。通过长读长进行的全基因组测序能够覆盖98%的新一代测序盲区，这些区域是传统行业标准的短读长测序无法解读的基因组区域。凭借长读长测序在这些区域明确识别变异的能力，我们在一名之前基因组测序结果为阴性的受试者中发现了由于IKBKG基因变异导致的免疫缺陷。此外，我们还展示了长读长测序在检测小变异方面与短读长测序相当的能力、在识别结构变异方面的卓越性能，以及在确定天然DNA中基因组甲基化缺陷方面的能力。尽管后两项技术能力已有相关证明，但我们展示了该技术的临床应用，即通过一次检测成功识别多种类型的变异。
