PDF(Pubmed)
Abstract：
BACKGROUND: Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown.
METHODS: In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform.
RESULTS: Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level.
CONCLUSIONS: Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
METHODS: In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform.
RESULTS: Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level.
CONCLUSIONS: Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
摘要：
背景：长读全基因组测序（lrWGS）有可能以短读WGS不可能的方式解决外显子组测序的技术局限性。然而,它在常染色体隐性孟德尔疾病中的效用在很大程度上是未知的。
方法：在一个由34个家族组成的队列中，其中可疑的常染色体隐性遗传疾病仍未通过外显子组测序诊断，lrWGS在PacificBioscienceSequelIIe平台上进行。
结果：在13（38%）的队列中发现了可能的因果变异。这些包括（1）TYMS中的纯合剪接SV作为致死性新生儿乳酸性酸中毒的新候选基因，（2）我们提出的纯合子非编码SV影响STK25表达并引起一种新型神经发育障碍，（3）在一个遗传性视网膜疾病家族中，RP1L1中具有复杂遗传模式的复合杂合SV，（4）LEMD2和SNAP91中的纯合深内含子变异体可作为两个家族神经发育障碍的新候选基因，和(5)引起非综合征性带状角膜病变的SLC4A4中的启动子SNV。令人惊讶的是,我们还遇到了可以通过短读段外显子组测序鉴定的7个家族的因果变异.后者强调了在口译层面特别具有挑战性的情况。
结论：我们的数据突出表明，在努力改进测序技术本身的同时，继续需要应对解释挑战。我们提出了在常染色体隐性疾病的背景下以最大化其效用的方式实施lrWGS测序的前进道路。
方法：在一个由34个家族组成的队列中，其中可疑的常染色体隐性遗传疾病仍未通过外显子组测序诊断，lrWGS在PacificBioscienceSequelIIe平台上进行。
结果：在13（38%）的队列中发现了可能的因果变异。这些包括（1）TYMS中的纯合剪接SV作为致死性新生儿乳酸性酸中毒的新候选基因，（2）我们提出的纯合子非编码SV影响STK25表达并引起一种新型神经发育障碍，（3）在一个遗传性视网膜疾病家族中，RP1L1中具有复杂遗传模式的复合杂合SV，（4）LEMD2和SNAP91中的纯合深内含子变异体可作为两个家族神经发育障碍的新候选基因，和(5)引起非综合征性带状角膜病变的SLC4A4中的启动子SNV。令人惊讶的是,我们还遇到了可以通过短读段外显子组测序鉴定的7个家族的因果变异.后者强调了在口译层面特别具有挑战性的情况。
结论：我们的数据突出表明，在努力改进测序技术本身的同时，继续需要应对解释挑战。我们提出了在常染色体隐性疾病的背景下以最大化其效用的方式实施lrWGS测序的前进道路。
