人类基因组包含“暗”基因区域,无法使用标准短读取测序技术充分组装或对齐,阻止研究人员识别这些基因区域内可能与人类疾病相关的突变。这里,我们通过深度来识别几乎没有可映射读数的区域,我们称之为黑暗,和其他有模糊对齐的人,叫做伪装。我们评估长读取或链接读取技术如何很好地解决这些区域。
基于标准全基因组Illumina测序数据,我们从对人类健康重要的途径中鉴定出6054个基因体中的36,794个暗区,发展,和繁殖。在这些基因体中,8.7%为完全黑暗,35.2%为≥5%黑暗。我们确定了748个基因的蛋白质编码外显子中存在的暗区。来自10x基因组学的链接读取或长读取测序技术,PacBio,牛津纳米孔技术将暗蛋白编码区减少到大约50.5%,35.6%,9.6%,分别。我们提出了一种算法来解决大多数伪装区域,并将其应用于阿尔茨海默病测序项目。我们拯救了CR1中罕见的十核苷酸移码缺失,CR1是阿尔茨海默病的顶级基因,在疾病病例中发现,但在对照中没有发现。
由于样本量不足,我们无法正式评估CR1移码突变与阿尔茨海默病的关联,我们认为值得在更大的队列中进行调查。仍有数千个潜在重要的基因组区域被短读取测序所忽略,这些区域主要由长读取技术解决。
The human genome contains \"dark\" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease. Here, we identify regions with few mappable reads that we call dark by depth, and others that have ambiguous alignment, called camouflaged. We assess how well long-read or linked-read technologies resolve these regions.
Based on standard whole-genome Illumina sequencing data, we identify 36,794 dark regions in 6054 gene bodies from pathways important to human health, development, and reproduction. Of these gene bodies, 8.7% are completely dark and 35.2% are ≥ 5% dark. We identify dark regions that are present in protein-coding exons across 748 genes. Linked-read or long-read sequencing technologies from 10x Genomics, PacBio, and Oxford Nanopore Technologies reduce dark protein-coding regions to approximately 50.5%, 35.6%, and 9.6%, respectively. We present an algorithm to resolve most camouflaged regions and apply it to the Alzheimer\'s Disease Sequencing Project. We rescue a rare ten-nucleotide frameshift deletion in CR1, a top Alzheimer\'s disease gene, found in disease cases but not in controls.
While we could not formally assess the association of the CR1 frameshift mutation with Alzheimer\'s disease due to insufficient sample-size, we believe it merits investigating in a larger cohort. There remain thousands of potentially important genomic regions overlooked by short-read sequencing that are largely resolved by long-read technologies.