视网膜母细胞瘤（RB）是儿童期最常见的眼内恶性肿瘤。 RB中的因果变异主要是通过以前使用的短读长测序（SRS）分析来表征的，该分析在识别结构变异（SV）和定相信息方面存在技术限制。长读长测序（LRS）技术在检测SV、定相遗传变异和甲基化方面比SRS具有优势。在这项研究中，我们使用 16 个 RB 肿瘤和 16 个匹配的血液样本的组合 LRS 和 SRS 全面描述了 RB 的遗传图谱。我们总共检测到 232 个体细胞 SV，在我们的队列中，整个基因组中每个样本平均有 14.5 个 SV。我们鉴定了 20 个破坏 RB1 基因的不同致病变异，包括三个新的小变异和五个体细胞 SV。我们发现，在具有 WGS 数据的 RB 样本中，LRS 比 SRS 检测到更多的体细胞 SV（140 比 122），特别是插入（18 比 1）。此外，我们的分析表明，除了一个缺乏甲基化数据的样本外，所有样本都呈现出各种形式的RB1双等位基因失活，其中包括两例具有双等位基因高甲基化启动子和四例具有SRS中缺失的复合杂合突变。分析。通过推断体细胞事件的相对时间，我们揭示了 RB 肿瘤发生过程中 RB1 早期破坏和随后拷贝数变化（包括 Chr2p 扩增和 Chr16q 缺失）的遗传进展。总而言之，我们描述了 RB 的全面遗传景观，为 RB 启动和发展的遗传改变和机制提供了新的见解。我们的工作还建立了一个基于 LRS 数据分析癌症基因组图谱的框架。版权所有 © 2024。由 Elsevier B.V. 出版。

Retinoblastoma (RB) is the most common intraocular malignancy in childhood. The causal variants in RB are mostly characterized by previously used short-read sequencing (SRS) analysis, which has technical limitations in identifying structural variants (SVs) and phasing information. Long-read sequencing (LRS) technology has advantages over SRS in detecting SVs, phased genetic variants, and methylation. In this study, we comprehensively characterized the genetic landscape of RB using combinatorial LRS and SRS of 16 RB tumors and 16 matched blood samples. We detected a total of 232 somatic SVs, with an average of 14.5 SVs per sample across the whole genome in our cohort. We identified 20 distinct pathogenic variants disrupting RB1 gene, including three novel small variants and five somatic SVs. We found more somatic SVs were detected from LRS than SRS (140 vs. 122) in RB samples with WGS data, particularly the insertions (18 vs. 1). Furthermore, our analysis shows that, with the exception of one sample who lacked the methylation data, all samples presented biallelic inactivation of RB1 in various forms, including two cases with the biallelic hypermethylated promoter and four cases with compound heterozygous mutations which were missing in SRS analysis. By inferring relative timing of somatic events, we reveal the genetic progression that RB1 disruption early and followed by copy number changes, including amplifications of Chr2p and deletions of Chr16q, during RB tumorigenesis. Altogether, we characterize the comprehensive genetic landscape of RB, providing novel insights into the genetic alterations and mechanisms contributing to RB initiation and development. Our work also establishes a framework to analyze genomic landscape of cancers based on LRS data.Copyright © 2024. Published by Elsevier B.V.