Kieran O'Neill, Erin Pleasance, Jeremy Fan, Vahid Akbari, Glenn Chang, Katherine Dixon, Veronika Csizmok, Signe MacLennan, Vanessa Porter, Andrew Galbraith, Cameron J Grisdale, Luka Culibrk, John H Dupuis, Richard Corbett, James Hopkins, Reanne Bowlby, Pawan Pandoh, Duane E Smailus, Dean Cheng, Tina Wong, Connor Frey, Yaoqing Shen, Eleanor Lewis, Luis F Paulin, Fritz J Sedlazeck, Jessica M T Nelson, Eric Chuah, Karen L Mungall, Richard A Moore, Robin Coope, Andrew J Mungall, Melissa K McConechy, Laura M Williamson, Kasmintan A Schrader, Stephen Yip, Marco A Marra, Janessa Laskin, Steven J M Jones
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引用次数: 0
摘要
长读数个性化肿瘤基因组学（POG）数据集包括使用牛津纳米孔技术公司（Oxford Nanopore Technologies）PromethION平台测序的189个患者肿瘤和41个匹配的正常样本。该数据集来自 POG 计划和马拉松希望癌症中心网络，包括 DNA 和 RNA 短读序列数据、分析和临床信息。我们展示了长线程测序在解析复杂的癌症相关结构变异、病毒整合和染色体外环状DNA方面的潜力。长程相位分析有助于发现等位基因差异甲基化区域（aDMR）和等位基因特异性表达，包括癌症基因 RET 和 CDKN2A 中反复出现的 aDMR。在林奇综合征中可以直接观察到 MLH1 的基因启动子甲基化。在没有发现编码驱动突变的情况下，BRCA1 和 RAD51C 的启动子甲基化可能是同源重组缺陷的驱动因素。该数据集展示了长线程测序在精准医疗中的应用，可作为利用该技术开发分析方法的资源。
Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes.
The Long-Read Personalized OncoGenomics (POG) dataset comprises a cohort of 189 patient tumors and 41 matched normal samples sequenced using the Oxford Nanopore Technologies PromethION platform. This dataset from the POG program and the Marathon of Hope Cancer Centres Network includes DNA and RNA short-read sequence data, analytics, and clinical information. We show the potential of long-read sequencing for resolving complex cancer-related structural variants, viral integrations, and extrachromosomal circular DNA. Long-range phasing facilitates the discovery of allelically differentially methylated regions (aDMRs) and allele-specific expression, including recurrent aDMRs in the cancer genes RET and CDKN2A. Germline promoter methylation in MLH1 can be directly observed in Lynch syndrome. Promoter methylation in BRCA1 and RAD51C is a likely driver behind homologous recombination deficiency where no coding driver mutation was found. This dataset demonstrates applications for long-read sequencing in precision medicine and is available as a resource for developing analytical approaches using this technology.
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