Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada.
Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
Cell Genom. 2024 Nov 13;4(11):100674. doi: 10.1016/j.xgen.2024.100674. Epub 2024 Oct 14.
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.
长读个性化肿瘤基因组学（POG）数据集包含 189 个患者肿瘤和 41 个匹配的正常样本，这些样本是使用牛津纳米孔技术 PromethION 平台进行测序的。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、分析结果和临床信息。我们展示了长读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 中的反复出现的 aDMR。林奇综合征中可以直接观察到 MLH1 中的种系启动子甲基化。BRCA1 和 RAD51C 中的启动子甲基化可能是同源重组缺陷的驱动因素，在这种情况下没有发现编码驱动突变。该数据集展示了长读测序在精准医学中的应用，并可作为使用该技术开发分析方法的资源。
