Lauhasurayotin Supanun, Cuvelier Geoff D, Klaassen Robert J, Fernandez Conrad V, Pastore Yves D, Abish Sharon, Rayar Meera, Steele MacGregor, Jardine Lawrence, Breakey Vicky R, Brossard Josee, Sinha Roona, Silva Mariana, Goodyear Lisa, Lipton Jeffrey H, Michon Bruno, Corriveau-Bourque Catherine, Sung Lillian, Shabanova Iren, Li Hongbing, Zlateska Bozana, Dhanraj Santhosh, Cada Michaela, Scherer Stephen W, Dror Yigal
1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.
2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada.
NPJ Genom Med. 2019 Dec 9;4:30. doi: 10.1038/s41525-019-0104-9. eCollection 2019.
Inherited bone marrow failure syndromes (IBMFSs) are genetically heterogeneous disorders with cytopenia. Many IBMFSs also feature physical malformations and an increased risk of cancer. Point mutations can be identified in about half of patients. Copy number variation (CNVs) have been reported; however, the frequency and spectrum of CNVs are unknown. Unfortunately, current genome-wide methods have major limitations since they may miss small CNVs or may have low sensitivity due to low read depths. Herein, we aimed to determine whether reanalysis of NGS panel data by normalized coverage value could identify CNVs and characterize them. To address this aim, DNA from IBMFS patients was analyzed by a NGS panel assay of known IBMFS genes. After analysis for point mutations, heterozygous and homozygous CNVs were searched by normalized read coverage ratios and specific thresholds. Of the 258 tested patients, 91 were found to have pathogenic point variants. NGS sample data from 165 patients without pathogenic point mutations were re-analyzed for CNVs; 10 patients were found to have deletions. Diamond Blackfan anemia genes most commonly exhibited heterozygous deletions, and included , , and . A diagnosis of -related disorder was made in a patient with myelodysplastic syndrome who was found to have a heterozygous deletion. Importantly, homozygous deletion were detected in a patient who could not be previously assigned a specific syndromic diagnosis. Lastly, we identified compound heterozygousity for deletions and pathogenic point variants in and genes. All deletions were validated by orthogonal methods. We conclude that careful analysis of normalized coverage values can detect CNVs in NGS panels and should be considered as a standard practice prior to do further investigations.
遗传性骨髓衰竭综合征（IBMFSs）是一类具有血细胞减少的基因异质性疾病。许多IBMFSs还伴有身体畸形以及患癌风险增加。约半数患者可检测到点突变。已有关于拷贝数变异（CNV）的报道；然而，CNV的频率和谱系尚不清楚。不幸的是，目前的全基因组方法存在重大局限性，因为它们可能会遗漏小的CNV，或者由于测序深度低而敏感性较差。在此，我们旨在确定通过标准化覆盖值对NGS panel数据进行重新分析是否能够识别CNV并对其进行特征描述。为实现这一目标，我们通过对已知IBMFS基因进行NGS panel检测，分析了IBMFS患者的DNA。在分析点突变后，通过标准化读取覆盖比率和特定阈值搜索杂合和纯合CNV。在258例接受检测的患者中，91例被发现存在致病性点变异。对165例无致病性点突变患者的NGS样本数据重新分析CNV；发现10例患者存在缺失。戴蒙德-布莱克范贫血基因最常表现为杂合缺失，包括 、 和 。一名骨髓增生异常综合征患者被发现存在杂合 缺失，从而被诊断为 -相关疾病。重要的是，在一名先前无法明确诊断为特定综合征的患者中检测到了纯合 缺失。最后，我们在 和 基因中鉴定出缺失和致病性点变异的复合杂合性。所有缺失均通过正交方法进行了验证。我们得出结论，仔细分析标准化覆盖值能够在NGS panel中检测到CNV，在进行进一步研究之前应将其视为标准操作。
