针对新型 SARS-CoV-2 (SCV-2) 菌株的诊断和疫苗依赖病毒基因组测序。研究人员倾向于采用成本效益高且高度敏感、基于扩增子的程序（例如 ARTIC）和杂交捕获测序（例如 SARS-CoV-2 NGS 检测），以选择性地靶向 SCV-2 基因组。为了证实杂交捕获用于病毒监测的优势，我们实施了预测建模，以评估 SCV-2 基因组中可能更容易发生突变的区域，而这些突变可能会影响扩增子测序期间多重 PCR 步骤中的引物效率。我们分析了来自 GISAID 的关切变异株 (VOC) 和关注变异株 (VOI) 分离株的 383,656 个基因组序列，发现 101,432 种病毒 (27%) 在来自 ARTIC 引物 3' 端的最后 6 个碱基对中存在 ≥1 个错配。相比之下，只有 38 种病毒 (0.01%) 具有足够的突变 (≥10)，预测对杂交捕获测序的影响相似。我们的方法鉴定了 4 个 ARTIC 引物过量突变的分离株，并生成了这些分离株的合成基因组，同时将 ARTIC 扩增子测序的性能与 Twist Bioscience 的 SARS-CoV-2 NGS 检测进行了比较。对于每个菌株，我们仅观察到扩增子文库测序覆盖度的下降，但未观察到杂交捕获的下降。我们还偶然观察到两个样本中 ARTIC 扩增子 72 丢失，因反向引物中反复出现的 1bp 错配引起。我们还使用不变参比对照品（Twist 合成 SARS-CoV-2 RNA 质控品 2）比较了丢失情况，发现杂交捕获测序了 99.5% 的碱基，覆盖度 ≥50 倍，而扩增子测序为 92.1%。总体而言，我们的结果证实杂交捕获对基因组变异更具稳定性，并且导致的丢失事件更少。尽管扩增子测序为病毒监测提供了一个低成本平台，但也增加了测序丢失的成本，可能会导致病毒谱系分类错误。突变肯定会在 SCV-2 中积累，这进一步加剧了这种情况，更多引物失效只是时间问题。因此，我们建议将杂交捕获作为病毒监测的一种稳定、全面的解决方案。

ASHG 2021 上的演讲

Pathogenic coding region mutations in BRCA1, BRCA2 and PALB2 are major contributors to hereditary breast cancer (HBC) but collectively explain less than a quarter of the families tested in clinical practice, leaving the majority with no identifiable genetic defect to inform cancer prevention strategies. Other HBC genes explain only a small fraction (5%) of families. In contrast to the intensive, but largely unsuccessful, international efforts aimed at discovering new HBC genes, little attention has been given to the possibility that many of these families are explained by known HBC genes but which are inactivated via alternative mechanisms that are not detected by current methodology. We hypothesize that a clinically important component of the uncovered inherited risk of breast cancer is due to inherited promoter hypermethylation. Promoter hypermethylation of specific genes in hereditary cancer syndromes have been reported, such as the MLH1 gene in a proportion of Lynch syndrome patients but whether the same mechanism explains some HBC families is largely unexplored. A significant limitation of the few studies that have tried to explore HBC is that most have used methods that interrogate single CpG dinucleotides rather than the entire gene promoter and few included cases with a strong cancer family history. To overcome the limitations of these previous attempts to resolve the role of inherited promoter hypermethylation we are performing targeted methylation sequencing (TWIST Bioscience) of the entire promoter regions of 13 HBC genes in germline DNA from over 1000 women from the BEACCON study (npj Breast Cancer 2021, 7:76) who have a very strong breast cancer family history but where all known genetic causes have been excluded. This represents the largest and most comprehensive study of its type to date, which will have the power to conclusively resolve the contribution of inherited promoter hypermethylation to HBC.