Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia.
Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia.
Genet Med. 2024 Oct;26(10):101220. doi: 10.1016/j.gim.2024.101220. Epub 2024 Jul 19.
The gold standard for identification of post-zygotic variants (PZVs) is droplet digital polymerase chain reaction or high-depth sequencing across multiple tissues types. These approaches are yet to be systematically implemented for monogenic disorders. We developed PZV detection pipelines for correct classification of de novo variants.
Our pipelines detect PZV in parents (gonosomal mosaicism [pGoM]) and children (somatic mosaicism, "M3"). We applied them to research exome sequencing (ES) data from the Australian Cerebral Palsy Biobank (n = 145 trios) and Simons Simplex Collection (n = 405 families). Candidate mosaic variants were validated using deep amplicon sequencing or droplet digital polymerase chain reaction.
69.2% (M3), 63.9% (M3), and 92.7% (pGoM) of detected variants were validated, with 48.6%, 56.7%, and 26.2% of variants, respectively, meeting strict criteria for mosaicism. In the Australian Cerebral Palsy Biobank, 16.6% of probands and 20.7% of parents had at least 1 true-positive somatic or pGoM variant, respectively. A large proportion of PZVs detected in Simons Simplex Collection parents (79.8%) and child (94.5%) were not previously reported. We reclassified 3.7% to 8.0% of germline de novo variants as mosaic.
Many PZVs were incorrectly classified as germline variants or missed by previous approaches. Systematic application of our pipelines could increase genetic diagnostic rate, improve estimates of recurrence risk in families, and benefit novel disease gene identification.
鉴定合子后变异（PZV）的金标准是在多种组织类型中进行液滴数字聚合酶链反应或高通量测序。这些方法尚未系统地应用于单基因疾病。我们开发了 PZV 检测管道，用于正确分类新生变异。
我们的管道在父母（性染色体嵌合体[ pGoM ]）和孩子（体细胞嵌合体，“M3”）中检测 PZV。我们将其应用于澳大利亚脑瘫生物库（n = 145 个三胞胎）和西蒙斯单纯性收藏（n = 405 个家庭）的研究外显子组测序（ES）数据。使用深度扩增子测序或液滴数字聚合酶链反应验证候选嵌合变体。
69.2%（M3）、63.9%（M3）和 92.7%（pGoM）的检测到的变异得到验证，分别有 48.6%、56.7%和 26.2%的变异符合嵌合体的严格标准。在澳大利亚脑瘫生物库中，16.6%的患者和 20.7%的父母分别至少有 1 个真正的阳性体细胞或 pGoM 变异。在西蒙斯单纯性收藏的父母（79.8%）和孩子（94.5%）中检测到的 PZV 很大一部分以前没有报道过。我们将西蒙斯单纯性收藏父母（79.8%）和孩子（94.5%）中检测到的 PZV 很大一部分以前没有报道过。我们将西蒙斯单纯性收藏父母（79.8%）和孩子（94.5%）中检测到的 PZV 很大一部分以前没有报道过。我们将西蒙斯单纯性收藏父母（79.8%）和孩子（94.5%）中检测到的 PZV 很大一部分以前没有报道过。我们将西蒙斯单纯性收藏中 3.7%至 8.0%的新生种系变体重新分类为嵌合体。
许多 PZV 被错误地归类为种系变体或被以前的方法遗漏。我们的管道的系统应用可以提高遗传诊断率，改善家族复发风险的估计，并有助于新疾病基因的鉴定。
