Preventive Health Division, Genepath, Sydney, NSW, Australia.
EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of NSW, Sydney, NSW, Australia.
Clin Chem. 2023 Aug 2;69(8):890-900. doi: 10.1093/clinchem/hvad066.
Newborn screening (NBS) is an effective public health intervention that reduces death and disability from treatable genetic diseases, but many conditions are not screened due to a lack of a suitable assay. Whole genome and whole exome sequencing can potentially expand NBS but there remain many technical challenges preventing their use in population NBS. We investigated if targeted gene sequencing (TGS) is a feasible methodology for expanding NBS.
We constructed a TGS panel of 164 genes which screens for a broad range of inherited conditions. We designed a high-volume, low-turnaround laboratory and bioinformatics workflow that avoids the technical and data interpretation challenges associated with whole genome and whole exome sequencing. A methods-based analytical validation of the assay was completed and test performance in 2552 newborns examined. We calculated annual birth estimates for each condition to assess cost-effectiveness.
Assay analytical sensitivity was >99% and specificity was 100%. Of the newborns screened, 1.3% tested positive for a condition. On average, each individual had 225 variants to interpret and 1.8% were variants of uncertain significance (VUS). The turnaround time was 7 to 10 days. Maximum batch size was 1536 samples.
We demonstrate that a TGS assay could be incorporated into an NBS program soon to increase the number of conditions screened. Additionally, we conclude that NBS using TGS may be cost-effective.
新生儿筛查（NBS）是一项有效的公共卫生干预措施，可以降低可治疗遗传疾病导致的死亡和残疾，但由于缺乏合适的检测方法，许多疾病都没有被筛查出来。全基因组和全外显子组测序有可能扩大 NBS 的范围，但仍存在许多技术挑战，阻碍了它们在人群 NBS 中的应用。我们研究了靶向基因测序（TGS）是否是扩大 NBS 的可行方法。
我们构建了一个包含 164 个基因的 TGS 面板，该面板可筛查多种遗传性疾病。我们设计了一种高通量、低周转的实验室和生物信息学工作流程，避免了与全基因组和全外显子组测序相关的技术和数据解释挑战。我们完成了该检测方法的基于方法的分析验证，并在 2552 名新生儿中进行了检测性能测试。我们计算了每种疾病的年度出生估计数，以评估成本效益。
检测分析灵敏度>99%，特异性为 100%。在筛查的新生儿中，有 1.3%的新生儿检测出患有某种疾病。平均而言，每个个体有 225 个需要解释的变异，1.8%的变异为意义不明的变异（VUS）。周转时间为 7 至 10 天。最大批处理量为 1536 个样本。
我们证明，TGS 检测可以很快被纳入 NBS 计划，以增加筛查的疾病数量。此外，我们得出结论，使用 TGS 的 NBS 可能具有成本效益。
