Table3_The Brazilian Rare Genomes Project: Validation of Whole Genome Sequencing for Rare Diseases Diagnosis.XLSX

Rare diseases affect up to 13.2 million individuals in Brazil. The Brazilian Rare Genomes Project is envisioned to further the implementation of genomic medicine into the Brazilian public healthcare system. Here we report the validation results of a whole genome sequencing (WGS) procedure for implementation in clinical laboratories. In addition, we report data quality for the first 1,200 real-world patients sequenced. We sequenced a well-characterized group of 76 samples, including seven gold standard genomes, using a PCR-free WGS protocol on Illumina Novaseq 6,000 equipment. We compared the observed variant calls with their expected calls, observing good concordance for single nucleotide variants (SNVs; mean F-measure = 99.82%) and indels (mean F-measure = 99.57%). Copy number variants and structural variants events detection performances were as expected (F-measures 96.6% and 90.3%, respectively). Our WGS protocol presented excellent intra-assay reproducibility (coefficients of variation ranging between 0.03% and 0.20%) and inter-assay reproducibility (coefficients of variation ranging between 0.02% and 0.09%). Limitations of the WGS protocol include the inability to confidently detect variants such as uniparental disomy, balanced translocations, repeat expansion variants, and low-level mosaicism. In summary, the observed performance of the WGS protocol was in accordance with that seen in the best centers worldwide. The Rare Genomes Project is an important initiative to bring pivotal improvements to the quality of life of the affected individuals.

巴西的罕见病患者人数多达1320万。巴西罕见基因组项目（Brazilian Rare Genomes Project）旨在推动基因组医学在巴西公共医疗体系中的落地应用。
本研究报道了适用于临床实验室落地的全基因组测序（whole genome sequencing, WGS）流程的验证结果；此外，还披露了首批1200名真实世界测序患者的数据质量情况。
本研究采用无PCR扩增的WGS建库方案，在Illumina NovaSeq 6000测序平台上对76份经过充分表征的样本进行测序，其中包含7份金标准基因组。研究将实测变异位点与预期变异位点进行比对，结果显示单核苷酸变异（single nucleotide variants, SNVs；平均F值为99.82%）与插入缺失变异（indels；平均F值为99.57%）均具有良好的一致性。拷贝数变异（copy number variants, CNVs）与结构变异（structural variants, SVs）的检测性能也符合预期（F值分别为96.6%与90.3%）。
本WGS流程展现出优异的批内重复性（变异系数区间为0.03%~0.20%）与批间重复性（变异系数区间为0.02%~0.09%）。
该WGS流程仍存在一定局限性，无法可靠检测单亲二体、平衡易位、重复扩增变异以及低水平嵌合等变异类型。
综上，本WGS流程的检测性能达到了全球顶尖临床测序中心的水准。巴西罕见基因组项目是一项旨在显著改善罕见病患者生活质量的重要举措。