Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, 2401 Gillham Rd., Kansas City, MO, USA.
Genomic Medicine Center, Children's Mercy Research Institute-Kansas City, 2420 Pershing Rd. Suite 100, Kansas City, MO, USA.
Clin Chem. 2022 Sep 1;68(9):1177-1183. doi: 10.1093/clinchem/hvac113.
Laboratories utilizing next-generation sequencing align sequence data to a standardized human reference genome (HRG). Several updated versions, or builds, have been released since the original HRG in 2001, including the Genome Reference Consortium Human Build 38 (GRCh38) in 2013. However, most clinical laboratories still use GRCh37, which was released in 2009. We report our laboratory's clinical validation of GRCh38.
Migration to GRCh38 was validated by comparing the coordinates (lifting over) of 9443 internally curated variants from GRCh37 to GRCh38, globally comparing protein coding sequence variants aligned with GRCh37 vs GRCh38 from 917 exomes, assessing genes with known discrepancies, comparing coverage differences, and establishing the analytic sensitivity and specificity of variant detection using Genome in a Bottle data.
Eight discrepancies, due to strand swap or reference base, were observed. Three clinically relevant variants had the GRCh37 alternate allele as the reference allele in GRCh38. A comparison of 88 295 calls between builds identified 8 disease-associated genes with sequence differences: ABO, BNC2, KIZ, NEFL, NR2E3, PTPRQ, SHANK2, and SRD5A2. Discrepancies in coding regions in GRCh37 were resolved in GRCh38.
There were a small number of clinically significant changes between the 2 genome builds. GRCh38 provided improved detection of nucleotide changes due to the resolution of discrepancies present in GRCh37. Implementation of GRCh38 results in more accurate and consistent reporting.
实验室利用下一代测序技术将序列数据与标准化的人类参考基因组（HRG）对齐。自 2001 年最初的 HRG 发布以来，已经发布了几个更新版本，包括 2013 年的基因组参考联盟人类构建 38 版（GRCh38）。然而，大多数临床实验室仍在使用 2009 年发布的 GRCh37。我们报告了我们实验室对 GRCh38 的临床验证。
通过将 9443 个内部管理的变体的坐标（提升）从 GRCh37 与 GRCh38 进行比较，对向 GRCh38 的迁移进行了验证，从 917 个外显子中全局比较与 GRCh37 相比与 GRCh38 对齐的蛋白质编码序列变体，评估具有已知差异的基因，比较覆盖差异，并使用基因组瓶中的数据建立变体检测的分析灵敏度和特异性。
观察到 8 个由于链交换或参考碱基引起的差异。在 GRCh38 中，有 3 个具有临床相关性的变体的 GRCh37 替代等位基因作为参考等位基因。在构建之间进行了 88,295 次调用比较，确定了 8 个具有序列差异的疾病相关基因：ABO、BNC2、KIZ、NEFL、NR2E3、PTPRQ、SHANK2 和 SRD5A2。GRCh37 中编码区域的差异在 GRCh38 中得到解决。
在这两个基因组构建之间，只有少数具有临床意义的变化。由于 GRCh37 中存在的差异得到解决，因此 GRCh38 提供了对核苷酸变化的更好检测。实施 GRCh38 可实现更准确和一致的报告。
