Background 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. Methods 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. Results 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. Conclusions 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.

中文翻译：

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利用下一代测序技术在实验室中对 Genome Reference Consortium Human Build 38 进行临床验证

背景 利用下一代测序的实验室将序列数据与标准化的人类参考基因组 (HRG) 进行比对。自 2001 年最初的 HRG 以来，已经发布了几个更新版本或构建，包括 2013 年的 Genome Reference Consortium Human Build 38 (GRCh38)。然而，大多数临床实验室仍然使用 2009 年发布的 GRCh37。我们报告我们实验室的GRCh38的临床验证。方法 通过比较从 GRCh37 到 GRCh38 的 9443 个内部策划变体的坐标（提升）来验证迁移到 GRCh38，全局比较与 GRCh37 与来自 917 个外显子组的 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，以及使用瓶中基因组数据建立变异检测的分析敏感性和特异性。结果 观察到由于链交换或参考碱基导致的八种差异。三个临床相关变体具有 GRCh37 替代等位基因作为 GRCh38 中的参考等位基因。比较构建之间的 88 295 个调用确定了 8 个具有序列差异的疾病相关基因：ABO、BN​​C2、KIZ、NEFL、NR2E3、PTPRQ、SHANK2 和 SRD5A2。GRCh37 中编码区的差异在 GRCh38 中得到解决。结论 2 个基因组构建之间存在少量临床显着变化。由于解决了 GRCh37 中存在的差异，GRCh38 提供了改进的核苷酸变化检测。GRCh38 的实施导致更准确和一致的报告。三个临床相关变体具有 GRCh37 替代等位基因作为 GRCh38 中的参考等位基因。比较构建之间的 88 295 个调用确定了 8 个具有序列差异的疾病相关基因：ABO、BN​​C2、KIZ、NEFL、NR2E3、PTPRQ、SHANK2 和 SRD5A2。GRCh37 中编码区的差异在 GRCh38 中得到解决。结论 2 个基因组构建之间存在少量临床显着变化。由于解决了 GRCh37 中存在的差异，GRCh38 提供了改进的核苷酸变化检测。GRCh38 的实施导致更准确和一致的报告。三个临床相关变体具有 GRCh37 替代等位基因作为 GRCh38 中的参考等位基因。比较构建之间的 88 295 个调用确定了 8 个具有序列差异的疾病相关基因：ABO、BN​​C2、KIZ、NEFL、NR2E3、PTPRQ、SHANK2 和 SRD5A2。GRCh37 中编码区的差异在 GRCh38 中得到解决。结论 2 个基因组构建之间存在少量临床显着变化。由于解决了 GRCh37 中存在的差异，GRCh38 提供了改进的核苷酸变化检测。GRCh38 的实施导致更准确和一致的报告。GRCh37 中编码区的差异在 GRCh38 中得到解决。结论 2 个基因组构建之间存在少量临床显着变化。由于解决了 GRCh37 中存在的差异，GRCh38 提供了改进的核苷酸变化检测。GRCh38 的实施导致更准确和一致的报告。GRCh37 中编码区的差异在 GRCh38 中得到解决。结论 2 个基因组构建之间存在少量临床显着变化。由于解决了 GRCh37 中存在的差异，GRCh38 提供了改进的核苷酸变化检测。GRCh38 的实施导致更准确和一致的报告。