Background Constitutional mismatch repair deficiency (CMMRD) is a rare and extraordinarily penetrant childhood-onset cancer predisposition syndrome. Genetic diagnosis is often hampered by the identification of mismatch repair (MMR) variants of unknown significance and difficulties in PMS2 analysis, the most frequently mutated gene in CMMRD. We present the validation of a robust functional tool for CMMRD diagnosis and the characterization of microsatellite instability (MSI) patterns in blood and tumors. Methods The highly sensitive assessment of MSI (hs-MSI) was tested on a blinded cohort of 66 blood samples and 24 CMMRD tumor samples. Hs-MSI scores were compared with low-pass genomic instability scores (LOGIC/MMRDness). The correlation of hs-MSI scores in blood with age of cancer onset and the distribution of insertion-deletion (indel) variants in microsatellites were analyzed in a series of 169 individuals (n = 68 CMMRD, n = 124 non-CMMRD). Results Hs-MSI achieved high accuracy in the identification of CMMRD in blood (sensitivity 98.5% and specificity 100%) and detected MSI in CMMRD-associated tumors. Hs-MSI had a strong positive correlation with whole low-pass genomic instability LOGIC scores (r = 0.89, P = 2.2e-15 in blood and r = 0.82, P = 7e-3 in tumors). Indel distribution identified PMS2 pathogenic variant (PV) carriers from other biallelic MMR gene PV carriers with an accuracy of 0.997. Higher hs-MSI scores correlated with younger age at diagnosis of the first tumor (r = −0.43, P = 0.011). Conclusions Our study confirms the accuracy of the hs-MSI assay as ancillary testing for CMMRD diagnosis, which can also characterize MSI patterns in CMMRD-associated cancers. Hs-MSI is a powerful tool to pinpoint PMS2 as the affected germline gene and thus potentially personalize cancer risk.

中文翻译：

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经验证的高灵敏度微卫星不稳定性测定可准确识别携带双等位基因种系 PMS2 致病性变异的个体，导致体质错配修复缺陷

背景 体质错配修复缺陷 (CMMRD) 是一种罕见且非常渗透的儿童期发病的癌症易感综合征。基因诊断常常受到意义未知的错配修复 (MMR) 变异的识别以及 PMS2 分析困难的阻碍，PMS2 是 CMMRD 中最常见的突变基因。我们验证了用于 CMMRD 诊断的强大功能工具以及血液和肿瘤中微卫星不稳定性 (MSI) 模式的表征。方法 在 66 个血液样本和 24 个 CMMRD 肿瘤样本的盲法队列中测试 MSI (hs-MSI) 的高灵敏度评估。将 Hs-MSI 评分与低通基因组不稳定性评分 (LOGIC/MMRDness) 进行比较。在 169 名个体（n = 68 CMMRD，n = 124 非 CMMRD）中分析了血液中 hs-MSI 评分与癌症发病年龄的相关性以及微卫星中插入缺失 (indel) 变异的分布。结果 Hs-MSI 在识别血液中 CMMRD 方面实现了高精度（敏感性 98.5%，特异性 100%），并检测了 CMMRD 相关肿瘤中的 MSI。 Hs-MSI 与整个低通基因组不稳定性 LOGIC 评分呈强正相关（血液中 r = 0.89，P = 2.2e-15，肿瘤中 r = 0.82，P = 7e-3）。 Indel分布从其他双等位错配修复基因PV携带者中识别出PMS2致病性变异(PV)携带者，准确度为0.997。较高的 hs-MSI 评分与诊断第一个肿瘤时的年龄较小相关（r = -0.43，P = 0.011）。结论 我们的研究证实了 hs-MSI 检测作为 CMMRD 诊断辅助检测的准确性，这也可以表征 CMMRD 相关癌症的 MSI 模式。 Hs-MSI 是一种强大的工具，可将 PMS2 确定为受影响的种系基因，从而潜在地个性化癌症风险。