Routine diagnostics for colorectal cancer patients suspected of having Lynch-Syndrome (LS) currently uses Next-Generation-Sequencing (NGS) of targeted regions within the DNA mismatch repair (MMR) genes. This analysis can reliably detect nucleotide alterations and copy-number variations (CNVs); however, CNV-neutral rearrangements comprising gene inversions or large intronic insertions remain undetected because their breakpoints are usually not covered. As several founder mutations exist for LS, we established PCR-based screening methods for five known rearrangements in MLH1, MSH2, or PMS2, and investigated their prevalence in 98 German patients with suspicion of LS without a causative germline variant or CNV detectable in the four MMR genes. We found no recurrence of CNV-neutral structural rearrangements previously described: Neither for two inversions in MLH1 (exon 1 and exon 16–19) within 33 MLH1-deficient patients, nor for two inversions in MSH2 (exon 1–7 and exon 2–6) within 48 MSH2-deficient patients. The PMS2 insertion in intron 7 was detected in one of 17 PMS2-deficient patients. None of the four genomic inversions constitutes a founder event within the German population, but we advise to test the rare cases with unsolved PMS2-deficiency upon the known insertion. As a next diagnostic step, tumour tissue of the unsolved patients should be sequenced for somatic variants, and germline analysis of additional genes with an overlapping clinical phenotype should be considered. Alternatively, full-length cDNA analyses may detect concealed MMR-defects in cases with family history.

中文翻译：

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在常规NGS诊断中无法检测到MLH1，MSH2和PMS2中CNV中性结构基因组重排的患病率。

对于怀疑患有Lynch综合征（LS）的结直肠癌患者，常规诊断目前使用DNA错配修复（MMR）基因内目标区域的下一代测序（NGS）。该分析可以可靠地检测核苷酸改变和拷贝数变异（CNV）。然而，包括基因倒置或大内含子插入在内的CNV中性重排仍然未被发现，因为它们的断点通常不被覆盖。由于LS存在多个创始人突变，因此我们针对MLH1，MSH2或PMS2中的五个已知重排建立了基于PCR的筛选方法，并调查了98名德国人的LS患病率，他们怀疑LS的4个MMR基因中没有可检测到的致病性种系变异或CNV。我们没有发现先前描述的CNV中性结构重新发生的复发：33例MLH1缺陷患者中既没有发生两次MLH1倒位（第1外显子和第16-19外显子），也没有出现两次MSH2倒位（第1-7外显子和第2外显子）。 6）48位MSH2缺陷患者中。该PMS2在17名PMS2缺陷患者中检测到内含子7插入。这四个基因组倒置均未构成德国人的奠基人事件，但我们建议在已知插入条件下测试未解决PMS2缺陷的罕见情况。作为下一步的诊断步骤，应对尚未解决的患者的肿瘤组织进行体细胞变体测序，并应考虑对具有重叠临床表型的其他基因进行种系分析。另外，在有家族史的情况下，全长cDNA分析可能会检测到隐蔽的MMR缺陷。