Genomic analysis has become a mainstay in the investigation of cancer patients, especially for those suspected of harboring a heritable cancer predisposition syndrome. With ubiquitous short-read next-generation sequencing (NGS) technologies, these analyses can be complicated by the inappropriate alignment of variants to homologous genomic regions or pseudogenes. Using distinct primer sets specific to the gene and pseudogene, a nonspecific primer set, and a highly gene-specific long-range polymerase chain reaction primer set, we have shown that in at least a subset of patients, the common African PMS2 variant NM_000535.5:c.2182_2184delACTinsG, classified as pathogenic in ClinVar, has been incorrectly assigned to PMS2 from its well-documented pseudogene, PMS2CL. This result is not only important for patients but also highlights a weakness in short-read NGS technologies and the racial inequity in genomic analysis.

中文翻译：

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从PMS2到非洲起源的常见变种重新分类为假基因PMS2CL。

基因组分析已成为癌症患者研究的主要手段，特别是对于那些怀疑患有遗传易感性癌症综合征的患者。使用普遍存在的短读下一代测序（NGS）技术，由于变体与同源基因组区域或假基因的不适当比对，这些分析可能会变得复杂。使用对基因和假基因具有特异性的独特引物组，非特异性引物组和高度基因特异性的远程聚合酶链反应引物组，我们已经证明，至少在一部分患者中，常见的非洲PMS2变体NM_000535。 5：c.2182_2184delACTinsG在ClinVar中被列为致病性，已从其有据可查的伪基因PMS2CL错误地分配给了PMS2。