With the discovery of circulating cell‐free fetal DNA (cffDNA) in maternal plasma, noninvasive prenatal testing became possible. However, analysis of low‐level cffDNA against high background maternal DNA remains complicated and challenging. To circumvent this limitation, selective amplification of cffDNA was used in this study. Two kinds of compound markers (namely DIP‐STR and SNP‐STR), both based on selective amplification, were used here for targeting fetal DNA. By designing two allele‐specific forward primers for DIP‐STR and SNP‐STR, DNA fragments with different DIP/SNP alleles can be selectively amplified. When analyzing maternal plasma DNA, these markers can selectively target paternally inherited fetal alleles whose DIP/SNP allele was not shared with the mother. In this study, 21 families were studied with six DIP‐STRs and 11 SNP‐STRs. Fetal DNA was successfully detected across plasma samples for at least one marker. Detection rate varied between DIP‐STR and SNP‐STR markers, and DIP‐STR outperforms SNP‐STR. Fetal alleles obtained from maternal plasma were double confirmed by genotyping paternal genomic DNA and fetal genomic DNA from amniocentesis. This study demonstrated that selective amplification strategy can be used to target cffDNA in maternal plasma, which will be a promising method for noninvasive prenatal paternity testing.

中文翻译：

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使用两种类型的复合标记检测母体血浆中游离胎儿 DNA

随着母体血浆中循环游离胎儿 DNA (cffDNA) 的发现，无创产前检测成为可能。然而，低水平 cffDNA 与高背景母体 DNA 的分析仍然复杂且具有挑战性。为了规避这一限制，本研究使用了 cffDNA 的选择性扩增。这里使用了两种基于选择性扩增的复合标记（即 DIP-STR 和 SNP-STR）来靶向胎儿 DNA。通过为 DIP-STR 和 SNP-STR 设计两个等位基因特异性正向引物，可以选择性地扩增具有不同 DIP/SNP 等位基因的 DNA 片段。在分析母体血浆 DNA 时，这些标记可以选择性地靶向 DIP/SNP 等位基因不与母亲共享的父系遗传胎儿等位基因。在这项研究中，对 21 个家族进行了研究，其中有 6 个 DIP-STR 和 11 个 SNP-STR。在血浆样本中成功检测到胎儿 DNA 的至少一种标志物。DIP-STR 和 SNP-STR 标记的检测率不同，DIP-STR 优于 SNP-STR。通过对来自羊膜穿刺术的父亲基因组 DNA 和胎儿基因组 DNA 进行基因分型，双重确认了从母体血浆中获得的胎儿等位基因。该研究表明，选择性扩增策略可用于靶向母体血浆中的 cffDNA，这将是一种有前途的无创产前亲子鉴定方法。