Noninvasive prenatal paternity testing using targeted massively parallel sequencing

作者：Ning Qu, Yifan Xie, Haiyan Li, Hao‐ Liang, Shaobin Lin, Erwen Huang, Jun Gao, Fang Chen, Yan‐Wei Shi, Xueling Ou · 发表于：Transfusion · 年份：2018 · DOI：10.1111/trf.14577 · 被引用次数：19 · 研究领域：Prenatal Screening and Diagnostics、Fetal and Pediatric Neurological Disorders、Genetic Syndromes and Imprinting

BACKGROUND: Recent advances in massively parallel sequencing (MPS) technology have provided efficient methods for noninvasive prenatal paternity testing (NIPAT). However, a well-accepted protocol has not been established. The present study developed an MPS-based approach for NIPAT and compared the performance of two recently reported methods for MPS data interpretation. STUDY DESIGN AND METHODS: We selected 1795 unlinked polymorphic single-nucleotide polymorphisms (SNPs) and performed paternity analysis in 34 real parentage test cases with maternal plasma samples using the Illumina HiSeq platform. Sequencing data were interpreted by the straightforward counting method for the identification of paternal alleles and mathematical algorithms for paternity index (PI) calculation, respectively. RESULTS: Based on the sequencing data from each family case, both of the two statistical approaches produced a significant separation between the biological father and 90 unrelated males (p < 0.0001) when sufficient effective loci were attained. Nevertheless, up to 30.82% of real paternal alleles were filtered by a predefined cutoff and resulted in insufficient effective loci, especially in plasma samples with low fetal fraction (approx. 90.60% were filtered). In contrast, the PI calculation model utilized all maternal homozygous SNPs as effective loci (approx. 40% of total SNPs) and successfully identified the correct biological father, with the log-transformed combined PI (Lg(CPI)) value v...