Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends
Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends
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DOI：
10.1073/pnas.1615800113
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发表时间：
2016-12-13
影响因子：
11.1
通讯作者：
Lo, Yuk Ming Dennis
中科院分区：
文献类型：
--
作者：
Chan, K. C. Allen;Jiang, Peiyong;Lo, Yuk Ming Dennis
从孕妇获得的血浆 DNA 进行了 270 倍单倍体基因组覆盖深度的测序。将母体血浆 DNA 测序数据与父母基因组 DNA 数据进行比较，并使用一系列生物信息学过滤器，检测到胎儿新生突变的灵敏度为 85%，阳性预测值为 74%。这些结果表明阳性预测值比之前的尝试提高了 169 倍。对基因组中每个碱基位置的序列信息解释的改进使我们能够询问胎儿的母体遗传，以找出母体基因组内 656,676 个 (94.2%) 杂合 SNP 中的 618,271 个。每个位点的胎儿基因型都是单独推导的，这与以前不同，以前是通过单倍型内的一组位点来确定遗传的。这些结果表明确定胎儿母系遗传的分辨率提高了 90 倍。选定的基因组位置更有可能出现在血浆 DNA 分子的末端。我们发现，此类优选末端的一部分对母体血浆中的胎儿或母体来源的 DNA 表现出选择性。具有胎儿优选末端的母体血浆DNA分子与具有母体优选末端的母体血浆DNA分子的数量之比显示出与胎儿DNA分数相关。最后，这种第二代非侵入性胎儿全基因组分析方法在诊断为心面皮肤综合征的妊娠中得到了验证，母体血浆 DNA 测序覆盖率达到 195 倍。通过母体血浆 DNA 分析成功检测到致病性 BRAF 新突变。
Plasma DNA obtained from a pregnant woman was sequenced to a depth of 270x haploid genome coverage. Comparing the maternal plasma DNA sequencing data with the parental genomic DNA data and using a series of bioinformatics filters, fetal de novo mutations were detected at a sensitivity of 85% and a positive predictive value of 74%. These results represent a 169-fold improvement in the positive predictive value over previous attempts. Improvements in the interpretation of the sequence information of every base position in the genome allowed us to interrogate the maternal inheritance of the fetus for 618,271 of 656,676 (94.2%) heterozygous SNPs within the maternal genome. The fetal genotype at each of these sites was deduced individually, unlike previously, where the inheritance was determined for a collection of sites within a haplotype. These results represent a 90-fold enhancement in the resolution in determining the fetus's maternal inheritance. Selected genomic locations were more likely to be found at the ends of plasma DNA molecules. We found that a subset of such preferred ends exhibited selectivity for fetal- or maternal-derived DNA in maternal plasma. The ratio of the number of maternal plasma DNA molecules with fetal preferred ends to those with maternal preferred ends showed a correlation with the fetal DNA fraction. Finally, this second generation approach for noninvasive fetal whole-genome analysis was validated in a pregnancy diagnosed with cardiofaciocutaneous syndrome with maternal plasma DNA sequenced to 195x coverage. The causative de novo BRAF mutation was successfully detected through the maternal plasma DNA analysis.