Maternal Plasma DNA Analysis with Massively Parallel Sequencing by Ligation for Noninvasive Prenatal Diagnosis of Trisomy 21
Maternal Plasma DNA Analysis with Massively Parallel Sequencing by Ligation for Noninvasive Prenatal Diagnosis of Trisomy 21
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DOI：
10.1373/clinchem.2009.136507
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发表时间：
2010-03-01
影响因子：
9.3
通讯作者：
Lo, Y. M. Dennis
中科院分区：
文献类型：
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作者：
Chiu, Rossa W. K.;Sun, Hao;Lo, Y. M. Dennis
背景：21三体(T21)的无创性产前诊断最近被证明可以通过在合成测序平台上对母体血浆进行大规模并行测序来实现。然而，包括18号和13号染色体在内的其他几条人类染色体的定量结果并不那么精确，定量偏差与染色体GC含量有关。方法：采用连接测序的方法对10例整倍体和5例T21妊娠的孕妇血浆DNA进行测序。我们计算了每条染色体的测序读数及其相关的测量CV的基因组表示(GRs)，并比较了整倍体和T21妊娠的21号染色体(Chr21)的GR。结果：我们获得了每个样本12×106个唯一读数的中位数(占总读数的21%)。GR偏离了某些染色体的预期，但以不同于先前报道的合成测序方法的方式。对18号和13号染色体的GRs的测量没有chr21的精确。结论：大规模平行测序连接母体血浆DNA对T21胎儿进行无创性鉴定是有效的。在某些染色体的GR之间观察到的数量偏差更有可能是基于分析因素而不是生物因素。需要进一步的研究来提高18号和13号染色体代表的测量精度。
BACKGROUND: Noninvasive prenatal diagnosis of trisomy 21 (T21) has recently been shown to be achievable by massively parallel sequencing of maternal plasma on a sequencing-by-synthesis platform. The quantification of several other human chromosomes, including chromosomes 18 and 13, has been shown to be less precise, however, with quantitative biases related to the chromosomal GC content.METHODS: Maternal plasma DNA from 10 euploid and 5 T21 pregnancies was sequenced with a sequencing-by-ligation approach. We calculated the genomic representations (GRs) of sequenced reads from each chromosome and their associated measurement CVs and compared the GRs of chromosome 21 (chr21) for the euploid and T21 pregnancies.RESULTS: We obtained a median of 12 X 106 unique reads (21% of the total reads) per sample. The GRs deviated from those expected for some chromosomes but in a manner different from that previously reported for the sequencing-by-synthesis approach. Measurements of the GRs for chromosomes 18 and 13 were less precise than for chr21. z Scores of the GR of chr21 were increased in the T21 pregnancies, compared with the euploid pregnancies.CONCLUSIONS: Massively parallel sequencing-by-ligation of maternal plasma DNA was effective in identifying T21 fetuses noninvasively. The quantitative biases observed among the GRs of certain chromosomes were more likely based on analytical factors than biological factors. Further research is needed to enhance the precision for measuring for the representations of chromosomes 18 and 13.