Noninvasive Detection of Fetal Subchromosome Abnormalities via Deep Sequencing of Maternal Plasma
Noninvasive Detection of Fetal Subchromosome Abnormalities via Deep Sequencing of Maternal Plasma
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DOI：
10.1016/j.ajhg.2012.12.006
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发表时间：
2013-02-07
影响因子：
9.8
通讯作者：
Rava, Richard P.
中科院分区：
文献类型：
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作者：
Srinivasan, Anupama;Bianchi, Diana W.;Rava, Richard P.
本研究的目的是确定从母体血液样本中检测整个基因组的胎儿亚染色体异常所需的深度测序和分析条件。无细胞（cf）DNA分离自11名孕妇的血浆中携带的胎儿亚染色体重复和缺失，易位，嵌合体，和三体20诊断中期核型。用25-mer标签进行大规模平行测序（MPS），每个样品约10（9）个标签，并映射到参考人类基因组组装hg 19。对标签进行计数并归一化至IMb或IOOkb的固定基因组箱大小，以检测与参考相比统计学上不同的拷贝数变化。所有7例微缺失、重复、易位和20三体的病例均通过MPS盲法检测，包括小至300 kb的微缺失。在其中两例中期核型显示来源不明的额外物质的情况下，MPS鉴定了额外物质的易位断点和染色体来源。在4例嵌合体病例中，MPS未显示亚染色体异常。这项工作表明，在非嵌合体的情况下，可以通过母体血浆cfDNA的MPS获得胎儿分子核型，其相当于染色体微阵列，并且在某些情况下优于中期核型。这种方法结合了增强胎儿基因组分辨率的优点和提高非侵入性母体血液检测的安全性。
The purpose of this study was to determine the deep sequencing and analytic conditions needed to detect fetal subchromosome abnormalities across the genome from a maternal blood sample. Cell-free (cf) DNA was isolated from the plasma of 11 pregnant women carrying fetuses with subchromosomal duplications and deletions, translocations, mosaicism, and trisomy 20 diagnosed by metaphase karyotype. Massively parallel sequencing (MPS) was performed with 25-mer tags at approximately 10(9) tags per sample and mapped to reference human genome assembly hg19. Tags were counted and normalized to fixed genome bin sizes of 1 Mb or 100 kb to detect statistically distinct copy-number changes compared to the reference. All seven cases of microdeletions, duplications, translocations, and the trisomy 20 were detected blindly by MPS, including a microdeletion as small as 300 kb. In two of these cases in which the metaphase karyotype showed additional material of unknown origin, MPS identified both the translocation breakpoint and the chromosomal origin of the additional material. In the four mosaic cases, the subchromosomal abnormality was not demonstrated by MPS. This work shows that in nonmosaic cases, it is possible to obtain a fetal molecular karyotype by MPS of maternal plasma cfDNA that is equivalent to a chromosome microarray and in some cases is better than a metaphase karyotype. This approach combines the advantage of enhanced fetal genomic resolution with the improved safety of a noninvasive maternal blood test.