Detection of aneuploidies by paralogous sequence quantification
Detection of aneuploidies by paralogous sequence quantification
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DOI：
10.1136/jmg.2004.023184
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发表时间：
2004-12-01
影响因子：
4
通讯作者：
Antonarakis, SE
中科院分区：
文献类型：
--
作者：
Deutsch, S;Choudhury, U;Antonarakis, SE
背景：染色体非整倍体是与认知障碍和多种畸形特征相关的先天性疾病的常见原因。产前诊断的非整倍体是最常见的进行胚胎细胞的核型分析获得的绒毛膜穿刺术或绒毛取样，但这种方法是劳动密集型的，需要约14天才能完成。方法：我们已经开发了一种基于PCR的方法检测有针对性的染色体数目异常称为旁系同源序列定量（PSQ），根据使用旁系同源基因。旁系同源序列具有高度的序列同一性，但以基因座特异性方式积累核苷酸取代。这些序列差异，我们称之为旁系同源序列错配（PSM），可以使用焦磷酸测序技术定量，以估计不同染色体之间的相对剂量。我们设计了10种检测方法来检测13号、18号和21号染色体三体以及性染色体非整倍性。结果：我们在175个高度富集异常样本的DNA上评估了该方法的性能。对120个非整倍体样本中的119个以及所有对照样本进行了正确和明确的诊断。一个样本，这给了一个中间值的染色体13检测不能被diagnosed.Conclusions：我们的数据表明，PSQ是一个强大的，易于解释，易于建立的方法，用于诊断常见的非整倍体，并可以在不到48小时内进行，代表了广泛使用的诊断实验室的竞争力的替代方案。
Background: Chromosomal aneuploidies are a common cause of congenital disorders associated with cognitive impairment and multiple dysmorphic features. Pre-natal diagnosis of aneuploidies is most commonly performed by the karyotyping of fetal cells obtained by amniocentesis or chorionic villus sampling, but this method is labour intensive and requires about 14 days to complete.Methods: We have developed a PCR based method for the detection of targeted chromosome number abnormalities termed paralogous sequence quantification (PSQ), based on the use of paralogous genes. Paralogous sequences have a high degree of sequence identity, but accumulate nucleotide substitutions in a locus specific manner. These sequence differences, which we term paralogous sequence mismatches (PSMs), can be quantified using pyrosequencing technology, to estimate the relative dosage between different chromosomes. We designed 10 assays for the detection of trisomies of chromosomes 13, 18, and 21 and sex chromosome aneuploidies.Results: We evaluated the performance of this method on 175 DNAs, highly enriched for abnormal samples. A correct and unambiguous diagnosis was given for 119 out of 120 aneuploid samples as well as for all the controls. One sample which gave an intermediate value for the chromosome 13 assays could not be diagnosed.Conclusions: Our data suggests that PSQ is a robust, easy to interpret, and easy to set up method for the diagnosis of common aneuploidies, and can be performed in less than 48 h, representing a competitive alternative for widespread use in diagnostic laboratories.