Molecular karyotyping using an SNP array for genomewide genotyping
Molecular karyotyping using an SNP array for genomewide genotyping
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DOI：
10.1136/jmg.2004.022855
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发表时间：
2004-12-01
影响因子：
4
通讯作者：
Nürnberg, P
中科院分区：
文献类型：
--
作者：
Rauch, A;Rüschendorf, F;Nürnberg, P
背景资料：染色体不平衡是发育缺陷和癌症的主要原因，并且通常构成鉴定新的疾病相关基因的关键。经典的细胞遗传学方法是有限的分辨率和依赖于高技能的劳动力，而具有更高分辨率的方法，基于分子细胞遗传学方法，如矩阵CGH，是不广泛提供。方法：我们已经开发和评估了一种方法，我们称之为“分子核型分析”，使用现成的和易于处理的寡核苷酸阵列最初设计的平行全基因组分析超过10 000个SNP。我们表明，我们可以很容易地和可靠地检测到各种大小的不平衡的染色体畸变，从一个单一的微阵列上的250纳克的DNA，基于荧光强度信息从簇SNPs.Results：我们确定了这种方法的分辨率，通过分析20 trios与21个先前确认的微妙的畸变大小之间的0.2和13 Mb。至少5 Mb大小的重复和缺失是可靠检测的，但较小畸变的检测取决于它们所含的SNP数量，因此分析的10种不同缺失中有7种（大小范围为0.2至3.7 Mb）由于相应区域的SNP密度不足而无法检测。在我们的一系列充分表征的患者中推导出阵列峰的可靠截止水平，允许使用GeneChip Mapping 10K SNP阵列从少量DNA进行快速分子核型分析，以高灵敏度检测甚至细微的缺失和重复和特异性。
Background: Chromosomal imbalances are a major cause of developmental defects as well as cancer and often constitute the key in identification of novel disease related genes. Classical cytogenetic methods are limited in resolution and dependent on highly skilled labour, while methods with higher resolution, based on molecular cytogenetics approaches such as matrix CGH, are not widely available.Methods: We have developed and evaluated a method we term "molecular karyotyping'', using readily available and easy to handle oligonucleotide arrays originally designed for parallel genomewide analysis of over 10 000 SNPs. We show that we can easily and reliably detect unbalanced chromosomal aberrations of various sizes from as little as 250 ng of DNA on a single microarray, based on fluorescence intensity information from clusters of SNPs.Results: We determined the resolution of this method through analysis of 20 trios with 21 previously confirmed subtle aberrations sizing between 0.2 and 13 Mb. Duplications and deletions of at least 5 Mb in size were reliably detectable, but detection of smaller aberrations was dependent on the number of SNPs they contained, thus seven of 10 different deletions analysed, with sizes ranging from 0.2 to 3.7 Mb, were not detectable due to insufficient SNP density in the respective region.Conclusions: Deduction of reliable cut off levels for array peaks in our series of well characterised patients allows the use of the GeneChip Mapping 10K SNP array for performing rapid molecular karyotyping from small amounts of DNA for the detection of even subtle deletions and duplications with high sensitivity and specificity.