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首页> 外文期刊>Genomics >High-resolution snp scan of chromosome 6p21 in pooled samples from patients with complex diseases.
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High-resolution snp scan of chromosome 6p21 in pooled samples from patients with complex diseases.

机译：来自复杂疾病患者的合并样本中6p21号染色体的高分辨率snp扫描。

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摘要

We apply a high-throughput protocol of chip-based mass spectrometry (matrix-assisted laser desorption/ionization time-of-flight; MALDI-TOF) as a method of screening for differences in single-nucleotide polymorphism (SNP) allele frequencies. Using pooled DNA from individuals with asthma, Crohn's disease (CD), schizophrenia, type 1 diabetes (T1D), and controls, we selected 534 SNPs from an initial set of 1435 SNPs spanning a 25-Mb region on chromosome 6p21. The standard deviations of measurements of time of flight at different dots, from different PCRs, and from different pools indicate reliable results on each analysis step. In 90% of the disease-control comparisons we found allelic differences of <10%. Of the T1D samples, which served as a positive control, 10 SNPs with significant differences were observed after taking into account multiple testing. Of these 10 SNPs, 5 are located between DQB1 and DRB1, confirming the known association with the DR3 and DR4 haplotypes whereas two additional SNPs also reproduced known associations of T1D with DOB and LTA. In the CD pool also, two earlier described associations were found with SNPs close to DRB1 and MICA. Additional associations were found in the schizophrenia and asthma pools. They should be confirmed in individual samples or can be used to develop further quality criteria for accepting true differences between pools. The determination of SNP allele frequencies in pooled DNA appears to be of value in assigning further genotyping priorities also in large linkage regions.
机译：我们应用基于芯片质谱的高通量协议（基质辅助激光解吸/电离飞行时间; MALDI-TOF）作为筛选单核苷酸多态性（SNP）等位基因频率差异的方法。使用来自患有哮喘，克罗恩病（CD），精神分裂症，1型糖尿病（T1D）和对照的个体的合并DNA，我们从最初的1435个SNP中选择了534个SNP，这些SNP跨越6p21染色体上的25-Mb区。不同点，不同PCR和不同池中的飞行时间测量值的标准偏差表明，每个分析步骤的结果可靠。在90％的疾病对照比较中，我们发现等位基因差异小于10％。在作为阳性对照的T1D样品中，考虑到多次测试后，观察到10个SNP具有显着差异。在这10个SNP中，有5个位于DQB1和DRB1之间，证实了与DR3和DR4单倍型的已知关联，而另外两个SNP也再现了T1D与DOB和LTA的已知关联。在CD池中，还发现了两个较早描述的与DRB1和MICA接近的SNP的关联。在精神分裂症和哮喘患者中还发现了其他关联。应该在单个样本中对它们进行确认，或者可以将其用于制定进一步的质量标准，以接受池之间的真实差异。合并DNA中SNP等位基因频率的确定对于在更大的连锁区域中分配进一步的基因分型优先级似乎也很有价值。

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