Identifying candidate Hirschsprung disease-associated RET variants
Identifying candidate Hirschsprung disease-associated RET variants
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DOI：
10.1086/429589
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发表时间：
2005-05-01
影响因子：
9.8
通讯作者：
Hofstra, RMW
中科院分区：
文献类型：
--
作者：
Burzynski, GM;Nolte, IM;Hofstra, RMW
散发性先天性巨结肠（HSCR）患者RET基因座5'区标记的等位基因共享增加，表明存在共同的祖先RET突变。在之前的研究中，我们发现了一个由6个SNP组成的单倍型，该单倍型在我们的患者中传播了55.6%，而在我们使用的对照中仅存在16.2%。在具有该单倍型的患者中，90.8%的患者在两条染色体上都具有该单倍型，这导致发生HSCR的风险比单倍型异质发生时高得多。为了更精确地定义HSCR相关区域并鉴定候选疾病相关变异体，我们在一个常见风险单倍型纯合子患者和一个最常见非风险单倍型纯合子对照个体中，对RET基因上游10 kb至内含子1和外显子2（共33 kb）的共有单倍型区域进行测序。这些序列的比较揭示了86个序列差异。在这86个变异中，有8个被证明是在不同脊椎动物之间高度保守的区域和假定的转录因子结合位点内。因此，我们认为这些是候选的疾病相关变异。随后对这八种变异的基因分型显示，八种标记中的六种与疾病有很强的关联。这六个标记也显示了等位基因传递的最大失真。种间比较表明，只有一个的六个变化是位于一个区域也保守的非哺乳动物物种，使其成为最有可能的候选人HSCR相关的变异。
Patients with sporadic Hirschsprung disease (HSCR) show increased allele sharing at markers in the 5' region of the RET locus, indicating the presence of a common ancestral RET mutation. In a previous study, we found a haplotype of six SNPs that was transmitted to 55.6% of our patients, whereas it was present in only 16.2% of the controls we used. Among the patients with that haplotype, 90.8% had it on both chromosomes, which led to a much higher risk of developing HSCR than when the haplotype occurred heterozygously. To more precisely define the HSCR-associated region and to identify candidate disease-associated variant(s), we sequenced the shared common haplotype region from 10 kb upstream of the RET gene through intron 1 and exon 2 (in total, 33 kb) in a patient homozygous for the common risk haplotype and in a control individual homozygous for the most common nonrisk haplotype. A comparison of these sequences revealed 86 sequence differences. Of these 86 variations, 8 proved to be in regions highly conserved among different vertebrates and within putative transcription factor binding sites. We therefore considered these as candidate disease-associated variants. Subsequent genotyping of these eight variants revealed a strong disease association for six of the eight markers. These six markers also showed the largest distortions in allele transmission. Interspecies comparison showed that only one of the six variations was located in a region also conserved in a nonmammalian species, making it the most likely candidate HSCR-associated variant.