Verlaan Dominique J, Ge Bing, Grundberg Elin, Hoberman Rose, Lam Kevin C L, Koka Vonda, Dias Joana, Gurd Scott, Martin Nicolas W, Mallmin Hans, Nilsson Olof, Harmsen Eef, Dewar Ken, Kwan Tony, Pastinen Tomi
Department of Human Genetics, McGill University, Montréal H3A 1B1, Canada.
Genome Res. 2009 Jan;19(1):118-27. doi: 10.1101/gr.084798.108. Epub 2008 Oct 29.
Regulatory cis-acting variants account for a large proportion of gene expression variability in populations. Cis-acting differences can be specifically measured by comparing relative levels of allelic transcripts within a sample. Allelic expression (AE) mapping for cis-regulatory variant discovery has been hindered by the requirements of having informative or heterozygous single nucleotide polymorphisms (SNPs) within genes in order to assign the allelic origin of each transcript. In this study we have developed an approach to systematically screen for heritable cis-variants in common human haplotypes across >1,000 genes. In order to achieve the highest level of information per haplotype studied, we carried out allelic expression measurements by using both intronic and exonic SNPs in primary transcripts. We used a novel RNA pooling strategy in immortalized lymphoblastoid cell lines (LCLs) and primary human osteoblast cell lines (HObs) to allow for high-throughput AE. Screening hits from RNA pools were further validated by performing allelic expression mapping in individual samples. Our results indicate that >10% of expressed genes in human LCLs show genotype-linked AE. In addition, we have validated cis-acting variants in over 20 genes linked with common disease susceptibility in recent genome-wide studies. More generally, our results indicate that RNA pooling coupled with AE read-out by second generation sequencing or by other methods provides a high-throughput tool for cataloging the impact of common noncoding variants in the human genome.
调控性顺式作用变异在人群基因表达变异性中占很大比例。顺式作用差异可通过比较样本中等位基因转录本的相对水平来具体测量。用于发现顺式调控变异的等位基因表达（AE）图谱绘制一直受到阻碍，因为需要基因内具有信息性或杂合的单核苷酸多态性（SNP），以便确定每个转录本的等位基因来源。在本研究中，我们开发了一种方法，用于系统筛选超过1000个基因的常见人类单倍型中的可遗传顺式变异。为了在所研究的每个单倍型中获得最高水平的信息，我们通过使用初级转录本中的内含子和外显子SNP进行等位基因表达测量。我们在永生化淋巴母细胞系（LCL）和原代人成骨细胞系（HOb）中使用了一种新型RNA混合策略，以实现高通量AE。通过在个体样本中进行等位基因表达图谱绘制，进一步验证了来自RNA池的筛选命中结果。我们的结果表明，人类LCL中超过10%的表达基因显示出与基因型相关的AE。此外，我们在最近的全基因组研究中验证了20多个与常见疾病易感性相关基因中的顺式作用变异。更普遍地说，我们的结果表明，RNA混合结合第二代测序或其他方法的AE读出，为编目人类基因组中常见非编码变异的影响提供了一种高通量工具。
