迄今为止，单核苷酸多态性（SNP）是全基因组关联研究（GWAS）中最深入研究的多态性类别，但插入-缺失或多核苷酸长度多态性（MNLPs）等其他类别也可能导致疾病风险。多份报告表明，5p15.33前列腺癌风险区是特别强的表达量性状定位基因（eQTL）Iroquois Homeobox 4（IRX4）转录本。在这里，我们使用表观基因组和基因组编辑证明了一个两等位（21和47个碱基对（bp））的MNLP是调控IRX4转录水平的因果变异。在LNCaP前列腺癌细胞（纯合子为21 bp短等位基因），47 bp长等位基因的单拷贝嵌合显著改变染色质状态，使雄激素受体（AR）可以结合，增加染色质可及性，组蛋白3赖氨酸27乙酰化（H3K27ac）和IRX4表达上调约3倍。我们进一步显示，在另外两个前列腺癌风险位点中，MNLP是最有力的候选易感性变异。我们估计，至少有5%的前列腺癌风险位点可以通过功能性非-SNP因果变异进行解释，这可能对其他癌症GWAS具有更广泛的影响。更一般地，我们的结果强调了研究其他遗传变异类别作为人类性状因果介质的重要性。© 2023. 施普林格自然出版集团有限公司。

To date, single-nucleotide polymorphisms (SNPs) have been the most intensively investigated class of polymorphisms in genome wide associations studies (GWAS), however, other classes such as insertion-deletion or multiple nucleotide length polymorphism (MNLPs) may also confer disease risk. Multiple reports have shown that the 5p15.33 prostate cancer risk region is a particularly strong expression quantitative trait locus (eQTL) for Iroquois Homeobox 4 (IRX4) transcripts. Here, we demonstrate using epigenome and genome editing that a biallelic (21 and 47 base pairs (bp)) MNLP is the causal variant regulating IRX4 transcript levels. In LNCaP prostate cancer cells (homozygous for the 21 bp short allele), a single copy knock-in of the 47 bp long allele potently alters the chromatin state, enabling de novo functional binding of the androgen receptor (AR) associated with increased chromatin accessibility, Histone 3 lysine 27 acetylation (H3K27ac), and ~3-fold upregulation of IRX4 expression. We further show that an MNLP is amongst the strongest candidate susceptibility variants at two additional prostate cancer risk loci. We estimated that at least 5% of prostate cancer risk loci could be explained by functional non-SNP causal variants, which may have broader implications for other cancers GWAS. More generally, our results underscore the importance of investigating other classes of inherited variation as causal mediators of human traits.© 2023. Springer Nature Limited.