Phased Haplotype Resolution of the SLC6A4 Promoter Using Long-Read Single Molecule Real-Time (SMRT) Sequencing.
Phased Haplotype Resolution of the SLC6A4 Promoter Using Long-Read Single Molecule Real-Time (SMRT) Sequencing.
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DOI：
10.3390/genes11111333
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发表时间：
2020-11-12
期刊：
影响因子：
3.5
通讯作者：
Scott SA
中科院分区：
文献类型：
--
作者：
Botton MR;Yang Y;Scott ER;Desnick RJ;Scott SA
SLC 6A 4基因与精神疾病易感性和抗抑郁反应变异性有关。SLC 6A 4启动子由可变数目的同源20-24 bp重复序列（5-HTTLPR）限定，长（L）和短（S）等位基因分别与较高和较低表达相关。然而，这种插入/缺失变异被认为是最具信息性的单倍型与rs 25531和rs 25532变异。因此，我们开发了一种长读单分子实时（SMRT）测序方法来询问SLC 6A 4启动子区域。对总共120个样品进行SLC 6A 4长读段SMRT测序，主要基于可用的短读段测序数据进行选择。来自1000个基因组（1 KG）项目（~5X）和遗传检测参考物质协调计划（~ 45 X）的短读基因组测序，以及基于高深度短读捕获的测序（~ 330 X），无法识别5-HTTLPR短（S）等位基因，短读测序也无法确定任何已识别的变体。相反，长读段SMRT测序明确鉴定了5-HTTLPR短（S）等位基因（频率为0.467）和定相SLC 6A 4启动子单倍型。此外，审查了不一致的rs 25531基因型，并确定为短读错误。总之，长读段SMRT测序是一种用于SLC 6A 4启动子分相解析的创新且稳健的方法，可以为研究和临床应用提供更准确的药物遗传学测试。
The SLC6A4 gene has been implicated in psychiatric disorder susceptibility and antidepressant response variability. The SLC6A4 promoter is defined by a variable number of homologous 20–24 bp repeats (5-HTTLPR), and long (L) and short (S) alleles are associated with higher and lower expression, respectively. However, this insertion/deletion variant is most informative when considered as a haplotype with the rs25531 and rs25532 variants. Therefore, we developed a long-read single molecule real-time (SMRT) sequencing method to interrogate the SLC6A4 promoter region. A total of 120 samples were subjected to SLC6A4 long-read SMRT sequencing, primarily selected based on available short-read sequencing data. Short-read genome sequencing from the 1000 Genomes (1KG) Project (~5X) and the Genetic Testing Reference Material Coordination Program (~45X), as well as high-depth short-read capture-based sequencing (~330X), could not identify the 5-HTTLPR short (S) allele, nor could short-read sequencing phase any identified variants. In contrast, long-read SMRT sequencing unambiguously identified the 5-HTTLPR short (S) allele (frequency of 0.467) and phased SLC6A4 promoter haplotypes. Additionally, discordant rs25531 genotypes were reviewed and determined to be short-read errors. Taken together, long-read SMRT sequencing is an innovative and robust method for phased resolution of the SLC6A4 promoter, which could enable more accurate pharmacogenetic testing for both research and clinical applications.
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