Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing.
Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing.
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DOI：
10.1038/s41397-017-0010-4
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发表时间：
2019-04
期刊：
影响因子：
--
通讯作者：
Yamamoto M
中科院分区：
文献类型：
--
作者：
Mimori T;Yasuda J;Kuroki Y;Shibata TF;Katsuoka F;Saito S;Nariai N;Ono A;Nakai-Inagaki N;Misawa K;Tateno K;Kawai Y;Fuse N;Hozawa A;Kuriyama S;Sugawara J;Minegishi N;Suzuki K;Kinoshita K;Nagasaki M;Yamamoto M
人类白细胞抗原(人类白细胞抗原)是一种基因复合体，因其在器官和血液干细胞移植中的重要性以及特定等位基因与各种疾病的相关性而在不同人群中具有特殊的多样性。我们通过单分子实时(SMRT)测序，对1070个全基因组日本人参考系统(1KJPN)中的208个个体进行了单分子、实时(SMRT)测序，构建了一个包含一组不同的人类白细胞抗原-A、人类白细胞抗原-B、人类白细胞抗原-C和人类白细胞抗原-H等位基因的日本人I类基因参考系统(ToMMo-HL A系统)。为了获得高质量的等位基因重构，我们开发了一种新的流水线，即引物分离组装和精化流水线(PSARP)，其中使用了SMRT测序和额外的短读数据。该组合由139个等位基因组成，均由已知的IPD-IMGT/HLA序列延伸而来，包含40个新的变异体，捕获了1KJPN中96.5%以上的等位基因多样性。这些新获得的序列将成为研究和临床应用的重要资源，包括高分辨率的HLA配型、遗传关联研究和顺式调控元件的分析。
Human leukocyte antigen (HLA) is a gene complex known for its exceptional diversity across populations, importance in organ and blood stem cell transplantation, and associations of specific alleles with various diseases. We constructed a Japanese reference panel of class I HLA genes (ToMMo HLA panel), comprising a distinct set of HLA-A, HLA-B, HLA-C, and HLA-H alleles, by single-molecule, real-time (SMRT) sequencing of 208 individuals included in the 1070 whole-genome Japanese reference panel (1KJPN). For high-quality allele reconstruction, we developed a novel pipeline, Primer-Separation Assembly and Refinement Pipeline (PSARP), in which the SMRT sequencing and additional short-read data were used. The panel consisted of 139 alleles, which were all extended from known IPD-IMGT/HLA sequences, contained 40 with novel variants, and captured more than 96.5% of allelic diversity in 1KJPN. These newly available sequences would be important resources for research and clinical applications including high-resolution HLA typing, genetic association studies, and analyzes of cis-regulatory elements.
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DOI：
10.1038/ejhg.2017.51
发表时间：
2017-06
期刊：
European journal of human genetics : EJHG
影响因子：
--
作者：
Mitt M;Kals M;Pärn K;Gabriel SB;Lander ES;Palotie A;Ripatti S;Morris AP;Metspalu A;Esko T;Mägi R;Palta P
通讯作者：
Palta P
影响因子：
--
作者：
Bentley G;Higuchi R;Hoglund B;Goodridge D;Sayer D;Trachtenberg EA;Erlich HA
通讯作者：
Erlich HA
影响因子：
3.5
作者：
Hosomichi K;Shiina T;Tajima A;Inoue I
通讯作者：
Inoue I
DOI：
10.1073/pnas.0710982105
发表时间：
2008-01-29
影响因子：
11.1
作者：
Korlach, Jonas;Marks, Patrick J.;Turner, Stephen W.
通讯作者：
Turner, Stephen W.
影响因子：
4.3
作者：
Dilthey, Alexander;Leslie, Stephen;McVean, Gil
通讯作者：
McVean, Gil