日本人群HLA I类和II类基因全长多态性参考级表征数据集

数据集获取（Figshare）

• 源站标题：Table_6_Reference Grade Characterization of Polymorphisms in Full-Length HLA Class I and II Genes With Short-Read Sequencing on the ION PGM System and Long-Reads Generated by Single Molecule, Real-Time Sequencing on the PacBio Platform.XLSX
• DOI：10.3389/fimmu.2018.02294.s010
• 发布日期：2018-10-04
• 文件数：1 个
• 文件总体积：20.03 KB
• 源站页面：https://frontiersin.figshare.com/articles/dataset/Table_6_Reference_Grade_Characterization_of_Polymorphisms_in_Full-Length_HLA_Class_I_and_II_Genes_With_Short-Read_Sequencing_on_the_ION_PGM_System_and_Long-Reads_Generated_by_Single_Molecule_Real-Time_Sequencing_on_the_PacBio_Platform_XLSX/7164074

命令行下载

curl -L -o "Table_6_Reference Grade Characterization of Polymorphisms in Full-Length HLA Class I and II Genes With Short-Read Sequencing on the ION PGM System and Long-Reads Generated by Single Molecule, Real-Time Sequencing on the PacBio Platform.XLSX" "https://ndownloader.figshare.com/files/13180805"

文件清单

• Table_6_Reference Grade Characterization of Polymorphisms in Full-Length HLA Class I and II Genes With Short-Read Sequencing on the ION PGM System and Long-Reads Generated by Single Molecule, Real-Time Sequencing on the PacBio Platform.XLSX（20.03 KB）

文件总体积 20.03 KB（源站 API 实测）。

数据加载示例（图像类）

from PIL import Image
import glob, os

files = (glob.glob(os.path.join(path, "**", "*.png"), recursive=True)
       + glob.glob(os.path.join(path, "**", "*.jpg"), recursive=True)
       + glob.glob(os.path.join(path, "**", "*.tif"), recursive=True))
print("图像文件数:", len(files))
img = Image.open(files[0]); print("尺寸/模式:", img.size, img.mode)

# torchvision Dataset 方式:
# from torchvision import datasets
# ds = datasets.ImageFolder(path)  # 要求 子目录=类别

目录组织与标注格式以源站说明和下载后实际文件为准。

数据说明

Although NGS technologies fuel advances in high-throughput HLA genotyping methods for identification and classification of HLA genes to assist with precision medicine efforts in disease and transplantation, the efficiency of these methods are impeded by the absence of adequately-characterized high-frequency HLA allele reference sequence databases for the highly polymorphic HLA gene system. Here, we report on producing a comprehensive collection of full-length HLA allele sequences for eight classical HLA loci found in the Japanese population. We augmented the second-generation short read data generated by the Ion Torrent technology with long amplicon spanning consensus reads delivered by the third-generation SMRT sequencing method to create reference grade high-quality sequences of HLA class I and II gene alleles resolved at the genomic coding and non-coding level. Forty-six DNAs were obtained from a reference set used previously to establish the HLA allele frequency data in Japanese subjects. The samples included alleles with a collective allele frequency in the Japanese population of more than 99.2%. The HLA loci were independently amplified by long-range PCR using previously designed HLA-locus specific primers and subsequently sequenced using SMRT and Ion PGM sequencers. The mapped long and short-reads were used to produce a reference library of consensus HLA allelic sequences with the help of the reference-aware software tool LAA for SMRT Sequencing. A total of 253 distinct alleles were determined for 46 healthy subjects. Of them, 137 were novel alleles: 101 SNVs and/or indels and 36 extended alleles at a partial or full-length level. Comparing the HLA sequences from the perspective of nucleotide diversity revealed that HLA-DRB1 was the most divergent among the eight HLA genes, and that the HLA-DPB1 gene sequences diverged into two distinct groups, DP2 and DP5, with evidence of independent polymorphisms generated in exon 2. We also identified two specific intronic variations in HLA-DRB1 that might be involved in rheumatoid arthritis. In conclusion, full-length HLA allele sequencing by third-generation and second-generation technologies has provided polymorphi

许可

CC BY 4.0

引用

学术使用请引用 DOI 10.3389/fimmu.2018.02294.s010（source: https://frontiersin.figshare.com/articles/dataset/Table_6_Reference_Grade_Characterization_of_Polymorphisms_in_Full-Length_HLA_Class_I_and_II_Genes_With_Short-Read_Sequencing_on_the_ION_PGM_System_and_Long-Reads_Generated_by_Single_Molecule_Real-Time_Sequencing_on_the_PacBio_Platform_XLSX/7164074）。