Human Genome Variation最新文献_第9页

Human leukocyte antigen super-locus: nexus of genomic supergenes, SNPs, indels, transcripts, and haplotypes. 人类白细胞抗原超级焦点：基因组超级基因、SNPs、indels、转录本和单倍型的联系。

IF 1

Human Genome Variation Pub Date : 2022-12-21 DOI: 10.1038/s41439-022-00226-5

Jerzy K Kulski, Shingo Suzuki, Takashi Shiina

{"title":"Human leukocyte antigen super-locus: nexus of genomic supergenes, SNPs, indels, transcripts, and haplotypes.","authors":"Jerzy K Kulski, Shingo Suzuki, Takashi Shiina","doi":"10.1038/s41439-022-00226-5","DOIUrl":"10.1038/s41439-022-00226-5","url":null,"abstract":"The human Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) super-locus is a highly polymorphic genomic region that encodes more than 140 coding genes including the transplantation and immune regulatory molecules. It receives special attention for genetic investigation because of its important role in the regulation of innate and adaptive immune responses and its strong association with numerous infectious and/or autoimmune diseases. In recent years, MHC genotyping and haplotyping using Sanger sequencing and next-generation sequencing (NGS) methods have produced many hundreds of genomic sequences of the HLA super-locus for comparative studies of the genetic architecture and diversity between the same and different haplotypes. In this special issue on 'The Current Landscape of HLA Genomics and Genetics', we provide a short review of some of the recent analytical developments used to investigate the SNP polymorphisms, structural variants (indels), transcription and haplotypes of the HLA super-locus. This review highlights the importance of using reference cell-lines, population studies, and NGS methods to improve and update our understanding of the mechanisms, architectural structures and combinations of human MHC genomic alleles (SNPs and indels) that better define and characterise haplotypes and their association with various phenotypes and diseases.","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"9 1","pages":"49"},"PeriodicalIF":1.0,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9772353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10513975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Acknowledgement to the Reviewers. 向审稿人致谢。

IF 1.5

Human Genome Variation Pub Date : 2022-12-20 DOI: 10.1038/s41439-022-00227-4

Issei Imoto

引用次数: 8

The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan. NBDC-DDBJ 估算服务器为使用日本受控访问参考面板数据集提供了便利。

IF 1

Human Genome Variation Pub Date : 2022-12-20 DOI: 10.1038/s41439-022-00225-6

Tsuyoshi Hachiya, Manabu Ishii, Yosuke Kawai, Seik-Soon Khor, Minae Kawashima, Licht Toyo-Oka, Nobutaka Mitsuhashi, Asami Fukuda, Yuichi Kodama, Takatomo Fujisawa, Katsushi Tokunaga, Toshihisa Takagi

引用次数: 0

Building cloud computing environments for genome analysis in Japan. 在日本为基因组分析构建云计算环境。

IF 1.5

Human Genome Variation Pub Date : 2022-12-14 DOI: 10.1038/s41439-022-00223-8

Osamu Ogasawara

{"title":"Building cloud computing environments for genome analysis in Japan.","authors":"Osamu Ogasawara","doi":"10.1038/s41439-022-00223-8","DOIUrl":"https://doi.org/10.1038/s41439-022-00223-8","url":null,"abstract":"This review article describes the current status of data archiving and computational infrastructure in the field of genomic medicine, focusing primarily on the situation in Japan. I begin by introducing the status of supercomputer operations in Japan, where a high-performance computing infrastructure (HPCI) is operated to meet the diverse computational needs of science in general. Since this HPCI consists of supercomputers of various architectures located across the nation connected via a high-speed network, including supercomputers specialized in genome science, the status of its response to the explosive increase in genomic data, including the International Nucleotide Sequence Database Collaboration (INSDC) data archive, is explored. Separately, since it is clear that the use of commercial cloud computing environments needs to be promoted, both in light of the rapid increase in computing demands and to support international data sharing and international data analysis projects, I explain how the Japanese government has established a series of guidelines for the use of cloud computing based on its cybersecurity strategy and has begun to build a government cloud for government agencies. I will also carefully consider several other issues of user concern. Finally, I will show how Japan's major cloud computing infrastructure is currently evolving toward a multicloud and hybrid cloud configuration.","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"9 1","pages":"46"},"PeriodicalIF":1.5,"publicationDate":"2022-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9751107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10863835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A novel FLNA variant in a fetus with skeletal dysplasia. 骨骼发育不良胎儿的FLNA新变异。

IF 1.5

Human Genome Variation Pub Date : 2022-12-13 DOI: 10.1038/s41439-022-00224-7

Kyoko Oshina, Yoshimasa Kamei, Asuka Hori, Fuyuki Hasegawa, Kosuke Taniguchi, Ohsuke Migita, Atsuo Itakura, Kenichiro Hata

引用次数: 0

TogoVar: A comprehensive Japanese genetic variation database. TogoVar:一个综合性的日本遗传变异数据库。

IF 1.5

Human Genome Variation Pub Date : 2022-12-12 DOI: 10.1038/s41439-022-00222-9

Nobutaka Mitsuhashi, Licht Toyo-Oka, Toshiaki Katayama, Minae Kawashima, Shuichi Kawashima, Kazunori Miyazaki, Toshihisa Takagi

{"title":"TogoVar: A comprehensive Japanese genetic variation database.","authors":"Nobutaka Mitsuhashi, Licht Toyo-Oka, Toshiaki Katayama, Minae Kawashima, Shuichi Kawashima, Kazunori Miyazaki, Toshihisa Takagi","doi":"10.1038/s41439-022-00222-9","DOIUrl":"https://doi.org/10.1038/s41439-022-00222-9","url":null,"abstract":"TogoVar ( https://togovar.org ) is a database that integrates allele frequencies derived from Japanese populations and provides annotations for variant interpretation. First, a scheme to reanalyze individual-level genome sequence data deposited in the Japanese Genotype-phenotype Archive (JGA), a controlled-access database, was established to make allele frequencies publicly available. As more Japanese individual-level genome sequence data are deposited in JGA, the sample size employed in TogoVar is expected to increase, contributing to genetic study as reference data for Japanese populations. Second, public datasets of Japanese and non-Japanese populations were integrated into TogoVar to easily compare allele frequencies in Japanese and other populations. Each variant detected in Japanese populations was assigned a TogoVar ID as a permanent identifier. Third, these variants were annotated with molecular consequence, pathogenicity, and literature information for interpreting and prioritizing variants. Here, we introduce the newly developed TogoVar database that compares allele frequencies among Japanese and non-Japanese populations and describes the integrated annotations.","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"9 1","pages":"44"},"PeriodicalIF":1.5,"publicationDate":"2022-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9744889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10524240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Novel BCL11B truncation variant in a patient with developmental delay, distinctive features, and early craniosynostosis. 发育迟缓、特征独特、早期颅缝闭合患者的新型BCL11B截断变异

IF 1.5

Human Genome Variation Pub Date : 2022-12-05 DOI: 10.1038/s41439-022-00220-x

Kaoru Eto, Osamu Machida, Tomoe Yanagishita, Keiko Shimojima Yamamoto, Kentaro Chiba, Yasuo Aihara, Yuuki Hasegawa, Miho Nagata, Yasuki Ishihara, Yohei Miyashita, Yoshihiro Asano, Satoru Nagata, Toshiyuki Yamamoto

引用次数: 1

A novel SLC5A2 heterozygous variant in a family with familial renal glucosuria. 一种新的SLC5A2杂合变异家族与家族性肾性糖尿症。

IF 1.5

Human Genome Variation Pub Date : 2022-12-01 DOI: 10.1038/s41439-022-00221-w

Maho Hatano, Tomohiro Udagawa, Toru Kanamori, Akito Sutani, Takayasu Mori, Eisei Sohara, Shinichi Uchida, Tomohiro Morio, Masato Nishioka

引用次数: 1

Atypical Sotos syndrome caused by a novel splice site variant. 由一种新的剪接位点变异引起的非典型索托斯综合征。

IF 1.5

Human Genome Variation Pub Date : 2022-11-16 DOI: 10.1038/s41439-022-00219-4

Mari Minatogawa, Taichi Tsuji, Mie Inaba, Noriaki Kawakami, Seiji Mizuno, Tomoki Kosho

引用次数: 1

Novel missense COL2A1 variant in a fetus with achondrogenesis type II. II型软骨发育不全胎儿的新型错义COL2A1变异。

IF 1.5

Human Genome Variation Pub Date : 2022-11-15 DOI: 10.1038/s41439-022-00218-5

Yukari Kobayashi, Yuki Ito, Kosuke Taniguchi, Kana Harada, Michihiro Yamamura, Taisuke Sato, Ken Takahashi, Hiroshi Kawame, Kenichiro Hata, Osamu Samura, Aikou Okamoto

引用次数: 0