Human Genome Variation最新文献

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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
{"title":"Acknowledgement to the Reviewers.","authors":"Issei Imoto","doi":"10.1038/s41439-022-00227-4","DOIUrl":"https://doi.org/10.1038/s41439-022-00227-4","url":null,"abstract":"","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2022-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10402549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
{"title":"The NBDC-DDBJ imputation server facilitates the use of controlled access reference panel datasets in Japan.","authors":"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","doi":"10.1038/s41439-022-00225-6","DOIUrl":"10.1038/s41439-022-00225-6","url":null,"abstract":"<p><p>Accurate genotype imputation requires large-scale reference panel datasets. When conducting genotype imputation on the Japanese population, researchers can use such datasets under collaborative studies or controlled access conditions in public databases. We developed the NBDC-DDBJ imputation server, which securely provides users with a web user interface to execute genotype imputation on the server. Our benchmarking analysis showed that the accuracy of genotype imputation was improved by leveraging controlled access datasets to increase the number of haplotypes available for analysis compared to using publicly available reference panels such as the 1000 Genomes Project. The NBDC-DDBJ imputation server facilitates the use of controlled access datasets for accurate genotype imputation.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2022-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9768127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10422706","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
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":"<p><p>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.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"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
{"title":"A novel FLNA variant in a fetus with skeletal dysplasia.","authors":"Kyoko Oshina,&nbsp;Yoshimasa Kamei,&nbsp;Asuka Hori,&nbsp;Fuyuki Hasegawa,&nbsp;Kosuke Taniguchi,&nbsp;Ohsuke Migita,&nbsp;Atsuo Itakura,&nbsp;Kenichiro Hata","doi":"10.1038/s41439-022-00224-7","DOIUrl":"https://doi.org/10.1038/s41439-022-00224-7","url":null,"abstract":"<p><p>Otopalatodigital spectrum disorder (OPDSD) is characterized by variable phenotypes, including skeletal dysplasia, and is caused by pathogenic variants in filamin A-encoding FLNA. FLNA variants associated with lethal OPDSD primarily alter the CH2 subdomain of the ABD of FLNA. Herein, we report a novel FLNA mutation in a fetus with severe skeletal dysplasia in a pregnant multigravida female with a history of repeated miscarriages and terminations.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2022-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9744731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10518651","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
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,&nbsp;Licht Toyo-Oka,&nbsp;Toshiaki Katayama,&nbsp;Minae Kawashima,&nbsp;Shuichi Kawashima,&nbsp;Kazunori Miyazaki,&nbsp;Toshihisa Takagi","doi":"10.1038/s41439-022-00222-9","DOIUrl":"https://doi.org/10.1038/s41439-022-00222-9","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"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
{"title":"Novel BCL11B truncation variant in a patient with developmental delay, distinctive features, and early craniosynostosis.","authors":"Kaoru Eto,&nbsp;Osamu Machida,&nbsp;Tomoe Yanagishita,&nbsp;Keiko Shimojima Yamamoto,&nbsp;Kentaro Chiba,&nbsp;Yasuo Aihara,&nbsp;Yuuki Hasegawa,&nbsp;Miho Nagata,&nbsp;Yasuki Ishihara,&nbsp;Yohei Miyashita,&nbsp;Yoshihiro Asano,&nbsp;Satoru Nagata,&nbsp;Toshiyuki Yamamoto","doi":"10.1038/s41439-022-00220-x","DOIUrl":"https://doi.org/10.1038/s41439-022-00220-x","url":null,"abstract":"<p><p>Intellectual developmental disorder with dysmorphic facies, speech delay, and T-cell abnormalities (MIM # 618092) is a congenital disorder derived from pathogenic variants of the B-cell leukemia/lymphoma 11B gene (BCL11B). Several variants have been reported to date. Here, through comprehensive genomic analysis, a novel BCL11B truncation variant, NM_138576.4(BCL11B_v001): c.2439_2452dup [p.(His818Argfs*31)], was identified in a Japanese male patient with developmental delay, distinctive features, and early craniosynostosis.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2022-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9722650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10863214","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: 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
{"title":"A novel SLC5A2 heterozygous variant in a family with familial renal glucosuria.","authors":"Maho Hatano,&nbsp;Tomohiro Udagawa,&nbsp;Toru Kanamori,&nbsp;Akito Sutani,&nbsp;Takayasu Mori,&nbsp;Eisei Sohara,&nbsp;Shinichi Uchida,&nbsp;Tomohiro Morio,&nbsp;Masato Nishioka","doi":"10.1038/s41439-022-00221-w","DOIUrl":"https://doi.org/10.1038/s41439-022-00221-w","url":null,"abstract":"<p><p>Familial renal glucosuria (FRG) is characterized by persistent glucosuria despite normal blood glucose levels in the absence of overt tubular dysfunction. SGLT2 is a sodium-glucose cotransporter expressed in the proximal tubule; loss-of-function variants in SLC5A2 are the primary cause of FRG. Heterozygous variants have rarely been reported in Japanese individuals. Here, we identified a novel SLC5A2 heterozygous variant, c.1348G>T: p.Gly450Trp, in a Japanese family comprising two children and their father.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9712647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10504185","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: 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
{"title":"Atypical Sotos syndrome caused by a novel splice site variant.","authors":"Mari Minatogawa,&nbsp;Taichi Tsuji,&nbsp;Mie Inaba,&nbsp;Noriaki Kawakami,&nbsp;Seiji Mizuno,&nbsp;Tomoki Kosho","doi":"10.1038/s41439-022-00219-4","DOIUrl":"https://doi.org/10.1038/s41439-022-00219-4","url":null,"abstract":"<p><p>Sotos syndrome is usually caused by haploinsufficiency of NSD1; it is characterized by overgrowth, craniofacial features, and learning disabilities. We describe a boy with Sotos syndrome caused by a splicing variant (c.4378+5G>A). The clinical manifestations included severe connective tissue involvement, including joint hypermobility, progressive scoliosis, pectus deformity, and skin hyperextensibility; no overgrowth was observed.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2022-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9666520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10498963","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: 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
{"title":"Novel missense COL2A1 variant in a fetus with achondrogenesis type II.","authors":"Yukari Kobayashi,&nbsp;Yuki Ito,&nbsp;Kosuke Taniguchi,&nbsp;Kana Harada,&nbsp;Michihiro Yamamura,&nbsp;Taisuke Sato,&nbsp;Ken Takahashi,&nbsp;Hiroshi Kawame,&nbsp;Kenichiro Hata,&nbsp;Osamu Samura,&nbsp;Aikou Okamoto","doi":"10.1038/s41439-022-00218-5","DOIUrl":"https://doi.org/10.1038/s41439-022-00218-5","url":null,"abstract":"<p><p>Achondrogenesis type II (ACG2) is a lethal skeletal disorder caused by pathogenic variants in COL2A1. We present a fetus with cystic hygroma and severe shortening of the limbs at 14 weeks of gestation. We performed postnatal genetic analysis of the parents and fetus to diagnose the disease. A novel missense variant of COL2A1 [NM_001844.5: c.2987G>A, (p. Gly996Asp)] was identified, which led to the ACG2 diagnosis.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2022-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9663423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10492076","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
Distal 2q duplication in a patient with intellectual disability. 智力残疾患者的远端2q重复。
IF 1.5
Human Genome Variation Pub Date : 2022-11-10 DOI: 10.1038/s41439-022-00215-8
Toshifumi Suzuki, Hitoshi Osaka, Noriko Miyake, Atsushi Fujita, Yuri Uchiyama, Rie Seyama, Eriko Koshimizu, Satoko Miyatake, Takeshi Mizuguchi, Satoru Takeda, Naomichi Matsumoto
{"title":"Distal 2q duplication in a patient with intellectual disability.","authors":"Toshifumi Suzuki,&nbsp;Hitoshi Osaka,&nbsp;Noriko Miyake,&nbsp;Atsushi Fujita,&nbsp;Yuri Uchiyama,&nbsp;Rie Seyama,&nbsp;Eriko Koshimizu,&nbsp;Satoko Miyatake,&nbsp;Takeshi Mizuguchi,&nbsp;Satoru Takeda,&nbsp;Naomichi Matsumoto","doi":"10.1038/s41439-022-00215-8","DOIUrl":"https://doi.org/10.1038/s41439-022-00215-8","url":null,"abstract":"<p><p>We report on a patient with a distal 16.4-Mb duplication at 2q36.3-qter, who presented with severe intellectual disability, microcephaly, brachycephaly, prominent forehead, hypertelorism, prominent eyes, thin upper lip, and progenia. Copy number analysis using whole exome data detected a distal 2q duplication. This is the first report describing a distal 2q duplication at the molecular level.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2022-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9649592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10491603","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: 1
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