Human Genome Variation最新文献_第4页

Allele frequency of pathogenic variants causing acid sphingomyelinase deficiency and Gaucher disease in the general Japanese population. 日本普通人群中导致酸性鞘磷脂酶缺乏症和戈谢病的致病变体的等位基因频率。

IF 1

Human Genome Variation Pub Date : 2024-06-12 DOI: 10.1038/s41439-024-00282-z

Shuhei Sako, Kimihiko Oishi, Hiroyuki Ida, Eri Imagawa

{"title":"Allele frequency of pathogenic variants causing acid sphingomyelinase deficiency and Gaucher disease in the general Japanese population.","authors":"Shuhei Sako, Kimihiko Oishi, Hiroyuki Ida, Eri Imagawa","doi":"10.1038/s41439-024-00282-z","DOIUrl":"10.1038/s41439-024-00282-z","url":null,"abstract":"Acid sphingomyelinase deficiency (ASMD) and Gaucher disease (GD) are lysosomal storage disorders associated with hepatosplenomegaly and thrombocytopenia. The incidences of ASMD and GD are known to be particularly high in the Ashkenazi Jewish population. Conversely, the number of reported patients with these diseases has been limited in Asian countries, including Japan. Here, we reviewed the allele frequencies of pathogenic variants causing ASMD and GD in the Japanese population and populations with various ancestry backgrounds using the Japanese Multi-Omics Reference Panel 54KJPN and the Genome Aggregation Database v4.0.0. The estimated carrier frequencies of ASMD- and GD-related variants were 1/180 and 1/154 in Japanese individuals, equivalent to disease occurrence frequencies of 1/128,191 and 1/94,791 individuals, respectively. These frequencies are much higher than previously expected. Our data also suggest that there are more patients with a milder form of ASMD and nonspecific clinical findings who have not yet been diagnosed.","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"24"},"PeriodicalIF":1.0,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11169237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141311849","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

Investigating mobile element variations by statistical genetics. 通过统计遗传学研究流动元素的变异。

IF 1

Human Genome Variation Pub Date : 2024-05-30 DOI: 10.1038/s41439-024-00280-1

Shohei Kojima

{"title":"Investigating mobile element variations by statistical genetics.","authors":"Shohei Kojima","doi":"10.1038/s41439-024-00280-1","DOIUrl":"10.1038/s41439-024-00280-1","url":null,"abstract":"The integration of structural variations (SVs) in statistical genetics provides an opportunity to understand the genetic factors influencing complex human traits and disease. Recent advances in long-read technology and variant calling methods for short reads have improved the accurate discovery and genotyping of SVs, enabling their use in expression quantitative trait loci (eQTL) analysis and genome-wide association studies (GWAS). Mobile elements are DNA sequences that insert themselves into various genome locations. Insertional polymorphisms of mobile elements between humans, called mobile element variations (MEVs), contribute to approximately 25% of human SVs. We recently developed a variant caller that can accurately identify and genotype MEVs from biobank-scale short-read whole-genome sequencing (WGS) datasets and integrate them into statistical genetics. The use of MEVs in eQTL analysis and GWAS has a minimal impact on the discovery of genome loci associated with gene expression and disease; most disease-associated haplotypes can be identified by single nucleotide variations (SNVs). On the other hand, it helps make hypotheses about causal variants or effector variants. Focusing on MEVs, we identified multiple MEVs that contribute to differential gene expression and one of them is a potential cause of skin disease, emphasizing the importance of the integration of MEVs in medical genetics. Here, I will provide an overview of MEVs, MEV calling from WGS, and the integration of MEVs in statistical genetics. Finally, I will discuss the unanswered questions about MEVs, such as rare variants.","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"23"},"PeriodicalIF":1.0,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11140006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141180068","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

Characteristic craniofacial defects associated with a novel USP9X truncation mutation. 与新型 USP9X 截断突变相关的特征性颅面缺陷。

IF 1.5

Human Genome Variation Pub Date : 2024-05-16 DOI: 10.1038/s41439-024-00277-w

Namiki Nagata, Hiroshi Kurosaka, Kotaro Higashi, Masaya Yamaguchi, Sayuri Yamamoto, Toshihiro Inubushi, Miho Nagata, Yasuki Ishihara, Ayumi Yonei, Yohei Miyashita, Yoshihiro Asano, Norio Sakai, Yasushi Sakata, Shigetada Kawabata, Takashi Yamashiro

引用次数: 0

NF1 with 47,XYY mosaicism diagnosed by mandibular neurofibromas. 通过下颌神经纤维瘤诊断出 NF1 与 47,XYY 嵌合。

IF 1

Human Genome Variation Pub Date : 2024-05-16 DOI: 10.1038/s41439-024-00279-8

Erina Tonouchi, Kei-Ichi Morita, Yosuke Harazono, Kyoko Hoshino, Tetsuya Yoda

引用次数: 0

Xq22 deletion involving TCEAL1 in a female patient with early-onset neurological disease trait. 一名女性早发性神经系统疾病患者体内涉及 TCEAL1 的 Xq22 缺失。

IF 1

Human Genome Variation Pub Date : 2024-05-15 DOI: 10.1038/s41439-024-00278-9

Keiko Shimojima Yamamoto, Yusuke Itagaki, Kazuki Tanaka, Nobuhiko Okamoto, Toshiyuki Yamamoto

引用次数: 0

Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data 通过短长线程测序数据检测到的 SNV、嵌合体和结构变异的比较评估

IF 1.5

Human Genome Variation Pub Date : 2024-04-17 DOI: 10.1038/s41439-024-00276-x

Shunichi Kosugi, Chikashi Terao

{"title":"Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data","authors":"Shunichi Kosugi, Chikashi Terao","doi":"10.1038/s41439-024-00276-x","DOIUrl":"https://doi.org/10.1038/s41439-024-00276-x","url":null,"abstract":"Short- and long-read sequencing technologies are routinely used to detect DNA variants, including SNVs, indels, and structural variations (SVs). However, the differences in the quality and quantity of variants detected between short- and long-read data are not fully understood. In this study, we comprehensively evaluated the variant calling performance of short- and long-read-based SNV, indel, and SV detection algorithms (6 for SNVs, 12 for indels, and 13 for SVs) using a novel evaluation framework incorporating manual visual inspection. The results showed that indel-insertion calls greater than 10 bp were poorly detected by short-read-based detection algorithms compared to long-read-based algorithms; however, the recall and precision of SNV and indel-deletion detection were similar between short- and long-read data. The recall of SV detection with short-read-based algorithms was significantly lower in repetitive regions, especially for small- to intermediate-sized SVs, than that detected with long-read-based algorithms. In contrast, the recall and precision of SV detection in nonrepetitive regions were similar between short- and long-read data. These findings suggest the need for refined strategies, such as incorporating multiple variant detection algorithms, to generate a more complete set of variants using short-read data.","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"3 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140617487","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: 0

Pediatric hypertrophic cardiomyopathy caused by a novel TNNI3 variant. 由新型 TNNI3 变异引起的小儿肥厚型心肌病。

IF 1

Human Genome Variation Pub Date : 2024-03-29 DOI: 10.1038/s41439-024-00272-1

Natsuko Inagaki, Tomoya Okano, Masatake Kobayashi, Masatsune Fujii, Yoshinao Yazaki, Yasuyoshi Takei, Hisanori Kosuge, Shinji Suzuki, Takeharu Hayashi, Masahiko Kuroda, Kazuhiro Satomi

引用次数: 0

Genomic insights into familial adenomatous polyposis: unraveling a rare case with whole APC gene deletion and intellectual disability. 家族性腺瘤性息肉病的基因组学见解：揭示一个全 APC 基因缺失和智力残疾的罕见病例。

IF 1

Human Genome Variation Pub Date : 2024-03-29 DOI: 10.1038/s41439-024-00270-3

Hiroki Tanabe, Masami Ijiri, Kenji Takahashi, Honoka Sasagawa, Tomomi Kamanaka, Shohei Kuroda, Hiroki Sato, Takeo Sarashina, Yusuke Mizukami, Yoshio Makita, Toshikatsu Okumura

引用次数: 0

End-stage ADPKD with a low-frequency PKD1 mosaic variant accelerated by chemoradiotherapy 低频 PKD1 马赛克变异的终末期 ADPKD 因化疗放疗而加速发展

IF 1.5

Human Genome Variation Pub Date : 2024-03-28 DOI: 10.1038/s41439-024-00273-0

Hiroaki Hanafusa, Hiroshi Yamaguchi, Naoya Morisada, Ming Juan YE, Riki Matsumoto, Hiroaki Nagase, Kandai Nozu

引用次数: 0

Ventriculosubgaleal shunt placement for hydrocephalus in osteogenesis imperfecta with novel compound heterozygous CRTAP variants 为伴有新型复合杂合CRTAP变异的成骨不全症脑积水患者实施脑室-次脑分流术

IF 1.5

Human Genome Variation Pub Date : 2024-03-28 DOI: 10.1038/s41439-024-00274-z

Shintaro Nakamura, Kyosuke Ibi, Hiroyuki Tanaka, Hirokazu Takami, Keita Okada, Nao Takasugi, Motohiro Kato, Naoto Takahashi, Takanobu Inoue

引用次数: 0