Human Genome Variation最新文献_第3页

Rare coinheritance of hemoglobin vancleave with severe beta-thalassemia mutation in a patient with secondary erythrocytosis 一名继发性红细胞增多症患者罕见的血红蛋白Vancleave与严重β地中海贫血突变共同遗传

IF 1.5

Human Genome Variation Pub Date : 2024-04-23 DOI: 10.1038/s41439-024-00275-y

Nur Aisyah Aziz, Nurul Hidayah Musa, Melina Mathews, Komalah Thevii Rajenderan, F. S. Abdul Hamid, S. Hassan, Syahira Lazira Omar, Wan Nurul Afiqha Binti Wan Yusoff, Melanie Ling Binti Mohd Din, Nurul Amira Jamaludin, W. R. Wan taib, E. Esa, Norafiza Mohd Yasin

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":"<p>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.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":null,"pages":null},"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 1.5

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 1.5

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

A novel splice site variant of the BBS2 gene in a patient with Bardet-Biedl syndrome. 一名巴尔德-比德尔综合征患者体内 BBS2 基因的一个新剪接位点变异。

IF 1.5

Human Genome Variation Pub Date : 2024-03-22 DOI: 10.1038/s41439-024-00269-w

Hasan Azizi, Mortaza Bonyadi, Abbas Rafat

引用次数: 0

A novel NFKB1 variant in a Japanese pedigree with common variable immunodeficiency. 日本常见变异性免疫缺陷症血统中的一种新型 NFKB1 变异体。

IF 1.5

Human Genome Variation Pub Date : 2024-03-22 DOI: 10.1038/s41439-024-00271-2

Naoko Nakatani, Akihiro Tamura, Hiroaki Hanafusa, Nanako Nino, Nobuyuki Yamamoto, Hiroyuki Awano, Yasuhiro Tanaka, Naoya Morisada, Suguru Uemura, Atsuro Saito, Daiichiro Hasegawa, Kandai Nozu, Yoshiyuki Kosaka

引用次数: 0

BARD1 deletion in a patient with suspected hereditary colorectal cancer. 一名疑似遗传性结直肠癌患者的 BARD1 缺失。

IF 1.5

Human Genome Variation Pub Date : 2024-03-15 DOI: 10.1038/s41439-024-00267-y

Nobue Takaiso, Issei Imoto, Akiyo Yoshimura, Akira Ouchi, Koji Komori, Hiroji Iwata, Yasuhiro Shimizu

引用次数: 0

A deletion variant in LMX1B causing nail-patella syndrome in Japanese twins. 导致日本双胞胎甲髌综合征的 LMX1B 基因缺失变异。

IF 1.5

Human Genome Variation Pub Date : 2024-02-29 DOI: 10.1038/s41439-024-00266-z

Nozomu Kishio, Kazuhiro Iwama, Sayuri Nakanishi, Ryosuke Shindo, Masaki Yasui, Naoki Nicho, Atsushi Takahashi, Mana Kohara, Michisato Hirata, Takahiro Kemmotsu, Miki Tanoshima, Shuichi Ito

引用次数: 0