Human Genome Variation最新文献

JG2: an updated version of the Japanese population-specific reference genome. JG2：日本特定人群参考基因组的更新版本。

IF 1

Human Genome Variation Pub Date : 2025-10-01 DOI: 10.1038/s41439-025-00326-y

Sirawit Sriwichaiin, Satoshi Makino, Takamitsu Funayama, Akihito Otsuki, Junko Kawashima, Yasunobu Okamura, Shu Tadaka, Fumiki Katsuoka, Kazuki Kumada, Shuichi Tsutsumi, Kengo Kinoshita, Masayuki Yamamoto, Gen Tamiya, Jun Takayama

{"title":"JG2: an updated version of the Japanese population-specific reference genome.","authors":"Sirawit Sriwichaiin, Satoshi Makino, Takamitsu Funayama, Akihito Otsuki, Junko Kawashima, Yasunobu Okamura, Shu Tadaka, Fumiki Katsuoka, Kazuki Kumada, Shuichi Tsutsumi, Kengo Kinoshita, Masayuki Yamamoto, Gen Tamiya, Jun Takayama","doi":"10.1038/s41439-025-00326-y","DOIUrl":"10.1038/s41439-025-00326-y","url":null,"abstract":"Here we present the construction of JG2, an updated population-specific reference genome for the Japanese population. Utilizing data from three individuals previously used in the construction of JG1, several methodologies were employed to enhance genomic coverage and assembly quality. Hi-C sequencing technology facilitated phase-aware assembly, generating two haploid assemblies per individual and enabling improved representation of genetic variation. A meta-assembly strategy and a majority decision approach further refined assembly quality by combining the best sequences from multiple assemblies and minimizing the inclusion of rare variants. The resulting JG2 genome comprises chromosome-level sequences, mitochondrial chromosomes and unplaced scaffolds, offering more comprehensive coverage of the Japanese genome. Comparative analyses with other reference genomes demonstrated the accuracy and representativeness of JG2, highlighting its utility for genetic research involving the Japanese population. Overall, by adopting the phased assembly technique, JG2 represents a substantial advancement over the collapsed assembly-based JG1, with improvements including a greater number of identified variants (3,115,695 variants, of which 298,644 had an allele frequency (AF) of 1.0 in the 3.5KJPNv2 AF panel) and a higher N50 value (152,668,378 bp). These enhancements provide researchers with a more precise and comprehensive resource for understanding the genetic landscape of the Japanese population. The sequences and annotations are available on the jMorp website ( https://jmorp.megabank.tohoku.ac.jp/ ).","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"12 1","pages":"21"},"PeriodicalIF":1.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12485050/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145201494","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

Juvenile/adult-type galactosialidosis with a homozygous CTSA variant without consanguinity. 少年/成人型半乳糖唾液中毒伴无血缘的纯合CTSA变异。

IF 1

Human Genome Variation Pub Date : 2025-09-26 DOI: 10.1038/s41439-025-00324-0

Machiko Toki, Kazushige Tsunoda, Tetsumin So, Motomichi Kosuga, Torayuki Okuyama, Masashi Miharu, Tomonobu Hasegawa, Kazuki Yamazawa

引用次数: 0

Osteogenesis imperfecta, intellectual disability and recurrent infections in a male with a pathogenic SASH3 variant. 致病性SASH3变异男性的成骨不全、智力残疾和复发性感染。

IF 1

Human Genome Variation Pub Date : 2025-09-15 DOI: 10.1038/s41439-025-00323-1

Jun Kido, Tomoyuki Mizukami, Yohei Misumi, Keishin Sugawara, Shouichirou Kusunoki, Naoto Nishimura, Takeshi Mizuguchi, Naomichi Matsumoto, Mitsuharu Ueda, Kimitoshi Nakamura

引用次数: 0

DHX37 variants in patients with 46,XY disorders or differences of sex development. 46、XY疾病患者DHX37变异或性别发育差异。

IF 1

Human Genome Variation Pub Date : 2025-09-08 DOI: 10.1038/s41439-025-00322-2

Yuko Katoh-Fukui, Daisuke Saito, Hiroko Narumi, Atsushi Hattori, Maki Igarashi, Erika Uehara, Hirohito Shima, Junko Kanno, Yukihiro Hasegawa, Reiko Horikawa, Keisuke Nagasaki, Maki Fukami

引用次数: 0

A case of Dravet syndrome with a novel SCN1A gross deletion involving the promoter region. Dravet综合征与涉及启动子区域的新型SCN1A严重缺失1例。

IF 1

Human Genome Variation Pub Date : 2025-09-03 DOI: 10.1038/s41439-025-00320-4

Eri Nakahara Sakamoto, Shino Shimada, Tokito Yamaguchi, Tomoya Ishida, Katsumi Imai, Hidetaka Eguchi, Yasushi Okazaki, Masami Arai

引用次数: 0

A case of Baraitser-Winter cerebrofrontofacial syndrome diagnosed by whole-exome sequencing. 全外显子组测序诊断Baraitser-Winter脑额面综合征1例。

IF 1

Human Genome Variation Pub Date : 2025-09-03 DOI: 10.1038/s41439-025-00319-x

Kenichi Suga, Hiroki Sato, Masashi Suzue, Yukako Honma, Yasunobu Hayabuchi, Ryuji Nakagawa, Kayo Shinomiya, Nobuhiko Okamoto, Yuta Inoue, Naomi Tsuchida, Naomichi Matsumoto, Hiroyuki Morino, Yuishin Izumi, Maki Urushihara

引用次数: 0

Distribution of CCR5-Δ32 and HLA-B*57:01 alleles in HIV-seropositive and HIV-exposed seronegative Peruvian individuals. 秘鲁hiv血清阳性和hiv暴露血清阴性个体CCR5-Δ32和HLA-B*57:01等位基因的分布

IF 1

Human Genome Variation Pub Date : 2025-08-26 DOI: 10.1038/s41439-025-00321-3

Susan M Echavarria-Correa, Daisy Obispo-Achallma, Susan Espetia Anco, Maria Luisa Guevara, Oscar Acosta Conchucos, María Isabel Dedios, Enrique Mamani Zapana, Ricardo Fujita Alarcón, Carlos Augusto Yabar

{"title":"Distribution of CCR5-Δ32 and HLA-B*57:01 alleles in HIV-seropositive and HIV-exposed seronegative Peruvian individuals.","authors":"Susan M Echavarria-Correa, Daisy Obispo-Achallma, Susan Espetia Anco, Maria Luisa Guevara, Oscar Acosta Conchucos, María Isabel Dedios, Enrique Mamani Zapana, Ricardo Fujita Alarcón, Carlos Augusto Yabar","doi":"10.1038/s41439-025-00321-3","DOIUrl":"10.1038/s41439-025-00321-3","url":null,"abstract":"Little information is available about CCR5-Δ32 and HLA-B*57:01 alleles in the Peruvian population, especially in human immunodeficiency virus (HIV)-negative people with high-risk sexual behavior. Here we describe the prevalence of these alleles in HIV-exposed seronegative individuals (PS) and HIV-seropositive individuals (PVV). For this purpose, 300 individuals were recruited: 150 from each group, and the selected alleles were characterized by endpoint PCR, real-time PCR and DNA sequencing. According to our results, the prevalence of CCR5/CCR5-Δ32 heterozygous was 2.7%, and no homozygous cases were found. The population was in Hardy-Weinberg equilibrium for the CCR5 locus. Regarding HLA-B*57:01, one case was identified in the PS group, while no cases were observed in the PVV group. No statistical difference was detected between groups (P > 0.05). In conclusion, we showed a low prevalence for CCR5-Δ32 as HLA-B*57:01 in the Peruvian population. As these alleles were found at similar frequencies among both HIV-positive and HIV-negative Peruvian individuals with high-risk sexual behavior, it is possible that other genetic factors play an important role in preventing HIV transmission in this population. The low frequency of the HLA-B*57:01 allele in the Peruvian population suggests that routine genotyping tests for abacavir hypersensitivity should be reevaluated in the public health policies of Peru's Ministry of Health, based on national epidemiological data.","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"12 1","pages":"15"},"PeriodicalIF":1.0,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12381279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144972701","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

Novel SKIC3 variants in tricho-hepato-enteric syndrome with hemochromatosis. 新的SKIC3变异在毛肝肠综合征合并血色素沉着症。

IF 1

Human Genome Variation Pub Date : 2025-07-18 DOI: 10.1038/s41439-025-00318-y

Kayo Ochiai, Yoshinori Aoki, Naoshi Yamada, Murasaki Aman, Atsushi Yamashita, Masatoshi Yamaguchi, Daisuke Nakato, Toshiki Takenouchi, Kenjiro Kosaki, Yuki Kodama, Hiroshi Moritake

引用次数: 0

A case of coexisting heterozygous NOTCH3 and HTRA1 mutations in cerebral small vessel disease. 脑小血管疾病中NOTCH3和HTRA1杂合突变共存1例。

IF 1

Human Genome Variation Pub Date : 2025-07-09 DOI: 10.1038/s41439-025-00317-z

Masataka Yamashiro, Daigo Yasutomi, Yuichiro Ohya, Satoshi Ohyama, Hiroshi Takashima, Takashi Tokashiki

引用次数: 0

Recurrent cellulitis associated with lymphoedema in Noonan syndrome: case reports with RIT1 variants and literature review. 努南综合征复发性蜂窝织炎伴淋巴水肿：RIT1变异病例报告及文献回顾

IF 1

Human Genome Variation Pub Date : 2025-06-04 DOI: 10.1038/s41439-025-00315-1

Yuki Kobayashi, Takeya Adachi, Umi Tahara, Moemi Tanaka, Hiroki Arakawa, Yohei Funatsu, Kazunori Moritani, Mamiko Yamada, Kenjiro Kosaki, Toyoko Inazumi

{"title":"Recurrent cellulitis associated with lymphoedema in Noonan syndrome: case reports with RIT1 variants and literature review.","authors":"Yuki Kobayashi, Takeya Adachi, Umi Tahara, Moemi Tanaka, Hiroki Arakawa, Yohei Funatsu, Kazunori Moritani, Mamiko Yamada, Kenjiro Kosaki, Toyoko Inazumi","doi":"10.1038/s41439-025-00315-1","DOIUrl":"10.1038/s41439-025-00315-1","url":null,"abstract":"Noonan syndrome (NS) is a RASopathy, a disorder caused by genetic alterations involving the Ras/mitogen-activated protein kinase pathway. It causes characteristic clinical manifestations, including facial dysmorphism and congenital cardiac defects. Occasionally, lymphoedema and recurrent cellulitis occur in patients with NS, potentially escalating to lethal conditions. Despite the frequent association of cellulitis with lymphoedema in NS, features susceptible to these complications have not been fully characterized. We encountered two patients with NS carrying RIT1 pathogenic variants, who were treated for recurrent lower leg cellulitis since their teenage years, which occasionally progressed to sepsis. Here we retrospectively examined these patients with NS and recurrent cellulitis on the background of lymphoedema and reviewed published cases of NS with lymphoedema and cellulitis up to March 2024 to elucidate the clinical and genetic features of this subgroup. Our literature review identified 16 additional patients with NS with similar complications. Among the 18 patients (15 men), genetic analyses revealed pathogenic variants in PTPN11 and RIT1 in 4 patients each, with the latter occurring more frequently than commonly observed. The patients developed lymphoedema by 15 years of age, predisposing them to cellulitis by 23 years of age. Notably, four of the five patients with sepsis had congenital heart defects, with a higher prevalence than that generally reported in NS. This study highlights the characteristics of genetic variants, congenital cardiac anomalies and heightened risk of recurrent cellulitis in patients with NS, emphasizing the need for early intervention with prophylactic antibiotics and surgical treatment to mitigate these risks.","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"12 1","pages":"12"},"PeriodicalIF":1.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12137658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227020","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