Erika Nakajima, Yuko Yokohama, Saori Sugiyama, Mio Taketazu, Kenrokuro Mitsube, Takahiro Yamada, Anna Hammarsjö, Giedre Grigelioniene, Gen Nishimura, Yoshio Makita
{"title":"Unclassifiable short-rib thoracic dysplasia diagnosed using targeted gene panel sequencing.","authors":"Erika Nakajima, Yuko Yokohama, Saori Sugiyama, Mio Taketazu, Kenrokuro Mitsube, Takahiro Yamada, Anna Hammarsjö, Giedre Grigelioniene, Gen Nishimura, Yoshio Makita","doi":"10.1038/s41439-024-00302-y","DOIUrl":"10.1038/s41439-024-00302-y","url":null,"abstract":"<p><p>We report a case of a fetus with short-rib thoracic dysplasia (SRTD) with polydactyly that also presented with atypical severe acro-mesomelic ossification defects. Genetic analysis using massively parallel sequencing of a skeletal dysplasia panel revealed compound heterozygous variants in DYNC2H1. This clinical report highlights the challenges associated with diagnosing the diverse phenotypes in the SRTD group and emphasizes the importance of genetic surveillance with a targeted gene panel for accurate diagnosis.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"44"},"PeriodicalIF":1.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11612155/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142773184","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}
{"title":"Simultaneous surgery for gastrostomy and laryngotracheal separation in a patient with Tay‒Sachs disease.","authors":"Masaharu Moroto, Uda Daisuke, Tomoya Yodoi, Yoshihiro Nitta, Yohei Sugimoto, Tomohiro Chiyonobu, Hiroyuki Yamada, Kayo Ozaki, Taichi Nakatani, Norio Sakai","doi":"10.1038/s41439-024-00300-0","DOIUrl":"10.1038/s41439-024-00300-0","url":null,"abstract":"<p><p>Genetic testing identified novel compound heterozygous missense variants in the HEXA gene (NM_00520.6: c.775A>C and NM_000520.6: c.508C>T) in a 16-month-old girl diagnosed with Tay‒Sachs disease. The patient gradually became unable to consume food orally. She suffered severe aspiration pneumonia and underwent gastrostomy and laryngotracheal separation at 2 years and 4 months of age. Despite an initially good prognosis, she died at 3 years of age.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"43"},"PeriodicalIF":1.0,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142751907","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}
{"title":"Genotypes and phenotypes of neurofibromatosis type 1 patients in Japan: A Hereditary Tumor Cohort Study.","authors":"Mashu Futagawa, Tetsuya Okazaki, Eiji Nakata, Chika Fukano, Risa Osumi, Fumino Kato, Yusaku Urakawa, Hideki Yamamoto, Toshifumi Ozaki, Akira Hirasawa","doi":"10.1038/s41439-024-00299-4","DOIUrl":"10.1038/s41439-024-00299-4","url":null,"abstract":"<p><p>Neurofibromatosis type 1 (NF1) presents with a broad spectrum of clinical manifestations, including an increased risk of tumor development and hypertension. Comprehensive data on genotype‒phenotype correlations in patients with NF1 are limited. Therefore, in this study, we aimed to elucidate the detailed genetic and clinical characteristics of NF1 in a hereditary tumor cohort. We performed sequencing and copy number assays in a clinical laboratory and analyzed the clinical data of 44 patients with suspected NF1. Germline pathogenic variants were detected in 36 patients (81.8%), and 20.7% of the variants were novel. Notably, 40.0% of adult patients presented with malignancies; female breast cancer occurred in 20.0% of patients, which was a higher rate than that previously reported. Hypertension was observed in 30.6% of the adult patients, with one patient experiencing sudden death and another developing pheochromocytoma. Three patients with large deletions in NF1 exhibited prominent cutaneous, skeletal, and neurological manifestations. These results highlight the importance of regular surveillance, particularly for patients with malignancies and hypertension. Our findings provide valuable insights for genetic counseling and clinical management, highlighting the multiple health risks associated with NF1 and the need for comprehensive and multidisciplinary care.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"42"},"PeriodicalIF":1.0,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11599849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142733290","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}
{"title":"CFAP43 variant in persistent respiratory symptoms after hematopoietic cell transplantation.","authors":"Shun Nagasawa, Toyoki Nishimura, Ai Yamada, Sachiyo Kamimura, Masataka Ishimura, Hiroshi Moritake","doi":"10.1038/s41439-024-00298-5","DOIUrl":"10.1038/s41439-024-00298-5","url":null,"abstract":"<p><p>We describe a case of RAS-associated autoimmune leukoproliferative disease with primary ciliary dyskinesia (PCD)-like symptoms, such as recurrent pneumonia, sinusitis, and otitis media, that occurred 7 years after hematopoietic cell transplantation. Whole-exome sequencing revealed a heterozygous CFAP43 nonsense variant. Environmental factors related to hematopoietic cell transplantation may have led to PCD symptoms in this patient with this variant. Genetic screening can help avoid subsequent complications during patient management.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"41"},"PeriodicalIF":1.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689122","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}
{"title":"A case of CDKL5 deficiency disorder with a novel intragenic multi-exonic duplication.","authors":"Takato Akiba, Shino Shimada, Katsumi Imai, Satoru Takahashi","doi":"10.1038/s41439-024-00296-7","DOIUrl":"10.1038/s41439-024-00296-7","url":null,"abstract":"<p><p>We present a case of suspected CDKL5 deficiency disorder (CDD) in which a novel intragenic multi-exonic duplication in the CDKL5 gene was identified using next-generation sequencing and multiple ligation-dependent probe amplification. This duplication was assumed to result in a shift of the reading frame and the introduction of a premature stop codon. This case highlights the importance of careful phenotyping and comprehensive genetic testing to detect rare structural variants in CDD patients.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"40"},"PeriodicalIF":1.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11544015/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142604617","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}
{"title":"A mild case of Cockayne syndrome with a novel start-loss variant of ERCC8.","authors":"Taro Matsuoka, Takeshi Yoshida, Kengo Kora, Naoko Yano, Yoshihiro Taura, Takashi Nakamura, Takenori Tozawa, Jun Mori, Tomohiro Chiyonobu","doi":"10.1038/s41439-024-00297-6","DOIUrl":"10.1038/s41439-024-00297-6","url":null,"abstract":"<p><p>Cockayne syndrome (CS) is a progressive multisystem disorder characterized by growth failure, microcephaly, developmental delay, and photosensitivity. The characteristic symptoms appear during early childhood in most patients with CS. Herein, we report a mild case of CS with a novel start-loss variant in ERCC8 that did not show the characteristic symptoms of CS during early childhood and exhibited sudden growth failure after the age of 10 years.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"39"},"PeriodicalIF":1.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11544238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605077","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}
Sílvia Pires, Paula Jorge, Thomas Liehr, Natália Oliva-Teles
{"title":"Challenges in classifying human chromosomal heteromorphisms using banding cytogenetics: From controversial guidelines to the need for a universal scoring system.","authors":"Sílvia Pires, Paula Jorge, Thomas Liehr, Natália Oliva-Teles","doi":"10.1038/s41439-024-00295-8","DOIUrl":"10.1038/s41439-024-00295-8","url":null,"abstract":"<p><p>Chromosomal heteromorphisms (CHs) are morphological variations predominantly found in constitutive heterochromatic regions of the genome, primarily composed of tandemly repetitive sequences of satellite DNA. Although not completely devoid of genes, these regions are typically not transcribed into proteins and lack obvious phenotypic impact. Nonetheless, their clinical importance is increasingly under scrutiny, with several studies aiming to assess their influence on human diseases and susceptibilities, especially as they are seemingly part of the long noncoding RNAs in certain tissues. This article summarizes the classification methods of human heterochromatic CHs documented in the literature over the last two decades. Multiple scoring systems have been identified, and previous approaches for CH assessment and reporting in genetic diagnosis have shown inconsistencies. Owing to the current heterogeneity in the classification of CHs, data analysis may be biased, impacting the quality of clinical reports and human genetic research. This review highlights the need for a universal scoring system, which is essential for scientific reproducibility and the accurate identification and clinical evaluation of human CHs.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"38"},"PeriodicalIF":1.0,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11499882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509745","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}
Moritz Otto, Yichen Zheng, Paul Grablowitz, Thomas Wiehe
{"title":"Detecting adaptive changes in gene copy number distribution accompanying the human out-of-Africa expansion.","authors":"Moritz Otto, Yichen Zheng, Paul Grablowitz, Thomas Wiehe","doi":"10.1038/s41439-024-00293-w","DOIUrl":"10.1038/s41439-024-00293-w","url":null,"abstract":"<p><p>Genes with multiple copies are likely to be maintained by stabilizing selection, which puts a bound to unlimited expansion of copy number. We designed a model in which copy number variation is generated by unequal recombination, which fits well with several genes surveyed in three human populations. Based on this theoretical model and computer simulations, we were interested in determining whether the gene copy number distribution in the derived European and Asian populations can be explained by a purely demographic scenario or whether shifts in the distribution are signatures of adaptation. Although the copy number distribution in most of the analyzed gene clusters can be explained by a bottleneck, such as in the out-of-Africa expansion of Homo sapiens 60-10 kyrs ago, we identified several candidate genes, such as AMY1A and PGA3, whose copy numbers are likely to differ among African, Asian, and European populations.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"37"},"PeriodicalIF":1.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11420239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308714","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}
{"title":"Novel MLH1 nonsense variant in a patient with suspected Lynch syndrome","authors":"Nobue Takaiso, Issei Imoto, Toshihiko Matsumoto, Akiyo Yoshimura","doi":"10.1038/s41439-024-00294-9","DOIUrl":"https://doi.org/10.1038/s41439-024-00294-9","url":null,"abstract":"<p>Loss-of-function germline variants of <i>MLH1</i> cause Lynch syndrome. Here, we present the case of a 43-year-old male patient diagnosed with cecal and transverse colon adenocarcinomas. The characteristics of the case met the revised Bethesda guidelines, and the tumors demonstrated a high frequency of microsatellite instability. Genetic testing for mismatch repair genes (indicative of Lynch syndrome) revealed a novel heterozygous germline pathogenic variant, NM_000249.4:c.856A>T/NP_000240.1:p.(Lys286Ter), in <i>MLH1</i>.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"27 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142255409","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}
Diana Mokhtari, Mohammad Jahanpanah, Nasim Jabbari, Hamed Azari, Sana Davarnia, Haleh Mokaber, Sara Arish, Rasol Molatefi, Vahid Abbasi, Behzad Davarnia
{"title":"Genetic investigation of patients with autosomal recessive ataxia and identification of two novel variants in the SQSTM1 and SYNE1 genes.","authors":"Diana Mokhtari, Mohammad Jahanpanah, Nasim Jabbari, Hamed Azari, Sana Davarnia, Haleh Mokaber, Sara Arish, Rasol Molatefi, Vahid Abbasi, Behzad Davarnia","doi":"10.1038/s41439-024-00292-x","DOIUrl":"10.1038/s41439-024-00292-x","url":null,"abstract":"<p><p>Hereditary ataxias are classified by inheritance patterns into autosomal dominant, autosomal recessive, X-linked, and mitochondrial modes of inheritance. A large group of adult hereditary ataxias have autosomal dominant inheritance, and autosomal recessive cerebellar ataxias (ARCAs) are rare, with greater diversity in phenotypic and genotypic features. Therefore, comprehensive genetic testing is useful for identifying the genes responsible for ARCAs. We identified two novel pathogenic variants of the SQSTM1 and SYNE1 genes via whole-exome sequencing in patients with ARCAs.</p>","PeriodicalId":36861,"journal":{"name":"Human Genome Variation","volume":"11 1","pages":"35"},"PeriodicalIF":1.0,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142113018","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}