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JOURNAL ARTICLE
Xiaoxi Liu, Satoshi Koyama, Kohei Tomizuka, Sadaaki Takata, Yuki Ishikawa, Shuji Ito, Shunichi Kosugi, Kunihiko Suzuki, Keiko Hikino, Masaru Koido, Yoshinao Koike, Momoko Horikoshi, Takashi Gakuhari, Shiro Ikegawa, Kochi Matsuda, Yukihide Momozawa, Kaoru Ito, Yoichiro Kamatani, Chikashi Terao
We generated Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL), a high-depth whole-genome sequencing dataset comprising 3256 individuals from across Japan. Analysis of JEWEL revealed genetic characteristics of the Japanese population that were not discernible using microarray data. First, rare variant-based analysis revealed an unprecedented fine-scale genetic structure. Together with population genetics analysis, the present-day Japanese can be decomposed into three ancestral components...
April 19, 2024: Science Advances
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JOURNAL ARTICLE
Chaker Aloui, Lisa Neumann, Françoise Bergametti, Eric Sartori, Marc Herbreteau, Arnaud Maillard, Thibault Coste, Hélène Morel, Dominique Hervé, Hugues Chabriat, Serge Timsit, Irina Viakhireva, Yves Denoyer, Rémi Allibert, Florence Demurger, Cedric Gollion, Patrick Vermersch, Florence Marchelli, Corinne Blugeon, Sophie Lemoine, Claire Tourtier-Bellosta, Alexis Brouazin, Anne-Louise Leutenegger, Eva Pipiras, Elisabeth Tournier-Lasserve
IMPORTANCE: Cerebral small vessel diseases (CSVDs) account for one-fifth of stroke cases. Numerous familial cases remain unresolved after routine screening of known CSVD genes. OBJECTIVE: To identify novel genes and mechanisms associated with familial CSVD. DESIGN, SETTING, AND PARTICIPANTS: This 2-stage study involved linkage analysis and a case-control study; linkage analysis and whole exome and genome sequencing were used to identify candidate gene variants in 2 large families with CSVD (9 patients with CSVD)...
April 1, 2024: JAMA Network Open
#3
JOURNAL ARTICLE
Nehal F Hassib, Mennat Mehrez, Mostafa I Mostafa, Mohamed S Abdel-Hamid
OBJECTIVE: Dentinogenesis imperfecta (DI) is an inherited dentin defect and may be isolated or associated with disorders such as osteogenesis imperfecta, odontochondrodysplasia Ehler-Danlos and others. Isolated DI is caused mainly by pathogenic variants in DSPP gene and around 50 different variants have been described in this gene. Herein, we report on 19 patients from two unrelated Egyptian families with isolated DI. Additionally, we focused on genetic counselling of the two families...
April 17, 2024: Clinical Oral Investigations
#4
REVIEW
Jianmei Zhang, Suhong Yang, Yan Zhang, Fei Liu, Lili Hao, Lianshu Han
BACKGROUND: This study aimed to characterize the clinical phenotype and genetic variations in patients with Kallmann syndrome (KS). METHODS: This study involved the collection and analysis of clinical data from an individual with sporadic KS. Following this, peripheral blood samples were obtained from the patient and his parents. Genomic deoxyribonucleic acid was extracted and subjected to whole-exome sequencing and genomic copy number variation (CNV) detection...
2024: Frontiers in Endocrinology
#5
Takuya Hiraide, Taiju Hayashi, Yusuke Ito, Rei Urushibata, Hiroshi Uchida, Ryoichi Kitagata, Hidetoshi Ishigaki, Tsutomu Ogata, Hirotomo Saitsu, Tokiko Fukuda
BACKGROUND: Galloway-Mowat syndrome (GAMOS) is a rare genetic disease characterized by early-onset nephrotic syndrome and microcephaly with central nervous system abnormalities. Pathogenic variants in genes encoding kinase, endopeptidase, and other proteins of small size (KEOPS) complex subunits cause GAMOS. The subunit TPRKB (TP53RK binding protein) has been reported in only two patients with GAMOS with homozygous missense variants. CLINICAL REPORT: Herein, we described a three-year-old male with GAMOS...
2024: Frontiers in Pediatrics
#6
Chennakeshava Thunga, Suvradeep Mitra, Devi Dayal, Sadhna Lal
Fatty acid oxidation defects are a heterogeneous group of disorders related to the mitochondrial fatty acid oxidation pathway. Carnitine acylcarnitine translocase (CACT) is an enzyme responsible for the unidirectional transport of acylcarnitine across the inner mitochondrial membrane. This enzyme plays a crucial role in the oxidation of fatty acids. The autopsy pathology of the CACT deficiency is described in only a few cases. We describe the autopsy pathology of a child with CACT deficiency dominantly in the form of microvesicular steatosis of the hepatocytes, renal proximal tubular epithelia, cardiac myocytes, and rhabdomyocytes...
2024: Autopsy & Case Reports
#7
JOURNAL ARTICLE
Minh Ho, Huynh-Nga Nguyen, Minh Van Hoang, Tien Thuy Thi Bui, Bao-Quoc Vu, Truc Huong Thi Dinh, Hoa Thi My Vo, Diana C Blaydon, Sherif A Eldirany, Christopher G Bunick, Chi-Bao Bui
BACKGROUND: Congenital ichthyosis (CI) is a collective group of rare hereditary skin disorders. Patients present with epidermal scaling, fissuring, chronic inflammation, and increased susceptibility to infections. Recently, there is increased interest in the skin microbiome; therefore, we hypothesized that CI patients likely exhibit an abnormal profile of epidermal microbes because of their various underlying skin barrier defects. Among recruited individuals of Southeast Asian ethnicity, we performed skin meta-genomics (i...
April 16, 2024: Human Genomics
#8
JOURNAL ARTICLE
Hui Zhang, Jian Gao, Hanjun Wang, Mengli Liu, Shuangshuang Lu, Hongen Xu, Wenxue Tang, Guoxi Zheng
OBJECTIVE: Branchio-oto-renal syndrome (BOR, OMIM#113,650) is a rare autosomal dominant disorder that presents with a variety of symptoms, including hearing loss (sensorineural, conductive, or mixed), structural abnormalities affecting the outer, middle, and inner ear, branchial fistulas or cysts, as well as renal abnormalities.This study aims to identify the pathogenic variants by performing genetic testing on a family with Branchio-oto-renal /Branchio-otic (BO, OMIM#602,588) syndrome using whole-exome sequencing, and to explore possible pathogenic mechanisms...
April 16, 2024: BMC Medical Genomics
#9
JOURNAL ARTICLE
Numrah Fadra, Laura E Schultz-Rogers, Pritha Chanana, Margot A Cousin, Erica L Macke, Alejandro Ferrer, Filippo Pinto E Vairo, Rory J Olson, Gavin R Oliver, Lindsay A Mulvihill, Garrett Jenkinson, Eric W Klee
BACKGROUND: X-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing one of two copies of the X chromosome in each cell. The preferential inactivation of either the maternal or paternal copy of the X chromosome in a majority of cells results in a skewed or non-random pattern of X inactivation and is observed in over 25% of adult females. Identifying skewed X inactivation is of clinical significance in patients with suspected rare genetic diseases due to the possibility of biased expression of disease-causing genes present on the active X chromosome...
April 16, 2024: BMC Genomics
#10
JOURNAL ARTICLE
Yunlu Zhu, Yun Bai, Wannian Yan, Ming Li, Fei Wu, Mingyuan Xu, Nanhui Wu, HongSong Ge, Yeqiang Liu
Acrokeratoelastoidosis (AKE) is a rare autosomal dominant hereditary skin disease characterized by small, round-oval, flat-topped keratotic papules on the palms, soles and dorsal aspect of hands or feet. The causative gene for AKE remains unidentified. This study aims to identify the causative gene of AKE and explore the underlying biological mechanisms. A large, three-generation Chinese family exhibiting classic AKE symptoms was identified. A genome-wide linkage analysis and whole-exome sequencing were employed to determine the causative gene...
April 16, 2024: European Journal of Human Genetics: EJHG
#11
REVIEW
Jennifer R Brown
Our understanding of risk factors for the development of chronic lymphocytic leukemia (CLL) is still incomplete and includes genetic and environmental factors. CLL is one of the most familial of all cancers, yet common high-penetrance risk alleles have not been identified. Genome-wide association studies have identified many common variants with low relative risks, whereas exome-wide rare variant analysis has implicated ATM in CLL causation. Environmental factors have also been challenging to identify given the limited understanding of the relevant time period of exposure relative to diagnosis, and the inability to quantify past exposures...
April 2024: Journal of the National Comprehensive Cancer Network: JNCCN
#12
JOURNAL ARTICLE
Sungwon Jeon, Hansol Choi, Yeonsu Jeon, Whan-Hyuk Choi, Hyunjoo Choi, Kyungwhan An, Hyojung Ryu, Jihun Bhak, Hyeonjae Lee, Yoonsung Kwon, Sukyeon Ha, Yeo Jin Kim, Asta Blazyte, Changjae Kim, Yeonkyung Kim, Younghui Kang, Yeong Ju Woo, Chanyoung Lee, Jeongwoo Seo, Changhan Yoon, Dan Bolser, Orsolya Biro, Eun-Seok Shin, Byung Chul Kim, Seon-Young Kim, Ji-Hwan Park, Jongbum Jeon, Dooyoung Jung, Semin Lee, Jong Bhak
BACKGROUND: Phenome-wide association studies (PheWASs) have been conducted on Asian populations, including Koreans, but many were based on chip or exome genotyping data. Such studies have limitations regarding whole genome-wide association analysis, making it crucial to have genome-to-phenome association information with the largest possible whole genome and matched phenome data to conduct further population-genome studies and develop health care services based on population genomics...
January 2, 2024: GigaScience
#13
JOURNAL ARTICLE
D Orsucci, A Tessa, E Caldarazzo Ienco, R Trovato, G Natale, G Bilancieri, M Giuntini, A Napolitano, S Salvetti, M Vista, F M Santorelli
OBJECTIVE: Essential Tremor (ET) is one of the most common neurological disorders. In most instances ET is inherited as an autosomal dominant trait with age-related penetrance (virtually complete in advanced age); however, ET genetics remains elusive. The current study aims to identify possibly pathogenic genetic variants in a group of well-characterized ET families. METHODS: 34 individuals from 14 families with dominant ET were clinically evaluated and studied by whole exome sequencing studies (after excluding trinucleotide expansion disorders)...
April 13, 2024: Journal of the Neurological Sciences
#14
JOURNAL ARTICLE
Stefania Bellone, Kyungjo Jeong, Mari Kyllesø Halle, Camilla Krakstad, Blair McNamara, Michelle Greenman, Levent Mutlu, Cem Demirkiran, Tobias Max Philipp Hartwich, Yang Yang-Hartwich, Margherita Zipponi, Natalia Buza, Pei Hui, Francesco Raspagliesi, Salvatore Lopez, Biagio Paolini, Massimo Milione, Emanuele Perrone, Giovanni Scambia, Gary Altwerger, Antonella Ravaggi, Eliana Bignotti, Gloria S Huang, Vaagn Andikyan, Mitchell Clark, Elena Ratner, Masoud Azodi, Peter E Schwartz, Charles M Quick, Roberto Angioli, Corrado Terranova, Samir Zaidi, Shuvro Nandi, Ludmil B Alexandrov, Eric R Siegel, Jungmin Choi, Joseph Schlessinger, Alessandro D Santin
High-grade neuroendocrine cervical cancers (NETc) are exceedingly rare, highly aggressive tumors. We analyzed 64 NETc tumor samples by whole-exome sequencing (WES). Human papillomavirus DNA was detected in 65.6% (42/64) of the tumors. Recurrent mutations were identified in PIK3CA, KMT2D/MLL2, K-RAS, ARID1A, NOTCH2, and RPL10. The top mutated genes included RB1, ARID1A, PTEN, KMT2D / MLL2, and WDFY3, a gene not yet implicated in NETc. Somatic CNV analysis identified two copy number gains (3q27.1 and 19q13.12) and five copy number losses (1p36...
April 23, 2024: Proceedings of the National Academy of Sciences of the United States of America
#15
JOURNAL ARTICLE
Marijana Nesic, Mads H Rasmussen, Tenna V Henriksen, Christina Demuth, Amanda Frydendahl, Iver Nordentoft, Lars Dyrskjøt, Claus L Andersen
Tumor-informed mutation-based approaches are frequently used for detection of circulating tumor DNA (ctDNA). Not all mutations make equally effective ctDNA markers. The objective was to explore if prioritizing mutations using mutational features-such as cancer cell fraction (CCF), multiplicity, and error rate-would improve the success rate of tumor-informed ctDNA analysis. Additionally, we aimed to develop a practical and easily implementable analysis pipeline for identifying and prioritizing candidate mutations from whole-exome sequencing (WES) data...
April 16, 2024: International Journal of Cancer. Journal International du Cancer
#16
JOURNAL ARTICLE
L L Cao, J G Yan, D N Feng, Y Dong, Z Q Xu, F C Wang, Y J Gao, S S Zhu, M Zhang
Objective: To analyze the clinical manifestations, pathology, and gene variant characteristics in children with progressive familial intrahepatic cholestasis type 3 (PFIC3). Methods: This retrospective study assessed the clinical manifestations, pathological features, gene variants, and prognosis data of 11 children with PFIC3 hospitalized in the Department of Hepatology, Fifth Medical Center, PLA General Hospital, from January 2015 to December 2022. Panel or whole exome sequencing was performed on the probands, followed by Sanger sequencing for verification within the family...
April 16, 2024: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
#17
JOURNAL ARTICLE
Shiqi Fan, Huanhuan Wu, Rongrong Wang, Qian Chen, Xue Zhang
BACKGROUND: Congenital disorders of glycosylation (CDG) are a type of inborn error of metabolism (IEM) resulting from defects in glycan synthesis or failed attachment of glycans to proteins or lipids. One rare type of CDG is caused by homozygous or compound heterozygous loss-of-function variants in mannosidase alpha class 2B member 2 (MAN2B2). To date, only two cases of MAN2B2-CDG have been reported worldwide. METHODS: Trio whole-exome sequencing (Trio-WES) was conducted to screen for candidate variants...
April 2024: Molecular Genetics & Genomic Medicine
#18
JOURNAL ARTICLE
Tugce Bozkurt-Yozgatli, Davut Pehlivan, Richard A Gibbs, Ugur Sezerman, Jennifer E Posey, James R Lupski, Zeynep Coban-Akdemir
BACKGROUND: Multilocus pathogenic variants (MPVs) are genetic changes that affect multiple gene loci or regions of the genome, collectively leading to multiple molecular diagnoses. MPVs may also contribute to intrafamilial phenotypic variability between affected individuals within a nuclear family. In this study, we aim to gain further insights into the influence of MPVs on a disease manifestation in individual research subjects and explore the complexities of the human genome within a familial context...
April 16, 2024: BMC Medical Genomics
#19
JOURNAL ARTICLE
Dilek Cavusoglu, Gulten Ozturk, Dilsad Turkdogan, Semra Hiz Kurul, Uluc Yis, Mustafa Komur, Faruk Incecik, Bulent Kara, Turkan Sahin, Olcay Unver, Cengiz Dilber, Gulen Gul Mert, Cagatay Gunay, Gamze Sarikaya Uzan, Ozlem Ersoy, Yavuz Oktay, Serdar Mermer, Gokcen Oz Tuncer, Olcay Gungor, Gul Demet Kaya Ozcora, Ugur Gumus, Ozlem Sezer, Gokhan Ozan Cetin, Fatma Demir, Arzu Yilmaz, Gurkan Gurbuz, Meral Topcu, Haluk Topaloglu, Ahmet Cevdet Ceylan, Serdar Ceylaner, Joseph G Gleeson, Dilara Fusun Icagasioglu, F Mujgan Sonmez
Pontocerebellar hypoplasia (PCH) is a heterogeneous group of neurodegenerative disorders characterized by hypoplasia and degeneration of the cerebellum and pons. We aimed to identify the clinical, laboratory, and imaging findings of the patients with diagnosed PCH with confirmed genetic analysis. We collected available clinical data, laboratory, and imaging findings in our retrospective multicenter national study of 64 patients with PCH in Turkey. The genetic analysis included the whole-exome sequencing (WES), targeted next-generation sequencing (NGS), or single gene analysis...
April 15, 2024: Cerebellum
#20
JOURNAL ARTICLE
Afsaneh Bazgir, Mehdi Agha Gholizadeh, Seyyed Mohammad Kahani, Ali Reza Tavasoli, Masoud Garshasbi
Developmental and epileptic encephalopathy (DEEs) (OMIM#618,328) is characterized by seizures, hypotonia, and brain abnormalities, often arising from mutations in genes crucial for brain function. Among these genes, GLS stands out due to its vital role in the central nervous system (CNS), with homozygous variants potentially causing DEE type 71. Using Whole Exome Sequencing (WES) on a patient exhibiting symptoms of epileptic encephalopathy, we identified a novel homozygous variant, NM_014905.5:c.1849G > T; p...
April 15, 2024: Neurogenetics
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