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JOURNAL ARTICLE
Meng-Ju Melody Tsai, Miao-Zi Hung, Yi-Lin Lin, Ni-Chung Lee, Yin-Hsiu Chien, Wuh-Liang Hwu
Lysosomal storage diseases (LSDs) are a group of metabolic disorders resulting from a deficiency in one of the lysosomal hydrolases. Most LSDs are inherited in an autosomal or X-linked recessive manner. As LSDs are rare, their true incidence in Taiwan remains unknown. In this study, we used high-coverage whole-genome sequencing data from 1,495 Taiwanese individuals obtained from the Taiwan Biobank. We found 3826 variants in 71 genes responsible for autosomal recessive LSDs. We first excluded benign variants by allele frequency and other criteria...
September 23, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Radwa Sharaf, Dexter X Jin, John Grady, Christine Napier, Ericka Ebot, Garrett M Frampton, Lee A Albacker, David M Thomas, Meagan Montesion
Tumor cells need to activate a telomere maintenance mechanism, enabling limitless replication. The bulk of evidence supports that sarcomas predominantly use alternative lengthening of telomeres (ALT) mechanism, commonly associated with alterations in ATRX and DAXX. In our dataset, only 12.3% of sarcomas harbored alterations in these genes. Thus, we checked for the presence of other genomic determinants of high telomeric content in sarcomas. Our dataset consisted of 13555 sarcoma samples, sequenced as a part of routine clinical care on the FoundationOne®Heme platform...
September 14, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Emma Strong, Carolyn B Mervis, Elaine Tam, Colleen A Morris, Bonita P Klein-Tasman, Shelley L Velleman, Lucy R Osborne
Williams-Beuren syndrome (WBS) and 7q11.23 duplication syndrome (Dup7) are rare neurodevelopmental disorders caused by deletion and duplication of a 1.5 Mb region that includes at least five genes with a known role in epigenetic regulation. We have shown that CNV of this chromosome segment causes dose-dependent, genome-wide changes in DNA methylation, but the specific genes driving these changes are unknown. We measured genome-wide whole blood DNA methylation in six participants with atypical CNV of 7q11...
September 14, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Roman Tremmel, Yitian Zhou, Matthias Schwab, Volker M Lauschke
Genetic variants in drug targets and genes encoding factors involved in drug absorption, distribution, metabolism and excretion (ADME) can have pronounced impacts on drug pharmacokinetics, response, and toxicity. While the landscape of genetic variability at the level of single nucleotide variants (SNVs) has been extensively studied in these pharmacogenetic loci, their structural variation is only poorly understood. Thus, we systematically analyzed the genetic structural variability across 908 pharmacogenes (344 ADME genes and 564 drug targets) based on publicly available whole genome sequencing data from 10,847 unrelated individuals...
September 8, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Erin R Bonner, Adam Dawood, Heather Gordish-Dressman, Augustine Eze, Surajit Bhattacharya, Sridevi Yadavilli, Sabine Mueller, Sebastian M Waszak, Javad Nazarian
Recent genomic data points to a growing role for somatic mutations altering core histone and linker histone-encoding genes in cancer. However, the prevalence and the clinical and biological implications of histone gene mutations in malignant tumors remain incompletely defined. To address these knowledge gaps, we analyzed somatic mutations in 88 linker and core histone genes across 12,743 tumors from pediatric, adolescent and young adult (AYA), and adult cancer patients. We established a pan-cancer histone mutation atlas contextualized by patient age, survival outcome, and tumor location...
August 28, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Ohad Wormser, Yonatan Perez, Vadim Dolgin, Bahman Kamali, Jared A Tangeman, Libe Gradstein, Yuval Yogev, Noam Hadar, Ofek Freund, Max Drabkin, Daniel Halperin, Inbar Irron, Erika Grajales-Esquivel, Katia Del Rio-Tsonis, Ramon Y Birnbaum, Gidon Akler, Ohad S Birk
Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive phenotypic continuum of microphthalmia, anophthalmia and ocular coloboma, with no apparent coding-region disease-causing mutation. Homozygosity mapping of several affected Jewish Iranian families, combined with whole genome sequence analysis, identified a 0.5 Mb disease-associated chromosome 2q35 locus (maximal LOD score 6.8) harboring an intronic founder variant in NHEJ1, not predicted to affect NHEJ1...
August 14, 2023: NPJ Genomic Medicine
#47
REVIEW
Macarena Las Heras, Benjamín Szenfeld, Rami A Ballout, Emanuele Buratti, Silvana Zanlungo, Andrea Dardis, Andrés D Klein
Niemann-Pick type C (NPC) disease is a lysosomal storage disease (LSD) characterized by the buildup of endo-lysosomal cholesterol and glycosphingolipids due to loss of function mutations in the NPC1 and NPC2 genes. NPC patients can present with a broad phenotypic spectrum, with differences at the age of onset, rate of progression, severity, organs involved, effects on the central nervous system, and even response to pharmacological treatments. This article reviews the phenotypic variation of NPC and discusses its possible causes, such as the remaining function of the defective protein, modifier genes, sex, environmental cues, and splicing factors, among others...
August 11, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Pankhuri Gupta, Kenji Nakamichi, Alyssa C Bonnell, Ryan Yanagihara, Nick Radulovich, Fuki M Hisama, Jennifer R Chao, Debarshi Mustafi
Phasing genetic variants is essential in determining those that are potentially disease-causing. In autosomal recessive inherited retinal diseases (IRDs), reclassification of variants of uncertain significance (VUS) can provide a genetic diagnosis in indeterminate compound heterozygote cases. We report four cases in which familial co-segregation demonstrated a VUS resided in trans to a known pathogenic variant, which in concert with other supporting criteria, led to the reclassification of the VUS to likely pathogenic, thereby providing a genetic diagnosis in each case...
August 10, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Hirotaka Miyashita, Razelle Kurzrock, Nicholas J Bevins, Kartheeswaran Thangathurai, Suzanna Lee, Sarabjot Pabla, Mary Nesline, Sean T Glenn, Jeffrey M Conroy, Paul DePietro, Eitan Rubin, Jason K Sicklick, Shumei Kato
Immune checkpoint blockade is effective for only a subset of cancers. Targeting T-cell priming markers (TPMs) may enhance activity, but proper application of these agents in the clinic is challenging due to immune complexity and heterogeneity. We interrogated transcriptomics of 15 TPMs (CD137, CD27, CD28, CD80, CD86, CD40, CD40LG, GITR, ICOS, ICOSLG, OX40, OX40LG, GZMB, IFNG, and TBX21) in a pan-cancer cohort (N = 514 patients, 30 types of cancer). TPM expression was analyzed for correlation with histological type, microsatellite instability high (MSI-H), tumor mutational burden (TMB), and programmed death-ligand 1 (PD-L1) expression...
August 8, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Zoe Fehlberg, Stephanie Best, Janet C Long, Tahlia Theodorou, Catherine Pope, Peter Hibbert, Sharon Williams, Lucinda Freeman, Sarah Righetti, Alison D Archibald, Jeffrey Braithwaite
An understanding of factors influencing implementation is essential to realise the benefits of population-based reproductive genetic carrier screening programs. The aim of this study was to synthesise data collected during the Australian Reproductive Genetic Carrier Screening Project (Mackenzie's Mission) to track how priorities shifted over time and identify important factors during scaling-up and for sustainment. We used a multi-method qualitative approach to integrate longitudinal project data collected from 10 project committees with 16 semi-structured interviews conducted with study team members...
July 31, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Yingjie Zhao, Yujue Wang, Lijie Shi, Donna M McDonald-McGinn, T Blaine Crowley, Daniel E McGinn, Oanh T Tran, Daniella Miller, Jhih-Rong Lin, Elaine Zackai, H Richard Johnston, Eva W C Chow, Jacob A S Vorstman, Claudia Vingerhoets, Therese van Amelsvoort, Doron Gothelf, Ann Swillen, Jeroen Breckpot, Joris R Vermeesch, Stephan Eliez, Maude Schneider, Marianne B M van den Bree, Michael J Owen, Wendy R Kates, Gabriela M Repetto, Vandana Shashi, Kelly Schoch, Carrie E Bearden, M Cristina Digilio, Marta Unolt, Carolina Putotto, Bruno Marino, Maria Pontillo, Marco Armando, Stefano Vicari, Kathleen Angkustsiri, Linda Campbell, Tiffany Busa, Damian Heine-Suñer, Kieran C Murphy, Declan Murphy, Sixto García-Miñaúr, Luis Fernández, Zhengdong D Zhang, Elizabeth Goldmuntz, Raquel E Gur, Beverly S Emanuel, Deyou Zheng, Christian R Marshall, Anne S Bassett, Tao Wang, Bernice E Morrow
Congenital heart disease (CHD) affecting the conotruncal region of the heart, occurs in 40-50% of patients with 22q11.2 deletion syndrome (22q11.2DS). This syndrome is a rare disorder with relative genetic homogeneity that can facilitate identification of genetic modifiers. Haploinsufficiency of TBX1, encoding a T-box transcription factor, is one of the main genes responsible for the etiology of the syndrome. We suggest that genetic modifiers of conotruncal defects in patients with 22q11.2DS may be in the TBX1 gene network...
July 18, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Yvonne Hort, Patricia Sullivan, Laura Wedd, Lindsay Fowles, Igor Stevanovski, Ira Deveson, Cas Simons, Andrew Mallett, Chirag Patel, Timothy Furlong, Mark J Cowley, John Shine, Amali Mallawaarachchi
Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic cause of kidney failure and is primarily associated with PKD1 or PKD2. Approximately 10% of patients remain undiagnosed after standard genetic testing. We aimed to utilise short and long-read genome sequencing and RNA studies to investigate undiagnosed families. Patients with typical ADPKD phenotype and undiagnosed after genetic diagnostics were recruited. Probands underwent short-read genome sequencing, PKD1 and PKD2 coding and non-coding analyses and then genome-wide analysis...
July 7, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Kevin S Guo, Alexander S Brodsky
The extracellular matrix (ECM) is a critical determinant of tumor fate that reflects the output from myriad cell types in the tumor. Collagens constitute the principal components of the tumor ECM. The changing collagen composition in tumors along with their impact on patient outcomes and possible biomarkers remains largely unknown. The RNA expression of the 43 collagen genes from solid tumors in The Cancer Genome Atlas (TCGA) was clustered to classify tumors. PanCancer analysis revealed how collagens by themselves can identify the tissue of origin...
July 6, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Takae Brewer, Lamis Yehia, Peter Bazeley, Charis Eng
Women with germline PTEN variants (PTEN hamartoma tumor syndrome, PHTS) have up to 85% lifetime risk of female breast cancer (BC). We previously showed that PHTS-derived BCs are distinct from sporadic BCs both at the clinical and genomic levels. In this study, we examined somatic copy number variations (CNV) and transcriptome data to further characterize the somatic landscape of PHTS-derived BCs. We analyzed exome sequencing data from 44 BCs from women with PHTS for CNV. The control group comprised of 558 women with sporadic BCs from The Cancer Genome Atlas (TCGA) dataset...
July 5, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Amy Nisselle, Emily King, Bronwyn Terrill, Belinda Davey, Belinda McClaren, Kate Dunlop, Debra Graves, Sylvia Metcalfe, Clara Gaff
Genomic medicine is being implemented on a global scale, requiring a genomic-competent health workforce. To inform education as part of implementation strategies to optimize adoption of genomics by non-genetics physicians, we investigated current practices, perceptions and preferences relating to genomic testing and education. Australian non-genetics physicians completed an online survey; we conducted univariate and multivariate analyses of determinants of confidence and engagement with genomic medicine. Confident or engaged respondents were more likely to be pediatricians, have completed continuing genomics education (CGE) and/or have genomics research experience...
June 24, 2023: NPJ Genomic Medicine
#56
Alessio Marcozzi, Myrthe Jager, Martin Elferink, Roy Straver, Joost H van Ginkel, Boris Peltenburg, Li-Ting Chen, Ivo Renkens, Joyce van Kuik, Chris Terhaard, Remco de Bree, Lot A Devriese, Stefan M Willems, Wigard P Kloosterman, Jeroen de Ridder
No abstract text is available yet for this article.
June 7, 2023: NPJ Genomic Medicine
#57
JOURNAL ARTICLE
Characteristics of Hepatitis B virus integration and mechanism of inducing chromosome translocation.
Xiaofang Cui, Yiyan Li, Hanshi Xu, Yuhui Sun, Shulong Jiang, Weiyang Li
Hepatitis B virus (HBV) integration is closely associated with the onset and progression of tumors. This study utilized the DNA of 27 liver cancer samples for high-throughput Viral Integration Detection (HIVID), with the overarching goal of detecting HBV integration. KEGG pathway analysis of breakpoints was performed using the ClusterProfiler software. The breakpoints were annotated using the latest ANNOVAR software. We identified 775 integration sites and detected two new hotspot genes for virus integration, N4BP1 and WASHP, along with 331 new genes...
June 2, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Anne Slavotinek, Shannon Rego, Nuriye Sahin-Hodoglugil, Mark Kvale, Billie Lianoglou, Tiffany Yip, Hannah Hoban, Simon Outram, Beatrice Anguiano, Flavia Chen, Jeremy Michelson, Roberta M Cilio, Cynthia Curry, Renata C Gallagher, Marisa Gardner, Rachel Kuperman, Bryce Mendelsohn, Elliott Sherr, Joseph Shieh, Jonathan Strober, Allison Tam, Jessica Tenney, William Weiss, Amy Whittle, Garrett Chin, Amanda Faubel, Hannah Prasad, Yusuph Mavura, Jessica Van Ziffle, W Patrick Devine, Ugur Hodoglugil, Pierre-Marie Martin, Teresa N Sparks, Barbara Koenig, Sara Ackerman, Neil Risch, Pui-Yan Kwok, Mary E Norton
The diagnostic yield of exome sequencing (ES) has primarily been evaluated in individuals of European ancestry, with less focus on underrepresented minority (URM) and underserved (US) patients. We evaluated the diagnostic yield of ES in a cohort of predominantly US and URM pediatric and prenatal patients suspected to have a genetic disorder. Eligible pediatric patients had multiple congenital anomalies and/or neurocognitive disabilities and prenatal patients had one or more structural anomalies, disorders of fetal growth, or fetal effusions...
May 26, 2023: NPJ Genomic Medicine
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Giuliana Giannuzzi, Nicolas Chatron, Katrin Mannik, Chiara Auwerx, Sylvain Pradervand, Gilles Willemin, Kendra Hoekzema, Xander Nuttle, Jacqueline Chrast, Marie C Sadler, Eleonora Porcu, Yann Herault, Bertrand Isidor, Brigitte Gilbert-Dussardier, Evan E Eichler, Zoltan Kutalik, Alexandre Reymond
No abstract text is available yet for this article.
May 24, 2023: NPJ Genomic Medicine
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JOURNAL ARTICLE
Patricio G Schlottmann, José D Luna, Natalia Labat, María Belén Yadarola, Silvina Bainttein, Evangelina Esposito, Agustina Ibañez, Evangelina Ivón Barbaro, Alejandro Álvarez Mendiara, Carolina P Picotti, Andrea Chirino Misisian, Luciana Andreussi, Julieta Gras, Luciana Capalbo, Mauro Visotto, José E Dipierri, Emilio Alcoba, Laura Fernández Gabrielli, Silvia Ávila, María Emilia Aucar, Daniel M Martin, Gerardo Juan Ormaechea, M Eugenia Inga, Aníbal A Francone, Martin Charles, Tamara Zompa, Pablo Javier Pérez, Vanesa Lotersztein, Pedro J Nuova, Ivana B Canonero, Omar A Mahroo, Michel Michaelides, Gavin Arno, Malena Daich Varela
This study corresponds to the first large-scale genetic analysis of inherited eye diseases (IED) in Argentina and describes the comprehensive genetic profile of a large cohort of patients. Medical records of 22 ophthalmology and genetics services throughout 13 Argentinian provinces were analyzed retrospectively. Patients with a clinical diagnosis of an ophthalmic genetic disease and a history of genetic testing were included. Medical, ophthalmological and family history was collected. A total of 773 patients from 637 families were included, with 98% having inherited retinal disease...
May 22, 2023: NPJ Genomic Medicine
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