36,989 results match your criteria variants compared


Cancer Predisposition Sequencing Reporter (CPSR): a flexible variant report engine for high-throughput germline screening in cancer.

Int J Cancer 2021 Jul 26. Epub 2021 Jul 26.

Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Norway.

The value of high-throughput germline genetic testing is increasingly recognized in clinical cancer care. Disease-associated germline variants in cancer patients are important for risk management and surveillance, surgical decisions, and can also have major implications for treatment strategies since many are in DNA repair genes. With the increasing availability of high-throughput DNA sequencing in cancer clinics and research, there is thus a need to provide clinically oriented sequencing reports for germline variants and their potential therapeutic relevance on a per-patient basis. Read More

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Impact of SARS-CoV-2 variant-associated RBD mutations on the susceptibility to serum antibodies elicited by COVID-19 infection or vaccination.

Clin Infect Dis 2021 Jul 26. Epub 2021 Jul 26.

State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.

Background: Several SARS-CoV-2 lineages with mutations at the spike protein receptor binding domain (RBD) have reduced susceptibility to antibody neutralization, and have been classified as Variants of Concern (VOCs) or Variants of Interest (VOIs). Here, we systematically compared the neutralization susceptibility and RBD binding of different VOCs/VOIs, including B.1. Read More

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Cost-minimization analysis of sequential genetic testing versus targeted next-generation sequencing gene panels in patients with pheochromocytoma and paraganglioma.

Ann Med 2021 Dec;53(1):1243-1255

Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.

Introduction: Pheochromocytomas and paragangliomas (PPGLs) are highly heritable tumours, with up to 40% of cases carrying germline variants. Current guidelines recommend genetic testing for all patients with PPGLs. Next-generation sequencing (NGS) enables accurate, fast, and inexpensive genetic testing. Read More

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December 2021

Genetics Contributes to Concomitant Pathology and Clinical Presentation in Dementia with Lewy Bodies.

J Alzheimers Dis 2021 Jul 23. Epub 2021 Jul 23.

Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.

Background: Dementia with Lewy bodies (DLB) is a complex, progressive neurodegenerative disease with considerable phenotypic, pathological, and genetic heterogeneity.

Objective: We tested if genetic variants in part explain the heterogeneity in DLB.

Methods: We tested the effects of variants previously associated with DLB (near APOE, GBA, and SNCA) and polygenic risk scores for Alzheimer's disease (AD-PRS) and Parkinson's disease (PD-PRS). Read More

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Interrelation between the rs2200733 polymorphism of the ATFB5 gene and atrial fibrillation in Uzbek patients.

Turk Kardiyol Dern Ars 2021 Jul;49(5):404-409

Department of Cardiology, Republican Specialized Scientific and Practical Medical Center of Cardiology, Tashkent, Uzbekistan.

Objective: Atrial fibrillation (AF) is one of the most common cardiac arrhythmias and a major predictor of morbidity and mortality. AF is a polygenic and polyetiological disease. In various ethnic groups, the strongest and most independent relationship with the development of AF was found with the 4q25 locus, where the ATFB5 gene is located. Read More

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Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases.

JACS Au 2021 May 23;1(5):646-659. Epub 2021 Apr 23.

Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States.

Catalysis by protein tyrosine phosphatases (PTPs) relies on the motion of a flexible protein loop (the WPD-loop) that carries a residue acting as a general acid/base catalyst during the PTP-catalyzed reaction. The orthogonal substitutions of a noncatalytic residue in the WPD-loops of YopH and PTP1B result in shifted pH-rate profiles from an altered kinetic p of the nucleophilic cysteine. Compared to wild type, the G352T YopH variant has a broadened pH-rate profile, similar activity at optimal pH, but significantly higher activity at low pH. Read More

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Understanding COVID-19 dynamics and the effects of interventions in the Philippines: A mathematical modelling study.

Lancet Reg Health West Pac 2021 Sep 14;14:100211. Epub 2021 Jul 14.

School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia.

Background: COVID-19 initially caused less severe outbreaks in many low- and middle-income countries (LMIC) compared with many high-income countries, possibly because of differing demographics, socioeconomics, surveillance, and policy responses. Here, we investigate the role of multiple factors on COVID-19 dynamics in the Philippines, a LMIC that has had a relatively severe COVID-19 outbreak.

Methods: We applied an age-structured compartmental model that incorporated time-varying mobility, testing, and personal protective behaviors (through a "Minimum Health Standards" policy, MHS) to represent the first wave of the Philippines COVID-19 epidemic nationally and for three highly affected regions (Calabarzon, Central Visayas, and the National Capital Region). Read More

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September 2021

Regulatory Status of Pesticide Residues in Cannabis: Implications to Medical Use in Neurological Diseases.

Curr Res Toxicol 2021 1;2:140-148. Epub 2021 Mar 1.

School of Mathematical and Natural Sciences, Arizona State University - West Campus, Glendale, AZ 85306.

Medical cannabis represents a potential route of pesticide exposure to susceptible populations. We compared the qualifying conditions for medical use and pesticide testing requirements of cannabis in 33 states and Washington, D.C. Read More

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Frequency of Pathogenic Germline Variants in Cancer-Susceptibility Genes in the Childhood Cancer Survivor Study.

JNCI Cancer Spectr 2021 Apr 23;5(2):pkab007. Epub 2021 Jan 23.

Basic Research Subdirection, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.

Background: Pediatric cancers are the leading cause of death by disease in children despite improved survival rates overall. The contribution of germline genetic susceptibility to pediatric cancer survivors has not been extensively characterized. We assessed the frequency of pathogenic or likely pathogenic (P/LP) variants in 5451 long-term pediatric cancer survivors from the Childhood Cancer Survivor Study. Read More

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Risk of COVID-19 variant importation - How useful are travel control measures?

Infect Dis Model 2021 11;6:875-897. Epub 2021 Jul 11.

Department of Mathematics & Data Science Nexus, University of Manitoba, Winnipeg, Manitoba, Canada.

We consider models for the importation of a new variant COVID-19 strain in a location already seeing propagation of a resident variant. By distinguishing contaminations generated by imported cases from those originating in the community, we are able to evaluate the contribution of importations to the dynamics of the disease in a community. We find that after an initial seeding, the role of importations becomes marginal compared to that of community-based propagation. Read More

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Simultaneous detection of SARS-CoV-2 and pandemic (H1N1) 2009 virus with real-time isothermal platform.

Heliyon 2021 Jul 15;7(7):e07584. Epub 2021 Jul 15.

Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China.

The recent ongoing outbreak of novel coronavirus SARS-CoV-2 (known as COVID-19) is a severe threat to human health worldwide. By press time, more than 3.3 million people have died from COVID-19, with many countries experiencing peaks in infections and hospitalizations. Read More

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Association Analysis of Candidate Variants in Admixed Brazilian Patients With Genetic Generalized Epilepsies.

Front Genet 2021 8;12:672304. Epub 2021 Jul 8.

Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil.

Genetic generalized epilepsies (GGEs) include well-established epilepsy syndromes with generalized onset seizures: childhood absence epilepsy, juvenile myoclonic epilepsy (JME), juvenile absence epilepsy (JAE), myoclonic absence epilepsy, epilepsy with eyelid myoclonia (Jeavons syndrome), generalized tonic-clonic seizures, and generalized tonic-clonic seizures alone. Genome-wide association studies (GWASs) and exome sequencing have identified 48 single-nucleotide polymorphisms (SNPs) associated with GGE. However, these studies were mainly based on non-admixed, European, and Asian populations. Read More

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Watch Out for a Second SNP: Focus on Multi-Nucleotide Variants in Coding Regions and Rescued Stop-Gained.

Front Genet 2021 7;12:659287. Epub 2021 Jul 7.

INRAE, INSTITUT AGRO, PEGASE UMR 1348, Saint-Gilles, France.

Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the fraction usually studied is harbored in protein-coding regions because potential impacts on proteins are relatively easy to predict by popular tools such as the Variant Effect Predictor. These tools annotate variants independently without considering the potential effect of grouped or haplotypic variations, often called "multi-nucleotide variants" (MNVs). Here, we used a large RNA-seq dataset to survey MNVs, comprising 382 chicken samples originating from 11 populations analyzed in the companion paper in which 9. Read More

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ROS/RNS Balancing, Aerobic Fermentation Regulation and Cell Cycle Control - a Complex Early Trait ('CoV-MAC-TED') for Combating SARS-CoV-2-Induced Cell Reprogramming.

Front Immunol 2021 7;12:673692. Epub 2021 Jul 7.

Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil.

In a perspective entitled 'From plant survival under severe stress to anti-viral human defense' we raised and justified the hypothesis that transcript level profiles of justified target genes established from somatic embryogenesis (SE) induction in plants as a reference compared to virus-induced profiles can identify differential virus signatures that link to harmful reprogramming. A standard profile of selected genes named 'ReprogVirus' was proposed for -scanning of early virus-induced reprogramming in critical primary infected cells/tissues as target trait. For data collection, the 'ReprogVirus platform' was initiated. Read More

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Endothelial Nitric Oxide Production and Antioxidant Response in Breath-Hold Diving: Genetic Predisposition or Environment Related?

Front Physiol 2021 9;12:692204. Epub 2021 Jul 9.

DAN Europe Research Division, DAN Europe Foundation, Roseto degli Abruzzi, Italy.

Introduction: Nitric oxide (NO) is an essential signaling molecule modulating the endothelial adaptation during breath-hold diving (BH-diving). This study aimed to investigate changes in NO derivatives (NOx) and total antioxidant capacity (TAC), searching for correlations with different environmental and hyperbaric exposure.

Materials And Methods: Blood samples were obtained from 50 breath-hold divers (BH-divers) before, and 30 and 60 min after the end of training sessions performed both in a swimming pool or the sea. Read More

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A Lightweight Multi-Scale Convolutional Neural Network for P300 Decoding: Analysis of Training Strategies and Uncovering of Network Decision.

Front Hum Neurosci 2021 8;15:655840. Epub 2021 Jul 8.

Department of Electrical, Electronic and Information Engineering "Guglielmo Marconi" (DEI), University of Bologna, Cesena, Italy.

Convolutional neural networks (CNNs), which automatically learn features from raw data to approximate functions, are being increasingly applied to the end-to-end analysis of electroencephalographic (EEG) signals, especially for decoding brain states in brain-computer interfaces (BCIs). Nevertheless, CNNs introduce a large number of trainable parameters, may require long training times, and lack in interpretability of learned features. The aim of this study is to propose a CNN design for P300 decoding with emphasis on its lightweight design while guaranteeing high performance, on the effects of different training strategies, and on the use of techniques to explain network decisions. Read More

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Genetic basis and hematologic manifestations of sitosterolemia in a group of Turkish patients.

J Clin Lipidol 2021 Jul 10. Epub 2021 Jul 10.

Department of Food Engineering, Ankara University, Faculty of Engineering, Ankara, Turkey.

Background: Sitosterolemia is a rare lipid disorder caused by mutations in adenosine triphosphate-binding cassette genes (ABCG) 5 and 8.

Objective: To evaluate the phenotypic/genotypic features of sitosterolemia in a group of Turkish patients.

Methods: Seven probands with unexplained hematologic abnormalities and their 13 relatives were enrolled. Read More

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A Comparison of Ten Polygenic Score Methods for Psychiatric Disorders Applied Across Multiple Cohorts.

Biol Psychiatry 2021 May 4. Epub 2021 May 4.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia; Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia. Electronic address:

Background: Polygenic scores (PGSs), which assess the genetic risk of individuals for a disease, are calculated as a weighted count of risk alleles identified in genome-wide association studies. PGS methods differ in which DNA variants are included and the weights assigned to them; some require an independent tuning sample to help inform these choices. PGSs are evaluated in independent target cohorts with known disease status. Read More

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An overview of the preclinical discovery and development of bamlanivimab for the treatment of novel coronavirus infection (COVID-19): reasons for limited clinical use and lessons for the future.

Expert Opin Drug Discov 2021 Jul 26. Epub 2021 Jul 26.

University Hospital of Pisa, North Western Tuscany Blood Bank, Pisa, Italy.

: In the COVID-19 pandemic emergency, research has been oriented towards the development of therapies that could cure critically ill patients and treatments that can reduce the number of hospitalized patients, in order to ease the pressure on healthcare systems. Bamlanivimab, developed from human convalescent plasma, was the first monoclonal antibody to become available for emergency use in several countries. Expectations related to its use in COVID-19 patients as a single agent have been largely disregarded, especially against E484K-carrying SARS-CoV-2 variants. Read More

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[Explore the value of whole exome sequencing in early diagnosis for children with language delay/disorder].

Zhonghua Yu Fang Yi Xue Za Zhi 2021 Jul;55(7):827-834

Department of Child Health Care, Children's Hospital, Capital Institute of Pediatrics, Beijing 100020, China.

To evaluate the utility of whole-exome sequencing (WES) in early diagnosis for children with language delay/disorder. Children with language delay/disorder who were admitted to the Department of Health Care, Children's Hospital Affiliated to the Capital Pediatric Institute from January 2019 to December 2020 were analyzed retrospectively. Based on informed consent, the peripheral blood of the children and their parents was collected for WES. Read More

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Inclusion of ALKBH5 as a candidate gene for the susceptibility of autoimmune thyroid disease.

Adv Med Sci 2021 Jul 22;66(2):351-358. Epub 2021 Jul 22.

Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China. Electronic address:

Purpose: RNA demethylase AlkB homolog 5 (ALKBH5) gene is pivotal in N6-methyladenosine (m6A) modification. Therefore, this study aimed to explore the potential relationship between polymorphisms of ALKBH5 gene and the development of autoimmune thyroid disease (AITD).

Material And Methods: A case-control study of 979 AITD patients, including 620 Graves' disease (GD) and 359 Hashimoto's thyroiditis (HT), and 732 normal controls of the Chinese Han population was performed using high-throughput sequencing (HiSeq) genotyping method for detecting 5 variants in ALKBH5 gene (rs12936694, rs2124370, rs4925144, rs8068517, and rs9913266). Read More

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Trajectory of Growth of SARS-CoV-2 Variants in Houston, Texas, January through May 2021 Based on 12,476 Genome Sequences.

Am J Pathol 2021 Jul 22. Epub 2021 Jul 22.

Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas, 77030; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York, 10065. Electronic address:

Certain genetic variants of SARS-CoV-2 are of substantial concern because they may be more transmissible or detrimentally alter the pandemic course and disease features in individual patients. We report SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist healthcare system diagnosed from January 1 through May 31, 2021. Prevalence of the B. Read More

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Differential mutation profile of SARS-CoV-2 proteins across deceased and asymptomatic patients.

Chem Biol Interact 2021 Jul 22:109598. Epub 2021 Jul 22.

Clinical and Applied Genomics (CAG) Laboratory, Department of Biological Sciences, Aliah University, Kolkata, India. Electronic address:

Background: The SARS-CoV-2 infection has spread at an alarming rate with many places showing multiple peaks in incidence. Present study analyzes a total of 332 SARS-CoV-2 genome sequences from 114 asymptomatic and 218 deceased patients from twenty-one different countries to assess the mutation profile therein in order to establish the correlation between the clinical status and the observed mutations.

Methods: The mining of mutations was carried out using the GISAID CoVSurver (www. Read More

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The coding microsatellite mutation profile of PMS2-deficient colorectal cancer.

Exp Mol Pathol 2021 Jul 21:104668. Epub 2021 Jul 21.

Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg, Heidelberg, Germany.

Lynch syndrome (LS) is caused by a pathogenic heterozygous germline variant in one of the DNA mismatch repair (MMR) genes: MLH1, MSH2, MSH6 or PMS2. LS-associated colorectal carcinomas (CRCs) are characterized by MMR deficiency and by accumulation of multiple insertions/deletions at coding microsatellites (cMS). MMR deficiency-induced variants at defined cMS loci have a driver function and promote tumorigenesis. Read More

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Interdomain Flexibility and Interfacial Integrity of β-Lactamase Inhibitory Protein (BLIP) Modulate Its Binding to Class A β-Lactamases.

J Biol Chem 2021 Jul 21:100980. Epub 2021 Jul 21.

State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China; State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen 518057, China. Electronic address:

β-Lactamase inhibitory protein (BLIP) consists of a tandem repeat of αβ domains conjugated by an interdomain loop and can effectively bind and inactivate class A β-lactamases, which are responsible for resistance of bacteria to β-lactam antibiotics. The varied ability of BLIP to bind different β-lactamases and the structural determinants for the significant enhancement of BLIP variants with a single point mutation are poorly understood. Here, we investigated the conformational dynamics of BLIP upon binding to three clinically prevalent class A β-lactamases (TEM1, SHV1, and PC1) with dissociation constants between subnanomolar and micromolar. Read More

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Safety and efficacy of itepekimab in patients with moderate-to-severe COPD: a genetic association study and randomised, double-blind, phase 2a trial.

Lancet Respir Med 2021 Jul 21. Epub 2021 Jul 21.

Sanofi, Chilly-Mazarin, France.

Background: Genetic data implicate IL-33 in asthma susceptibility. Itepekimab, a monoclonal antibody targeting IL-33, demonstrated clinical activity in asthma, with potential in chronic obstructive pulmonary disease (COPD). In this study we first aimed to test the hypothesis that genetic variants in the IL-33 pathway were also associated with COPD. Read More

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Physiological Response of Maize Plants ( L.) to the Use of the Potassium Quercetin Derivative.

Int J Mol Sci 2021 Jul 9;22(14). Epub 2021 Jul 9.

Department of Food Chemistry and Toxicology, University of Rzeszow, Ćwiklińskiej 1A, 35-601 Rzeszów, Poland.

Plant production technologies based solely on the improvement of plants themselves face obstacles resulting from the natural limitations of the biological potential of varieties. Therefore, new substances are sought that positively influence the growth and development of plants and increase resistance to various biotic and abiotic stresses, which also translates into an increase in obtained yields. The exogenous application of various phytoprotectants shows great promise in terms of cost effectiveness compared to traditional breeding methods or transgenic approaches in relation to increasing plant tolerance to abiotic stresses. Read More

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Development of Multidrug Resistance in Acute Myeloid Leukemia Is Associated with Alterations of the LPHN1/GAL-9/TIM-3 Signaling Pathway.

Cancers (Basel) 2021 Jul 20;13(14). Epub 2021 Jul 20.

Faculty of Chemical and Food Technology, Institute of Biochemistry and Microbiology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia.

P-glycoprotein (known as ABCB1 transporter) expression in myeloid blasts of acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS) leads to the commonly observed multidrug resistance. Overexpression of latrophilin-1 was detected in leukemic cells from AML patients. In a previous study, we showed that ABCB1 overexpression is associated with decreased latrophilin-1 expression in MOLM-13/VCR and SKM-1/VCR AML cell variants derived from MOLM-13 and SKM-1 cells by vincristine selection/adaptation. Read More

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NPM1 Mutational Status Underlines Different Biological Features in Pediatric AML.

Cancers (Basel) 2021 Jul 10;13(14). Epub 2021 Jul 10.

Department of Women's and Children's Health, Haematology-Oncology Clinic and Lab, University of Padova, 35128 Padova, Italy.

Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling protein, predominantly located in the nucleolus, that regulates a multiplicity of different biological processes. NPM1 localization in the cell is finely tuned by specific signal motifs, with two tryptophan residues (Trp) being essential for the nucleolar localization. In acute myeloid leukemia (AML), several NPM1 mutations have been reported, all resulting in cytoplasmic delocalization, but the putative biological and clinical significance of different variants are still debated. Read More

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Next-generation sequencing to confirm clinical familial hypercholesterolemia.

Eur J Prev Cardiol 2021 Jul;28(8):875-883

Department of Clinical Genetics, University of Amsterdam, The Netherlands.

Background: Familial hypercholesterolemia is characterised by high low-density lipoprotein-cholesterol levels and is caused by a pathogenic variant in LDLR, APOB or PCSK9. We investigated which proportion of suspected familial hypercholesterolemia patients was genetically confirmed, and whether this has changed over the past 20 years in The Netherlands.

Methods: Targeted next-generation sequencing of 27 genes involved in lipid metabolism was performed in patients with low-density lipoprotein-cholesterol levels greater than 5 mmol/L who were referred to our centre between May 2016 and July 2018. Read More

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