5,726 results match your criteria amplification loci

Estimating population genetics and forensic efficiency of the GlobalFiler PCR amplification kit in the population of Sardinia (Italy).

Gene 2021 Jun 11:145775. Epub 2021 Jun 11.

Dept. of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato Ca, Italy.

GlobalFiler is a new PCR amplification kit that includes 21 autosomal short tandem repeats and three sex-determining loci. In the present research, for the first time, the GlobalFiler kit was tested to analyze a sample of 500 unrelated individuals from 18 villages encompassing the entire area of Sardinia (Italy). We tested if the kit, which is a powerful tool in forensic studies, may also find application in the field of population genetics. Read More

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Post-Transformation IGHV-IGHD-IGHJ Mutations in Chronic Lymphocytic Leukemia B Cells: Implications for Mutational Mechanisms and Impact on Clinical Course.

Front Oncol 2021 25;11:640731. Epub 2021 May 25.

The Feinstein Institutes for Medical Research, Institute for Molecular Medicine, Northwell Health, Manhasset, NY, United States.

Analyses of IGHV gene mutations in chronic lymphocytic leukemia (CLL) have had a major impact on the prognostication and treatment of this disease. A hallmark of IGHV-mutation status is that it very rarely changes clonally over time. Nevertheless, targeted and deep DNA sequencing of IGHV-IGHD-IGHJ regions has revealed intraclonal heterogeneity. Read More

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Development, characterization, functional annotation and validation of genomic and genic-SSR markers using de novo next generation sequencing in Cav.

3 Biotech 2021 Jul 4;11(7):310. Epub 2021 Jun 4.

Genetics and Tree Improvement Division, Institute of Wood Science and Technology, 18th Cross Malleswaram, Bengaluru, India.

Cav. (Meliaceae), a fast-growing tropical tree finds use in plywood, pulp and high-value solid wood products. To increase its productivity, we must essentially capture genetic diversity and identify genotypes with superior wood properties. Read More

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Large-scale comparative analysis of cytogenetic markers across Lepidoptera.

Sci Rep 2021 Jun 9;11(1):12214. Epub 2021 Jun 9.

Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.

Fluorescence in situ hybridization (FISH) allows identification of particular chromosomes and their rearrangements. Using FISH with signal enhancement via antibody amplification and enzymatically catalysed reporter deposition, we evaluated applicability of universal cytogenetic markers, namely 18S and 5S rDNA genes, U1 and U2 snRNA genes, and histone H3 genes, in the study of the karyotype evolution in moths and butterflies. Major rDNA underwent rather erratic evolution, which does not always reflect chromosomal changes. Read More

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DNA degradation in human teeth exposed to thermal stress.

Sci Rep 2021 Jun 9;11(1):12118. Epub 2021 Jun 9.

Department of Forensic Dentistry and Medicine, Instituto de Investigación Biomédica de Málaga-IBIMA (CE-18), School of Medicine, University of Malaga, 29071, Malaga, Spain.

Human identification from burned remains poses a challenge to forensic laboratories, and DNA profiling is widely used for this purpose. Our aim was to evaluate the effect of temperature on DNA degradation in human teeth. Thirty teeth were exposed to temperatures of 100, 200, or 400 °C for 60 min. Read More

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Forensic characterization and genomic diversity of Assam population viewed from 23 autosomal STRs.

Int J Legal Med 2021 Jun 8. Epub 2021 Jun 8.

DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001, India.

In order to find out the genetic structure and characterize the forensic features of 23 autosomal STRs in the population of Assam, PowerPlex® Fusion 6C amplification kit was employed to genotype 292 unrelated individuals from Assam, India. A total of 79 different alleles were observed across 23 autosomal STRs with the corresponding frequency of alleles, which ranges from 0.002 to 0. Read More

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Association of Gene Polymorphism rs10865035 with Rheumatoid Arthritis: A Population-Based Case-Control Study on a Pakistani Cohort.

Genet Res (Camb) 2021 15;2021:5544198. Epub 2021 May 15.

Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan.

Rheumatoid arthritis (RA) is one of the complex diseases with the involvement of the genetic as well as environmental factors in its onset and severity. Different genome-wide association and candidate gene studies have shown the role of several genetic variants in multiple loci/genes with ethnical and geographical variations. This study was designed to detect the association of a single-nucleotide polymorphism (SNP) rs10865035 in the gene with the genetic background of rheumatoid arthritis (RA) in the Pakistani cohort. Read More

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DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms ().

Front Microbiol 2021 17;12:624347. Epub 2021 May 17.

Key Laboratory of Shandong Province for Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China.

Oyster mushrooms (genus ) are widespread and comprise the most commonly cultivated edible mushrooms in the world. Species identification of oyster mushroom spawn based on cultural, morphological, and cultivated characteristics is time consuming and can be extraordinarily difficult, which has impeded mushroom breeding and caused economic loss for mushroom growers. To explore a precise and concise approach for species identification, the nuclear ribosomal internal transcribed spacer (ITS), 28S rDNA, and the widely used protein-coding marker translation elongation factor 1α (EF-1α) gene were evaluated as candidate DNA barcode markers to investigate their feasibility in identifying 13 oyster mushroom species. Read More

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Modulatory effect of single nucleotide polymorphism in Xmn1, BCL11A and HBS1L-MYB loci on foetal haemoglobin levels in β-thalassemia major and Intermedia patients.

J Pak Med Assoc 2021 May;71(5):1394-1398

Institute of Bio Health Sciences, University of Health Sciences, Lahore, Pakistan.

Objective: To evaluate the influence of certain genetic modifiers on foetal haemoglobin levels in thalassemia major and thalassemia intermedia.

Methods: The cohort study was conducted from November 2018 to August 2019, at Department of Haematology, University of Health Sciences, Lahore and comprised beta thalassemia intermedia and thalassemia major patients who were referred by various healthcare facilities across Punjab, Pakistan. Foetal haemoglobin was quantified by high performance liquid chromatography. Read More

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First report of the prevalence and genetic characterization of Giardia duodenalis and Cryptosporidium spp. in Yunling cattle in Yunnan Province, southwestern China.

Microb Pathog 2021 Jun 6;158:105025. Epub 2021 Jun 6.

Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan Province, 650201, PR China. Electronic address:

Yunling cattle is an unique cattle breed distributed in Yunnan Province, southwestern China. It is yet to know whether Yunling cattle are infected with Giardia duodenalis and Cryptosporidium spp.. Read More

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Genetic variants associated with expression of contribute to the risk of head and neck cancer in Chinese population.

J Med Genet 2021 Mar 5. Epub 2021 Mar 5.

Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China

Background: Squamous cell carcinoma of the head and neck (SCCHN) is one of the most common cancers worldwide and includes cancers arising from the oral cavity, pharynx and larynx. Genome-wide association studies have found several genetic variants related to the risk of SCCHN; however, they could only explain a small fraction of the heritability. Thus, more susceptibility loci associated with SCCHN need to be identified. Read More

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Amplifications of Stemness Gene Loci-New Markers for the Determination of the Need for Neoadjuvant Chemotherapy for Patients with Breast Cancer. A Prospective Study.

J Pers Med 2021 May 11;11(5). Epub 2021 May 11.

Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634050 Tomsk, Russia.

In this prospective study, a new strategy for the prescription of neoadjuvant chemotherapy (NAC) was prospectively tested and depended on the presence of stemness gene amplifications in the tumor before treatment, which in our early studies showed a connection with metastasis. The study included 92 patients with grade IIA-IIIB luminal B breast cancer. Patients underwent a biopsy before treatment, and with the use of a CytoScan HD Array microarray (Affymetrix, Santa Clara, CA, USA), the presence of stemness gene amplifications (3q, 5p, 6p, 7q, 8q, 13q, 9p, 9q, 10p, 10q21. Read More

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Targeted amplification and MinION nanopore sequencing of key azole and echinocandin resistance determinants of clinically relevant Candida spp. from blood culture bottles.

Lett Appl Microbiol 2021 Jun 1. Epub 2021 Jun 1.

Department of Laboratory Medicine, National University Hospital, Singapore.

The objective of the study was to evaluate the use of targeted multiplex Nanopore MinION amplicon re-sequencing of key Candida spp. from blood culture bottles to identify azole and echinocandin resistance associated SNPs. Targeted PCR amplification of azole (ERG11 and ERG3) and echinocandin (FKS) resistance-associated loci was performed on positive blood culture media. Read More

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Molecular characterization of ctDNA from Chinese patients with advanced gastric adenocarcinoma reveals actionable alterations for targeted and immune therapy.

J Mol Med (Berl) 2021 May 31. Epub 2021 May 31.

Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China.

Circulating tumor DNA (ctDNA) is considered an ideal sample type for genotyping patients with advanced unresectable cancer to inform treatment decision. It may better capture tumor heterogeneity, especially in gastric adenocarcinoma (GAC). However, there exists little evidence regarding genomic profiling of Chinese advanced GAC patients from ctDNA. Read More

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Applicability of human-specific STR systems, GlobalFiler™ PCR Amplification Kit, Investigator 24plex QS Kit, and PowerPlex® Fusion 6C in chimpanzee (Pan troglodytes).

BMC Res Notes 2021 May 29;14(1):212. Epub 2021 May 29.

State Forensic Science Laboratory, Directorate of Forensic Services, Junga, Shimla, 171218, Himachal Pradesh, India.

Objectives: Human identification systems based on STRs are widely used in human population genetics and forensic analysis. This study aimed to validate the cross-reactivity of three widely known human-specific STR identification systems i.e. Read More

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Organ-, sex- and age-dependent patterns of endogenous L1 mRNA expression at a single locus resolution.

Nucleic Acids Res 2021 06;49(10):5813-5831

Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.

Expression of L1 mRNA, the first step in the L1 copy-and-paste amplification cycle, is a prerequisite for L1-associated genomic instability. We used a reported stringent bioinformatics method to parse L1 mRNA transcripts and measure the level of L1 mRNA expressed in mouse and rat organs at a locus-specific resolution. This analysis determined that mRNA expression of L1 loci in rodents exhibits striking organ specificity with less than 0. Read More

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Identification and characterization of microsatellite markers for population genetic studies of Panstrongylus megistus (Burmeister, 1835) (Triatominae: Reduviidae).

Parasit Vectors 2021 May 22;14(1):273. Epub 2021 May 22.

Laboratory of Triatomíneos, Institute René Rachou/FIOCRUZ-MG, Belo Horizonte, Brazil.

Background: Panstrongylus megistus is the most important vector of Chagas disease in Brazil. Studies show that the principal factor hindering the control of triatomines is reinfestation of houses previously treated with insecticides. Studies at the microgeographic level are therefore necessary to better understand these events. Read More

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A Schistosoma mansoni tri- and tetramer microsatellite catalog for genetic population diversity and differentiation.

Int J Parasitol 2021 May 19. Epub 2021 May 19.

Department of Tropical Medicine, Tulane School of Public Health and Tropical Medicine, Tidewater Building, 1440 Canal Street, New Orleans, LA 70112, USA. Electronic address:

All Schistosoma mansoni tri- and tetranucleotide repeat microsatellites published as of December 2018 were identified. All 52 were evaluated for autosomal location, strength of amplification, scorability and behavior as single-copy loci by polyacrylamide and capillary gel electrophoresis. Of these, 27 were unique, autosomal, polymorphic, easily scored and single copy as assessed on pooled adult worm DNA from two different continental origins and adult worm clones. Read More

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Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD.

BMC Infect Dis 2021 May 21;21(1):464. Epub 2021 May 21.

Department of Parasitology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China.

Background: Leishmaniasis is one of the most neglected tropical diseases in the world and remains endemic in some underdeveloped regions, including western China. The phylogeny and classification of Chinese Leishmania has not been completely clarified to date, especially within the Leishmania (L.) donovani complex, although phylogenetic analyses based on a series of gene markers have been performed. Read More

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Druggable epigenetic suppression of interferon-induced chemokine expression linked to amplification in neuroblastoma.

J Immunother Cancer 2021 May;9(5)

Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, Bonn, Germany

Background: Amplification of the oncogene is a molecular hallmark of aggressive neuroblastoma (NB), a childhood cancer of the sympathetic nervous system. There is evidence that promotes a non-inflamed and T-cell infiltration-poor ('cold') tumor microenvironment (TME) by suppressing interferon signaling. This may explain, at least in part, why patients with NB seem to have little benefit from single-agent immune checkpoint blockade (ICB) therapy. Read More

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Evaluation of probability distribution models for stutter ratios in the typing system of GlobalFiler and 3500xL Genetic Analyzer.

Leg Med (Tokyo) 2021 May 13;52:101906. Epub 2021 May 13.

Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.

As DNA typing systems have become increasingly sensitive in recent years, probability distribution models for back, forward, double-back, and minus 2-nt stutter ratios have been desired to be considered in DNA evidence interpretation using specific software programs. However, experimental investigations have been insufficient, especially for forward, double-back, and minus 2-nt stutters. In this study, we experimentally reevaluated the probability distribution models for each stutter ratio in the typing systems of GlobalFiler™ PCR Amplification Kit and 3500xL Genetic Analyzer from Thermo Fisher Scientific. Read More

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Amplification of the human epidermal growth factor receptor 2 () gene is associated with a microsatellite stable status in Chinese gastric cancer patients.

J Gastrointest Oncol 2021 Apr;12(2):377-387

Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China.

Background: Gastric cancer (GC) is one of the most common cancers worldwide. However, little is known about the combination of HER2 amplification and microsatellite instability (MSI) status in GC. This study aimed to analyze the correlation of amplification with microsatellite instability (MSI) status, clinical characteristics, and the tumor mutational burden (TMB) of patients. Read More

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Chromosome 20q11.21 Amplifications in Colorectal Cancer.

Cancer Genomics Proteomics 2021 May-Jun;18(3 Suppl):487-496

Algoma District Cancer Program, Sault Area Hospital, Sault Ste. Marie, ON, Canada;

Background: Colorectal cancer is the most common gastrointestinal carcinoma in western countries. Prognosis of metastatic colorectal cancer has improved in the last decades, but the disease continues to carry an adverse outcome in most cases. An improved understanding of molecular pathogenesis has provided incremental benefits in survival outcomes with the introduction of targeted therapies for specific sub-types and gives hope for further improvements. Read More

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Developmental validation of the Microreader™ Y Prime Plus ID System: An advanced Y-STR 38-plex system for forensic applications.

Sci Justice 2021 May 30;61(3):260-270. Epub 2021 Jan 30.

Forensic Science Service of the Beijing Public Security Bureau, 100192 Beijing, China. Electronic address:

Y-STR is widely used in sexual assaults and familial searches of suspects. Here, we reported a novel 38-plex STR genotyping system designed for forensic applications. Microreader™ Y Prime Plus ID System (YPP) amplifies 38 loci in one reaction, including 29 loci from commonly used Yfiler® Plus PCR Amplification Kit & PowerPlex® Y23 System (DYS393, DYS570, DYS19, DYS392, DYS549, Y GATA H4, DYS460, DYS458, DYS481, DYS635, DYS448, DYS533, DYS449, DYS456, DYS389I, DYS390, DYS389Ⅱ, DYS438, DYS391, DYS439, DYS437, DYS385a/b, DYS643, DYS518, DYS576, DYF387S1a/b, and DYS627), 6 commonly used loci for the Y-STR database (DYS444, DYS447, DYS596, DYF404a/b, DYS527a/b, DYS557) and one Y-indel specific for the Chinese population. Read More

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Genetic polymorphism of 23 autosomal STR loci in Han population from Yuncheng, Shanxi Province.

Zhong Nan Da Xue Xue Bao Yi Xue Ban 2021 Apr;46(4):351-360

Key Laboratory of Cell Engineering in Guizhou Province; Affiliated Hospital of Zunyi Medical University, Zunyi Guizhou 563099.

Objectives: Due to the genetic feature of high diversity than other DNA markers, short tandem repeat (STR) plays key roles in forensic, anthropology, and population genetics. Newly introduced multiple STR kit is more valuable because of the greatly improved discriminatory power with the increase in the number of STR loci. The genetic polymorphic data are essential for the application and research in specific population. Read More

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DNA barcoding of some medicinally important plant species of Lamiaceae family in India.

Mol Biol Rep 2021 Apr 28;48(4):3097-3106. Epub 2021 Apr 28.

Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur, 482004, India.

Several species of the Lamiaceae family are the primary source of bioactive aromatic oils and secondary metabolites, having broader applications in the cosmetics, pharmaceuticals, food, confectionery and liquor industries. Due to the scarcity of raw materials and high costs of this family's economically vital species, its products often adulterated to cater to the market's high demand. The present study provides a DNA based approach for identifying different species of this family. Read More

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Evaluation of the and Polymorphisms with Autosomal Recessive Nonsyndromic Hearing Loss in Iranian Population.

Iran J Otorhinolaryngol 2021 Mar;33(115):79-86

Department of Genetics, Zanjan Branch, Islamic Azad University, Zanjan, Iran .

Introduction: Hearing loss (HL), with more than 100 gene loci, is the most common sensorineural defects in humans. The mutations in two and (Gap Junction Protein Beta 2, 6) genes are responsible for nearly 50% of autosomal recessive nonsyndromic hearing loss. The aim of the present study was to evaluate polymorphisms of 111C>T (rs7329857) and 337G>T (rs7333214) in (encoding connexin 26) and (encoding connexin 32) genes, respectively. Read More

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Obtaining deeper insights into microbiome diversity using a simple method to block host and nontargets in amplicon sequencing.

Mol Ecol Resour 2021 Apr 27. Epub 2021 Apr 27.

Plant Microbiosis Laboratory, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany.

Profiling diverse microbiomes is revolutionizing our understanding of biological mechanisms and ecologically relevant problems, including metaorganism (host + microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci has therefore become an instrumental tool for many researchers. Investigations in many systems are hindered, however, since essential sequencing depth can be lost by amplification of nontarget DNA from hosts or overabundant microorganisms. Read More

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Tenacibaculum maritimum CRISPR loci analysis and evaluation of isolate spoligotyping.

J Appl Microbiol 2021 Apr 27. Epub 2021 Apr 27.

Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey.

Aims: We performed in silico analysis of CRISPRcas loci from Tenacibaculum maritimum, evaluated spoligotyping as a subtyping method and genotyped uncharacterized Turkish isolates from European sea bass by multilocus sequence typing (MLST).

Methods And Results: Spoligotyping was performed with primers designed to allow amplification and sequencing of whole CRISPR-arrays from 23 T. maritimum isolates. Read More

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A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants.

Methods Mol Biol 2021 ;2250:1-14

Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Plant genomes harbor a particularly rich landscape of repetitive sequences. Transposable elements (TEs) represent a major fraction of this diversity and are intimately linked with plasticity and evolution of genomes across the tree of life (Fedoroff, Science 338:758-767, 2012). Amplification of Long Terminal Repeats (LTR) retrotransposons have shaped the genomic landscape by reshuffling genomic regions, altering gene expression, and providing new regulatory sequences, some of which have been instrumental for crop domestication and breeding (Lisch, Nat Rev Genet 14:49-61, 2013; Vitte et al. Read More

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January 2021