Journal of Genetics and Genome Research publishes articles on all aspects of inheritance and novel insights into the genome biology of all organisms, including advances in genomic medicine. JGGR focuses on Gene Structure and Organization, Gene Expression, Mutation Detection and Analysis, Linkage Analysis and Genetic Mapping, Physical Mapping, Cytogenetics, Genomic Imaging, Genome Structure and Organization, Disease Association Studies, Comparative Genomics, Molecular Evolution, Genome-Scale Quantitative and Population Genetics, Proteomics, Epigenomics and systems biology.
Journal of Genetics and Genome Research is peer-review open access journal that ensures the publication of high quality articles in the form of original work, reviews, commentaries, shorts communications, letters, oral presentations and case studies. JGGR follows a standard peer-review process with the support of its eminent Editorial board members. Two independent review comments followed by editor's decision will be considered to publish the article. JGGR provides the readers with free and immediate access to its content and is a permanent archive of genetic information under open access category serves the scientific community.
Title: Journal of Genetics and Genome Research
Editor-in-chief: Ming Zhan
NLM title abbreviation: J Genet Genome Res
ISO abbreviation: J Genet Genome Res
Other titles: JGGR
Peer review: Double blind
Review speed: 3 weeks
Fast-track review: 10 days
Publication format (s): Electronic and print
Publication policy: Open Access; COPE guide
Publication type(s): Periodicals
Publisher: ClinMed International Library
Country of publication: USA
Contact email: firstname.lastname@example.org
Articles Search by Keyword | Journal title | Author name | DOI
Open Access DOI:10.23937/2378-3648/1410054
m6A Demethylase FTO Regulates Nasopharyngeal Carcinoma Invasion, Migration
Zhencheng Liao, Fan Ye, Ying Tao, Jun Wang, Guan Huang, Siyi Yang, Zhaoqun Lu, Honglei Zhu and Pingan Wu
Article Type: Original Article | First Published: February 03, 2023
In recent years, the research interest in m6A has remained high, and the reason is that N6- methyladenosine (m6A) is the most common reversible methylation modification of eukaryotic mRNA and plays a significant role in tumorigenesis. However, abnormalities of the RNA m6A regulators (writers, erasers, and readers) have rarely been reported in nasopharyngeal carcinoma. The expression of m6A regulators in nasopharyngeal carcinoma is highly diverse, and this diversity has important implications for...
Open Access DOI:10.23937/2378-3648/1410053
Systematic Review of microRNAs in the SARS-CoV-2 Infection: Are microRNAs Potential Therapy for COVID-19?
Omer SEVGIN and Kubra SEVGIN
Article Type: Review Article | First Published: April 21, 2021
COVID-19 is a highly infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Although the exact diagnosis, clinical and treatment features for SARS-CoV-2 infection have not been determined yet, the accumulation of knowledge is increasing day by day. However, there is still insufficient information about the cellular and molecular regulation of SARS-CoV-2. The development of miRNA targeting anti-viral therapies in the literature has attracted great interest and ...
Open Access DOI:10.23937/2378-3648/1410052
Y Chromosome Sequences in Turner Syndrome: Multiplex PCR, a New Method for Diagnosis
Lene Garcia Barbosa Maria Anunciação Souza, Adriana Aparecida Siviero-Miachon, Magnus Régius Dias-da-Silva and Angela Maria Spinola-Castro
Article Type: Brief Report | First Published: December 02, 2020
Turner’s syndrome is characterized by the partial or complete absence of one of the sex chromosomes in women in association with one or more clinical exposures. Molecular techniques such as polymerase chain reaction (PCR) are useful when it comes to complementing the genetic approach, as they present greater sensitivity in recognizing mosaicism. Considering the high percentage of mosaicism and the possible clinical impact of the presence of Y chromosome in these patients, we proposed in this s...
Open Access DOI:10.23937/2378-3648/1410051
Novel Variant in COL4A5 Gene Associated with X-linked Alport Syndrome
Eranga Sanjeewa Wijewickrama, Dineshani Hettiarachchi, Hwai Liang Loh, Lye Wai Choong and Vajira HW Dissanayake
Article Type: Case Report | First Published: August 22, 2020
Alport syndrome is an inherited disease of collagen IV leading to progressive glomerular sclerosis associated with variable degrees of proteinuria and haematuria, sensorineural deafness and ocular abnormalities. Here we describe a novel mutation involving the COL4A5 gene leading to X-linked Alport syndrome (XLAS) in a Singhalese family of six children born to nonconsanguineous parents of Sri Lankan origin. The eldest 19-year-old male was found to have microscopic haematuria and proteinuria. His ...
Open Access DOI:10.23937/2378-3648/1410050
SARS-CoV-2 Global Spreading Investigation Using Principal Component Analysis of Sequence Variants
Christiane Scherer, James Grover, Darby Kammeraad, Gabe Rudy and Andreas Scherer
Article Type: Research Article | First Published: August 13, 2020
As COVID-19 has spread from its origin in Wuhan, China, into a global pandemic, there has been a number of efforts to understand the mutations and clusters of genetic lineages of the SARS-CoV-2 virus. The high mutation rate and rapid spread makes this analysis capable of tracking chains of infections as well as putting individual sequences in context. So far, phylogenetic analysis methods have recently found a broader application in this regard. Here we demonstrate that Principal Component Analy...
Open Access DOI:10.23937/2378-3648/1410049
Ancestral European Origins and Population Structure of Helicobacter pylori Strains from an Iranian Population
Article Type: Editorial | First Published: May 13, 2020
Helicobacter pylori is a spiral, microaerophilic and motile bacterium originated by its polar flagella that is the etiological reason of chronic gastritis, peptic ulcer, gastric cancer, and extra-gastrointestinal diseases. The human stomach is considered the only host of this bacterium. This bacterium has been residing in the human stomach for many years and has been coevolved simultaneously with its host, especially since the horizontally transmitted condition is not observed in Helicobacter py...
Open Access DOI:10.23937/2378-3648/1410048
Which Aligner Software is the Best for Our Study?
Article Type: Short Report | First Published: May 13, 2020
Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Many algorithms have been developed for this alignment step. Due to the increasing growth in the use of aligning and mapping software, this software has become particularly important. This seemingly worthless issue but it is confusing and difficult to compare results from different approaches. We performed a comprehensive benchmarking of 4 popular and common aligners and...
Open Access DOI:10.23937/2378-3648/1410047
Cytogenetics of Chrysichthys nigrodigitatus as Bioindicator of Environmental Pollution from Two Polluted Lagoons, South- Western Nigeria
Bassey OB, Chukwu LO and Alimba GC
Article Type: Research Article | First Published: November 14, 2019
Pollution of aquatic ecosystems from anthropogenic activities has heightened in recent times and this has elicited national and international concern on the impacts on aquatic biota. This study investigated the genotoxic effects in C. nigrodigitatus from two polluted lagoons. Micronuclei (MN) test, as an index of chromosomal damage, is widely applied in field studies. The peripheral erythrocytes from C. nigrodigitatus were subjected to MN analysis and physicochemical parameters were evaluated fo...
Open Access DOI:10.23937/2378-3648/1410046
Modifiers of Severity in Autism Spectrum Disorder
Sandra P Smiesze, Will Bush, and Jonathan Haines
Article Type: Research Article | First Published: September 14, 2019
Autism Spectrum Disorder (ASD) comprises a complex of neurodevelopmental disorders primarily characterized by deficits in verbal communication, impaired social interaction and repetitive behaviors. The complex genetic architecture of ASD encompasses profound clinical heterogeneity, which poses huge challenges in understanding its pathophysiology. We conducted a large scale association analysis of the MSSNG whole genome sequencing data to elucidate potential modifiers of ASD severity. Using linea...
Open Access DOI:10.23937/2378-3648/1410045
In silico Characterization of Rad51a Interactions with Cancer-Related Proteins
Kleber Santiago Freitas e Silva
Article Type: Research Article | First Published: June 28, 2019
RAD51a is a highly conserved protein and its major role is the repair of DNA double strand breaks. Endogenous species are generated during normal cell metabolic activities and can cause damage to DNA, as well as several environmental factors. The interactions RAD51a perform with other proteins help the maintenance of oncogenetic metabolism within cells. RAD51a interacts with PCNA, FANCD2 and ABL1, among many other cancer-related proteins. PCNA acts as a DNA clamp and is related to the replicatio...
Open Access DOI:10.23937/2378-3648/1410044
SVMOneClAS: Pipeline for Efficient Splicing Events Calling
Sokolov A, Mazur A, Zhigalova N, Prokhortchouk A, Gruzdeva N and Prokhortchouk E
Article Type: Research Article | First Published: June 05, 2019
Splicing is a part of mRNA maturation process when exons of pre-mRNA transcript are joined in multiple ways. In case of alternative splicing, some exons may be excluded from the final mRNA, and the resulting ensemble of mRNAs creates different protein isoforms, allowing multiple proteins to be coded by a single gene. To detect new events of alternative splicing in human blood cells, we used RNA-seq technology. A pipeline based on Python "Scikit-Learn" library was developed for efficient splicing...
Open Access DOI:10.23937/2378-3648/1410043
The Role of Genetic Mutations in Gene RBM8A in Thrombocytopenia-Absent Radius Syndrome
Article Type: Scientific Advocacy | First Published: March 18, 2019
TAR syndrome is a genetic disorder characterized by a lack of radial bone in the forearm and a lack of blood platelets. Thrombocytopenia prevents normal blood clotting and causes bleeding easily and often bleeds from the nose. The TAR syndrome is caused by the mutation of the RBM8A gene, which is based on the long arm of chromosome 1, which is based on 1q21.1. TAR syndrome is a genetic disorder characterized by a lack of radial bone in the forearm and a lack of blood platelets. Thrombocytopenia ...
Open Access DOI:10.23937/2378-3648/1410042
The Association of piR-36707 and piR-36741 with Clear Cell Renal Cell Carcinoma
Sercan ERGUN, Diler US ALTAY, Sezgin GUNEŞ, Recep BUYUKALPELLI and Oguz AYDIN
Article Type: Research Article | First Published: February 16, 2019
The expression levels of piR-36707 and piR-36741 were found higher in tumor samples than control ones. Also, piR-36707 expression showed significantly different pattern in terms of gender. Moreover, piR-36707 and piR-36741 expressions displayed statistically significant difference with respect to some TNM staging comparisons. piR-36707 and piR-36741 expressions were significantly differed between Fuhrman nuclear grade 2 and 4. Furthermore, piR-36741 expression change was significantly associated...
Open Access DOI:10.23937/2378-3648/1410041
Identification of the Single Nucleotide Polymorphisms Affecting Normal Phenotypic Variability in Human Craniofacial Morphology Using Candidate Gene Approach
Mark Barash, Philipp E Bayer and Angela van Daal
Article Type: Research Article | First Published: December 08, 2018
There is a remarkable variety of human facial appearances, almost exclusively the result of genetic differences, as exemplified by the striking resemblance of identical twins. Despite intensive research on the genetics of craniofacial morphology using animal models and human craniofacial syndromes, the genetic variation that underpins normal human facial appearance is still largely elusive....
Open Access DOI:10.23937/2378-3648/1410040
HLA DRB1*/DQA1*Alleles and TNF-alpha G308A Polymorphism Protect against Neuromyelitis Optica in the Cuban Population
Fernandez-de-Cossio ME, Cintado A, Nazabal M, Camacho H, Diaz T, Villarreal A, Ale M, Grass D, Cervantes-Llanos M, Pavon-Fuentes N, Benitez JV, Cabrera-Gomez JA, Diaz de la Fe A and Penton-Rol G
Article Type: Research Article | First Published: November 23, 2018
Neuromyelitis optica (NMO) is a complex immune-mediated disease whose prevalence differs among ethnic groups, most likely due to genetic factors. The presence of the Human Leucocyte Antigens (HLA) extended haplotype is a risk for NMO. The tumor necrosis factor-alpha (TNF-a) is believed to play a role in NMO pathogenesis. Although single nucleotide polymorphisms (SNPs) in the TNF-a promoter region (pTNF-a) has been shown to influence levels of TNF-a production, such an association is not evident ...
Open Access DOI:10.23937/2378-3648/1410039
A Novel Mutation in the MFN2 Gene Associated with Hereditary Sensory and Motor Neuropathy with Proximal Predominance (HMSN-P)- A Case Report
D Hettiaracchchi, K Weththasigha, N Nethikumara, S Pathirana and WHV Dissanayaka
Article Type: Case Report | First Published: October 17, 2018
Mutations in mitofusin 2 gene have been reported in Charcot-Marie-Tooth type 2 disease also known as Hereditary Sensory and Motor Neuropathy. With its cytogenetic location: 1p36.22. A 43-year-old female with a family history of neuropathy was experiencing gradual detrition and proximal weakness of the bilateral lower limb for the past 3 years. Her MRI scan (Brain and whole Spinal) was normal and Electromyography (EMG) report was suggestive of motor & sensory demyelinating polyneuropathy with fea...
Open Access DOI:10.23937/2378-3648/1410038
Molecular Landscape and Clonal Evolution of Acute Mast Cell Leukemia: Case Study
Ricardo Sanchez, Maria Liz Paciello, Rosa M Ayala, Leyre Lorza, Teresa Cedena, M Pilar Martinez and Joaquin Martinez-Lopez
Article Type: Case Report | First Published: September 20, 2018
Systemic mastocytosis is a rare disorder characterized by clonal proliferation, which results in abnormally high numbers of mast cells in the skin, bone marrow, and internal organs, such as liver, spleen, or lymph nodes. Mast cell leukemia and subvariants were stratified by the World Health Organization in 2016, as a subtype of systemic mastocytosis. The World Health Organization classification of tumors that arise in hematopoietic and lymphoid tissues represents the worldwide consensus on hemat...
Open Access DOI:10.23937/2378-3648/1410037
Combination of Vitamin K2 and Phosphatidylcholine Inhibits Hepatocarcinogenesis via Mir-16 Regulating
Ruicheng Yan, Jianfei Luo, Fusheng Lin, Chao Hu, and Shiqiang Shen
Article Type: ORIGINAL RESEARCH | First Published: September 12, 2018
Vitamin K2 and phosphatidylcholine are two common drugs in clinical treatment. Studies carried out in the past several years demonstrated vitamin K2 and phosphatidylcholine could separately inhibit hepatocarcinogenesis. In this study, we sought to investigate the synergy of vitamin K2 and phosphatidylcholine and the potential mechanism. Multiple assays were performed to evaluate the effect of combination administration in vitro and in vivo. Then microRNA microarray, bioinformatics analysis and w...
Open Access DOI:10.23937/2378-3648/1410036
Comprehensive Leaf Transcriptome of a Non-model Plant, Abelmoschus esculentus for the Functional Genomics Studies
Padmanabhan Priyavathi, Srikakulam Nagesh, Velayudha Vimala Kumar Kavitha, Christdas Johnson and Pandi Gopal
Article Type: Research Article | First Published: August 25, 2018
Abelmoschus esculentus is widely cultivated and consumed across the globe for its nutritional and medicinal purpose. In spite of the growing demand, its cultivation is massively affected by various insects, fungi, nematodes and viruses. Due to lack of genomic and limited transcriptomic resources, genetic manipulation studies concerning the crop improvement against various environmental factors is scarce for this crop. Thereby, the present study aims to develop high quality transcriptome of A. es...
Open Access DOI:10.23937/2378-3648/1410035
Identification of Expression QTLs Targeting Candidate Genes for Residual Feed Intake in Dairy Cattle Using Systems Genomics
Salleh MS, Mazzoni G, Nielsen MO, Lovendahl P and Kadarmideen HN
Article Type: Research Article | First Published: July 16, 2018
Residual feed intake (RFI) is the difference between actual and predicted feed intake and an important factor determining feed efficiency (FE). Recently, 170 candidate genes were associated with RFI, but no expression quantitative trait loci (eQTL) mapping has hitherto been performed on FE related genes in dairy cows. In this study, an integrative systems genetics approach was applied to map eQTLs in Holstein and Jersey cows fed two different diets to improve identification of candidate genes fo...
Open Access DOI:10.23937/2378-3648/1410034
Investigation of Aeromonas: A Medical and Biotechnological Perspective
Zeynep Yegin and Cumhur Avsar
Article Type: Research Article | First Published: June 23, 2018
The genus Aeromonas is widely distributed in aquatic environments and certain strains are serious pathogens in poikilothermic animals and humans. Human infections related with this pathogen include gastroenteritis, urinary tract infections, pneumonia, wound infections and septicemia. In this study, both the correct medical diagnosis with taking advantages of molecular approaches and a brief investigation of the enzymatic activity potential of Aeromonas were aimed....
Open Access DOI:10.23937/2378-3648/1410033
A Review of NEMO Protein and its Relationship with Genetic Diseases
Mohammad Reza Zinatizadeh, Zahra Masoumalinejad, Azim Nejatizadeh, Mohammad Shekari, Farzaneh Parnak and Faeghe Zaree
Article Type: Review Article | First Published: May 30, 2018
NF-κB essential modulator (NEMO) syndrome is an immunodeficiency disease. NF-κB proteins, which regulate the expression of genes that moderate important physiological processes, are called regulatory of cell homeostasis. NEMO is a protein in the IKK inhibitor complex that many organ systems normally do not grow. Cells (as well as organ and tissues) do not grow proteins they express proteins....
Open Access DOI:10.23937/2378-3648/1410032
Sequence and Expression Analysis of Procine GLI3 gene
Ying Wang, Zhengwei Zhang, Yifan Dai and Haiyuan Yang
Article Type: Research Article | First Published: October 11, 2017
GLI family zinc finger 3 (GLI3) has been shown to play a critical role in the regulation of Hedgehog signaling, with important implications in embryonic and postnatal development. However, the molecular characteristics of GLI3 gene and its expression profile in pig tissues have yet to be elucidated....
Open Access DOI:10.23937/2378-3648/1410031
Deriving Transition Probabilities and Evolutionary Distances from Substitution Rate Matrix by Probability Reasoning
Article Type: Review Article | First Published: July 27, 2017
Substitution rate matrices are used to correct multiple hits at the same sites, which requires the derivation of transition probabilities and evolutionary distances from substitution rate matrices. The derivation is essential in molecular phylogenetics and phylogenomics....
Open Access DOI:10.23937/2378-3648/1410030
Thermo Stability of DNA Methylation Marks in Human Sperm
Timothy G Jenkins, Monis B Shamsi, Emma James, Kenneth I Aston and Douglas T Carrell
Article Type: Research Article | First Published: June 12, 2017
Shipping of various tissues, including sperm, for the purposes of diagnostic testing and/or collaborative scientific pursuits is commonly performed. While many sample attributes are largely stable during the shipping process regardless of shipping environment, some physical factors such as temperature, duration of storage and other handling conditions may affect certain features of these samples including a commonly assessed epigenetic mark, DNA methylation....
Open Access DOI:10.23937/2378-3648/1410029
Testing the Mutagenicity Potential of Chemicals
Geert R Verheyen, Koen Van Deun and Sabine Van Miert
Article Type: Research Article | First Published: May 15, 2017
All information for the proper development, functioning and reproduction of organisms is coded in the sequence of matched base-pairs of DNA. DNA mutations can result in harmful effects and play a role in genetic disorders and cancer. As mutations can arise through exposure to chemical substances, testing needs to be done on substances that humans and animals can be exposed to....
Open Access DOI:10.23937/2378-3648/1410028
Generation of Epstein-Barr Virus Immortalized-B Lymphocytes Cell Line of Orang Asli
Mohd Helmy Yusof, Sharifah Izwan Tuan Othman, Siti Shuhada Mokhtar, Yushimah Yunus, Abu Thalhah Abdul Aziz and Hoh Boon Peng
Article Type: Original Article | First Published: September 26, 2016
Obtaining sustainable source of cells or DNA from a single individual has always been a constraint in biomedical research. Generation of lymphoblastoid cell lines (LCLs) as a surrogate for replacement of isolated peripheral blood mononuclear cells (PBMCs) has substantially accelerated the process of biological investigations. LCLs can be established by transfection of B lymphocytes from peripheral blood with Epstein Barr Virus (EBV), bearing minor genetic and phenotypic alterations....
Open Access DOI:10.23937/2378-3648/1410027
An Overview on the Phylogeny of Aerobic Metabolism and the Preponderance of Mitochondrial Functions in Evolution
Article Type: Review Article | First Published: September 15, 2016
Aerobic oxidation of carbohydrates by mitochondria has been a great invention of nature, marking a big step in early evolution. This biological system has greatly multiplied the energy production of the cell by supplying this energy to different metabolic units, with increased temporal and spatial specificities. The numerous mitochondrial functions that have emerged and developed along evolution constitute strong signatures of evolution pressures, driving toward higher order, more complex and mo...
Open Access DOI:10.23937/2378-3648/1410026
Sequence Characterization of Bovine Antisense to Insulin-Like Growth Factor Type 2 Receptor Non-Coding RNA (AIRN)
W T Farmer, J R Sommer and C E Farin
Article Type: Review Article | First Published: August 22, 2016
Bovine insulin-like growth factor type 2 receptor (IGF2R) is an imprinted gene whose aberrant expression has been implicated in development of abnormal offspring syndrome. Bovine AIRN (AIRN) is expressed in post-implantation fetal tissues coinciding with imprinted expression of IGF2R. Although expression patterns of bovine AIRN have been reported based on PCR analysis, characteristics of this transcript are unknown....
Open Access DOI:10.23937/2378-3648/1410025
Sedaghatian-Type Spondylometaphyseal Dysplasia: A Case of Rapid Demise with Evidence of Myocardial Injury
Mehmet Sah Ipek and Alper Akin
Article Type: Case Report | First Published: June 02, 2016
Sedaghatian-type spondylometaphyseal dysplasia (SSMD) is a lethal neonatal form of spondylometaphyseal dysplasias that is reported rarely. The case of a female infant demonstrating a clinical phenotype consistent with a diagnosis of SSMD was presented. She died with acute evidence of myocardial injury. In SSMD, certain organ systems including the central nervous, cardiac, and skeletal systems, are clearly involved. Although the exact cause of the uniform fatality remains unclear, cardiac involve...
Open Access DOI:10.23937/2378-3648/1410024
Susceptibility of Patients with Manganese Superoxide Dismutase Ala16val Genetic Polymorphism to Type 2 Diabetes Mellitus and its Complications in a Sample of Lebanese Population
Abir M Zahreddine, Mohamed E Moustafa and Hala A Chamieh
Article Type: Original Article | First Published: May 24, 2016
Oxidative stress has been frequently associated with the development of type 2 diabetes mellitus. Manganese superoxide dismutase (MnSOD) is one of the most important enzymes responsible for the defense against oxidative damage in the mitochondria. A polymorphism in the second exon of the MnSOD at position 16 that changes Ala into Val, induces changes in the structural conformation and mitochondrial transport of MnSOD. This polymorphism affects the scavenger activity of the enzyme and generates h...
Open Access DOI:10.23937/2378-3648/1410023
A Perspective on the Algorithms Predicting and Evaluating the RNA Secondary Structure
Giulia Fiscon, Giulio Iannello and Paola Paci
Article Type: Review Article | First Published: May 20, 2016
Investigating the RNA structure contributes greatly to understand RNA roles in cellular processes. Indeed, functional RNAs show specific instrumental sub-structures for their interaction with other molecules. The RNA structure prediction will provide fundamental insights into developing hypothesis connecting function to structure, but it is a challenging and unsolved task yet. We aim at discussing the current status of the widespread RNA folding tools and comparing their performances on RNA fami...
Open Access DOI:10.23937/2378-3648/1410022
Microevolutionary History of Helicobacter Pylori During Infection: A Review
Mendoza-Elizalde S, Olivares-Cervantes AL, Zuniga G, Valencia-Mayoral P, Vigueras-Galindo JC and Velazquez-Guadarrama N
Article Type: Review Article | First Published: April 13, 2016
Helicobacter pylori is a bacterium that has evolved with humans, is transmitted from person to person and persistently colonizes the stomach. During its long coexistence with humans, H. Pylori has developed complex strategies to limit the degree and extent of inflammation and damage to the gastric mucosa. It is capable of altering the physiology and immune response of the host, thereby allowing it to persist throughout life. Infection with H. pylori has been linked to such diseases as severe gas...
Open Access DOI:10.23937/2378-3648/1410020
Data-driven Biomarker and Drug Discovery using Network-based Approach
Fuhai Li and Ming Zhan
Article Type: Review Article | First Published: November 05, 2015
An increasing body of large-scale genomic profiling data has been being generated on many diseases including cancers and on a number of drugs and compounds. The exploration of such big data has led to data-driven biomedical research. The data-driven studies include exploring disease subtypes with distinct molecular patterns, uncovering novel diagnosis biomarkers or treatments, and discovering new indications of drugs along with novel mechanisms of drug action, among others....
Open Access DOI:10.23937/2378-3648/1410021
A Comparison of SNaPshot Minisequencing and HRM Analysis in mtSNP Genotyping with Reference Samples from East Timor
Luis Souto, Filipa Tavares, Helena Moreira and Fatima Pinheiro
Article Type: Research Article | First Published: December 28, 2015
The analysis of mtDNA in forensic samples is commonly carried out by direct sequencing of the hyper variable regions of the control region, although with limited power of discrimination. Genotyping SNPs in the coding region of mtDNA can provide additional information and increase the discrimination power of mtDNA typing. In this study, we compare two methodologies for the detection of 9 SNPs in the control region of mtDNA: SNaPshot minisequencing and Real Time PCR, through High-Resolution Meltin...
Open Access DOI:10.23937/2378-3648/1410019
Development of a Comprehensive NGS Workflow for the Analysis of Tumor BRCA1 and BRCA2 Mutations and Large Rearrangements
Zhengwei Dong, Hua Dong, Xiaorong Zhong, Zuxiang Peng, Xuehua Zhu, Yun Sun, Yunqin Chen, Changting Liu, Xiaolu Yin, Guanshan Zhu, Hong Zheng and Yi Gu
Article Type: Research Article | First Published: September 28, 2015
Patients with germ line or somatic BRCA1 and BRCA2 mutations are sensitive to PARP inhibitor treatment. However, current clinical testing of BRCA1/2 is limited to germ line mutations in blood samples. In the present study, we have developed and validated a work flow for BRCA1/2 mutation test in patient tumor samples, which can identify both germ line and somatic mutations. Our approach combined targeted capturing with the BRCA MASTR assay and consequent sequencing using Miseq, a benchtop next-ge...
Open Access DOI:10.23937/2378-3648/1410018
Enhanced Detection of Longer Insertions and Deletions in Clinical Exome Sequencing Improves Diagnostic Yield
Deepali N. Shinde, Jefferey Chen, Soren Fischbach, David J. Salvador, Kelly Farwell, Hsiao-Mei Lu and Sha Tang
Article Type: Research Article | First Published: September 17, 2015
Whole exome sequencing (WES) has been remarkably successful as both a diagnostic and novel gene discovery tool since its introduction to the clinical laboratory in 2011. Where traditional diagnostic methods have been uninformative in discovering the pathogenic etiology in patients, diagnostic exome sequencing (DES) has provided answers for roughly one-third of patients tested, thus contributing to the management of patients' overall healthcare. Single nucleotide variants are generally efficientl...
Open Access DOI:10.23937/2378-3648/1410017
Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC)
Heather S.L. Jim, Hui-Yi Lin, Jonathan P. Tyrer, Kate Lawrenson, Joe Dennis, Ganna Chornokur, Zhihua Chen, Ann Y. Chen, Jennifer Permuth-Wey, Katja KH. Aben, Hoda Anton-Culver, Natalia Antonenkova, Fiona Bruinsma, Elisa V. Bandera, Yukie T. Bean, Matthias W. Beckmann, Maria Bisogna, Line Bjorge, Natalia Bogdanova, Louise A. Brinton, Angela Brooks-Wilson, Clareann H. Bunker, Ralf Butzow, Ian G. Campbell, Karen Carty, Jenny Chang-Claude, Linda S. Cook, Daniel W. Cramer, Julie M. Cunningham, Cezary
Article Type: Research Article | First Published: September 15, 2015
Disruption in circadian gene expression, whether due to genetic variation or environmental factors (e.g., light at night, shiftwork), is associated with increased incidence of breast, prostate, gastrointestinal and hematologic cancers and gliomas. Circadian genes are highly expressed in the ovaries where they regulate ovulation; circadian disruption is associated with several ovarian cancer risk factors (e.g., endometriosis). However, no studies have examined variation in germline circadian gene...
Open Access DOI:10.23937/2378-3648/1410016
Understanding the Host Epigenetics in Mycobacterium tuberculosis Infection
Vinod Yadav, Ved Prakash Dwivedi, Debapriya Bhattacharya, Ashwan
Article Type: Research Article | First Published: June 27, 2015
It was in 1942 when C.H. Waddington first coined the term epigenetics. According to him there is no direct relationship between a gene and its phenotype. He considered epigenetics as a part of development biology and in his opinion many times genotype and phenotype variations are not associated and phenotype differences do not necessarily involve change in genotype. Since 40s epigenetics became the topic of interest among the scientific community. Now everybody wants to know that what goes on be...
Open Access DOI:10.23937/2378-3648/1410015
Transplantation of hBMSCs Loaded on Collagen Scaffolds for the Regeneration of Canine Tissue-Engineered Urethras
Jianjian Wu, Weisheng Jia, Wei Chen, Feng Zhou, Zhenqiang Fang, Xianglin Hou, Bing Chen, Gang Ye, and Jianwu Dai
Article Type: Research Article | First Published: June 21, 2015
A 5cm long urethra segment near the penis bone was excised surgically. A collagen scaffold seeded with hBMSCs was sutured to two ends of the host urethra for the urethral repair in the experimental group, whereas the unseeded scaffold was used in the control group. Retrograde urethrography was performed before the operation and at 6 months after the surgery. At 6 months postsurgery, the animals were sacrificed, and the reconstructed urethras were collected for histological observation....
Open Access DOI:10.23937/2378-3648/1410014
Genomic and Genotyping Characterization of Haplotype-Based Polymorphic Microsatellites in Prunus
Chunxian Chen, Clive H. Bock, Tom G. Beckman, Bruce W. Wood and William R. Okie
Article Type: Research Article | First Published: May 30, 2015
Efficient utilization of microsatellites in genetic studies remains impeded largely due to the unknown status of their primer reliability, chromosomal location, and allele polymorphism. Discovery and characterization of microsatellite polymorphisms in a taxon will disclose the unknowns and gain new insights into the polymorphic alleles....
Open Access DOI:10.23937/2378-3648/1410013
Application of Synthetic Standard Curves for Absolute Quantification of Hepatitis A and E by Real-Time PCR
Renata Santos Tourinho, Camilla Rodrigues de Almeida, Andreza Salvio Lemos, Noemi Rovaris Gardinali, Yasmine Rangel Vieira, Jonas Schmidt-Chanasit and Vanessa Salete de Paula
Article Type: Short Communication | First Published: March 23, 2015
Hepatitis A, which presents a major health problem globally, is caused by hepatitis A virus (HAV). This virus, whose primary site of replication is the liver, is the most common agent causing acute liver disease worldwide. Hepatitis E virus (HEV) is the most recently discovered of the hepatotropic viruses, its genome having been identified in 1991. Despite the similarity with hepatitis A virus in their pathogenesis and transmission form, HEV has a zoonotic potential....
Open Access DOI:10.23937/2378-3648/1410012
Analysis of the Methylation Pattern of SOX2 and OCT4 Genes in Astrocytomas
Wallax Augusto Silva Ferreira, Mariana Diniz Araujo, Nilson Praia Anselmo, Maria Lucia Harada and Barbara do Nascimento Borges
Article Type: Research Article | First Published: February 27, 2015
Astrocytoma is a common aggressive intracranial tumor and a formidable challenge in clinic. Association of the altered DNA methylation pattern of the promoter CpG islands has been found in many human tumors. OCT4 and SOX2 are essential transcription factors for embryonic development and play key roles in determining the fate of stem cells....
Open Access DOI:10.23937/2378-3648/1410011
Relationship of Mitochondrial DNA Haplogroups with Complex Diseases
Carlos G Urzua-Traslavina, Maria G Moreno-Trevino, Denisse A Martinez-Trevino, Hugo A Barrera-Saldana and Rafael BR Leon-Cachon
Article Type: Review Article | First Published: December 16, 2014
Mitochondria are responsible for energy production in unicellular and multicellular eukaryotes. Apart from their major role in metabolism, mitochondria are involved in many other cellular processes. A new paradigm is needed to understand aging, aging-related illnesses, and complex diseases. Because of the long co-evolution of mitochondria with the cells, subtle variations in the function of these organelles could influence many organ systems. Understanding the extent of this influence will shed ...
Open Access DOI:10.23937/2378-3648/1410010
Oxidative Stress and the Epigenome in Human Disease
Adriana Arita and Max Costa
Article Type: Review Article | First Published: December 15, 2014
Epigenetics refers to the study of the changes in gene expression that occur without changes in the DNA sequence. There is growing evidence that epigenetic modifications such as changes in the levels of DNA methylation or post-translational histone modifications are involved in the pathogenesis of many human diseases including cancer. Oxidative stress as a result of metabolic or environmental factors leads to excessive production of reactive oxygen species (ROS). ROS plays a role in many human d...
Open Access DOI:10.23937/2378-3648/1410009
Discordant Disease Course in a Monozygotic Twin Pair with Juvenile Myelomonocytic Leukemia
Silvia Bresolin, Paola De Filippi, Claudia Cagioni, Simone Cesaro, Annamaria Di Meglio, Anna Leszl, Fiorenza Aprili, Chiara Cugno, Chiara Frasson, Marco Zecca, Cesare Danesino and Geertruyte Kronnie
Article Type: Research Article | First Published: December 14, 2014
Juvenile myelomonocytic leukemia is a rare neoplastic disorder occurring in early childhood often showing an aggressive progression. We report a case of a twin pair with concordant JMML but an extremely different disease course. Both twins presented with somatic aberrations of chromosome 7 and mutations in PTPN11. Analysis of sorted BM and PB cell populations revealed the clonal nature of the disease and indicated that genomic aberrations arise from common hematopoietic precursor cells. PTPN11 m...
Open Access DOI:10.23937/2378-3648/1410008
Experimental Detection of Mitochondrial DNA Insertions in Nuclear Genome of Chicken Embryos Developed from X-Ray Irradiated Eggs
Serazhutdin A. Abdullaev and Azhub I. Gaziev
Article Type: Research Article | First Published: December 08, 2014
The transfer of mitochondrial DNA (mtDNA) into the nuclear genome is a dynamic process, resulting in the formation of nuclear mitochondrial (numt) pseudogenes or numt-insertions. Experimental determination of de novo numt-insertions is limited by the extensive homology of mtDNA in the nuclear DNA (nDNA) of eukaryotes. Since chicken nDNA contains only 13 numtpseudogenes, we tried to follow experimentally the induction of numt-insertions de novo in the nDNA of chicken (Gallus gallus) embryos devel...
Open Access DOI:10.23937/2378-3648/1410007
Variation H452Y in HTR2A Gene Effects Immediate Visual Memory
Nesli Avgan, Heidi G. Sutherland, Lauren K. Spriggens, Astrid J. Rodriguez-Acevedo, Larisa M. Haupt, David H. K. Shum and Lyn R. Griffihs
Article Type: Research Article | First Published: November 12, 2014
Serotonin and its receptors, including the 5-Hydroxytryptamine Receptor 2A encoded by the HTR2A gene, are important for learning and memory in animals and humans.Polymorphic variation in the HTR2A gene, which encodes the 5-HT2Aserotonin receptor, has previously been shown to associate with some memory traits,in particular effecting delayed verbal memory. In the current study we have examined the HTR2A His452Tyr (H452Y) substitution for association in a cohort of healthy individuals whose memory ...
Open Access DOI:10.23937/2378-3648/1410006
Identification of Ten Novel Mutations in Factor VIII Gene: A Study of A Cohort of 52 Haemophilia A Patients
Rosa Santacroce, Angelica Leccese, Roberta Trunzo, Giuseppe Lassandro, Paola Giordano, Cosimo Ettorre, Stefano Antoncecchi, Isabella Cantori, Alfredo Dragani, Donata Belvini, Roberta Salviato and Maurizio Margaglione
Article Type: Research Article | First Published: October 14, 2014
Introduction: Haemophilia A (HA) is the most common X-linked recessive genetic disease caused by mutations in the gene coding for coagulation factor VIII (FVIII) resulting in spontaneous bleeding. Aim: The aim of our study is to provide additional information about the genetic causes of HA describing the correlation between the observed mutations and the clinical phenotype in a cohort of 52 patients suffering from HA to different degrees. Methods: First we performed a search of inversion 22 ...
Open Access DOI:10.23937/2378-3648/1410005
Aspergillus flavus Blast2GO Gene Ontology Database: Elevated Growth Temperature Alters Amino Acid Metabolism
Perng-Kuang Chang and Leslie L. Scharfenstein
Article Type: Research Article | First Published: October 05, 2014
The availability of a representative Gene Ontology (GO) database is a prerequisite for a successful functional genomics study. Using the online Blast2GO tool we constructed a GO database of Aspergillus flvus, a plant and human pathogen. Of the predicted total 13,485 A. flvus genes 8,987 were annotated with GO terms. The mean GO level was 5.64. Using a low stringency setting of a sequence cut-off number of 10 and a node score of 20, we obtained 1,177 GO terms associated with biological process, 3...
Open Access DOI:10.23937/2378-3648/1410004
Replacing CFTR Sanger Sequencing in the Clinical Lab with a Reliable, Targeted Next-Generation Sequencing Assay
Shela Lee, Joy Radecki, Hsiao-Mei Lu, and Aaron M. Elliott
Article Type: Research Article | First Published: October 05, 2014
The clinical implementation of new target enrichment methods and next-generation sequencing (NGS) technology has rapidly transformed genetic testing. Diagnostic labs can now offer a wide variety of large comprehensive multi-gene panels or even full exome sequencing to help clinicians diagnose and treat patients. The unmatched sensitivity, accuracy and throughput of NGS compared to traditional Sanger sequencing make it an ideal technology not only for panels but also high volume single gene assay...
Open Access DOI:10.23937/2378-3648/1410003
Correlation of Killer Immunoglobulin like Receptor Genes with the Rate of Cytomegalovirus Infection in Renal Transplantation Cases
Tejendra Singh Chauhan, Swayam Prakash, Raj Kumar Sharma and Suraksha Agrawal
Article Type: Research Article | First Published: October 04, 2014
Aim: Immune mechanisms of Cytomegalovirus (CMV) infection suggest a possible relationship between CMV with development of acute graft rejection. Current immune suppression impairs antiviral specifi T-cell immunity in solid organ transplantation. Inhibitory/ activating NK receptor bindings activated by self HLA antigens confront allogeneic cells that lack a ligand for specifi receptor. KIR ligand incompatibility caused due to presence/absence of KIR receptor in recipient and corresponding HLA lig...
Open Access DOI:10.23937/2378-3648/1410002
Association of XmnI (-158 γG) Polymorphism and Response to Hydroxyurea in Omani S/S and S/β Patients
Hassan SM, Al Muslahi M, Al Riyami M, Bakker E, Harteveld CL and Giordano PC
Article Type: Research Article | First Published: September 26, 2014
Objective: To describe the effect of Hydroxyurea (HU) treatment in Omani Sickle Cell Disease (SCD) patients with different beta-globin gene cluster haplotypes. Materials and methods: A total of 52 cases treated with HU were enrolled in this study. Response to the drug was compared between patients with and without the XmnI polymorphism in the different betaglobin gene cluster haplotypes. We have classified our cohort into three categories: good responders to HU for those patients who had no cr...
Open Access DOI:10.23937/2378-3648/1410001
Extremely High Carrier Frequency of the GJB2 Splice Site IVS1+1G>A Mutation in Eastern Siberia is Comparable to the Carrier Frequency of the Sickle Cell Anemia in Africa
Nikolay A. Barashkov, Aisen V. Solovyev, Fedor M. Teryutin, Vera G. Pshennikova1, Leonid A. Klarov, Georgii P. Romanov, Sergey S. Nakhodkin, Kyunney E. Savvinova, Nyurgun N. Gotovtsev, Natalya A. Solovyeva, Andrei A. Kozhevnikov, Lena M. Vasilyeva, Elvira E. Fedotova, Maria V. Pak, Sargylana N. Lekhanova, Elena V. Zakharova, Adyum M. Rafailov, Nikolay V. Luginov, Anatoliy N. Alexeev, Olga L. Posukh, Lilya U. Dzhemileva, Elza K. Khusnutdinova and Sardana A. Fedorova
Article Type: Research article | First Published: September 01, 2014
This study presents data on the carrier frequencies of IVS1+1 G>A mutation in GJB2 gene, causing by autosomal recessive form of deafness among various ethno-geographical groups of Yakut population and in a random sample of the Yakuts. 350 DNA samples of hearing individuals from various ethno-geographical groups of Yakut population: Central (n=60), Vilyui (n=60), Northern (n=60) and random samples of Yakuts (n=170) were obtained from the DNA Bank of the Department of Molecular Genetics of Yakut R...
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ClinMed Journals Index Copernicus Values
Clinical Medical Image Library: 93.51
International Journal of Critical Care and Emergency Medicine: 92.83
International Journal of Sports and Exercise Medicine: 91.84
International Journal of Womens Health and Wellness: 91.79
Journal of Musculoskeletal Disorders and Treatment: 91.73
Journal of Geriatric Medicine and Gerontology: 91.55
Journal of Infectious Diseases and Epidemiology: 91.55
Clinical Medical Reviews and Case Reports: 91.40
International Archives of Nursing and Health Care: 90.87
International Journal of Ophthalmology and Clinical Research: 90.80
International Archives of Urology and Complications: 90.73
Journal of Clinical Nephrology and Renal Care: 90.33
Journal of Family Medicine and Disease Prevention: 89.99
Journal of Clinical Gastroenterology and Treatment: 89.54
Journal of Dermatology Research and Therapy: 89.34
International Journal of Clinical Cardiology: 89.24
International Journal of Radiology and Imaging Technology: 88.88
Obstetrics and Gynaecology Cases - Reviews: 88.42
International Journal of Blood Research and Disorders: 88.22
International Journal of Diabetes and Clinical Research: 87.97