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Genetics Research

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https://www.readbyqxmd.com/read/30221607/an-efficient-classification-algorithm-for-ngs-data-based-on-text-similarity
#1
Xiangyu Liao, Xingyu Liao, Wufei Zhu, Lu Fang, Xing Chen
With the advancement of high-throughput sequencing technologies, the amount of available sequencing data is growing at a pace that has now begun to greatly challenge the data processing and storage capacities of modern computer systems. Removing redundancy from such data by clustering could be crucial for reducing memory, disk space and running time consumption. In addition, it also has good performance on reducing dataset noise in some analysis applications. In this study, we propose a high-performance short sequence classification algorithm (HSC) for next generation sequencing (NGS) data based on efficient hash function and text similarity...
September 17, 2018: Genetics Research
https://www.readbyqxmd.com/read/30086807/comprehensive-review-on-the-molecular-genetics-of-autosomal-recessive-primary-microcephaly-mcph
#2
Muhammad Naveed, Syeda Khushbakht Kazmi, Mariyam Amin, Zainab Asif, Ushna Islam, Kinza Shahid, Sana Tehreem
Primary microcephaly (MCPH) is an autosomal recessive sporadic neurodevelopmental ailment with a trivial head size characteristic that is below 3-4 standard deviations. MCPH is the smaller upshot of an architecturally normal brain; a significant decrease in size is seen in the cerebral cortex. At birth MCPH presents with non-progressive mental retardation, while secondary microcephaly (onset after birth) presents with and without other syndromic features. MCPH is a neurogenic mitotic syndrome nevertheless pretentious patients demonstrate normal neuronal migration, neuronal apoptosis and neural function...
August 8, 2018: Genetics Research
https://www.readbyqxmd.com/read/30047344/epigenetics-and-bone-diseases
#3
Tu Huang, Xiu Peng, Zhenxia Li, Quan Zhou, Shishu Huang, Yuting Wang, Juan Li, Youqiang Song
Owing to the development of new technologies, the epigenome, a second dimensional method for genome analysis has emerged. Epigenetic mechanisms, including DNA methylation, histone modifications and noncoding RNAs, regulate gene expression without changing the genetic sequence. These epigenetic mechanisms normally modulate gene expression, trans-generational effects and inherited expression states in various biological processes. Abnormal epigenetic patterns typically cause pathological conditions, including cancers, age-related diseases, and specific cartilage and bone diseases...
July 26, 2018: Genetics Research
https://www.readbyqxmd.com/read/30014809/stage-specific-differential-dna-methylation-data-analysis-during-human-erythropoiesis-in-chromosome-16
#4
Najyah A Garoot, Byung Guk Kim
Previous studies have generated controversial findings regarding the correlation between DNA methylation in the human genome and gene expression. Some reports have indicated that promoter methylation is negatively correlated with gene expression levels; however, in some cases, a poor or positive correlation was reported. Most previous findings were based on general trends observed with whole-genome data analysis. Here, we present a novel chromosome-specific statistical analysis design of empirical Bayes differential tests for five phases of erythroid development...
July 17, 2018: Genetics Research
https://www.readbyqxmd.com/read/29502537/association-of-tribbles-homologue-1-gene-expression-in-human-umbilical-vein-endothelial-cells-with-duration-of-intrauterine-exposure-to-hyperglycaemia
#5
Polina V Popova, Liudmila B Vasileva, Alexandra S Tkachuk, Maxim V Puzanov, Yana A Bolotko, Evgenii A Pustozerov, Andrey S Gerasimov, Irina E Zazerskaya, Olga A Li, Elena Y Vasilyeva, Anna A Kostareva, Renata I Dmitrieva, Elena N Grineva
Maternal gestational diabetes mellitus (GDM) is considered to be an important factor that epigenetically predisposes offspring to metabolic and cardiovascular diseases. However, the mechanisms of how intrauterine hyperglycaemia affects offspring have not been thoroughly studied. The mammalian tribbles homologue 1 (TRIB1) gene is associated with plasma lipid concentrations and coronary artery disease (CAD). Our aim was to study the effect of GDM and its treatment terms on the level of TRIB1 gene expression in human umbilical vein endothelial cells (HUVECs) of newborns from women with and without GDM...
March 5, 2018: Genetics Research
https://www.readbyqxmd.com/read/29386085/dna-methylation-is-not-involved-in-dietary-restriction-induced-lifespan-extension-in-adult-drosophila
#6
Ting Lian, Uma Gaur, Q I Wu, Jianbo Tu, Boyuan Sun, Deying Yang, Xiaolan Fan, Xueping Mao, Mingyao Yang
Dietary restriction (DR) is widely regarded as a viable intervention to extend lifespan and healthspan in diverse organisms. The precise molecular regulatory mechanisms are largely unknown. Epigenetic modifications are not stable upon DR and also keep changing with age. Here, we employed whole genome bisulfite sequencing to determine the DNA methylation changes upon DR in adult Drosophila. Our results indicate that although a low level of DNA methylation exists in the adult Drosophila genome, there is no significant difference in DNA methylation levels upon DR when compared to unrestricted flies...
February 1, 2018: Genetics Research
https://www.readbyqxmd.com/read/29386084/association-analysis-of-rare-and-common-variants-with-multiple-traits-based-on-variable-reduction-method
#7
Lili Chen, Yong Wang, Yajing Zhou
Pleiotropy, the effect of one variant on multiple traits, is widespread in complex diseases. Joint analysis of multiple traits can improve statistical power to detect genetic variants and uncover the underlying genetic mechanism. Currently, a large number of existing methods target one common variant or only rare variants. Increasing evidence shows that complex diseases are caused by common and rare variants. Here we propose a region-based method to test both rare and common variant associated multiple traits based on variable reduction method (abbreviated as MULVR)...
February 1, 2018: Genetics Research
https://www.readbyqxmd.com/read/28851476/analysis-of-pathogenic-variants-from-the-clinvar-database-in-healthy-people-using-next-generation-sequencing
#8
Tautvydas Rančelis, Justas Arasimavičius, Laima Ambrozaitytė, Ingrida Kavaliauskienė, Ingrida Domarkienė, Dovilė Karčiauskaitė, Zita Aušrelė Kučinskienė, Vaidutis Kučinskas
Next-generation sequencing (NGS) became an effective approach for finding novel causative genomic variants of genetic disorders and is increasingly used for diagnostic purposes. Public variant databases that gather data of pathogenic variants are being relied upon as a source for clinical diagnosis. However, research of pathogenic variants using public databases data could be carried out not only in patients, but also in healthy people. This could provide insights into the most common recessive disorders in populations...
August 30, 2017: Genetics Research
https://www.readbyqxmd.com/read/28583209/fine-mapping-by-composite-genome-wide-association-analysis
#9
Joaquim Casellas, Jhon Jacobo Cañas-Álvarez, Marta Fina, Jesús Piedrafita, Alessio Cecchinato
Genome-wide association (GWA) studies play a key role in current genetics research, unravelling genomic regions linked to phenotypic traits of interest in multiple species. Nevertheless, the extent of linkage disequilibrium (LD) may provide confounding results when significant genetic markers span along several contiguous cM. In this study, we have adapted the composite interval mapping approach to the GWA framework (composite GWA), in order to evaluate the impact of including competing (possibly linked) genetic markers when testing for the additive allelic effect inherent to a given genetic marker...
June 6, 2017: Genetics Research
https://www.readbyqxmd.com/read/28502252/differential-analysis-of-mutations-in-the-jewish-population-and-their-implications-for-diseases
#10
Yaron Einhorn, Daphna Weissglas-Volkov, Shai Carmi, Harry Ostrer, Eitan Friedman, Noam Shomron
Sequencing large cohorts of ethnically homogeneous individuals yields genetic insights with implications for the entire population rather than a single individual. In order to evaluate the genetic basis of certain diseases encountered at high frequency in the Ashkenazi Jewish population (AJP), as well as to improve variant annotation among the AJP, we examined the entire exome, focusing on specific genes with known clinical implications in 128 Ashkenazi Jews and compared these data to other non-Jewish populations (European, African, South Asian and East Asian)...
May 15, 2017: Genetics Research
https://www.readbyqxmd.com/read/28132660/grin3b-missense-mutation-as-an-inherited-risk-factor-for-schizophrenia-whole-exome-sequencing-in-a-family-with-a-familiar-history-of-psychotic-disorders
#11
COMPARATIVE STUDY
Tobias Hornig, Björn Grüning, Kousik Kundu, Torsten Houwaart, Rolf Backofen, Knut Biber, Claus Normann
Glutamate is the most important excitatory neurotransmitter in the brain. The N-methyl-D-aspartate (NMDA) receptor is a glutamate-gated ionotropic cation channel that is composed of several subunits and modulated by a glycine binding site. Many forms of synaptic plasticity depend on the influx of calcium ions through NMDA receptors, and NMDA receptor dysfunction has been linked to a number of neuropsychiatric disorders, including schizophrenia. Whole-exome sequencing was performed in a family with a strong history of psychotic disorders over three generations...
January 30, 2017: Genetics Research
https://www.readbyqxmd.com/read/28132651/effective-experimental-validation-of-mirna-targets-using-an-improved-linker-reporter-assay
#12
Cheolwon Choi, James Han, Nguyen Thi Thao Tran, Seulgi Yoon, Goeun Kim, Sujung Song, Youngjo Kim, Seongho Ryu
miRNAs are small, non-coding RNAs that play critical roles in various cellular processes. Although there are several algorithms that can predict the potential candidate genes that are regulated by a miRNA, these algorithms require further experimental validation in order to demonstrate genuine targets of miRNAs. Moreover, most algorithms predict hundreds to thousands of putative target genes for each miRNA, and it is difficult to validate all candidates using the whole 3'-untranslated region (UTR) reporter assay...
January 30, 2017: Genetics Research
https://www.readbyqxmd.com/read/27834158/investigating-genetic-characteristics-of-hepatitis-b-virus-associated-and-non-associated-hepatocellular-carcinoma
#13
COMPARATIVE STUDY
Xi-Hua Fu, Min Li, Hai-Bo Lou, Ming-Shou Huang, Chun-Long Liu
BACKGROUND: Hepatocellular carcinoma (HCC) is a primary liver malignancy that mainly occurs in patients with chronic liver disease and cirrhosis. Risk factors for HCC include hepatitis B virus (HBV) infection. However, the specific role of HBV infection in HCC development is not yet completely understood. In order to reveal the effects of HBV on HCC, we compare the genes of HCC patients infected with HBV with those who are not infected. METHODS: We encoded the genes of these two types of HCC in databases using enrichment scores of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway terms...
November 11, 2016: Genetics Research
https://www.readbyqxmd.com/read/27834155/whole-genome-fetal-and-maternal-dna-methylation-analysis-using-medip-ngs-for-the-identification-of-differentially-methylated-regions
#14
Anna Keravnou, Marios Ioannides, Kyriakos Tsangaras, Charalambos Loizides, Michael D Hadjidaniel, Elisavet A Papageorgiou, Skevi Kyriakou, Pavlos Antoniou, Petros Mina, Achilleas Achilleos, Maria Neofytou, Elena Kypri, Carolina Sismani, George Koumbaris, Philippos C Patsalis
DNA methylation is an epigenetic marker that has been shown to vary significantly across different tissues. Taking advantage of the methylation differences between placenta-derived cell-free DNA and maternal blood, several groups employed different approaches for the discovery of fetal-specific biomarkers. The aim of this study was to analyse whole-genome fetal and maternal methylomes in order to identify and confirm the presence of differentially methylated regions (DMRs). We have initially utilized methylated DNA immunoprecipitation (MeDIP) and next-generation sequencing (NGS) to identify genome-wide DMRs between chorionic villus sampling (CVS) and female non-pregnant plasma (PL) and peripheral blood (WBF) samples...
November 11, 2016: Genetics Research
https://www.readbyqxmd.com/read/27724990/identification-of-fbn1-gene-mutations-in-ukrainian-marfan-syndrome-patients
#15
Rustam Zhurayev, Dorien Proost, Dmytro Zerbino, Viktor Fedorenko, Josephina A N Meester, Lut VAN Laer, Bart L Loeys
Marfan syndrome is an autosomal dominant connective tissue disorder, predominantly affecting the ocular, skeletal and cardiovascular systems. Here, we present the results of the first genetic testing in 40 Ukrainian Marfan (-like) patients and 10 relatives. We applied a targeted next generation sequencing panel comprising FBN1 and 13 thoracic aortic aneurysm genes. We identified 27 causal mutations in FBN1, obtaining a mutation yield of 67·5%. A significant difference in age at aortic surgery between mutation positive and negative patients was observed...
October 11, 2016: Genetics Research
https://www.readbyqxmd.com/read/27376979/the-molecularization-of-identity-science-and-subjectivity-in-the-21st-century
#16
Ian Vincent McGONIGLE, Ruha Benjamin
Recent advances in biological and computational technologies are changing the way different social groups imagine race, gender, kinship, citizenship and disease risk. Existing taxonomies are being displaced or reconfigured, impacting the ways in which people are governed, how lives are lived, how groups are known and how power is exercised. Herein we report on a two-day international symposium that we co-organized, titled 'The molecularization of identity: science and subjectivity in the 21st century,' that was held on 29-30 April 2016 at the Program on Science, Technology and Society, at Harvard University...
July 5, 2016: Genetics Research
https://www.readbyqxmd.com/read/27350105/fmr1-gene-mutations-in-patients-with-fragile-x-syndrome-and-obligate-carriers-30-years-of-experience-in-chile
#17
Lorena Santa María, Solange Aliaga, Víctor Faundes, Paulina Morales, Ángela Pugin, Bianca Curotto, Paula Soto, M Ignacia Peña, Isabel Salas, M Angélica Alliende
Fragile X syndrome (FXS) is the most common form of inherited intellectual disability (ID) and co-morbid autism. It is caused by an amplification of the CGG repeat (>200), which is known as the full mutation, within the 5'UTR of the FMR1 gene. Expansions between 55-200 CGG repeats are termed premutation and are associated with a greater risk for fragile X-associated tremor/ataxia syndrome and fragile X-associated premature ovarian insufficiency. Intermediate alleles, also called the grey zone, include approximately 45-54 repeats and are considered borderline...
June 28, 2016: Genetics Research
https://www.readbyqxmd.com/read/27265430/exome-sequencing-identified-a-novel-de-novo-opa1-mutation-in-a-consanguineous-family-presenting-with-optic-atrophy
#18
Lior Cohen, Shay Tzur, Nitza Goldenberg-Cohen, Concetta Bormans, Doron M Behar, Eyal Reinstein
Inherited optic neuropathies are a heterogeneous group of disorders characterized by mild to severe visual loss, colour vision deficit, central or paracentral visual field defects and optic disc pallor. Optic atrophies can be classified into isolated or non-syndromic and syndromic forms. While multiple modes of inheritance have been reported, autosomal dominant optic atrophy and mitochondrial inherited Leber's hereditary optic neuropathy are the most common forms. Optic atrophy type 1, caused by mutations in the OPA1 gene is believed to be the most common hereditary optic neuropathy, and most patients inherit a mutation from an affected parent...
June 6, 2016: Genetics Research
https://www.readbyqxmd.com/read/27193946/power-considerations-for-%C3%AE-inflation-factor-in-meta-analyses-of-genome-wide-association-studies
#19
Georgios Georgiopoulos, Evangelos Evangelou
The genomic control (GC) approach is extensively used to effectively control false positive signals due to population stratification in genome-wide association studies (GWAS). However, GC affects the statistical power of GWAS. The loss of power depends on the magnitude of the inflation factor (λ) that is used for GC. We simulated meta-analyses of different GWAS. Minor allele frequency (MAF) ranged from 0·001 to 0·5 and λ was sampled from two scenarios: (i) random scenario (empirically-derived distribution of real λ values) and (ii) selected scenario from simulation parameter modification...
May 19, 2016: Genetics Research
https://www.readbyqxmd.com/read/27174043/molecular-genetics-of-thyroid-cancer
#20
REVIEW
Maha Rebaї, Ahmed Rebaї
The pathogenesis of the development and progression of thyroid cancer (TC) is far from being clear at present. Accumulated evidence suggests that it is a complex polygenic disorder for which genetic factors play an important role in disease aetiology. Here we review the literature to report the genetic variations and alterations that have been described in the aetiology of TC. The functional effects of some mutations and single nucleotide polymorphisms on TC are validated, establishing the role of sequence variations in this cancer...
May 13, 2016: Genetics Research
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