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Genetics Research

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https://www.readbyqxmd.com/read/28583209/fine-mapping-by-composite-genome-wide-association-analysis
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27173948/exome-sequencing-identified-mutations-in-cask-and-mybpc3-as-the-cause-of-a-complex-dilated-cardiomyopathy-phenotype
#13
Eyal Reinstein, Shay Tzur, Concetta Bormans, Doron M Behar
Whole-exome sequencing for clinical applications is now an integral part of medical genetics practice. Though most studies are performed in order to establish diagnoses in individuals with rare and clinically unrecognizable disorders, due to the constantly decreasing costs and commercial availability, whole-exome sequencing has gradually become the initial tool to study patients with clinically recognized disorders when more than one gene is responsible for the phenotype or in complex phenotypes, when variants in more than one gene can be the cause for the disease...
May 13, 2016: Genetics Research
https://www.readbyqxmd.com/read/26996452/rare-high-impact-disease-variants-properties-and-identifications
#14
Leeyoung Park, Ju Han Kim
Although many genome-wide association studies have been performed, the identification of disease polymorphisms remains important. It is now suspected that many rare disease variants induce the association signal of common variants in linkage disequilibrium (LD). Based on recent development of genetic models, the current study provides explanations of the existence of rare variants with high impacts and common variants with low impacts. Disease variants are neither necessary nor sufficient due to gene-gene or gene-environment interactions...
March 21, 2016: Genetics Research
https://www.readbyqxmd.com/read/26947005/defining-the-polyposis-colorectal-cancer-phenotype-associated-with-the-ashkenazi-grem1-duplication-counselling-and-management-recommendations
#15
James Ziai, Ellen Matloff, Jaehyuk Choi, Ninani Kombo, Miguel Materin, Allen E Bale
Hereditary mixed polyposis is a genetically heterogeneous, autosomal dominant condition with adenomatous, hyperplastic and juvenile polyps. We conducted a comprehensive clinical evaluation of a large Ashkenazi Jewish family with this phenotype and performed extensive genetic testing. As seen in one previous report, a 40 kb duplication upstream of GREM1 segregated with the polyposis/colon cancer phenotype in this kindred. Our study confirms the association of GREM1 with mixed polyposis and further defines the phenotype seen with this mutation...
March 7, 2016: Genetics Research
https://www.readbyqxmd.com/read/26864234/the-future-of-ips-cells-in-advancing-regenerative-medicine
#16
Peng Liu, K E Li, Shaohua Xu
Induced pluripotent stem (iPS) cells have great potential in regenerative medicine, including cell replacement therapies and disease modelling in vitro. However, with this potential comes several challenges, including clinical safety, reprogramming and differentiation efficiency, and compromised functionality of differentiated cell types after transplantation. Many of these issues arise from imprecise control of cell fate. With large-scale sequencing and genome-editing technologies we can now precisely manipulate the genome, which has expanded our knowledge of functional cell types and cell identity...
February 11, 2016: Genetics Research
https://www.readbyqxmd.com/read/26792757/the-collective-nature-of-personalized-medicine
#17
Ian Vincent McGonigle
Precision medicine, incorporating personalized medicine, is an emerging medical model that holds great promise for improving the prevention, diagnosis and treatment of many diseases. The future success of precision medicine, however, depends on the establishment of large databases that collate diverse data, including family genealogies, disease histories, drug sensitivities and genomic data. Herein I raise some of the social and ethical challenges that such a system faces, specifically: the enrolment of volunteers into large genetic databases; the need for a change in mindset of clinicians, patients and the wider public; and the need for interdisciplinary ethics considering the emerging issues...
January 21, 2016: Genetics Research
https://www.readbyqxmd.com/read/26763729/privacy-anonymity-and-subjectivity-in-genomic-research
#18
EDITORIAL
Ian McGonigle, Noam Shomron
The use of non-anonymized human genome data is becoming increasingly popular in research. Here we review the proceedings of a special meeting on this topic that took place at European Molecular Biology Organization (EMBO) in December 2014. The main points discussed centered on how to achieve 'anonymity,' 'trust,' and 'protection of data' in relation to new genomic technologies and research. Following our report of this meeting, we also raise three further issues for future consideration: the harmonization of international law in relation to genetic data protection; the complex issues around the 'dividual' nature of genetic data; and the growing commercial value of personal data...
January 14, 2016: Genetics Research
https://www.readbyqxmd.com/read/27159928/a-nonparametric-method-to-test-for-associations-between-rare-variants-and-multiple-traits
#19
Ying Zhou, Yangyang Cheng, Wensheng Zhu, Qian Zhou
More and more rare genetic variants are being detected in the human genome, and it is believed that besides common variants, some rare variants also explain part of the phenotypic variance for human diseases. Due to the importance of rare variants, many statistical methods have been proposed to test for associations between rare variants and human traits. However, in existing studies, most methods only test for associations between multiple loci and one trait; therefore, the joint information of multiple traits has not been considered simultaneously and sufficiently...
2016: Genetics Research
https://www.readbyqxmd.com/read/26707058/a-refined-high-carbohydrate-diet-is-associated-with-changes-in-the-serotonin-pathway-and-visceral-obesity
#20
Paola A Spadaro, Helen L Naug, Eugene F DU Toit, Daniel Donner, Natalie J Colson
Consumption of palatable foods high in refined carbohydrate has been implicated as a contributing factor to the epidemic levels of obesity. Such foods may disrupt appetite regulation in the hypothalamus through alterations in hunger and satiety signalling. This investigation examined whether a palatable high refined carbohydrate (HRC) diet with the potential to induce obesity was linked to modulation of serotonin and dopamine signalling within the hypothalamus of rats. Male Wistar rats were allowed ad libitum access to either a palatable refined carbohydrate enriched (HRC) diet or standard chow (SC)...
December 28, 2015: Genetics Research
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