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iMEGES: integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes

Atlas Khan, Qian Liu, Kai Wang
2018 BMC Bioinformatics  
used in population studies to help the prioritization of novel genes or variants that might be associated with the susceptibility to mental disorders, and also on individual patients to help the identification  ...  of genes or variants related to mental diseases.  ...  The enhancer and promoter data of brain from Roadmap Epigenomics Project ( was also used in variant prioritization.  ... 
doi:10.1186/s12859-018-2469-7 pmid:30591030 pmcid:PMC6309067 fatcat:74h7p5ifpjceheqv25iyhcj33e

Computational Methods for the Pharmacogenetic Interpretation of Next Generation Sequencing Data

Yitian Zhou, Kohei Fujikura, Souren Mkrtchian, Volker M. Lauschke
2018 Frontiers in Pharmacology  
We anticipate that these methodologies will provide a useful toolkit to facilitate the integration of the vast extent of rare genetic variability into drug response predictions in a precision medicine  ...  Importantly, the rapid progress in Next Generation Sequencing technologies in recent years unveiled the true complexity of the genetic landscape in pharmacogenes with tens of thousands of rare genetic  ...  However, while these variants are likely to be depleted of pathogenic variants in haploinsufficient genes, many common variants entail functional consequences in their respective gene product, particularly  ... 
doi:10.3389/fphar.2018.01437 pmid:30564131 pmcid:PMC6288784 fatcat:w5z2qrm47fh25nannvs6h7zqfe

Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder

Rebeca Borges-Monroy, Chong Chu, Caroline Dias, Jaejoon Choi, Soohyun Lee, Yue Gao, Taehwan Shin, Peter J. Park, Christopher A. Walsh, Eunjung Alice Lee
2021 Mobile DNA  
Results We analyzed WGS data from a cohort of 2288 ASD families from the Simons Simplex Collection by establishing a scalable computational pipeline for retrotransposon insertion detection.  ...  adequate sensitivity from whole genome sequencing (WGS) data and a large enough cohort for this analysis has only recently become available.  ...  We acknowledge the clinicians who contributed to the collection of samples and phenotypic data, the SSC principal investigators, and the SFARI staff, in particular, S. Xiao and R.  ... 
doi:10.1186/s13100-021-00256-w pmid:34838103 pmcid:PMC8627061 fatcat:4js5y6v5lzghveftmj64crw4hy

A tissue-aware machine learning framework enhances the mechanistic understanding and genetic diagnosis of Mendelian and rare diseases [article]

Eyal Simonovsky, Moran Sharon, Maya Ziv, Omry Mauer, Idan Hekselman, Juman Jubran, Ekaterina Vinogradov, Chanan M. Argov, Omer Basha, Lior Kerber, Yuval Yogev, Ayellet V. Segrè (+5 others)
2021 bioRxiv   pre-print
Patient-specific models of candidate disease-causing genes from 50 patients successfully prioritized the pathogenic gene in 86% of the cases, implying that the tissue-selectivity of rare diseases aids  ...  ABSTRACTGenetic studies of Mendelian and rare diseases face the critical challenges of identifying pathogenic gene variants and their modes-of-action.  ...  For example, ML helped identify interactomerewired genes in tissue-specific cancers 27 , infer gene modules for complex diseases 35 , and predict diabetes-causing variants from epigenomes of pancreatic  ... 
doi:10.1101/2021.02.16.430825 fatcat:lllxhii55fdhzemxmyfbyikk6q

Gene expression profiling in MDS and AML: potential and future avenues

K Theilgaard-Mönch, J Boultwood, S Ferrari, K Giannopoulos, J M Hernandez-Rivas, A Kohlmann, M Morgan, B Porse, E Tagliafico, C M Zwaan, J Wainscoat, M M Van den Heuvel-Eibrink (+2 others)
2011 Leukemia  
funded by the 6th Framework Program of the European Community (WP13 Gene Profiling).  ...  Acknowledgements This work is based on the joint research activities under the framework of the European Program for Cooperation in Science and Technology (COST, Action BM0801, WG1) and the European LeukemiaNet  ...  Subsequent validation using quantitative PCR and an independent data set of gene expression profiles obtained from relapsed or refractory AML patients treated with single agent tipifarnib confirmed the  ... 
doi:10.1038/leu.2011.48 pmid:21445077 fatcat:3wxqrh32cff6phf5azsuchcdoy

Chen_columbia_0054D_16308.pdf [article]

The first project, Episcore, predicts haploinsufficient genes based on a large integrated epigenomic profiles from multiple tissues and cell lines by supervised machine learning methods.  ...  Integration of Functional Genomic Data in Genetic Analysis Siying Chen Identifying disease risk genes is a central topic of human genetics.  ...  Based on this model, we developed a Random Forest-based method ("Episcore") using epigenomic data from the Epigenomic Roadmap (Roadmap Epigenomics et al., 2015) and ENCODE Projects (Consortium et al  ... 
doi:10.7916/d8-rfyj-v449 fatcat:5nvfnzlybnhd7flrpjdubngib4

Human genome meeting 2016

A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson, R. Polimanti, J. Gelernter, X. Lin (+828 others)
2016 Human Genomics  
Further, targeted quantitative analysis of a subset of discriminating metabolites using tandem mass spectrometry provided a reliable laboratory method to detect children with ASD.  ...  Methods Plasma samples from a clinically well-defined cohort of 100 male individuals, ages 2-16+ years, with ASD and 32 age-matched typically developing (TD) controls were subjected to global metabolomic  ...  Acknowledgements Funding for research and development is acknowledged for Project: "Research Oriented Data Management and Analysis" at the Ucar Lab by The Jackson Laboratory, USA.  ... 
doi:10.1186/s40246-016-0063-5 pmid:27294413 pmcid:PMC4896275 fatcat:ycjj53ixrbauvnusibuz76y7bm

General sessions (1A-01 – 3E-13)

2014 Genes & Genetic Systems  
The Gc gene Gc3-C1 derived from chromosome 3C of Ae. triuncialis (2n = 4x = 28, CCUU) induces chromosomal breakage in a wheat cultivar 'Chinese Spring' (CS) but not in 'Norin 26' (N26), because N26 carries  ...  Radiation hybrid mapping of the genes related to the gametocidal action in wheat Several species of the genus Aegilops, wild relatives of wheat, carry gametocidal (Gc) genes.  ...  The use of marker information from syntenic genes led to the identification of chromosomal segments that were highly conserved or frequently rearranged, which is very useful for our understanding of the  ... 
doi:10.1266/ggs.89.304 fatcat:wnqmfki5yzdxlm3ibgd474lybm

HGM 2010 Programme / Abstract

2010 The HUGO Journal  
The identification of an EYS mutation in a dog affected with retinal progressive atrophy would provide a useful model for establishing future therapies for retinitis pigmentosa.  ...  We are currently RT-PCR-amplifying RNA from the lymphocytes of patients to identify aberrant transcripts.  ...  Results obtained from the 5 DNAs allowed the detection of specific breakpoints of chromosomal rearrangements and the causative disease gene in 2 of the patients, the identification of candidate genes for  ... 
doi:10.1007/s11568-010-9143-0 fatcat:oykxd6u7snfi5o7m6tst7wi6yq

16th International Conference on Malignant Lymphoma, Virtual Edition, 18-22 June, 2021

2021 Hematological Oncology  
genomic landscape of CLL. 9,10 From these studies we have learned that genes regulating inflammatory pathways, BCR signaling and differentiation, Notch signaling, Wnt signaling, DNA damage control, chromatin  ...  Biology: The use of genetic and genomic technologies has led to an improved understanding of the biology of CLL.  ...  of fruitful cooperation.  ... 
doi:10.1002/hon.2879 pmid:34105791 fatcat:3eg6websqfgvrgq6zucmwmgbey

Program and Abstracts of the 15th Transgenic Technology Meeting (TT2019)

2019 Transgenic research  
We will present data using these methodologies to generate a variety of designed-null alleles and gene knock-in alleles, as well as flox alleles.  ...  The data flow from the deposit of mice to the publishing information of the mouse strains on WWW is efficiently achieved by the developed system using Spring Boor, PostgreSQL, Tomcat and etc.  ... 
doi:10.1007/s11248-019-00115-8 fatcat:wg6w4sarinatnpjztxslhdw5hu

Panel and Study Groups

2013 Neuropsychopharmacology  
Methods: We have studied over 238 normal human brains in both DLPFC and hippocampus ranging in age from week 14 in the fetus to 80 years of age, using Illumina microchip arrays, qRT-PCR and RNA Seq.  ...  Results: First and foremost, there are a number of previously unknown transcripts for each of these genes.  ...  Together, these data combined with other work on comparative genomes and epigenomes will pioneer an innovative approach for understanding the functional consequences of genes, gene evolution, and gene  ... 
doi:10.1038/npp.2013.278 fatcat:expu2u3f3reypazj7tt7jhybfa

ACNP 57th Annual Meeting: Poster Session II

2018 Neuropsychopharmacology  
We tested the hypothesis that increased CRP after gene transfer using an adeno-associated virus (AAV8) encoding murine CRP may confer a higher risk for PTSD-like behaviors after predator stress.  ...  Post-traumatic stress disorder (PTSD) remains a growing and often debilitating psychiatric disorder resulting from severe trauma.  ...  Methods: We generated predictive models of gene expression across 14 datasets by using a weighted elastic net model that integrates epigenome data.  ... 
doi:10.1038/s41386-018-0267-6 fatcat:febeq6uwefgdzm65ccmzrmjwjy

Abstracts of the Lectures During Haematocon 2013

2013 Indian Journal of Hematology and Blood Transfusion  
result from haploinsufficiency of ribosomal protein S19 (RPS19).  ...  The EBMT risk score was later validated using separate data from the International Bone Marrow Transplant Registry.  ...  However, identification of founder mutations/recurrent mutations makes rapid and cost effective diagnosis possible.  ... 
doi:10.1007/s12288-013-0303-y fatcat:pmhm2mkmpzhpbhozgqpjbvgyd4

Clinical Sciences and Therapeutics for health

Natalia Neophytou, Kerith Aginsky, Natalie Benjamin
2017 Southern African Journal of Infectious Diseases  
We identified a 7.67 kb tandem duplication within the KWE critical region, upstream of the CTSB gene and encompassing two enhancers.  ...  Reads were aligned to the reference genome using BWA. GATK and PINDEL were used to call small and large structural variants, respectively.  ...  . 25 single nucleotide polymorphisms (SNPs) within this region will be Familial Hypercholesterolaemia (FH) is a common, autosomal dominant, single-gene disorder resulting from haploinsufficiency of the  ... 
doi:10.4102/sajid.v32i2.50 fatcat:rg67lmnm7rh4hairc5llrzye6q
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