Results 71 to 80 of about 153,555 (331)

GAWMerge expands GWAS sample size and diversity by combining array-based genotyping and whole-genome sequencing

Communications Biology, 2022
GAWMerge is a computational tool that allows users to integrate SNP genotyping data from array techniques or whole-genome sequencing, providing a feasible method to leverage existing cohorts to increase sample size in genetic studies.
Ravi Mathur, Fang Fang, Nathan Gaddis, Dana B. Hancock, Michael H. Cho, John E. Hokanson, Laura J. Bierut, Sharon M. Lutz, Kendra Young, Albert V. Smith, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Edwin K. Silverman, Grier P. Page, Eric O. Johnson   +13 more
doaj   +1 more source

Molecular Epidemiology of Aspergillus fumigatus in Chronic Pulmonary Aspergillosis Patients

Journal of Fungi, 2021
Molecular fungal genotyping techniques developed and employed for epidemiological studies have understandably concentrated on establishing the genetic diversity of Aspergillus fumigatus in invasive aspergillosis due to its severity, the urgency for ...
Mireille H. van der Torre, Hongwei Shen, Riina Rautemaa-Richardson, Malcolm D. Richardson, Lilyann Novak-Frazer   +4 more
doaj   +1 more source

Improved Imputation of Common and Uncommon Single Nucleotide Polymorphisms (SNPs) with a New Reference Set [PDF]

, 2011
Statistical imputation of genotype data is an important technique for analysis of genome-wide association studies (GWAS). We have built a reference dataset to improve imputation accuracy for studies of individuals of primarily European descent using ...
Amy Hutchinson, Ann W. Hsing, Brian E. Henderson, Charles C. Chung, Christopher M. Haiman, Daniel Stram, Demetrius Albanes, Jarmo Virtamo, Jennifer L. Stone, Joshua Sampson, Kevin Jacobs, Lauren R. Teras, Margaret Tucker, Mark P. Purdue, Meredith Yeager, Michael A. Eberle, Nilanjan Chatterjee, Phil Taylor, Sonja I. Berndt, Stephen Chanock, Susan M. Gabstur, W. Ryan Diver, Xiang Deng, Zhaoming Wang   +23 more
core   +2 more sources

Comparing self‐reported race and genetic ancestry for identifying potential differentially methylated sites in endometrial cancer: insights from African ancestry proportions using machine learning models

Molecular Oncology, EarlyView.
Integrating ancestry, differential methylation analysis, and machine learning, we identified robust epigenetic signature genes (ESGs) and Core‐ESGs in Black and White women with endometrial cancer. Core‐ESGs (namely APOBEC1 and PLEKHG5) methylation levels were significantly associated with survival, with tumors from high African ancestry (THA) showing ...
Huma Asif, J. Julie Kim
wiley   +1 more source

An HMM-based Comparative Genomic Framework for Detecting Introgression in Eukaryotes [PDF]

, 2013
One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species.
Dai, Jingxuan, Kohn, Michael H., Liu, Kevin J., Nakhleh, Luay, Song, Ying, Truong, Kathy   +5 more
core   +5 more sources

Data‐driven discovery of gene expression markers distinguishing pediatric acute lymphoblastic leukemia subtypes

Molecular Oncology, EarlyView.
This study investigates gene expression differences between two major pediatric acute lymphoblastic leukemia (ALL) subtypes, B‐cell precursor ALL, and T‐cell ALL, using a data‐driven approach consisting of biostatistics and machine learning methods. Following analysis of a discovery dataset, we find a set of 14 expression markers differentiating the ...
Mona Nourbakhsh, Nikola Tom, Anna Schrøder Lassen, Helene Brasch Lind Petersen, Ulrik Kristoffer Stoltze, Karin Wadt, Kjeld Schmiegelow, Matteo Tiberti, Elena Papaleo   +8 more
wiley   +1 more source

Cross Species use of Human Microarray Genotyping Technology for Bornean Orangutan (Pongo pygmaeus) SNP Discovery

Hayati Journal of Biosciences, 2021
Previous genetic studies of orangutans (Pongo spp.) have relied mainly upon mitochondrial DNA or microsatellite short tandem repeats (STR) for genomic genotyping analysis.
Ruth Ella Linsky, R. Steven Wagner, Reniastoetie Djojoasmoro, Joseph Lorenz, Biruté M. F. Galdikas   +4 more
doaj   +1 more source

Beijing genotype is the most dominant genotype among clinical isolates of m.tuberculosis in Kazakhstan [PDF]

, 2014
Methods of genotyping of M. tuberculosis play important role in tuberculosis (TB) infection control. These techniques are used to detect or exclude laboratory errors, control recurrent cases and determine ways of TB transmission.
Akhmetova, А., Akilzhanova, A., Bismilda, V., Chingissova, L., Kozhamkulov, U.   +4 more
core   +1 more source

ITGAV and SMAD4 influence the progression and clinical outcome of pancreatic ductal adenocarcinoma

Molecular Oncology, EarlyView.
In SMAD4‐positive pancreatic ductal adenocarcinoma (PDAC), integrin subunit alpha V (ITGAV) activates latent TGF‐β, which binds to the TGF‐β receptor and phosphorylates SMAD2/3. The activated SMAD2/3 forms a complex with SMAD4, and together they translocate to the nucleus, modulating gene expression to promote proliferation, migration, and invasion. In
Daniel K. C. Lee, Keyue Chen, Ryan Loke, Xiang Li, David Liubart, Golam T. Saffi, Jonathan T. S. Chow, Ché M. P. Melo, Lydia To, Leonardo Salmena   +9 more
wiley   +1 more source

Joint Haplotype Assembly and Genotype Calling via Sequential Monte Carlo Algorithm [PDF]

, 2015
Genetic variations predispose individuals to hereditary diseases, play important role in the development of complex diseases, and impact drug metabolism. The full information about the DNA variations in the genome of an individual is given by haplotypes,
Ahn, Soyeon, Vikalo, Haris
core   +3 more sources