Results 51 to 60 of about 451,573 (269)

High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing

Plant Methods, 2022
Background In addition to heterogeneity and artificial selection, natural selection is one of the forces used to combat climate change and improve agrobiodiversity in evolutionary plant breeding. Accurate identification of the specific genomic effects of
Michael Schneider, Asis Shrestha, Agim Ballvora, Jens Léon   +3 more
doaj   +1 more source

Classification of acute myeloid leukemia based on multi‐omics and prognosis prediction value

Molecular Oncology, EarlyView.
The Unsupervised AML Multi‐Omics Classification System (UAMOCS) integrates genomic, methylation, and transcriptomic data to categorize AML patients into three subtypes (UAMOCS1‐3). This classification reveals clinical relevance, highlighting immune and chromosomal characteristics, prognosis, and therapeutic vulnerabilities.
Yang Song, Zhe Wang, Guangji Zhang, Jiangxue Hou, Kaiqi Liu, Shuning Wei, Yan Li, Chunlin Zhou, Dong Lin, Min Wang, Hui Wei, Jianxiang Wang, Tao Cheng, Yingchang Mi   +13 more
wiley   +1 more source

SVAT: Secure outsourcing of variant annotation and genotype aggregation

BMC Bioinformatics, 2022
Background Sequencing of thousands of samples provides genetic variants with allele frequencies spanning a very large spectrum and gives invaluable insight into genetic determinants of diseases.
Miran Kim, Su Wang, Xiaoqian Jiang, Arif Harmanci   +3 more
doaj   +1 more source

Adverse prognosis gene expression patterns in metastatic castration‐resistant prostate cancer

Molecular Oncology, EarlyView.
We aggregated a cohort of 1012 mCRPC tissue samples from 769 patients and investigated the association of gene expression‐based pathways with clinical outcomes. Loss of AR signaling, high proliferation, and a glycolytic phenotype were independently prognostic for poor outcomes, and an adverse transcriptional feature score incorporating these pathways ...
Marina N. Sharifi, Eric Feng, Nicholas R. Rydzewski, Amy K. Taylor, Jamie M. Sperger, Yue Shi, Kyle T. Helzer, Matthew L. Bootsma, Viridiana Carreno, Alex H. Chang, Luke A. Nunamaker, Grace C. Blitzer, Tianfu Andy Shang, Aishwarya Subramanian, Anders Bjartell, Andreas Josefsson, Pernilla Wikström, Emily Feng, Manish Kohli, Rendong Yang, Scott M. Dehm, Eric J. Small, Rahul Aggarwal, David A. Quigley, Joshua M. Lang, Shuang G. Zhao, Martin Sjöström   +26 more
wiley   +1 more source

Family and case–control genetic study of MSX1 polymorphisms in peg-shaped teeth Jordanian population

BMC Oral Health, 2022
Background This study aimed to investigate the genetic association of specific Single Nucleotide Polymorphisms (SNPs) within the muscle segment homeobox gene 1 (MSX1) with susceptibility to the peg-shaped teeth in 36 Jordanian Arab families and case ...
Rami Alkhatib, Razan Hawamdeh, Laith Al-Eitan, Nour Abdo, Fadi Obeidat, Mohamed Al-Bataineh, Hatem Aman   +6 more
doaj   +1 more source

Why Mutant Allele Frequencies in Oncogenes Peak Around 0.40 and Rapidly Decrease? [PDF]

arXiv, 2016
The mutant allele frequencies in oncogenes peak around 0.40 and rapidly decrease. In this article, we explain why this is the case. Invoking a key result from mathematical analysis in our model, namely, the inverse function theorem, we estimate the selection pressures of the mutations as a function of germline allele frequencies.
arxiv  

Highly multiplexed digital PCR assay for simultaneous quantification of variant allele frequencies and copy number alterations of KRAS and GNAS in pancreatic cancer precursors

Molecular Oncology, EarlyView.
Combining melting curve analysis enhances the multiplexing capability of digital PCR. Here, we developed a 14‐plex assay to simultaneously measure single nucleotide mutations and amplifications of KRAS and GNAS, which are common driver genes in pancreatic cancer precursors. This assay accurately quantified variant allele frequencies in clinical samples
Junko Tanaka, Tatsuo Nakagawa, Yusuke Ono, Yoshio Kamura, Takeshi Ishida, Hidemasa Kawabata, Kenji Takahashi, Hiroki Sato, Andrew S. Liss, Yusuke Mizukami, Takahide Yokoi   +10 more
wiley   +1 more source

A powerful allele based test for case-control association studies [PDF]

arXiv, 2015
In a case-control study aimed at localizing disease variants, association between a marker and the disease status is often tested by comparing the marker allele frequencies among cases and controls. These marker allele frequencies are expected to be different if the marker is associated with the disease. The power of the commonly used allele based test
arxiv  

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

Features of the genetic structure of the Simmental breed cattle

Науковий вісник Львівського національного університету ветеринарної медицини та біотехнологій імені С.З. Гжицького. Серія: Сільськогосподарські науки, 2020
Breeds of farm animals are characterized by the presence of their genetic structure, in particular, the distribution of allelic and genotypic frequencies by individual genetic and biochemical systems.
V. Y. Bodnaruk, L. I. Muzyka, Y. G. Kropyvka, P. V. Bodnar, A. J. Zhmur, T. V. Orikhivskyj   +5 more
doaj   +1 more source