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Your search keyword '"Krejci, Adam"' showing total 2 results
Start Over Author "Krejci, Adam" Topic genetics
2 results on '"Krejci, Adam"'

1. Copy number variation: A prognostic marker for young patients with squamous cell carcinoma of the oral tongue.

Author

Gu, Xiaolian, Coates, Philip J., Boldrup, Linda, Wang, Lixiao, Krejci, Adam, Hupp, Ted, Fahraeus, Robin, Norberg‐Spaak, Lena, Sgaramella, Nicola, Wilms, Torben, Nylander, Karin, and Norberg-Spaak, Lena

Subjects
SQUAMOUS cell carcinoma, TONGUE cancer, DISEASE incidence, CANCER prognosis, GENETIC markers, RNA sequencing, EXOMES, AGE distribution, GENETICS, PROGNOSIS, RESEARCH funding, SURVIVAL, TONGUE tumors
Abstract

Background: The incidence of squamous cell carcinoma of the oral tongue (SCCOT) is increasing in people under age 40. There is an urgent need to identify prognostic markers that help identify young SCCOT patients with poor prognosis in order to select these for individualized treatment.Materials and Methods: To identify genetic markers that can serve as prognostic markers for young SCCOT patients, we first investigated four young (≤40 years) and five elderly patients (≥50 years) using global RNA sequencing and whole-exome sequencing. Next, we combined our data with data on SCCOT from the cancer genome atlas (TCGA), giving a total of 16 young and 104 elderly, to explore the correlations between genomic variations and clinical outcomes.Results: In agreement with previous studies, we found that SCCOT from young and elderly patients was transcriptomically and also genomically similar with no significant differences regarding cancer driver genes, germline predisposition genes, or the burden of somatic single nucleotide variations (SNVs). However, a disparate copy number variation (CNV) was found in young patients with distinct clinical outcome. Combined with data from TCGA, we found that the overall survival was significantly better in young patients with low-CNV (n = 5) compared to high-CNV (n = 11) burden (P = 0.044).Conclusions: Copy number variation burden is a useful single prognostic marker for SCCOT from young, but not elderly, patients. CNV burden thus holds promise to form an important contribution when selecting suitable treatment protocols for young patients with SCCOT. [ABSTRACT FROM AUTHOR]

Published
2019
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2. GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data

Author

Nikos Darzentas, Martin Demko, Adam Krejčí, Tasoula Touloumenidou, Šárka Pospíšilová, Jitka Malčíková, Boris Tichy, Karol Pál, Vojtech Bystry, Kostas Stamatopoulos, Tomáš Reigl, Paolo Ghia, Evangelia Stalika, Pal, Karol, Bystry, Vojtech, Reigl, Toma, Demko, Martin, Krejci, Adam, Touloumenidou, Tasoula, Stalika, Evangelia, Tichy, Bori, Ghia, Paolo, Stamatopoulos, Kosta, Pospisilova, Sarka, Malcikova, Jitka, and Darzentas, Nikos

Subjects
0301 basic medicine, Statistics and Probability, Genotyping Techniques, Computer science, genetic processes, information science, Standardized test, Computational biology, 02 engineering and technology, Biology, computer.software_genre, Biochemistry, 03 medical and health sciences, symbols.namesake, Computational Theory and Mathematic, 0202 electrical engineering, electronic engineering, information engineering, Humans, natural sciences, Molecular Biology, Gene, 030304 developmental biology, TRACE (psycholinguistics), Genetics, Sanger sequencing, 0303 health sciences, Polymorphism, Genetic, Sequence Analysis, RNA, business.industry, Computer Science Applications1707 Computer Vision and Pattern Recognition, 020207 software engineering, Sequence Analysis, DNA, eye diseases, Computer Science Applications, Trace (semiology), Computational Mathematics, Alternative Splicing, 030104 developmental biology, Computational Theory and Mathematics, symbols, Human genome, Artificial intelligence, Tumor Suppressor Protein p53, Genotyping Technique, business, computer, Software, Natural language processing, Human
Abstract

MotivationSanger sequencing remains the reference method for sequence variant detection, especially in a clinical setting. However, chromatogram interpretation often requires manual inspection and in some cases considerable expertise. Additionally, variant reporting and nomenclature is typically left to the user, which can lead to inconsistencies.ResultsWe introduce GLASS, a tool built to assist with the assessment of gene variations in Sanger sequencing data. Critically, it provides a standardized variant output as recommended by the Human Genome Variation Society.AvailabilityThe program is freely available online at http://bat.infspire.org/genomepd/glass/.Contactnikos.darzentas@gmail.com, malcikova.jitka@fnbrno.czSupplementary informationSupplementary data are available at Bioinformatics online.

Published
2016
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