Results 81 to 90 of about 144,950 (282)

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

Nature Communications, 2021
Variable number tandem repeats (VNTRs) are difficult to analyze by short-read sequencing in disease studies. Here, the authors describe a VNTR mapping strategy for short-read analyses using a repeat pangenome graph.
Tsung-Yu Lu, The Human Genome Structural Variation Consortium, Mark J. P. Chaisson   +2 more
doaj   +1 more source

lobSTR: A Short Tandem Repeat Profiler for Personal Genomes [PDF]

Genome Research, 2012
Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task.
Gymrek, Melissa, Golan, David, Rosset, Saharon, Erlich, Yaniv   +3 more
openaire   +2 more sources

Keratin 19 as a prognostic marker and contributing factor of metastasis and chemoresistance in high‐grade serous ovarian cancer

Molecular Oncology, EarlyView.
Keratin 19 (KRT19) is overexpressed in high‐grade serous ovarian cancer with high levels of Kallikrein‐related peptidases (KLK) 4–7 and is associated with poor survival. In vivo analyses demonstrate that elevated KRT19 increases peritoneal tumour burden.
Sophia Bielesch, Isabel Vogel, Sina Nokodian, Johanna Moeller, Antonia Blechschmidt, Vicky Hecht, Vanessa Kuentzel, Katharina Thiedig, Melissa Schwab, Oliver Schilling, Holger Bronger, Marion Kiechle, Viktor Magdolen, Tobias Dreyer   +13 more
wiley   +1 more source

REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats

Genome Medicine, 2022
Background Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others.
Egor Dolzhenko, Ben Weisburd, Kristina Ibañez, Indhu-Shree Rajan-Babu, Christine Anyansi, Mark F. Bennett, Kimberley Billingsley, Ashley Carroll, Samuel Clamons, Matt C. Danzi, Viraj Deshpande, Jinhui Ding, Sarah Fazal, Andreas Halman, Bharati Jadhav, Yunjiang Qiu, Phillip A. Richmond, Christopher T. Saunders, Konrad Scheffler, Joke J. F. A. van Vugt, Ramona R. A. J. Zwamborn, Genomics England Research Consortium, Samuel S. Chong, Jan M. Friedman, Arianna Tucci, Heidi L. Rehm, Michael A. Eberle   +26 more
doaj   +1 more source

A Small Family of Elements with Long Inverted Repeats is Located Near Sites of Developmentally Regulated DNA Rearrangement in \u3cem\u3eTetrahymena thermophila\u3c/em\u3e [PDF]

, 1994
Extensive DNA rearrangement occurs during the development of the somatic macronucleus from the germ line micronucleus in ciliated protozoans. The micronuclear junctions and the macronuclear product of a developmentally regulated DNA rearrangement in ...
Berger, Patricia J., Catt, Diana M., Ellingson, Jay Lee Edward, Karrer, Kathleen M., Wells, John M.   +4 more
core   +1 more source

Somatic mutational landscape in von Hippel–Lindau familial hemangioblastoma

Molecular Oncology, EarlyView.
The causes of central nervous system (CNS) hemangioblastoma in Von Hippel–Lindau (vHL) disease are unclear. We used Whole Exome Sequencing (WES) on familial hemangioblastoma to investigate events that underlie tumor development. Our findings suggest that VHL loss creates a permissive environment for tumor formation, while additional alterations ...
Maja Dembic, Anne Nørremølle, Lilian Bomme Ousager, Lars van Brakel Andersen, Marie Louise Mølgaard Binderup, Mads Thomassen   +5 more
wiley   +1 more source

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci

Genome Medicine
Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp motifs.
Laurel Hiatt, Ben Weisburd, Egor Dolzhenko, Vincent Rubinetti, Akshay K. Avvaru, Grace E. VanNoy, Nehir Edibe Kurtas, Heidi L. Rehm, Aaron R. Quinlan, Harriet Dashnow   +9 more
doaj   +1 more source

The impact of short tandem repeat variation on gene expression. [PDF]

, 2019
Short tandem repeats (STRs) have been implicated in a variety of complex traits in humans. However, genome-wide studies of the effects of STRs on gene expression thus far have had limited power to detect associations and provide insights into putative ...
Fotsing, Stephanie Feupe, Goren, Alon, Gymrek, Melissa, Margoliash, Jonathan, Saini, Shubham, Shleizer-Burko, Sharona, Wang, Catherine, Yanicky, Richard   +7 more
core   +1 more source

De novo Development and Characterization of Tetranucleotide Microsatellite Loci Markers from a Southeastern Population of the House Finch (Haemorhous mexicanus) [PDF]

, 2019
Microsatellites are short tandem repeats (e.g. TAGATAGA) of base pairs in a species’ genome. High mutation rates in these regions produce variation in the number of repeats across individuals that can be utilized to study patterns of population- and ...
Barron, Douglas G, Maddox, J Dylan, Sanchez, Edgar E   +2 more
core   +3 more sources

E2A selectively regulates TGF‐β–induced apoptosis in KRAS‐mutant non‐small cell lung cancer

Molecular Oncology, EarlyView.
Ability to induce apoptosis by TGF‐β is frequently lost in advanced lung adenocarcinoma despite intact TGF‐β signaling. We identify E2A as a mutant KRAS–dependent mediator of resistance to TGF‐β–induced apoptosis. TGF‐β induces E2A via SMAD3 in mutant KRAS cells, and E2A silencing restores apoptosis and enhances radiation response in cell lines ...
Sergei Chuikov, Shiva Krishna Katkam, Zhefan Wang, Venkateshwar G. Keshamouni   +3 more
wiley   +1 more source