Results 1 to 10 of about 2,058,071 (297)

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

Truvari: refined structural variant comparison preserves allelic diversity

Genome Biology, 2022
The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same.
Adam C. English, Vipin K. Menon, Richard A. Gibbs, Ginger A. Metcalf, Fritz J. Sedlazeck   +4 more
doaj   +1 more source

The effects of common structural variants on 3D chromatin structure

BMC Genomics, 2020
Background Three-dimensional spatial organization of chromosomes is defined by highly self-interacting regions 0.1–1 Mb in size termed Topological Associating Domains (TADs).
Omar Shanta, Amina Noor, Human Genome Structural Variation Consortium (HGSVC), Jonathan Sebat   +3 more
doaj   +1 more source

Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach

BMC Bioinformatics, 2021
Background The widespread use of next-generation sequencing has identified an important role for somatic mosaicism in many diseases. However, detecting low-level mosaic variants from next-generation sequencing data remains challenging.
Jeffrey N. Dudley, Celine S. Hong, Marwan A. Hawari, Jasmine Shwetar, Julie C. Sapp, Justin Lack, Henoke Shiferaw, NISC Comparative Sequencing Program, Jennifer J. Johnston, Leslie G. Biesecker   +9 more
doaj   +1 more source

Genome maps across 26 human populations reveal population-specific patterns of structural variation. [PDF]

, 2019
Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in ...
Cao, Han, Chan, Ting-Fung, Chow, Eugene YC, Chu, Catherine, Chung, Claire YL, Hastie, Alex R, Jin, Nana, Kwok, Pui-Yan, Lam, Ernest T, Leung, Alden KY, Levy-Sakin, Michal, Li, Le, Lin, Chin, Ma, Walfred, McCaffrey, Jennifer, Mostovoy, Yulia, Naguib, Ahmed, Pastor, Steven, Poon, Annie, Rajagopalan, Ramakrishnan, Sibert, Justin, Wang, Wei-Ping, Wong, Karen HY, Xiao, Ming, Yip, Kevin Y, Young, Eleanor   +25 more
core   +2 more sources

Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism. [PDF]

, 2015
Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from
A Conesa, A Ecker, A Pain, A Sinha, AR Quinlan, B Langmead, B Singh, B Singh, C Aurrecoechea, C Daneshvar, C Hertz-Fowler, CJ Sutherland, EV Meyer, FA Fatih, H Li, I Kozarewa, J Cox-Singh, J Cox-Singh, Janet Cox-Singh, JB Koenderink, JC Barrett, JC Barrett, JC de Roode, JC Rayner, Julian C. Rayner, K Rutherford, KS Lee, L Mamanova, LH Miller, LH Miller, M Ashburner, M Rougemont, M Yuda, MA Ahmed, Md Atique Ahmed, Miguel M. Pinheiro, Osamu Kaneko, P Jones, P Librado, PC Divis, PM Jones, R Leinonen, R Tanizaki, R Tripathi, S Iwanaga, S Purcell, Sanjeev Krishna, Scott B. Millar, SE Lindner, SO Oyola, SW Roy, T Carver, T William, TC Yeo, Theo Sanderson, Thomas D. Otto, U Bronner, Woon Chan Lu, YL Lau   +58 more
core   +4 more sources

Expansión clónica y caracterización genómica del proceso de integración del virus linfotrópico humano tipo I en la leucemia/linfoma de células T en adultos

Biomédica: revista del Instituto Nacional de Salud, 2009
Introducción. Aunque la integración del virus linfotrópico humano tipo I no es al azar, se desconocen muchos de los detalles de este proceso. Objetivo. Evaluar las características de la cromatina celular adyacente a secuencias provirales en pacientes con
Mercedes Salcedo-Cifuentes, Jesús Cabrera, Yesid Cuesta-Astroz, Edwin Carrascal, Yoshito Eizuru, Martha C. Domínguez, Adalberto Sánchez, Felipe García-Vallejo   +7 more
doaj   +1 more source

The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration

npj Regenerative Medicine, 2021
Throughout their lifetime, fish maintain a high capacity for regenerating complex tissues after injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio, which serves as an ideal model of appendage regeneration due to its easy ...
Jason W. Sinclair, David R. Hoying, Erica Bresciani, Damian Dalle Nogare, Carli D. Needle, Alexandra Berger, Weiwei Wu, Kevin Bishop, Abdel G. Elkahloun, Ajay Chitnis, Paul Liu, Shawn M. Burgess   +11 more
doaj   +1 more source

Unified theory of human genome reveals a constrained spatial chromosomal arrangement in interphase nuclei [PDF]

, 2015
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across all pairs of ...
Fatakia, Sarosh N., Mehta, Ishita S., Rao, Basuthkar J.   +2 more
core   +2 more sources

Phenotypic variance explained by local ancestry in admixed African Americans

Frontiers in Genetics, 2015
We surveyed 26 quantitative traits and disease outcomes to understand the proportion of phenotypic variance explained by local ancestry in admixed African Americans. After inferring local ancestry as the number of African-ancestry chromosomes at hundreds
Daniel eShriner, Amy R. Bentley, Ayo Priscille Doumatey, Guanjie eChen, Jie eZhou, Adebowale eAdeyemo, Charles N. Rotimi   +6 more
doaj   +1 more source