Results 51 to 60 of about 105,918 (288)

Comparative assessments of indel annotations in healthy and cancer genomes with next-generation sequencing data

BMC Medical Genomics, 2020
Background Insertion and deletion (indel) is one of the major variation types in human genomes. Accurate annotation of indels is of paramount importance in genetic variation analysis and investigation of their roles in human diseases.
Jing Chen, Jun-tao Guo
doaj   +1 more source

Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak

Viruses, 2023
Australia experienced widespread COVID-19 outbreaks from infection with the SARS-CoV-2 Delta variant between June 2021 and February 2022. A 17-nucleotide frameshift-inducing deletion in ORF7a rapidly became represented at the consensus level (Delta ...
Charles S. P. Foster, Rowena A. Bull, Nicodemus Tedla, Fernando Santiago, David Agapiou, Anurag Adhikari, Gregory J. Walker, Lok Bahadur Shrestha, Sebastiaan J. Van Hal, Ki Wook Kim, William D. Rawlinson   +10 more
doaj   +1 more source

Programmable base editing of zebrafish genome using a modified CRISPR-Cas9 system. [PDF]

, 2017
Precise genetic modifications in model animals are essential for biomedical research. Here, we report a programmable "base editing" system to induce precise base conversion with high efficiency in zebrafish. Using cytidine deaminase fused to Cas9 nickase,
Bai, Haipeng, Huang, Haigen, Li, Song, Lin, Shuo, Lu, Xiaochan, Qin, Wei, Xu, Jason, Zhang, Yihan   +7 more
core   +1 more source

A redefined InDel taxonomy provides insights into mutational signatures

Nature Genetics
Despite their deleterious effects, small insertions and deletions (InDels) have received far less attention than substitutions. Here we generated isogenic CRISPR-edited human cellular models of postreplicative repair dysfunction (PRRd), including ...
G. Koh, A. S. Nanda, Giuseppe Rinaldi, Soraya Boushaki, A. Degasperi, Cherif Badja, A. Pregnall, S. Zhao, Lucia Chmelova, Daniella Black, Laura Heskin, João M. L. Dias, Jamie Young, Yasin Memari, Scott Shooter, Jan Czarnecki, Matthew A. Brown, H. Davies, Xueqing Zou, S. Nik-Zainal   +19 more
semanticscholar   +1 more source

A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions

bioRxiv, 2020
Insertions and deletions (indels) are common molecular evolutionary events. However, probabilistic models for indel evolution are under-developed due to their computational complexity.
Gil Loewenthal, Dana Rapoport, Oren Avram, Asher Moshe, Alon Itzkovitch, Omer Israeli, Dana Azouri, R. Cartwright, I. Mayrose, T. Pupko   +9 more
semanticscholar   +1 more source

Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations

Cell Genomics
Summary: Antiviral proteins often evolve rapidly at virus-binding interfaces to defend against new viruses. We investigated whether antiviral adaptation via missense mutations might face limits, which insertion or deletion mutations (indels) could ...
Jeannette L. Tenthorey, Serena del Banco, Ishrak Ramzan, Hayley Klingenberg, Chang Liu, Michael Emerman, Harmit S. Malik   +6 more
doaj   +1 more source

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population. [PDF]

, 2015
Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology.
Cardeno, Charis M, Corbett-Detig, Russell B, Crepeau, Marc W, Lack, Justin B, Langley, Charles H, Pool, John E, Stevens, Kristian A, Taylor, William   +7 more
core   +1 more source

Deep indel mutagenesis reveals the impact of amino acid insertions and deletions on protein stability and function

bioRxiv
Amino acid insertions and deletions (indels) are an abundant class of genetic variants. However, compared to substitutions, the effects of indels on protein stability are not well understood and are poorly predicted.
Magdalena Topolska, Antoni Beltran, Ben Lehner   +2 more
semanticscholar   +1 more source

Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery

Genome Biology, 2020
Accurate discovery of somatic variants is of central importance in cancer research. However, count statistics on discovered somatic insertions and deletions (indels) indicate that large amounts of discoveries are missed because of the quantification of ...
Johannes Köster, L. Dijkstra, T. Marschall, A. Schönhuth   +3 more
semanticscholar   +1 more source

Genetic insights and evaluation of forensic features in Mongolian and Ewenki groups using the InDel variations

Frontiers in Bioscience-Landmark, 2022
Background: InDel polymorphisms show great potential for use with challenging DNA samples in forensic practice due to having similar advantages to STRs and SNPs.
Qiong Lan, Congying Zhao, Cong Wei, Hui Xu, Chunmei Shen, Bofeng Zhu   +5 more
doaj   +1 more source