Results 21 to 30 of about 5,783,756 (283)

Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments. [PDF]

PLoS ONE, 2015
Nucleotide alterations detected by next generation sequencing are not always true biological changes but could represent sequencing errors. Even highly accurate methods can yield substantial error rates when applied to millions of nucleotides.
Yuan Qi, Xiuping Liu, Chang-Gong Liu, Bailing Wang, Kenneth R Hess, W Fraser Symmans, Weiwei Shi, Lajos Pusztai   +7 more
doaj   +1 more source

Single Nucleotide Variants in the TLR1, TLR2 and TLR6 Genes: A Case–Control Study in a Colombian Population

Tropical Medicine and Infectious Disease, 2023
Background: Single nucleotide variants in toll-like receptor genes play a crucial role in leprosy susceptibility or resistance. Methods: With an epidemiology case–control study, associations between SNVs rs5743618 in TLR1, rs5743708 in TLR2, and ...
Luz D. Gutierrez-Castañeda, Carmen R. Acosta, Mónica A. Bustos, Diana K. García, Diana P. Bohada, Raúl Rodríguez, Martha Inirida Guerrero   +6 more
doaj   +1 more source

Using SomaticSniper to Detect Somatic Single Nucleotide Variants [PDF]

Current Protocols in Bioinformatics, 2014
AbstractDetecting somatic single nucleotide variants (SNVs) is an essential component of cancer research with next‐generation sequencing data. This unit describes how to run the SomaticSniper somatic SNV detector and then filter the output to eliminate most false positives.
David E, Larson, Travis E, Abbott, Richard K, Wilson   +2 more
openaire   +2 more sources

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

BMC Genomics, 2020
Background Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we
Zeinab Amiri Ghanatsaman, Guo-Dong Wang, Hojjat Asadollahpour Nanaei, Masood Asadi Fozi, Min-Sheng Peng, Ali Esmailizadeh, Ya-Ping Zhang   +6 more
doaj   +1 more source

Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders—an important consideration for resource-constrained settings

Frontiers in Genetics, 2023
Exome sequencing (ES) is a recommended first-tier diagnostic test for many rare monogenic diseases. It allows for the detection of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in coding exonic regions of the genome in a single ...
Nadja Louw, Nadia Carstens, Nadia Carstens, Zané Lombard, for DDD-Africa as members of the H3Africa Consortium   +4 more
doaj   +1 more source

VCF2Networks: applying genotype networks to single-nucleotide variants data [PDF]

Bioinformatics, 2014
Abstract Summary: A wealth of large-scale genome sequencing projects opens the doors to new approaches to study the relationship between genotype and phenotype. One such opportunity is the possibility to apply genotype networks analysis to population genetics data. Genotype networks are a representation of the set of genotypes associated
Giovanni Marco Dall'Olio, Ali R. Vahdati, Jaume Bertranpetit, Andreas Wagner, Hafid Laayouni   +4 more
openaire   +8 more sources

A resource of variant effect predictions of single nucleotide variants in model organisms

Molecular Systems Biology, 2018
Abstract The effect of single nucleotide variants (SNVs) in coding and noncoding regions is of great interest in genetics. Although many computational methods aim to elucidate the effects of SNVs on cellular mechanisms, it is not straightforward to comprehensively cover different molecular effects. To address this,
Omar Wagih, Marco Galardini, Bede P Busby, Danish Memon, Athanasios Typas, Pedro Beltrao   +5 more
openaire   +5 more sources

Investigation of Naturally Occurring Single-Nucleotide Variants in Human TAAR1 [PDF]

Frontiers in Pharmacology, 2017
Activation of trace amine-associated receptor 1 (TAAR1) in endocrine pancreas is involved in weight regulation and glucose homeostasis. The purpose of this study was the identification and characterization of potential TAAR1 variants in patients with overweight/obesity and disturbed glucose homeostasis. Screening for TAAR1 variants was performed in 314
Jessica Mühlhaus, Juliane Dinter, Sabine Jyrch, Alexander Teumer, Simon F. Jacobi, Georg Homuth, Peter Kühnen, Susanna Wiegand, Annette Grüters, Henry Völzke, Henry Völzke, Klemens Raile, Klemens Raile, Gunnar Kleinau, Gunnar Kleinau, Heiko Krude, Heike Biebermann   +16 more
openaire   +4 more sources

SomaticSignatures: Inferring Mutational Signatures from Single Nucleotide Variants [PDF]

Bioinformatics, 2014
Mutational signatures are patterns in the occurrence of somatic single nucleotide variants (SNVs) that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable, and easy-to-use tools that identify such signatures in cancer sequencing data.
Gehring, Julian S., Fischer, Bernd, Lawrence, Michael, Huber, Wolfgang   +3 more
openaire   +3 more sources

Interaction of CCND2, CDKN1A, and POLD3 Variants in Mexican Patients with Colorectal Cancer

The Turkish Journal of Gastroenterology, 2022
Background: Colorectal cancer is the second cause of death by cancer around the world. Sporadic colorectal cancer is the most frequent (75%), and it is produced by the interaction of environmental, epigenetic, and genetic factors.
Carlos Rogelio Alvizo-Rodríguez, María de la Luz Ayala-Madrigal, Beatriz Armida Flores-López, Miriam Partida-Pérez, Nelly Margarita Macías-Gómez, Jorge Peregrina-Sandoval, Alexis Sayuri Suárez-Villanueva, José Miguel Moreno-Ortiz, Sergio Cervantes-Ortiz, Víctor Manuel Maciel-Gutiérrez, Melva Gutiérrez-Angulo   +10 more
doaj   +1 more source