Cargando…

A Novel Quality-Control Procedure to Improve the Accuracy of Rare Variant Calling in SNP Arrays

Background: Single-nucleotide polymorphism (SNP) arrays are an ideal technology for genotyping genetic variants in mass screening. However, using SNP arrays to detect rare variants [with a minor allele frequency (MAF) of <1%] is still a challenge because of noise signals and batch effects. An app...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sun, Ting-Hsuan, Shao, Yu-Hsuan Joni, Mao, Chien-Lin, Hung, Miao-Neng, Lo, Yi-Yun, Ko, Tai-Ming, Hsiao, Tzu-Hung
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Frontiers Media S.A. 2021
Materias:	Genetics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8577504/ https://www.ncbi.nlm.nih.gov/pubmed/34764980 http://dx.doi.org/10.3389/fgene.2021.736390

Ejemplares similares

Evaluation of calling algorithms for array-CGH
por: Roy, Siddharth, et al.
Publicado: (2013)

Multi-omics analysis reveals the BRCA1 mutation and mismatch repair gene signatures associated with survival, protein expression, and copy number alterations in prostate cancer
por: Hsiao, Tzu-Hung, et al.
Publicado: (2019)

Clinical Utility of SNP Array Analysis in Prenatal Diagnosis: A Cohort Study of 5000 Pregnancies
por: Xiang, Jingjing, et al.
Publicado: (2020)

Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy
por: Kendig, Katherine I., et al.
Publicado: (2019)

Comparison of Genotype Imputation for SNP Array and Low-Coverage Whole-Genome Sequencing Data
por: Deng, Tianyu, et al.
Publicado: (2022)

Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays
por: Wang, Zhipeng, et al.
Publicado: (2020)

Exploring the optimal strategy of imputation from SNP array to whole-genome sequencing data in farm animals
por: Jiang, Yifan, et al.
Publicado: (2022)

Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping
por: Bernard, Maria, et al.
Publicado: (2022)

scdNet: a computational tool for single-cell differential network analysis
por: Chiu, Yu-Chiao, et al.
Publicado: (2018)

Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut
por: Peng, Ze, et al.
Publicado: (2020)

RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species
por: Jehl, Frédéric, et al.
Publicado: (2021)

Development and Validation of 58K SNP-Array and High-Density Linkage Map in Nile Tilapia (O. niloticus)
por: Joshi, Rajesh, et al.
Publicado: (2018)

Genome-wide association study and identification of systemic comorbidities in development of age-related macular degeneration in a hospital-based cohort of Han Chinese
por: Shih, Chien-Hung, et al.
Publicado: (2023)

Identifying putative breast cancer-associated long intergenic non-coding RNA loci by high density SNP array analysis
por: Jiang, Zhengyu, et al.
Publicado: (2012)

Read trimming has minimal effect on bacterial SNP-calling accuracy
por: Bush, Stephen J.
Publicado: (2020)

Design and characterization of a high-resolution multiple-SNP capture array by target sequencing for sheep
por: Guo, Yingwei, et al.
Publicado: (2022)

Linkage Disequilibrium and Effective Population Size of Buffalo Populations of Iran, Turkey, Pakistan, and Egypt Using a Medium Density SNP Array
por: Rahimmadar, Shirin, et al.
Publicado: (2021)

Whole-genome DNA methylome analysis of different developmental stages of the entomopathogenic fungus Beauveria bassiana NCHU-157 by nanopore sequencing
por: Li, Yi-Hsuan, et al.
Publicado: (2023)

Reference-free SNP calling: improved accuracy by preventing incorrect calls from repetitive genomic regions
por: Dou, Jinzhuang, et al.
Publicado: (2012)

SNP Arrays
por: Louhelainen, Jari
Publicado: (2016)

An Integrative Co-localization (INCO) Analysis for SNV and CNV Genomic Features With an Application to Taiwan Biobank Data
por: Yu, Qi-You, et al.
Publicado: (2021)

Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data
por: Liu, Qi, et al.
Publicado: (2012)

Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays
por: Chai, High Seng, et al.
Publicado: (2010)

Vitis Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls
por: Miller, Allison J., et al.
Publicado: (2013)

Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon (Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array
por: Barría, Agustín, et al.
Publicado: (2019)

Construction of a novel Wheat 55 K SNP array-derived genetic map and its utilization in QTL mapping for grain yield and quality related traits
por: Fan, Xiaoli, et al.
Publicado: (2022)

Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP
por: Yoshimura, Dai, et al.
Publicado: (2019)

SNP–SNP Interactions of Surfactant Protein Genes in Persistent Respiratory Morbidity Susceptibility in Previously Healthy Children
por: Gandhi, Chintan K., et al.
Publicado: (2022)

Evaluation of a Custom SNP Panel for Identifying and Rectifying of Misjudged Paternity in Deficiency Cases
por: Chang, Liao, et al.
Publicado: (2021)

Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array
por: Xie, Xinke, et al.
Publicado: (2023)

Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing
por: Zhang, Rangran, et al.
Publicado: (2022)

Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens
por: Liu, Zhuang, et al.
Publicado: (2021)

Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance
por: Kumar, Pankaj, et al.
Publicado: (2014)

Integrated study of copy number states and genotype calls using high-density SNP arrays
por: Sun, Wei, et al.
Publicado: (2009)

Correction: Vitis Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls
por: Miller, Allison J., et al.
Publicado: (2014)

Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success
por: Humble, Emily, et al.
Publicado: (2016)

SNP Array in Hematopoietic Neoplasms: A Review
por: Song, Jinming, et al.
Publicado: (2015)

Use of High Density Single Nucleotide Polymorphism (SNP) Arrays to Assess Genetic Diversity and Population Structure of Dairy Cattle in Smallholder Dairy Systems: The Case of Girinka Programme in Rwanda
por: Chagunda, Mizeck G. G., et al.
Publicado: (2018)

SAQC: SNP Array Quality Control
por: Yang, Hsin-Chou, et al.
Publicado: (2011)

Examining SNP-SNP interactions and risk of clinical outcomes in colorectal cancer using multifactor dimensionality reduction based methods
por: Curtis, Aaron, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_n47nqavbn34svqsluhoge4te2i