SynthesisBriefings in bioinformatics2022
Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.
Synthesis in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- An increased number of heterozygous calls in the AxiomTM Equine Genotyping Array.G3 (Bethesda, Md.) · 2026Article
- Recovery and analysis of ancient DNA: challenges, methods, and applications in forensic and archaeological science.Journal, genetic engineering & biotechnology · 2026Article
- Development and application of a genotyping by target sequencing single-nucleotide polymorphism array panel in Salix suchowensis.BMC genomics · 2026Article
- Article
- A PCA-random forest pipeline for high-resolution SNP-based cultivar discrimination in Leymus chinensis.BMC plant biology · 2026Article
- Exploring chromosomal variations in garden roses: Insights from high-density SNP array data and a new tool, Qploidy.The plant genome · 2025Article
- Investigating the Performance of Oxford Nanopore Long-Read Sequencing with Respect to Illumina Microarrays and Short-Read Sequencing.International journal of molecular sciences · 2025Article
- Prediction of Skin Color Using Forensic DNA Phenotyping in Asian Populations: A Focus on Thailand.Biomolecules · 2025Review
- DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.Genetics, selection, evolution : GSE · 2025Article
- A High-Throughput Screening Strategy forMicroorganisms · 2025Article
- Influence of ADRB2 variants on bronchodilator response and asthma control in a mixed population.Jornal brasileiro de pneumologia : publicacao oficial da Sociedade Brasileira de Pneumologia e Tisilogia · 2025Article
- Uniparental disomy (UPD) exclusion in embryos following Preimplantation Genetic Testing for Structural Rearrangements (PGT-SR).Journal of assisted reproduction and genetics · 2025Article
- Asthma-Genomic Advances Toward Risk Prediction.Clinics in chest medicine · 2024Review
- Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle.BMC genomics · 2024Article
- Potential Association of Cytochrome P450 Copy Number Alteration in Tumour with Chemotherapy Resistance in Lung Adenocarcinoma Patients.International journal of molecular sciences · 2023Article
- Article
- Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference.Life (Basel, Switzerland) · 2023Review
- Cytogenomic epileptology.Molecular cytogenetics · 2023Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.
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Registered trials
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