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Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development
Genetic polymorphisms, particularly single nucleotide polymorphisms (SNPs), have been widely used to advance quantitative, functional and evolutionary genomics. Ideally, all genetic variants among individuals should be discovered when next generation sequencing (NGS) technologies and platforms are u...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Ivyspring International Publisher
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679402/ https://www.ncbi.nlm.nih.gov/pubmed/26722221 http://dx.doi.org/10.7150/ijbs.13498 |
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author | Jiang, Zhihua Wang, Hongyang Michal, Jennifer J. Zhou, Xiang Liu, Bang Woods, Leah C. Solberg Fuchs, Rita A. |
author_facet | Jiang, Zhihua Wang, Hongyang Michal, Jennifer J. Zhou, Xiang Liu, Bang Woods, Leah C. Solberg Fuchs, Rita A. |
author_sort | Jiang, Zhihua |
collection | PubMed |
description | Genetic polymorphisms, particularly single nucleotide polymorphisms (SNPs), have been widely used to advance quantitative, functional and evolutionary genomics. Ideally, all genetic variants among individuals should be discovered when next generation sequencing (NGS) technologies and platforms are used for whole genome sequencing or resequencing. In order to improve the cost-effectiveness of the process, however, the research community has mainly focused on developing genome-wide sampling sequencing (GWSS) methods, a collection of reduced genome complexity sequencing, reduced genome representation sequencing and selective genome target sequencing. Here we review the major steps involved in library preparation, the types of adapters used for ligation and the primers designed for amplification of ligated products for sequencing. Unfortunately, currently available GWSS methods have their drawbacks, such as inconsistency in the number of reads per sample library, the number of sites/targets per individual, and the number of reads per site/target, all of which result in missing data. Suggestions are proposed here to improve library construction, genotype calling accuracy, genome-wide marker density and read mapping rate. In brief, optimized GWSS library preparation should generate a unique set of target sites with dense distribution along chromosomes and even coverage per site across all individuals. |
format | Online Article Text |
id | pubmed-4679402 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Ivyspring International Publisher |
record_format | MEDLINE/PubMed |
spelling | pubmed-46794022016-01-01 Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development Jiang, Zhihua Wang, Hongyang Michal, Jennifer J. Zhou, Xiang Liu, Bang Woods, Leah C. Solberg Fuchs, Rita A. Int J Biol Sci Review Genetic polymorphisms, particularly single nucleotide polymorphisms (SNPs), have been widely used to advance quantitative, functional and evolutionary genomics. Ideally, all genetic variants among individuals should be discovered when next generation sequencing (NGS) technologies and platforms are used for whole genome sequencing or resequencing. In order to improve the cost-effectiveness of the process, however, the research community has mainly focused on developing genome-wide sampling sequencing (GWSS) methods, a collection of reduced genome complexity sequencing, reduced genome representation sequencing and selective genome target sequencing. Here we review the major steps involved in library preparation, the types of adapters used for ligation and the primers designed for amplification of ligated products for sequencing. Unfortunately, currently available GWSS methods have their drawbacks, such as inconsistency in the number of reads per sample library, the number of sites/targets per individual, and the number of reads per site/target, all of which result in missing data. Suggestions are proposed here to improve library construction, genotype calling accuracy, genome-wide marker density and read mapping rate. In brief, optimized GWSS library preparation should generate a unique set of target sites with dense distribution along chromosomes and even coverage per site across all individuals. Ivyspring International Publisher 2016-01-01 /pmc/articles/PMC4679402/ /pubmed/26722221 http://dx.doi.org/10.7150/ijbs.13498 Text en © Ivyspring International Publisher. Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. See http://ivyspring.com/terms for terms and conditions. |
spellingShingle | Review Jiang, Zhihua Wang, Hongyang Michal, Jennifer J. Zhou, Xiang Liu, Bang Woods, Leah C. Solberg Fuchs, Rita A. Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development |
title | Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development |
title_full | Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development |
title_fullStr | Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development |
title_full_unstemmed | Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development |
title_short | Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development |
title_sort | genome wide sampling sequencing for snp genotyping: methods, challenges and future development |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679402/ https://www.ncbi.nlm.nih.gov/pubmed/26722221 http://dx.doi.org/10.7150/ijbs.13498 |
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