Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling
Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the next-generation DNA sequencer (NGS) Roc...
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| Format: | Article |
| Language: | English |
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Korea Genome Organization
2012-03-01
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| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gni-10-1.pdf |
| _version_ | 1818909458877644800 |
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| author | Jong-Sung Lim Beom-Soon Choi Jeong-Soo Lee Chanseok Shin Tae-Jin Yang Jae-Sung Rhee Jae-Seong Lee Ik-Young Choi |
| author_facet | Jong-Sung Lim Beom-Soon Choi Jeong-Soo Lee Chanseok Shin Tae-Jin Yang Jae-Sung Rhee Jae-Seong Lee Ik-Young Choi |
| author_sort | Jong-Sung Lim |
| collection | DOAJ |
| description | Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the next-generation DNA sequencer (NGS) Roche/454 and Illumina/Solexa systems, along with bioinformation analysis technologies of whole-genome de novo assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing de novo assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least 2× and 30× depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive short-length reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20× and 50× coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average 30× coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence. |
| first_indexed | 2024-12-19T22:27:14Z |
| format | Article |
| id | doaj.art-7318ed03a6bb419e9836c35476dfdecc |
| institution | Directory Open Access Journal |
| issn | 1598-866X 2234-0742 |
| language | English |
| last_indexed | 2024-12-19T22:27:14Z |
| publishDate | 2012-03-01 |
| publisher | Korea Genome Organization |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj.art-7318ed03a6bb419e9836c35476dfdecc2022-12-21T20:03:28ZengKorea Genome OrganizationGenomics & Informatics1598-866X2234-07422012-03-011011810.5808/GI.2012.10.1.14Survey of the Applications of NGS to Whole-Genome Sequencing and Expression ProfilingJong-Sung Lim0Beom-Soon Choi1Jeong-Soo Lee2Chanseok Shin3Tae-Jin Yang4Jae-Sung Rhee5Jae-Seong Lee6Ik-Young Choi7National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 133-791, Korea.Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 133-791, Korea.National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the next-generation DNA sequencer (NGS) Roche/454 and Illumina/Solexa systems, along with bioinformation analysis technologies of whole-genome de novo assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing de novo assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least 2× and 30× depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive short-length reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20× and 50× coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average 30× coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.http://genominfo.org/upload/pdf/gni-10-1.pdf assemblyexpression profilingmultiplatformNGSresequencingwhole genome |
| spellingShingle | Jong-Sung Lim Beom-Soon Choi Jeong-Soo Lee Chanseok Shin Tae-Jin Yang Jae-Sung Rhee Jae-Seong Lee Ik-Young Choi Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling Genomics & Informatics assembly expression profiling multiplatform NGS resequencing whole genome |
| title | Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling |
| title_full | Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling |
| title_fullStr | Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling |
| title_full_unstemmed | Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling |
| title_short | Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling |
| title_sort | survey of the applications of ngs to whole genome sequencing and expression profiling |
| topic | assembly expression profiling multiplatform NGS resequencing whole genome |
| url | http://genominfo.org/upload/pdf/gni-10-1.pdf |
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