Multiple issues context February 2009 expert Genetics date February 2009 refimprove January 2010 SOLiD Sequencing by Oligonucleotide Ligation and Detection is a https en.wikipedia.org wiki DNA sequencing High throughput sequencing next generation sequencing technology developed by Life Technologies and has been commercially available since 2008. This next generation technology generates hundreds of millions to billions of small sequence reads at one time. This method should not be confused with sequencing by synthesis, a principle used by Roche 454 pyrosequencing introduced in 2005, generating millions of 200 400bp reads in 2009 , and the Solexa system now owned by Illuimina introduced in 2006, generating hundreds of millions of 50 100bp reads in 2009 These methods have reduced the cost from 0.01 base in 2004 to nearly 0.0001 base in 2006 and increased the sequencing capacity from 1,000,000 bases machine day in 2004 to more than 5,000,000,000 bases machine day in 2009. Over 30 publications exist describing its use first for nucleosome positioning from Valouev et al., ref cite journal author Valouev A, Ichikawa J, Tonthat T, et al. title A high resolution, nucleosome position map of C. elegans reveals a lack of universal sequence dictated positioning journal Genome Research volume 18 issue 7 pages 1051 63 year 2008 month July pmid 18477713 pmc 2493394 doi 10.1101 gr.076463.108 ref transcriptional profiling or strand sensitive RNA Seq with Cloonan et al., ref cite journal author Cloonan N, Forrest AR, Kolle G, et al. title Stem cell transcriptome profiling via massive scale mRNA sequencing journal Nature Methods volume 5 issue 7 pages 613 9 year 2008 month July pmid 18516046 doi 10.1038 nmeth.1223 ref single cell transcriptional profiling with Tang et al. ref cite journal author Tang F, Barbacioru C, Wang Y, et al. title mRNA Seq whole transcriptome analysis of a single cell journal Nature Methods volume 6 issue 5 pages 377 82 year 2009 month May pmid 19349980 doi 10. ... more details
The Illumina company Illumina Methylation Assay using the Infinium II platform uses BeadChip technology Clarify date August 2011 to generate a comprehensive genome wide profiling of human DNA methylation . Similar to bisulfite sequencing and pyrosequencing , this method quantifies methylation levels at specific locus genetics loci within the genome . Although the assay does not encompass the entire human genome , it can measure methylation level at 27,578 CpG site CpG dinucloeotides in 14,495 genes. ref name weisen Weisenberger, DJ. et al. 2008 Comprehensive DNA Methylation Analysis on the Illumina Infinium Assay Platform. http www.illumina.com downloads InfMethylation AppNote.pdf ref Background DNA methylation plays a significant role in the epigenetics epigenetic regulation of chromatin structure, which in the last decade has been recognized to be important in the regulation of gene expression , developmental biology development and genomic imprinting genetic imprinting in vertebrates. ref name weisen Changes in the methylation pattern and level have been shown to contribute to cancer and various developmental diseases. ref name go DNA methylation in development and human disease. Gopalakrishnan S, Van Emburgh BO, Robertson KD. Mutation Research. 2008 Dec 1 647 1 2 30 8. Epub 2008 Aug 20. Review. ref For example, hypermethylation at the promoter CpG islands of a tumor suppressor gene tumour suppressor gene , which in turn leads to its gene silencing silencing , is frequently associated with Carcinogenesis tumourgenesis . ref name go A large scale measurement of DNA methylation patterns from a wide selection of gene s may enable us to understand better the relationships between epigenetic changes and the genesis of different diseases and a better understanding of the role that epigenetics plays in tissue specific cellular differentiation differentiation . File MethylationBeadChipStats.png thumb 500px Table 1. Methylation Statistics Material The chip contains 27,578 ... more details
High throughput sequencing high throughput sequencing , in this case massively parallel pyrosequencing ... used massively parallel pyrosequencing 454 pyrosequencing . ref name Poinar2005 Two other technologies ... for sequencing DNA generate shorter fragments than Sanger sequencing 454 pyrosequencing typically ... 2006 title Using pyrosequencing to shed light on deep mine microbial ecology journal BMC Genomics ... and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454 Pyrosequencing ... more details
pyrosequencing are yielding insights into the range of microbial diversity in the human vagina .... Recent studies use shotgun Sanger sequencing or pyrosequencing to recover the sequences of the reads ... through methods such as the pyrosequencing of extracted RNA. ref name ShiTyson2009 Cite pmid ... more details
2 Base Encoding , also called SOLiD Sequencing by Oligonucleotide Ligation and Detection , is a next generation sequencing technology developed by Applied Biosystems and has been commercially available since 2008. These technologies generate hundreds of thousands of small sequence reads at one time. Well known examples of such DNA sequencing methods include 454 pyrosequencing introduced in 2005 , the Solexa system introduced in 2006 and the SOLiD system introduced in 2007 . These methods have reduced the cost from 0.01 base in 2004 to nearly 0.0001 base in 2006 and increased the sequencing capacity from 1,000,000 bases machine day in 2004 to more than 100,000,000 bases machine day in 2006. Similar to Shendure et al. , ref Jay Shendure et al. 2005 Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome. Science 309 5741 , 1728 1732 ref 2 base encoding is based on ligation sequencing rather than sequencing by synthesis. However, instead of using fluorescent labeled 9 mer probes that distinguish only 6 bases, 2 base encoding takes advantage of fluorescent labeled 8 mer probes that distinguish the two 3 prime most bases but can be cycled similar to the Macevicz method, thus greater than 6bp reads can be obtained 25 50bp published, ref Sequence and structural variation in a human genome uncovered by short read, massively parallel ligation sequencing using two base encoding. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP. Genome Res. 2009 Sep 19 9 1527 41. Epub 2009 Jun 22. ref 50bp in NCBI in Feb 2008 . The ... more details
DNA barcoding is a Taxonomy taxonomic method that uses a short genetic marker in an organism s DNA to identify it as belonging to a particular species . It differs from molecular phylogeny in that the main goal is not to determine classification but to identify an unknown sample in terms of a known classification. ref name Kress Although barcodes are sometimes used in an effort to identify unknown species or assess whether species should be combined or separated, ref Koch, H. 2010. Combining morphology and DNA barcoding resolves the taxonomy of Western Malagasy Liotrigona Moure, 1961. African Invertebrates 51 2 413 421. http www.africaninvertebrates.org.za Koch 2010 51 2 474.aspx http www.tb1.ethz.ch PublicationsEO PDFpapers Koch AFRICAN INVERTEBRATES 2010 51 413 421.pdf PDF fulltext ref the utility of DNA barcoding for these purposes is subject to debate. ref name seberg2009 Cite journal journal PLoS ONE year 2009 volume 4 issue 2 pages e4598 title How Many Loci Does it Take to DNA Barcode a Crocus? author Seberg O, Petersen G. pmid 19240801 pmc 2643479 doi 10.1371 journal.pone.0004598 editor1 last Stout editor1 first Jane Catherine ref Applications include, for example, identifying plant leaves even when flowers or fruit are not available, identifying insect larvae which typically have fewer diagnostic characters than adults , identifying the diet of an animal based on stomach contents or faeces, ref Cite journal title Analysing diet of small herbivores the efficiency of DNA barcoding coupled with high throughput pyrosequencing for deciphering the composition of complex plant mixtures author Eeva M Soininen journal Frontiers in Zoology year 2009 volume 6 pages 16 doi 10.1186 1742 9994 6 16 pmid 19695081 pmc 2736939 author separator , display authors 1 last2 Valentini first2 Alice last3 Coissac first3 Eric last4 Miquel first4 Christian last5 Gielly first5 Ludovic last6 Brochmann first6 Christian last7 Brysting first7 Anne K last8 S nsteb first8 J rn H last9 Ims fi ... more details
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