Asset Details

  • Description:
  • Overview of the next generation DNA sequencing workflow. Nucleic acid sources from blood, tissue and cell culture are all compatible with next generation sequencing (NGS). Nucleic acids including DNA and RNA from germ-line as well as somatic sources can be used in the NGS assays. Depending on the choice of experimental design, samples can be enriched for specific targets (eg, the complete coding sequence of the human genome or exome, individual gene(s), or other custom needs); RNA specimens in most cases are converted to ds-cDNA at this time (the exception being direct sequencing of RNA molecules on the Heliscope). Following fragmentation, if needed, nucleic acid samples are end-repaired, A-tailed, linker-modified and, in most cases, amplified prior to sequencing. Linker-modified and amplified nucleic acids can be sequenced using any number of NGS approaches depending on the needs of the study design. Raw sequence data are processed via a stabilising but still dynamic pipeline; the highlights of the procedure are identified here. Numerous public and commercially available programmes are used for variant calling, data visualisation and annotation. Finally, annotation of the identified variants along with other analyses can be used to improve the understanding of the genetic basis of disease. Of course, additional studies will likely be required for a complete understanding of the functional consequences of the identified variant(s). Specific details on all of the processes depicted here can be found in the references cited in the text as well as references contained within. *Depending on the RNA isolation protocol(s), total RNA, messenger RNA, micro RNA, long non-coding RNAs can be studied. CNV, copy number variation; SNP, single nucleotide polymorphism SV, structural variants.
  • License:
  • Rights Managed
  • Rights Holder:
  • BMJ
  • License Rights Holder:
  • Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions
  • Asset Type:
  • Image
  • Asset Subtype:
  • Photo
  • Image Orientation:
  • Landscape
  • Image Dimensions:
  • 1280 x 725
  • Image File Size:
  • 122 KB
  • Creator:
  • Graham Casey, David Conti, Robert Haile, David Duggan
  • Credit:
  • Casey, G., et al., Gut, 62(6), 920.
  • Collection:
  • Keywords:
  • Next generation sequencing, colorectal cancer, GI malignancies, genetics, genomics, epigenetics, germ-line, somatic, DNA, RNA
  • Restrictions:
  • Property Release:
  • No
  • Model Release:
  • No
  • Purchasable:
  • Yes
  • Sensitive Materials:
  • No
  • Article Authors:
  • Graham Casey, David Conti, Robert Haile, David Duggan
  • Article Copyright Year:
  • 2013
  • Publication Title:
  • Gut
  • Publication Volume:
  • 62
  • Publication Issue:
  • 6
  • Publication Date:
  • 05/01/2012
  • DOI:
  • https://doi.org/10.1136/gutjnl-2011-301935

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