Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--Modern Genome Sequencing Technology

Given the workshop will be moving quite quickly the organizer(s) suggested for those of us with less background to do some reading up in certain topics which they outline and include links to on the website in a section called Preparation.

This page, with respect to the workshop on genomics, is broken down into sections. Total there are a suggested 23 readings or websites, unfortunately many (11 of 23) of the links, you have to have a subscription to view the articles beyond the abstract; which unfortunately I do not have and my institution has limited subscriptions; besides most of my preparation is being done at home where I would't have access to the institutional subscriptions anyway. I'll be going section by section with the papers linked and offer some additional suggestions for those unable to access articles due to lack of subscription.



Section 1: Modern Genome Sequencing Technology

• Three of the suggested readings are from Elaine Mardis who has been great at formulating pipelines of analysis for next generation sequencing and I encourage you to check out her page (linked with her name above). Unfortunately clicking on the paper links within the website I was blocked due to a lack of subscription. I've linked the papers below in case you have a subscription in which case I highly recommend the readings. Alternatively, for YouTube junkies, she's done an excellent talk that is an excellent introduction to sequencing technology today.
• Mardis, ER. 2011. A decades perspective on DNA sequencing technology. Nature. 470: 198-203.
• Mardis, ER. 2008. Next generation sequencing technologies. Annual Review of Genomics and Human Genetics. 9:387402.
• Mardis, ER. 2008. The impact of next generation sequencing technology on genetics. Trends in Genetics. 24:133-141.
• Her great video on Sequencing Technologies, 84 of the best minutes you'll spend bringing yourself up to date on sequencing technology and how it works today (uploaded Feb 2012).

• There were two more articles/readings suggested neither are available without a subscription or buying the book:
• Glenn, TC. 2011. Field guide to next generation DNA sequencers. Molecular Ecology Resources. 11:759-769.
• Rodriguez-Ezpeleta, N; M Hackenberg and AM Aransay (eds). 2012. Bioinformatics for high throughput sequencing. Springer Book. (ISBN: 978-4614-0782). The book is quite pricey, but the Springer site does have a link to a free preview. Also the workshop website link provides a preview of the book as well and may provide a preview of more pages than the springer site.

• A PubMed search focusing on 'DNA sequencing technologies' with filters for the last 5 years, review articles and Free full text availability yielded 206 results spanning from general to field specific so I encourage you take a gander:

1. Lin L et al., 2012. Comparison of next generation sequencing systems. J Biomed Biotechnol
2. Mestan et al., 2011. Genomic sequencing in clinical trials. J Transl Med. 9: 222
3. Shekhar Pareek, C; R Smoczynski and A Tretyn. 2011. Sequencing technologies and genome sequencing. J Appl Genet. 52:413-435. (gives a nice review of 1st generation sequencers and the development of high throughput sequencing).

Some nice video lectures/seminars on high throughput sequencing:

• Dr. Matthew W. Anderson, Stanford University School of Medicine geared toward applications in genomic medicine is also available. Unfortunately I could not embed this video for some reason so I linked it to his name above. (low sound so headphones in and turn your volume up, of course it could've been my computer as well).
• Professor Mark Pallen who discusses high-throughput sequencing in terms of clinical microbiology.

• There is also a group on YouTube that posts quite a few genomics seminars including Dr. Anderson's I posted above. They are the genomiclectures group and there are several interesting videos uploaded fairly recently on DNA sequencing, pharmacogenomics, and personal genomics--so if you enjoy watching videos and like learning through seminar format as opposed to just reading articles, check this out.

• One of the other tools I am a fan of is SlideShare where you can search for slide presentations on any subject that are freely available. The only caveat is you don't have context on some of the simpler slides and therefore may interpret differently than if the slides were being orally presented. However, it is still a great tool for visualizing topics of interest and all usually contain names of presenters/authors so if you have questions or further interest you can look them up directly. Doing a search on SlideShare of 'dna sequencing' pulls up over 50 pages of slide sets, sifting through about 20 sets of slides I found these two which satisfy my criteria of being understandible without someone talking and having to 'explain' what is going on in the slide, I could put 1 and 2 together. So kudos to the slide creators for these presentations, very helpful.

1. From presenters Thomas Keane and Jan Aerts from the Wellcome Trust Sanger Institute, they offer a tutorial on working with next generation sequencing data. The slides are fairly self explanatory and will give you an idea of what things to consider when it comes to next generation sequence data. This was from the European Conference on Computational Biology (2010) so be aware given it's now 2012 we will encounter some updates most likely in our workshop. Great primer though.
2. Another good primer, also from 2010, also from Europe is Bioinformatics for high-throughput sequencing. Presented by Misha Kapushesky, but the slides were made by Nicolas Delhomme and Simon Anders from EMBL-EBI. Quite understandible just from the slides and a nice little crib sheet of again things to consider in bioinformatic analysis of sequence data.

Modern sequencing technology has made it possible for huge strides to be made in cancer genomics, whole genome studies of both environmental and pathogenic bacteria/viruses and metagenomic surveys of various environments from soil to sea to the human microbiome--I know right? How much more fantastically vague can I get? I'm sure we'll touch on many of these applications during the workshop. In the meantime if you'd like to 'jump ahead' to how sequencing in all its forms has impacted research and application/pipeline developments, see the links below--more to come on much of this:

• Human metagenomics: Human Microbiome Project
• Environmental metagenomics: Sequencing of the Sargasso Sea (you can get this free with registration on Science), Global Ocean Sampling (applications of shotgun sequencing via random-insert clone libraries) and Hypersaline microbial communities.
• Microbial Genomes
• Cancer genomics (check out their pubs, some highlight next generation sequencing such as Xu et al., 2012)
• Vaccine development

Hopefully I have given some options for the readers, video viewers and powerpoint slide addicts as well as 'over-achievers' who like to jump ahead in terms of coming up to speed on sequencing today. If you have any other resources or links to open access papers, videos, slideshare please feel free to link them below in the comments!

Next Up: Preparation--Genome Structure and Transcriptomics