This is a web-based collaboration area for learning about the science and technology of the Broad. The emphasis is on introductory materials appropriate for new employees or those wanting to learn about areas other than their own. If you have corrections or additions please feel free to edit this page or e-mail zleber@broadinstitute.org. Thank you.
Table of Contents
Genetics
The Cartoon Guide to Genetics: This 1991 book remains a great introduction to genetics and is a highly enjoyable read. See Zach Leber to borrow a copy.
Primer on Molecular Genetics: A 1992 PDF primer from the Human Genome Project.
Sequencing
https://apps.broadinstitute.org/twiki/pub/TechnicalTraining/WebHome/Sequencing_tech_2011.pdf - Niall Lennon's technology poster
Sanger Sequencing
This video by Broad member Chad Nusbaum describes the Sanger sequencing techniques that have already been superseded by the Broad's next-gen machines. But the video is certainly worth viewing as it describes the fundamental breakthrough of dye-terminator sequencing. This video plays at 7CC in the DNAtruim.
Next-gen Sequencing
Next-generation sequencing uses very different sample preparation, chemistry, and imaging to produce much more data per run than the Sanger-type machines used for almost 30 years. The Broad started using next-generation sequencing in 2005. You can read an overview of the transition to next-gen or an in-depth review of the technology. Presentations from a 2010 Broad workshop on next-gen sequencing can be found here.
Illumina/Solexa
Illumina machines
Sequencing
Here at 320C, we used to work with a variety of sequencing technologies (Sanger, ABI Solid, Roche 454, Ion Torrent, Helicos, Pacific Biosciences, etc.), but now we have scaled up to production-level sequencing on Illumina machines.
Illumina
Illumina sequencers are the current workhorses of the Broad. This short whitepaper is a good introduction to their technology. You can also watch the Technology section of this video. Illuminia Illumina bought Solexa in 2006 so the terms Illumina and Solexa are often used interchangeably.
Roche/454
454 machines were the first of the next-gen machines and can produce significantly longer base pair (bp) read lengths than the Illumina machines (~400 bp vs. ~100 bp). They are used by the Broad for projects where these extended reads are helpful such as de novo assembly of new fungal and microbial genomes. 454 machines use PicoTiterPlates rather than flow cells. Their chemistry is described here and the process is more fully described by some of their videos.
ABI/SOLiD
SOLiD machines are the third type of next-gen machines used at the Broad. The most distinguishing feature of these systems is their use of color space.
Third-gen Sequencing
The Broad is investigating new machines being developed by Helicos Biosciences, Pacific Biosciences, Oxford Nanopore Technologies, and Complete Genomics. Sequencing's new race is a good introduction to these systems.
term "Solexa" is still used in some places in our LIMS.
Glossary of Sequencing Terms
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