1. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Progress in genome sequencing  Human Genome Project  10 years to complete  Billions of dollars  Current sequencing technology  $10-25 million to sequence a human genome  Mammalian genomes sequenced in months  Microbial genomes sequenced in weeks  Massively parallel sequencing  25 million base pairs in 4 hours!

2. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Sample preparation  Fragment DNA into short single strands  Use “adaptor” sequences to attach DNA to micron-scale beads  Encase beads in oil droplets containing PCR reagents  Amplify bead DNA  Load beads into picoliter wells From Figure 1 in Margulies, M. et al. (2005) “Genome sequencing in microfabricated high-density picolitre reactors” Nature 437: 376-380. Figures 1 and 2 used by permission by Jonathan Rothberg.

3. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 The instrument  Load beads into slide containing 1.6 million picoliter wells  Sequentially pass A, G, C, and T into picoliter wells  Presence of a particular base emits light from individual well  CCD reads emitted light from each picoliter well From Figure 2 in Margulies, M. et al. (2005) “Genome sequencing in microfabricated high-density picolitre reactors” Nature 437: 376-380.

4. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Caveats  Only reads short lengths of sequence  80-120 bp  Accuracy of individual reads is lower than conventional methods  Though speed can compensate to some extent  Can not read paired-ends  Makes sequence assembly less efficient