Computational Molecular Biology and Genomics
Assignment 2
02-711/03-711/15-856
Due Nov 9, 2012
Article:
 S. C. Schuster, Next-generation sequencing transforms today’s biology. Nature Methods, 5(1):
16-18, 2008
Last week’s articles discussed the history of sequencing technologies, especially the development of
Sanger sequencing, and the influence of sequencing technologies on how science is conducted. The
current article focusses on how the characteristics of next generation sequencing technology, in
comparison to Sanger sequencing, lead to different tradeoffs between speed, cost, and accuracy.
Further, it considers some new questions and approaches that next generation sequencing enables,
from a 2008 perspective.
Read this article and briefly answer the following questions. You may read additional materials, if you
wish. If you do, you must cite your sources. You may not quote verbatim without attribution.
1. Craig Venter’s genome was sequenced using Sanger sequencing at a cost of $70M. This effort
took several years. Using next-generation sequencing, Jim Watson’s genome was sequenced in
two months at a cost of $1M. The rapid, low cost sequencing of Watson’s genome depended
crucially on the fact that the human genome had already been sequenced. Why?
2. Schuster states next-generation sequencing was more readily accepted for sequencing bacterial
genomes than for other projects. Why might next-generation sequencing work better for
sequencing a bacterial genome than the human genome?
3. The Roche 454 sequencer uses emulsion PCR for DNA amplification rather than cloning. Give
two reasons why this is advantageous.
4. The two figures in the article show two different modes of sequencing: Sanger sequencing in
“factory-like outfits” requiring “large numbers of personnel” versus next-generation sequencing
machines, whose scale and cost make sequencing technology accessible to individual
laboratories. How does this technological shift change how individual PI’s do science?
5. What kinds of questions can be asked with next generation sequencing that do not lend
themselves to Sanger sequencing? Give two examples.
6. Resequencing:
 What is resequencing?

Give two examples of resequencing applications.

Why does resequencing require less coverage than de novo sequencing?

Why does next-gen resequencing require more coverage than Sanger sequencing?
7. The application of next-gen sequencing to cancer genetics takes advantage of the fact that a
large number of short sequence reads can be obtain efficiently at low cost. What is the
advantage of many short reads for this application? Why is Sanger sequencing not appropriate
for cancer genetics?