Essay on Next Generation Sequencing and Metagenomics
Write a short essay (roughly 2+2 pages long) introducing
next generation sequenceing and ,
and discussing their connection, i.e. how next generation sequencing is
used as a key technology in metagenomics.
The essay should start with a short introduction to a couple of the main next
generation sequencing platforms and some of the challenges that arise in the
interpretation of data from these. Focus either on:
resequencing, that is the sequencing of a genome with a previously
sequenced reference genome.
A major application of resequencing is identification of disease-causing
mutations in the human genome.
de novo sequencing, that is the characterization of a completely
new genome for an organism where there is no or little previously knowledge.
Metagenomics is a technique where microorganisms are studied by sequencing DNA
directly from a sample.
This means that single individual organisms are ignored.
Instead, metagenomics investigates the entire genetic composition of a
community of microorganisms. Samples typically studied in metagenomics
includemicroorganisms in soil, bacteria in he human gut, for example from both
healthy or sick patient(s).
Discuss metagenomics, its dependence on next generation DNA sequencing and the
challenges in analyzing the resulting metagenomic data.
Identify also (at least) one application of metagenomics and next generation
sequencing and give a brief summary of it (them).
Start your reading with the following papers:
Robinson, E.R. and
Pallen, M.J. (2012)
"High-throughput bacterial genome sequencing: an embarrassment of choice, a
a world of opportunity",
Nature Reviews Microbiology, 10, 599-606
Hugenholtz, P. and Tyson, G.W. (2008)
Nature, 455, 481-483
De Meo, P.D.,
Picardi, E. and
Pesole, G (2010)
"Bioinformatics approaches for genomics and post genomics applications of
Brief. Bioinform., 11, 181-197
Metzker, M.L. (2010)
"Sequencing technologies - the next generation",
Nature Reviews Genetics, 11, 31-46
Mardis, E.R. (2008)
"The impact of next-generation sequencing technology on genetics",
Trends in Genetics, 24, 133-141
Pop, M. and Salzberg, S.L. (2008)
"Bioinformatics challenges of new sequencing technology",
Trends in Genetics, 24, 142-149.
All of these papers can be accessed from within the "chalmers.se" domain.
You should be aware of these guidelines:
Honesty and Integity at Chalmers.
Hand-in and deadline
Send your essay as a PDF file to email@example.com and firstname.lastname@example.org before
17:00 on Monday 3 March 2014.
Ensure that your name is included in the document.
Last Modified: 12 February 2014
by Graham Kemp