The biggest genome sequencing projects: the uber-list!

03 Dec 2013

I am just writing a short presentation for a meeting in Hinxton. I wanted to demonstrate the profound effect that whole-genome sequencing is having on the study of biology, and the size and scope of recent studies.

So I thought it would be fun to catalogue the largest - in terms of samples - genome projects that have been published so far.

A few things are notable here. As expected, many of the biggest studies in terms of numbers are bacterial, enabled partly due to their smaller genome size.

Update: My attention has just been drawn to a study of 2,007 C. elegans genomes!

I found it interesting that all the bacterial studies listed herald from the UK, we are clearly blazing a trail in this field of study!

A PhD for sequencing a gene? A single genome? A hundred genomes? How about a thousand genomes? A million?

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So, what's coming up that could potentially knock these studies off their perch?

• The Million Human Genome Project
• 100,000 foodborne pathogen genome project
• Up to 100,000 NHS patients
• 50,000 Faroe Islanders Project 
• 20,000 Global pneumococcal project
• 10,000 Genome 10k vertebrate sequencing project
• UK 10K human genome project
• 10,000 autism genome project
• 5,000 arthropod genome sequencing project
• 3,000 NCTC culture collection sequencing

Did I miss a study? Please drop a comment below.

Rules for inclusion:

• whole-genome sequencing >10X average per sample (no exome, target capture)
• at least one library per sample (e.g. no pooled species, quasispecies)
• not a meta-analysis, fresh data for the paper

Thanks to: Casey Bergman, Scott Edmunds, Prashant, Liz Batty, Craig Duffy, Cui Yujun, Lex Nederbragt for suggestions!

Update 10-02-2014: Added Chewapreecha et al, Casali et al, now occupying positions 1 and 4 respectively in the uber-list!
Update 15-04-2014: Added Nasser et al, new position 1!
Update 29-05-2014: Added 3,000 rice genome project, new position 3!

Name	Number	Reference
S. pyogenes	3,615	Nasser et al. 2014</td. </tr>
S. pneumoniae	3,085	Chewapreecha et al. 2014
Rice (Oryza sativa)	3,000	The 3,000 rice genomes project
C. elegans	2,007	Thompson et al. 2013
Clostridium difficile	1,250	Eyre et al. 2013
The thousand genome project	1092 human genomes	1000 Genome Project Consortium, 2013
Mycobacterium tuberculosis	1,000	Casali et al. 2014
Plasmodium falciparum	825	Miotto et al, 2013
Streptococcus pneumoniae	616	Croucher et al. 2013
Mycobacterium tuberculosis	390	Walker et al. 2013
Salmonella in cattle and humans	373	Mather et al. 2013
Shigella sonnei	263	Holt et al. 2013
Mycobacterium tuberculosis	259	Comas et al. 2013
Streptococcus pneumoniae	240	Croucher at al. 2011
Methicillin-resistant Staphylococcus aereus	193	Holden et al. 2013
Campylobacter jejuni	192	Sheppard et al. 2013
Mycobacterium abscessus in CF	170	Bryant et al. 2013