Thursday 14 November 2013

$100million for the Broad: what have they done for genomics?

When the Prime Minister announced £100M and the creation of Genome England we thought we had made the big time here in the UK. But compare that to the Broad's latest gift of $100M and our national effort suddenly doesn't look so big!

The Broad was formally opened in 2003 and grew out of MIT and Harvard communities including the Whitehead Institute and Harvard Medical School. It has been built primarily on the generosity of Eli and Edythe Broad who have given a total of $700 million to the institute that bears their name. And it has been an incredible and unqualified success.  There are almost 1400 publications listed on the Broad website and taking a look at through these highlights some of the impacts Broad science has had on the rest of us using NGS. I don't want to suggest that without the Broad none of this work would ever have happened but they have undoubtedly made a huge impact on the work all of us are doing.

The Broad's are not the only philanthropists out there, in fact the Cancer Research UK Cambridge Institute where I work was founded with the help of Sir Li Ka Shing. His funding, along with that from  Cambridge University, Hutchison Whampoa Ltd., Cancer Research UK and The Atlantic Philanthropies, plus several other donors allowed us to open the £50 million Li Ka Shing Centre on the Cambridge Biomedical Campus in 2007. And we've not done too badly ourselves!

Here were some publications from the Broad over the last few years that stood out for me:

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 2007/08/02, Volume 448, Issue 7153, p.553-60, (2007) 

Somatic mutations affect key pathways in lung adenocarcinoma. Nature, 2008/10/23, Volume 455, Issue 7216, p.1069-75, (2008) 
 High-resolution mapping of copy-number alterations with massively parallel sequencing. (2008)  

Mapping and sequencing of structural variation from eight human genomes. Nature, 2008/05/01, Volume 453, Issue 7191, p.56-64, (2008) 

ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome research, 2008/05/01, Volume 18, Issue 5, p.810-20, (2008)  

Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature, 2008/08/07, Volume 454, Issue 7205, p.766-70, (2008) 

Sequencing the nuclear genome of the extinct woolly mammoth. Nature, 2008/11/20, Volume 456, Issue 7220, p.387-90, (2008)  

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature biotechnology, 2009/02/01, Volume 27, Issue 2, p.182-9, (2009) 

Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (New York, N.Y.), 2009/10/09, Volume 326, Issue 5950, p.289-93, (2009) 

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome research, 2010/09/01, Volume 20, Issue 9, p.1297-303, (2010)  

Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nature methods, 2010/09/01, Volume 7, Issue 9, p.709-15, (2010) 

Quantitative comparison of genome-wide DNA methylation mapping technologies.Nature biotechnology, 2010/10/01, Volume 28, Issue 10, p.1106-14, (2010)  

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nature protocols, 2011/04/01, Volume 6, Issue 4, p.468-81, (2011) 

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic acids research, 2011/12/08, Volume 33, Issue 18, p.5868-77, (2011) 

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome biology, 2012/01/09, Volume 12, Issue 2, p.R18, (2012) 

Absolute quantification of somatic DNA alterations in human cancer. Nature biotechnology, 2012/04/29, (2012) 

RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics (Oxford, England), 2012/06/01, Volume 28, Issue 11, p.1530-2, (2012)  

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome biology, 2012/10/03, Volume 13, Issue 10, p.R92, (2012) 

Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nature methods, 2013/05/19, (2013) 

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