30 July 2012
ByAppeared in BioNews 667
On 12 and 13 July, the project's team met with the wider genomics community at the University of Michigan, Ann Arbor, USA, to discuss the progression, applications and challenges of the project, as well as future directions for community sequencing.
This year's meeting was an enjoyable and engaging event, providing an overview of the scientific advances allowed by the project, including analysis, community resources and research applications. There was also a useful discussion of what to prioritise in terms of future requirements and next steps.
Talks by a host of leading geneticists and statisticians included Professors Gonçalo Abecasis, who organised the meeting, Richard Durbin (Wellcome Trust Sanger Institute), Gil McVean (University of Oxford) and Nancy Cox (University of Chicago).
The 1000 Genomes Project offers an unprecedented opportunity to chart genetic variation between individuals. Because the data is being made freely available, ideas can be shared and numerous researchers have been instrumental in solving technical and analytical challenges. Despite not being completely finished, this resource has become indispensable as a reference panel of variants for genetic studies.
Professor Gonçalo Abecasis highlighted other important contributions of the project, notably the creation of a standardised data format to allow the results to be stored and shared more easily and the development of methods and tools for analysing this type of data.
He added that collaboration between three groups involved in the analysis, from the Broad Institute in Boston, the University of Michigan and Wellcome Trust Sanger Institute, Cambridge, resulted in an overall reduction in error rates of 40 percent.
The meeting covered various methods used for sequence analysis, their applications and potential future uses. One of the remaining challenges discussed was that the human genome reference, which is used to align genetic sequences to their correct position in the genome, is only 95 percent complete. This means that an individual's genetic code can't be completed using just this reference. Improvements are therefore needed to fill this gap in the genetic sequence.
Another challenge is to accurately assess complicated mutations – current techniques are very good at identifying single changes in the letters making up the genetic code, but not as efficient for more complex alterations.
Further discussions involved using large scale sequencing studies for understanding the genetic basis of human diseases, including schizophrenia. Others talked about using data from the project to help genetic studies of conditions such as Crohn's disease and type II diabetes.
Professor Cisca Wijmenga talked about the influence of the 1000 Genomes on the Genomes of the Netherlands project, in terms of development of techniques and tools. However, she noted that 40 percent of the genetic variations identified in this project were not present in the 1000 Genomes' data, bringing home the importance of sequencing additional populations.
The meeting closed with a discussion of the future of large scale sequencing studies, which allowed the audience to contribute their own thoughts and what they think should take priority. The wish lists of many speakers were nicely summarised by Professor Durbin as: sequencing more individuals from different ancestry; achieving greater accuracy and more complete genomes by improving analysis; and eventually sequencing more individuals more thoroughly to improve data quality.
He added that we now need ideas and vision, and new people who will take these challenges on.
The #1000genomes Twitter coverage of the meeting has been Storfied here, and more information on the 1000 Genomes Project is available here. The meeting was sponsored by Illumina, Complete Genomics and Roche.