, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.
An integrated map of genetic variation from 1,092 human genomes.
Nature. 2012 Nov 1;491(7422):56-65.
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Clearly, the 1000 Genomes Project and related projects are very important for those of us who are interested in the genetic determinants of all diseases. These projects give us the background information for disease association studies. One of the major goals of our lab and other similar labs is to find variants that are present in the order of 0.1-5.0 percent of the general population and substantively increase disease risk. These types of projects tell us what variability is out there in this range. Obviously, as more and more people are sequenced, the lower limit for our studies can fall below even the 0.1 percent level.
This study is a major achievement.
In the International Genomics of Alzheimer’s Project (IGAP), which gathers the four largest GWAS consortia on AD, we have been using the 1000 Genomes information since the beginning of our collaboration to perform imputations. This has allowed us to identify around eight million SNPs in common for all the studies. Depending on the study, we were able to impute SNP with minor allele frequency of lower than 0.01 percent for half of the samples. In our present GWAS, 1000 Genomes and similar projects help us to identify specific genome areas where such rare SNPs are located. Once these are found, we have to confirm this imputed information by performing genotyping or deep sequencing. But it is clearly progress in deciphering what is called "hidden heritability."
Indeed, this 1000 Genomes map will help to more efficiently identify rare variants that may be implicated in neurodegenerative diseases. However, you will need very large population samples (as we have obtained in IGAP) to be able to detect variations in rare variants between cases and controls.
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