Genomics from Inner Asia
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ABSTRACT:
PROVIDER: EGAD00010001557 | EGA |
REPOSITORIES: EGA
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Project description:502 genotypes obtained from Illumina DNA-arrays. Available as plink formatted files
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Project description:503 genotypes from Inner Asia used in "Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy" publication
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Project description:In order to benchmark the reproducibility of Affymetrix Genome-Wide Human SNP Array 6.0 for detecting copy-number alterations, we performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numbers at each SNP probeset by a custom copy-number pipeline (PMID: 18772890). For each cell line, copy number data from replicate arrays are supplied in the accompanying matrix files. For each SNP probeset, we calculated the median copy number across replicate arrays. We compared the copy-number alterations detected by Circular Binary Segmentation segmentation of these arrays with statistical analyses of short sequence reads obtained from the Illumina/Solexa 1G GenomeAnalyzer. Shotgun sequencing results can be found in the NCBI Short Read Archive, accession number SRP000246 Keywords: disease state analysis
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Project description:The experiment was based on 3 arrays (3 Illumina HumanHap300 and 3 Affymetrix Genechip HindIII arrays) of each type being hybridized to a single pool which contained equal amounts of DNA from each of 384 individuals. The goal is to estimate a pooling allele frequency, the average frequency of allele 1, say, in the set of 384 individuals. After processing, the raw data are summarized to give pooling allele frequency estimates for each array. Abstract from paper comparing two arrays (one affy, one illumina) is as follows; Genome wide association (GWA) studies to map genes for complex traits are powerful yet costly. DNA pooling strategies have the potential to dramatically reduce the cost of GWA studies. Pooling using Affymetrix arrays has been proposed and used but the efficiency of these arrays has not been quantified. We compared and contrasted Affymetrix Genechip HindIII and Illumina HumanHap300 arrays on the same DNA pools and show that the HumanHap300 arrays are substantially more efficient. In terms of effective sample size, HumanHap300 based pooling extracts >80% of the information available with individual genotyping (IG). In contrast, Genechip HindIII based pooling only extracts ~30% of the available information. With HumanHap300 arrays concordance with IG data is excellent. Guidance is given on best study design and it is shown that even after taking into account pooling error, one stage scans can be performed for >100 fold reduced cost compared with IG. With appropriately designed two stage studies, IG can provide confirmation of pooling results whilst still providing ~20 fold reduction in total cost compared with IG based alternatives. The large cost savings with Illumina HumanHap300 based pooling imply that future studies need only be limited by the availability of samples and not cost. Keywords: DNA pooling experiment
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