Nonparametric estimation of LOH using Affymetrix SNP genotyping arrays for unpaired samples
Abstract Studies of loss of heterozygosity (LOH) play an important role in cancer research. In this paper, we developed a two-step
procedure to examine LOH by comparing unpaired tumour and normal samples. In the first step we determined which chromosomes
significantly differ between the two sets of samples by using nonparametric procedures. We then used the biplot data visualisation
technique and homozygosity intensity estimates to determine the regions of these chromosomes that required further examination.
We illustrated our method by examining 22 autosomes in samples of 95 normal controls and 14 acute lymphoblastic leukaemia
patients. The genomewide scan of LOH with the Affymetrix Human Mapping 100K Set successfully identified the important tumour
suppressor gene, CDKN2...
Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms
Whole-genome microarrays with large-insert clones designed to determine DNA copy number often show variation in hybridization intensity that is related to the genomic position of the clones. We found these ‘genomic waves’ to be present in Illumina and Affymetrix SNP genotyping arrays, confirming that they are not platform-specific. The causes of genomic waves are not well-understood, and they may prevent accurate inference of copy number variations (CNVs). By measuring DNA concentration for 1444 samples and by genotyping the same sample multiple times with varying DNA quantity, we demonstrated that DNA quantity correlates with the magnitude of waves. We further showed that wavy signal patterns correlate best with GC content, among multiple genomic features considered. To measur...
Improvements to bead-based oligonucleotide ligation SNP genotyping assays.
We describe a bead-based, multiplexed, oligonucleotide ligation assay (OLA) performed on the Luminex flow cytometer. Differences between this method and those previously reported include the use of far fewer beads and the use of a universal oligonucleotide for signal detection. These innovations serve to significantly reduce the cost of the assay, while maintaining robustness and accuracy. Comparisons are made between the Luminex OLA and both pyrosequencing and direct sequencing. Experiments to assess conversion rates, call rates, and concordance across technical replicates are also presented.
PMID: 19007340 [PubMed - in process] (Source: BioTechniques)
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