Journal:

Article Title: Linkage Disequilibrium and Heritability of Copy-Number Polymorphisms within Duplicated Regions of the Human Genome

doi:

Figure Lengend Snippet: CNP ACNF and corroboration with other data sources. When stratified by frequency, the variants more commonly seen in the HapMap population samples were more often supported by other sources of CNP data, such as previous reports,1–3,13 and by our own comparison with oligonucleotide-array data. This is partly because of the nature of rare variants, in that they are less likely to be seen by other studies of small populations, but also implies that a proportion may be false-positive results and should be considered with more caution until sequence data are generated to fully document the variant in question.

Article Snippet: Oligonucleotide-Based Array CGH A custom oligonucleotide array (NimbleGen Systems) was designed that consisted of 385,000 isothermal probes (45–70 bp) that covered the identical regions represented on the segmental duplication array, with an overall mean probe density of one probe per 733 bp.

Techniques: Comparison, Sequencing, Generated, Variant Assay

Journal:

Article Title: Linkage Disequilibrium and Heritability of Copy-Number Polymorphisms within Duplicated Regions of the Human Genome

doi:

Figure Lengend Snippet: Fine structure variation of a common CNP. The CNP initially observed in BAC RP11-142H6 was observed as a common variant found in all subgroups of the HapMap population samples (ACNF 0.46). BAC-based array CGH results (top panel) for eight BAC clones spanning ∼1.5 Mb of chromosome 19 show continuous variability. Fine-tiling oligonucleotide array CGH profiles of the same individuals confirms subtle copy-number differences over the 156-kb interval encompassed by RP11-142H6. Note the close correlation between the log2 hybridization data from BAC-based array CGH and oligonucleotide microarray data. The recurrent pattern of log2 ratio data corresponds to a tandem organization of a 60-kb region composed of intrachromosomal segmental duplication (gray bars). Avg. = average.

Article Snippet: Oligonucleotide-Based Array CGH A custom oligonucleotide array (NimbleGen Systems) was designed that consisted of 385,000 isothermal probes (45–70 bp) that covered the identical regions represented on the segmental duplication array, with an overall mean probe density of one probe per 733 bp.

Techniques: Variant Assay, Clone Assay, Hybridization, Microarray

Journal:

Article Title: Linkage Disequilibrium and Heritability of Copy-Number Polymorphisms within Duplicated Regions of the Human Genome

doi:

Figure Lengend Snippet: Oligonucleotide array data underlying CNPs detected via BAC array. Each plot displays the oligonucleotide hybridization data for a subset of samples tested. The BAC ID and build 34 interval for that BAC are indicated at the top left corner of each plot. The average log2 ratio determined by BAC array CGH is listed in parentheses within the graph key. The tracks depicting segmental duplications detected using a whole-genome depth of coverage statistic (WSSD) and known genes, extracted from the UCSC Genome Browser, are shown below each plot. Note that a three-point moving average of the oligonucleotide data is plotted. Avg. = average.

Article Snippet: Oligonucleotide-Based Array CGH A custom oligonucleotide array (NimbleGen Systems) was designed that consisted of 385,000 isothermal probes (45–70 bp) that covered the identical regions represented on the segmental duplication array, with an overall mean probe density of one probe per 733 bp.

Techniques: Hybridization