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    Results: 20

    1.

    Towards a comprehensive structural variation map of an individual human genome for personalized medicine

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Homo sapiens
    Type:
    SNP genotyping by SNP array; Genome variation profiling by SNP array; Genome variation profiling by genome tiling array
    87 related Platforms
    100 Samples
    Download data:
    GEO (CEL, CHP, GFF, PAIR, TXT)
    Series
    Accession:
    GSE20290
    ID:
    200020290
    2.

    NimbleGen 42M data for the HuRef individual

    (Submitter supplied) The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array
    60 related Platforms
    60 Samples
    Download data:
    GEO (GFF, PAIR)
    Series
    Accession:
    GSE20289
    ID:
    200020289
    3.

    Agilent custom 24M array CGH data for the HuRef individual

    (Submitter supplied) The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array
    24 related Platforms
    24 Samples
    Download data:
    GEO (GFF, TXT)
    Series
    Accession:
    GSE20288
    ID:
    200020288
    4.

    Agilent custom 244K array CGH data for the HuRef individual

    (Submitter supplied) The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array
    Platform:
    GPL16619
    14 Samples
    Download data:
    GEO (GFF, TXT)
    Series
    Accession:
    GSE20287
    ID:
    200020287
    5.

    Illumina SNP and CNV data for the HuRef individual

    (Submitter supplied) The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. more...
    Organism:
    Homo sapiens
    Type:
    SNP genotyping by SNP array; Genome variation profiling by SNP array
    Platform:
    GPL6983
    1 Sample
    Download data:
    GEO (GFF, TXT)
    Series
    Accession:
    GSE20284
    ID:
    200020284
    6.

    Affymetrix SNP and CNV data for the HuRef individual

    (Submitter supplied) The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. more...
    Organism:
    Homo sapiens
    Type:
    SNP genotyping by SNP array; Genome variation profiling by SNP array
    Platform:
    GPL6801
    1 Sample
    Download data:
    GEO (CEL, CHP, GFF)
    Series
    Accession:
    GSE20275
    ID:
    200020275
    7.

    Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes

    (Submitter supplied) Goal: To identify copy number variation in normal individuals using high density, non-polymorphic oligonucleotide probes Background DNA sequence diversity within the human genome may be more greatly affected by copy number variations (CNVs) than single nucleotide polymorphisms (SNPs). Although the importance of CNVs in genome wide association studies (GWAS) is becoming widely accepted, the optimal methods for identifying these variants are still under evaluation. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array
    Platforms:
    GPL6659 GPL6660
    42 Samples
    Download data:
    GEO (CEL)
    Series
    Accession:
    GSE9053
    ID:
    200009053
    8.

    The Complete Genome of a Single Individual by Massively Parallel DNA Sequencing

    (Submitter supplied) The association of genetic variation with disease and drug response, together with improvements in nucleic acids technologies, has given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome has prevented the routine application of sequencing methods to deciphering complete individual human genomes, and has so far limited the realization of the full potential of genomics for science and human health. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array; Genome variation profiling by SNP array; SNP genotyping by SNP array
    Platforms:
    GPL4544 GPL3720 GPL3718
    6 Samples
    Download data:
    GEO (CEL, TXT)
    Series
    Accession:
    GSE10668
    ID:
    200010668
    9.

    DNA copy-number changes

    (Submitter supplied) Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by array
    Platform:
    GPL179
    10 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE49
    ID:
    200000049
    10.

    An initial comparative map of copy number variations in the goat (Capra hircus) genome

    (Submitter supplied) Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. more...
    Organism:
    Capra hircus; Bos taurus
    Type:
    Genome variation profiling by genome tiling array
    Platform:
    GPL10990
    9 Samples
    Download data:
    GEO (PAIR)
    Series
    Accession:
    GSE24436
    ID:
    200024436
    11.

    Canine CNVs associated with canFam2 segmental duplications

    (Submitter supplied) This study centered on using a custom made Nimblegen aCGH chip that targeted all segmental duplications in the canine genome to identify associated CNVs. A total of 19 hybridizations were performed in a panel of diverse dogs and a single wolf.
    Organism:
    Canis lupus familiaris; Canis lupus
    Type:
    Genome variation profiling by genome tiling array
    Platform:
    GPL7501
    19 Samples
    Download data:
    GEO (PAIR, TXT)
    Series
    Accession:
    GSE13266
    ID:
    200013266
    12.

    Combined arrayCGH and SNP-loss of heterozygosity analysis in cervical cancer

    (Submitter supplied) BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by array; Genome variation profiling by genome tiling array; Genome variation profiling by SNP array; SNP genotyping by SNP array
    Platforms:
    GPL4012 GPL2641 GPL201
    40 Samples
    Download data:
    GEO (CEL, GPR)
    Series
    Accession:
    GSE8605
    ID:
    200008605
    13.

    The fine-scale and complex architecture of human copy number variation

    (Submitter supplied) Despite considerable excitement over the potential functional significance of copy number variants (CNVs), we still lack knowledge of the fine-scale architecture of the large majority of CNV regions in the human genome. In this study, we used a high-resolution array-based comparative genomic hybridization (aCGH) platform that targeted known CNV regions of the human genome at ~1 kb resolution to interrogate the genomic DNAs of 30 individuals from four HapMap populations. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array
    Platforms:
    GPL6251 GPL6250
    144 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE9831
    ID:
    200009831
    14.

    8-chip high-resolution aCGH experiment NA15510 vs. NA18505

    (Submitter supplied) We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome sequencing method to identify SVs 3 kb or larger that combines the rescue and capture of paired-ends of 3 kb fragments, massive 454 Sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an African and putatively European individual and identified shared and divergent SVs relative to the reference genome. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array
    8 related Platforms
    8 Samples
    Download data:
    GEO (PAIR)
    Series
    Accession:
    GSE9002
    ID:
    200009002
    15.

    Supervised Lowess normalization of comparative genome hybridization data: application to lactococcal strain comparisons.

    (Submitter supplied) Background Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. In aCGH data, systematic errors are comparable to those occurring in transcriptome data. However, especially for microbes, an additional source of variation exists: differences in hybridization due to gene sequence divergence between the strains hybridized. Current normalization methods do not take this source of variation into consideration. more...
    Organism:
    Lactococcus lactis subsp. cremoris MG1363; Lactococcus lactis subsp. lactis Il1403
    Type:
    Genome variation profiling by array
    Platform:
    GPL2545
    4 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE9039
    ID:
    200009039
    16.

    A first comparative map of copy number variations in the sheep genome

    (Submitter supplied) We carried out a cross species cattle-sheep array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the sheep genome analysing animals of Italian dairy breeds (Sarda, Bagnolese, Laticauda, Massese and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs) covering about 10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and median equal to 77.6 kb and 55.9 kb, respectively. more...
    Organism:
    Bos taurus; Ovis aries
    Type:
    Genome variation profiling by genome tiling array
    Platform:
    GPL10990
    11 Samples
    Download data:
    GEO (PAIR)
    Series
    Accession:
    GSE25122
    ID:
    200025122
    17.

    HapMap Yoruban individuals vs CEPH reference

    (Submitter supplied) It is becoming clear that copy number polymorphism in the human genome is a significant form of genetic variation. We have developed a new method that uses SNP genotype data from parent-offspring trios and applied it to HapMap to conduct high-resolution detection of deletion polymorphism. Of the delections uncovered, approximately 100 have been experimentally validated using comparative genome hybridization on these tiling-resolution oligonucleotide microarrays. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array
    Platform:
    GPL2988
    8 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE3474
    ID:
    200003474
    18.

    CGH validation of de novo CNVs in asthma and CEU HapMap samples

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array
    Platforms:
    GPL10780 GPL10779
    60 Samples
    Download data:
    GEO (PAIR, TXT)
    Series
    Accession:
    GSE23645
    ID:
    200023645
    19.

    Custom array CGH validation of de novo CNVs in CEU HapMap samples

    (Submitter supplied) This is the validation data for candidate de novo CNV calls made in the CEU Hapmap by Itsara et al., Genome Research 2010. In this study, de novo CNV calls were initially made with Illumina 1M SNP arrays. Validation of CNV calls was performed with Nimblegen custom array CGH using the extended CEPH pedigrees. A truly de novo CNV would be unobserved in the first generation (CEU trio parents), validated in the second generation (CEU trio children), and assuming no selective effects, transmitted to approximately half of the individuals in the third generation. more...
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array
    Platform:
    GPL10780
    36 Samples
    Download data:
    GEO (PAIR, TXT)
    Series
    Accession:
    GSE23575
    ID:
    200023575
    20.

    Custom array CGH validation of de novo CNVs in asthma samples

    (Submitter supplied) This is the validation data for candidate de novo CNV calls made in the asthma trios by Itsara et al., Genome Research 2010. In this study, de novo CNV calls in the asthma data set were initially made with Illumina 550K SNP arrays. Validation was performed with custom Nimblegen array CGH for which DNA was available. de novo CNVs would be expected to validate in the child of each trio tested, and not be detected in either parent.
    Organism:
    Homo sapiens
    Type:
    Genome variation profiling by genome tiling array
    Platform:
    GPL10779
    24 Samples
    Download data:
    GEO (PAIR, TXT)
    Series
    Accession:
    GSE23572
    ID:
    200023572

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