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estd198 (Chia et al. 2013)

Organism:
Human
Study Type:
Control Set
Submitter:
Nicole Chia
Description:
We performed high density array analysis of 64 unrelated healthy Caucasian females using Illumina Omni1-Quad SNP microarray. Two CNV detection algorithms were applied to the raw data and the calls were merged to ensure a robust analysis of copy number variation. The results of a comprehensive investigation of CNVs on chromosome 18 in relation to distribution, incidence, gene density, population frequency and association with genomic architecture are described. Two CNV regions were confirmed by sequencing and precise breakpoints defined demonstrating a 2bp microhomology at the breakpoint junction of both CNVs. The investigation of associations of CNVs with repetitive elements on chromosome 18 shows that one third do not involve breakpoints in repeat sequences and the results of investigations suggests that the mechanism of derivation of CNVs in the normal population may be multi-factorial. The population frequencies of two CNVs were determined using a simple screening test that was designed to differentiate genotypes. This is the first specific investigation of CNVs on chromosome 18 with high resolution microarray of normal individuals using DNA extracted from whole blood. See Variant Summary counts for estd198 in dbVar Variant Summary.
Publication(s):
Chia et al. 2013

Detailed Information: Download 381 Variant Regions, Download 399 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI36 (hg18)

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000018.10Chr18381399RemappedNC_000018.10
NT_187666.1Chr18|NT_187666.1910RemappedNT_187666.1
NW_003315961.1Chr18|NW_003315961.1910RemappedNW_003315961.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000018.9Chr18381399RemappedNC_000018.9
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000018.8Chr18381399SubmittedNC_000018.8

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000018.8Chr1838138100003993990000
Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000018.8Chr18381372000939938900010

Samplesets

Number of Samplesets: 1

Name:
AN_18(Chromosome 18)
Description:
Whole blood from 64 healthy female individuals were investigated for copy number variation. The study presented here represents the investigation of chromosome 18. A total of 500 DNA samples from The Aussie Normal Collection and anonymous Australian Red Cross blood donors were used in the population analysis.
Size:
64
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported
Sex:
Female
  • Download Samples as CSV file
    • Samples for sampleset 1
    Sample IDCell TypeSubject ID SexEthnicitySubject Phenotype
    2378 [56]Whole bloodAN2378 [56]FemaleAustralianNot reported
    2243 [60]Whole bloodAN2243 [60]FemaleAustralianNot reported
    2349 [43]Whole bloodAN2349 [43]FemaleAustralianNot reported
    2326 [24]Whole bloodAN2326 [24]FemaleAustralianNot reported
    2315 [14]Whole bloodAN2315 [14]FemaleAustralianNot reported
    2358 [52]Whole bloodAN2358 [52]FemaleAustralianNot reported
    2242 [59]Whole bloodAN2242 [59]FemaleAustralianNot reported
    2319 [17]Whole bloodAN2319 [17]FemaleAustralianNot reported
    2311 [10]Whole bloodAN2311 [10]FemaleAustralianNot reported
    2334 [31]Whole bloodAN2334 [31]FemaleAustralianNot reported
    2340 [36]Whole bloodAN2340 [36]FemaleAustralianNot reported
    2361 [54]Whole bloodAN2361 [54]FemaleAustralianNot reported
    2338 [34]Whole bloodAN2338 [34]FemaleAustralianNot reported
    2354 [48]Whole bloodAN2354 [48]FemaleAustralianNot reported
    2304 [3]Whole bloodAN2304 [3]FemaleAustralianNot reported
    2356 [50]Whole bloodAN2356 [50]FemaleAustralianNot reported
    2353 [47]Whole bloodAN2353 [47]FemaleAustralianNot reported
    2379 [57]Whole bloodAN2379 [57]FemaleAustralianNot reported
    2352 [46]Whole bloodAN2352 [46]FemaleAustralianNot reported
    2355 [49]Whole bloodAN2355 [49]FemaleAustralianNot reported
    2332 [29]Whole bloodAN2332 [29]FemaleAustralianNot reported
    2333 [30]Whole bloodAN2333 [30]FemaleAustralianNot reported
    2303 [2]Whole bloodAN2303 [2]FemaleAustralianNot reported
    2345 [40]Whole bloodAN2345 [40]FemaleAustralianNot reported
    2347 [42]Whole bloodAN2347 [42]FemaleAustralianNot reported
    2309 [8]Whole bloodAN2309 [8]FemaleAustralianNot reported
    2323 [21]Whole bloodAN2323 [21]FemaleAustralianNot reported
    2245 [62]Whole bloodAN2245 [62]FemaleAustralianNot reported
    2320 [18]Whole bloodAN2320 [18]FemaleAustralianNot reported
    2246 [63]Whole bloodAN2246 [63]FemaleAustralianNot reported
    2328 [26]Whole bloodAN2328 [26]FemaleAustralianNot reported
    2360 [53]Whole bloodAN2360 [53]FemaleAustralianNot reported
    2350 [44]Whole bloodAN2350 [44]FemaleAustralianNot reported
    2305 [4]Whole bloodAN2305 [4]FemaleAustralianNot reported
    2357 [51]Whole bloodAN2357 [51]FemaleAustralianNot reported
    2244 [61]Whole bloodAN2244 [61]FemaleAustralianNot reported
    2346 [41]Whole bloodAN2346 [41]FemaleAustralianNot reported
    2313 [12]Whole bloodAN2313 [12]FemaleAustralianNot reported
    2325 [23]Whole bloodAN2325 [23]FemaleAustralianNot reported
    2327 [25]Whole bloodAN2327 [25]FemaleAustralianNot reported
    2339 [35]Whole bloodAN2339 [35]FemaleAustralianNot reported
    2329 [27]Whole bloodAN2329 [27]FemaleAustralianNot reported
    2324 [22]Whole bloodAN2324 [22]FemaleAustralianNot reported
    2316 [15]Whole bloodAN2316 [15]FemaleAustralianNot reported
    2337 [33]Whole bloodAN2337 [33]FemaleAustralianNot reported
    2351 [45]Whole bloodAN2351 [45]FemaleAustralianNot reported
    2343 [38]Whole bloodAN2343 [38]FemaleAustralianNot reported
    2344 [39]Whole bloodAN2344 [39]FemaleAustralianNot reported
    2307 [6]Whole bloodAN2307 [6]FemaleAustralianNot reported
    2312 [11]Whole bloodAN2312 [11]FemaleAustralianNot reported
    2317 [16]Whole bloodAN2317 [16]FemaleAustralianNot reported
    2314 [13]Whole bloodAN2314 [13]FemaleAustralianNot reported
    2380 [58]Whole bloodAN2380 [58]FemaleAustralianNot reported
    2301 [1]Whole bloodAN2301 [1]FemaleAustralianNot reported
    2322 [20]Whole bloodAN2322 [20]FemaleAustralianNot reported
    2321 [19]Whole bloodAN2321 [19]FemaleAustralianNot reported
    2377 [55]Whole bloodAN2377 [55]FemaleAustralianNot reported
    2306 [5]Whole bloodAN2306 [5]FemaleAustralianNot reported
    2310 [9]Whole bloodAN2310 [9]FemaleAustralianNot reported
    2331 [28]Whole bloodAN2331 [28]FemaleAustralianNot reported
    2342 [37]Whole bloodAN2342 [37]FemaleAustralianNot reported
    2336 [32]Whole bloodAN2336 [32]FemaleAustralianNot reported
    2308 [7]Whole bloodAN2308 [7]FemaleAustralianNot reported
    2290 [64]Whole bloodAN2290 [64]FemaleAustralianNot reported

    Experimental Details

    Experiment IDTypeMethodAnalysisPlatformsNumber of Variant Calls
    1DiscoveryMerging of experiments 3,7Merging of experiments 3,7See merged experiments399
    3DiscoverySNP arraySNP genotyping analysisIlluminaOmni1-QUAD0
    7DiscoverySNP arraySNP genotyping analysisIlluminaOmni1-QUAD0
    2ValidationKaryotypingManual observation399
    4ValidationPCRManual observation14
    5ValidationSequencingSequence alignment5
    6ValidationPCRManual observation14

    Validations

    Experiment IDMethodAnalysisNumber of Variant Calls Validated
    2KaryotypingManual observation399
    4PCRManual observation14
    5SequencingSequence alignment5
    6PCRManual observation14
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