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Database/ list of Common CNVs in humans
2
8
Entering edit mode
6.8 years ago
Kizuna ▴ 830

Hi All,

I am searching for a database or even list for common CNVs in humans, I found one database published by Donald F. Conrad et al in Nature 2010.

I would like to ask if you know other useful sources !

Best regards

Kiz

gene cnv database • 3.8k views
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5
Entering edit mode
6.8 years ago

search for CNV in the UCSC: http://genome.ucsc.edu/cgi-bin/hgTracks ('track search')

e.g: UCSC dgv: http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=dgvMerged

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/dgvMerged.txt.gz" |
gunzip -c |grep -i cnv |  head -n 2 | verticalize -n | more

>>> 1
$1    73
$2    chr1
$3    632917
$4    998289
$5    essv4734
$6    0
$7    +
$8    632917
$9    632917
$10    9127187
$11    CNV
$12    Redon et al 2006
$13    17122850
$14    BAC aCGH, MassSpec, PCR, qPCR, SNP array
$15    Agilent
$16    
$17    
$18    271
$19    0
$20    0
$21    Samples from several populations that are part of the HapMap project.
$22    AGRN, C1orf170, FAM41C, HES4, ISG15, KLHL17, LINC00115, LOC100130417, LOC100133331, LOC100288069, LOC643837,
 NOC2L, PLEKHN1, SAMD11
$23    NA18620
<<< 1

>>> 2
$1    73
$2    chr1
$3    752565
$4    1018704
$5    essv2408
$6    0
$7    +
$8    752565
$9    752565
$10    9127187
$11    CNV
$12    Redon et al 2006
$13    17122850
$14    BAC aCGH, MassSpec, PCR, qPCR, SNP array
$15    Affymetrix GeneChip Mapping 500K Early Access Array (250K_Sty_SNP + 250K_Nsp_SNP)
$16    
$17    
$18    271
$19    0
$20    0
$21    Samples from several populations that are part of the HapMap project.
$22    AGRN, C1orf159, C1orf170, FAM41C, HES4, ISG15, KLHL17, LINC00115, LOC100130417, LOC643837, NOC2L, PLEKHN1, R
NF223, SAMD11
$23    NA18976
<<< 2

 

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3
Entering edit mode
6.8 years ago
Robert Sicko ▴ 630

Also check out CHOP (High-resolution mapping of copy number variations in 2,026 healthy individuals) 

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1
Entering edit mode

r.j.sicko : thank you, 

In fact, I found the Database of Genomic variants , which currently contains information from 53 different peer reviewed studies, corresponding to ~ 265,000 CNV regions and ~1k inversions. Among the 53 studies, I found the one you are mentioning (shaikh et al , Genome Research 2009).

 

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