Global CNV assessment (Redon et al, 2006)

Browse data

Browse Data by Individual

Individual chromosome genome assembly browser

Individual

NA06985 NA06991 NA06993 NA06994 NA07000 NA07019 NA07022 NA07029 NA07034 NA07048 NA07055 NA07056 NA07345 NA07348 NA07357 NA10830 NA10831 NA10835 NA10838 NA10839 NA10846 NA10847 NA10854 NA10855 NA10856 NA10857 NA10859 NA10860 NA10861 NA10863 NA11829 NA11830 NA11831 NA11832 NA11839 NA11840 NA11881 NA11882 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12005 NA12006 NA12043 NA12044 NA12056 NA12057 NA12144 NA12145 NA12146 NA12154 NA12155 NA12156 NA12234 NA12236 NA12239 NA12248 NA12249 NA12264 NA12707 NA12716 NA12717 NA12740 NA12750 NA12751 NA12752 NA12753 NA12760 NA12761 NA12762 NA12763 NA12801 NA12802 NA12812 NA12813 NA12814 NA12815 NA12864 NA12865 NA12872 NA12873 NA12874 NA12875 NA12878 NA12891 NA12892 NA18500 NA18501 NA18502 NA18503 NA18504 NA18505 NA18506 NA18507 NA18508 NA18515 NA18516 NA18517 NA18521 NA18522 NA18523 NA18524 NA18526 NA18529 NA18532 NA18537 NA18540 NA18542 NA18545 NA18547 NA18550 NA18552 NA18555 NA18558 NA18561 NA18562 NA18563 NA18564 NA18566 NA18570 NA18571 NA18572 NA18573 NA18576 NA18577 NA18579 NA18582 NA18592 NA18593 NA18594 NA18603 NA18605 NA18608 NA18609 NA18611 NA18612 NA18620 NA18621 NA18622 NA18623 NA18624 NA18632 NA18633 NA18635 NA18636 NA18637 NA18852 NA18853 NA18854 NA18855 NA18856 NA18857 NA18858 NA18859 NA18860 NA18861 NA18862 NA18863 NA18870 NA18871 NA18872 NA18912 NA18913 NA18914 NA18940 NA18942 NA18943 NA18944 NA18945 NA18947 NA18948 NA18949 NA18951 NA18952 NA18953 NA18956 NA18959 NA18960 NA18961 NA18964 NA18965 NA18966 NA18967 NA18968 NA18969 NA18970 NA18971 NA18972 NA18973 NA18974 NA18975 NA18976 NA18978 NA18980 NA18981 NA18987 NA18990 NA18991 NA18992 NA18994 NA18995 NA18997 NA18998 NA18999 NA19000 NA19003 NA19005 NA19007 NA19012 NA19092 NA19093 NA19094 NA19098 NA19099 NA19100 NA19101 NA19102 NA19103 NA19116 NA19119 NA19120 NA19127 NA19128 NA19129 NA19130 NA19131 NA19132 NA19137 NA19138 NA19139 NA19140 NA19141 NA19142 NA19143 NA19144 NA19145 NA19152 NA19153 NA19154 NA19159 NA19160 NA19161 NA19171 NA19172 NA19173 NA19192 NA19193 NA19194 NA19200 NA19201 NA19202 NA19203 NA19204 NA19205 NA19206 NA19207 NA19208 NA19209 NA19210 NA19211 NA19221 NA19222 NA19223 NA19238 NA19239 NA19240

chromosome

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y

genome assembly

NCBI35 NCBI36

browser

UCSC Ensembl

How to browse a sample

Choose the sample, the chromosome, the genome assembly and the browser that you would like to use, then click on "Browse".

This will redirect you to the first 1Mb of the chosen chromosome.

UCSC

The UCSC browser will show up to four tracks:

• The clones on the WGTP array (Track "Sanger_WGTP_clones")
• The log2ratio of copy number at each clone (Track "DyeSwap Ratios for ...")
• The clones called as losses relative to the reference DNA (Track "Loss calls ...")
• The clones called as gains relative to the reference DNA (Track "Gain calls ...")
• The distribution of log2ratios across all 270 HapMap samples can be visualised for each clone on the array by clicking on the desired clone in the track "Sanger_WGTP_Clones" to show the details page for that clone and then clicking on the link entitled "Outside Link".

For help about the UCSC browser use, please visit UCSC help

Ensembl

Choosing to display the CNVs for an individual in the Ensembl browser will show four tracks. These will be :

• The clones on the WGTP array (Track "Sanger_WGTP_clones" )
• A histogram track of the probe/clone intensity log2ratios.
• The clones called as losses relative to the reference DNA (Track "cnvs_loss_NAxxxxx")
• The clones called as gains relative to the reference DNA (Track "cnvs_gain_NAxxxxxx")
• By clicking on any of the clone features in the Sanger_WGTP_clones you can follow a link (click 'details') to view a distribution of the log2ratio scores for each clone across the whole dataset of 270 HapMap individuals.

Note that due to software issues with the Ensembl website, when viewing CNVs on the NCBI35 assembly the histogram track of log2ratios will appear as a track of vertical bars. When you mouse over these the log2ratio will be displayed as a tool tip. Ideally, use the NCBI36 assembly display as it is much more illustrative.

For help about the Ensembl browser use, please visit Ensembl help

Browse Copy Number Variable regions identified within the 270 HapMap samples

Hapmap CNVs

WGTP_CNVs 500KEA_CNVs Redon_CNVs

genome assembly

NCBI35 NCBI36

browser

UCSC Ensembl

Hapmap CNVs genome assembly browser

• WGTP_CNVs - CNV identified using the WGTP array among all 270 HapMap samples
• 500KEA_CNVs - CNV identified using the Affymetrix 500k GeneChip Early Access arrays among all 270 HapMap samples
• Redon_CNVs - merged CNVs from both 500KEA and WGTP platforms for the 270 HapMap Samples

Data download

Data access summary

• Gene Expression Omnibus - access raw data from the 500K EA as well as the 500K commercial arrays, with accession numbers GSE5013 and GSE5173
• ArrayExpress - access WGTP data, with accession number E-TABM-107
• Database of Genomic Variants - access CNV calls integrated with all other CNV data

The data can be downloaded in four formats:

• A single text file containing the mean dye-swap intensity for each clone in each individual
• Raw extracted intensities for each image (BlueFuse format) in Excel-compatible text files
• Normalized extracted intensities, with low intensity spots removed and log2ratios calculated.
• Some sample image files for dye-swap experiment and a mapping file for use with the image files

Download data

The data were generated using the WGTP array with dye-swap for 269 HapMap individuals and using a single male reference : HapMap individual NA10851.

WGTP Intensities Data

Alternatively you can download all the pre and post-processed intensities for all of the 269 individuals:

• part1/3 ( ~782Mo )
• part2/3 ( ~785Mo )
• part3/3 ( ~541Mo )

Or you can download the individual's intensities of your interest:

Hapmap sample

NA06985 NA06991 NA06993 NA06994 NA07000 NA07019 NA07022 NA07029 NA07034 NA07048 NA07055 NA07056 NA07345 NA07348 NA07357 NA10830 NA10831 NA10835 NA10838 NA10839 NA10846 NA10847 NA10854 NA10855 NA10856 NA10857 NA10859 NA10860 NA10861 NA10863 NA11829 NA11830 NA11831 NA11832 NA11839 NA11840 NA11881 NA11882 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12005 NA12006 NA12043 NA12044 NA12056 NA12057 NA12144 NA12145 NA12146 NA12154 NA12155 NA12156 NA12234 NA12236 NA12239 NA12248 NA12249 NA12264 NA12707 NA12716 NA12717 NA12740 NA12750 NA12751 NA12752 NA12753 NA12760 NA12761 NA12762 NA12763 NA12801 NA12802 NA12812 NA12813 NA12814 NA12815 NA12864 NA12865 NA12872 NA12873 NA12874 NA12875 NA12878 NA12891 NA12892 NA18500 NA18501 NA18502 NA18503 NA18504 NA18505 NA18506 NA18507 NA18508 NA18515 NA18516 NA18517 NA18521 NA18522 NA18523 NA18524 NA18526 NA18529 NA18532 NA18537 NA18540 NA18542 NA18545 NA18547 NA18550 NA18552 NA18555 NA18558 NA18561 NA18562 NA18563 NA18564 NA18566 NA18570 NA18571 NA18572 NA18573 NA18576 NA18577 NA18579 NA18582 NA18592 NA18593 NA18594 NA18603 NA18605 NA18608 NA18609 NA18611 NA18612 NA18620 NA18621 NA18622 NA18623 NA18624 NA18632 NA18633 NA18635 NA18636 NA18637 NA18852 NA18853 NA18854 NA18855 NA18856 NA18857 NA18858 NA18859 NA18860 NA18861 NA18862 NA18863 NA18870 NA18871 NA18872 NA18912 NA18913 NA18914 NA18940 NA18942 NA18943 NA18944 NA18945 NA18947 NA18948 NA18949 NA18951 NA18952 NA18953 NA18956 NA18959 NA18960 NA18961 NA18964 NA18965 NA18966 NA18967 NA18968 NA18969 NA18970 NA18971 NA18972 NA18973 NA18974 NA18975 NA18976 NA18978 NA18980 NA18981 NA18987 NA18990 NA18991 NA18992 NA18994 NA18995 NA18997 NA18998 NA18999 NA19000 NA19003 NA19005 NA19007 NA19012 NA19092 NA19093 NA19094 NA19098 NA19099 NA19100 NA19101 NA19102 NA19103 NA19116 NA19119 NA19120 NA19127 NA19128 NA19129 NA19130 NA19131 NA19132 NA19137 NA19138 NA19139 NA19140 NA19141 NA19142 NA19143 NA19144 NA19145 NA19152 NA19153 NA19154 NA19159 NA19160 NA19161 NA19171 NA19172 NA19173 NA19192 NA19193 NA19194 NA19200 NA19201 NA19202 NA19203 NA19204 NA19205 NA19206 NA19207 NA19208 NA19209 NA19210 NA19211 NA19221 NA19222 NA19223 NA19238 NA19239 NA19240

Download WGTP Individual Sample CNVs

Hapmap CNVs (sample level)

NCBI35 NCBI36

Download Copy Number Variable regions identified within the 270 HapMap samples

Hapmap CNVs

WGTP_CNVs 500KEA_CNVs Redon_CNVs

genome assembly

NCBI35 NCBI36

To browse data within a genome browser, please visit the 'Browse Data' tab.

Related files

• FTP_README
• Mapping files WGTP Array and Genomic clones mapping files
• log2ratios Intensities for the 269 Hapmap Individuals

Validation data

Two types of experiments are available: replicates and add_in experiments.

Their pre-processed and post-processed intensities (as defined in data description) are fully available. Only samples of raw scanner images files are available, for any interest in downloading the Raw Scanner images please contact Matthew Hurles.

Validation data:

All the validation datafiles are in the same format as the one provided for the WGTP Array.

Pre & Post processed intensities data
Replicates experiments	All replicates data (~322Mo)		FTP
Add_in experiments	Human chromosome validation (~380Mo)	Hamster, Mouse & self experiments validation (~118Mo)	FTP

Replicates Raw Images
NA15510A	reference_red	reference_green	sample_green	sample_red	FTP
NA12144A	reference_red	reference_green	sample_green	sample_red	FTP
self_A	reference_red	reference_green	sample_green	sample_red	FTP

Add_in experiments Raw Images
chrom10		FTP
chrom10 exp 1489-16	chr10_red_1489-16	chr10_green_1489-16
chrom10 exp 1489-17	chr10_red_1489-17	chr10_green_1489-17
chrom10 exp 1489-18	chr10_red_1489-18	chr10_green_1489-18
chrom10 exp 1489-19	chr10_red_1489-19	chr10_green_1489-19
chrom11		FTP
chrom11 exp 1489-20	chr11_red_1489-20	chr11_green_1489-20
chrom11 exp 1489-21	chr11_red_1489-21	chr11_green_1489-21
chrom11 exp 1489-22	chr11_red_1489-22	chr11_green_1489-22
chrom11 exp 1489-23	chr11_red_1489-23	chr11_green_1489-23

Data release

Sample

It corresponds to the HapMap Individual that has been used for the WGTP array.

Mapping files

The 2 GAL file are for the mapping on the WGTP array

WGTP_array_map1.gal is to use with experiments until 23/09/2005 and WGTP_array_map2.gal with experiments from 27/09/2005.

The text file WGTP_clone_map_NCBIxx.txt contains the mapping of the Human clones ( for both assembly NCBI35 (May 2004) and NCBI36 (March 2006) ).

Log2ratios Intensities for the 269 Hapmap Individuals

This single text file contains the mean dye-swap intensity for each clone in each individual.

All experimental artefacts, as provided in this list, have been removed from this file.

Pre processed ( Raw ) intensities ( from BlueFuse)

Foreach individual there are 2 files: one per intensity signal ( red, green )

Fluorescence intensities and log2 ratio values were extracted using the Bluefuse software (Bluegnome Ltd) from the scanner (raw) images.

Post processed intensities ( from BlueFuse )

For each individual there are 2 files : one per intensity signal ( red, green ).

These excel files are derived from the Raw intensities excel file after a post processing from the software BlueFuse.

This post processing consisted in:

• Any spot giving low signal intensities ("amplitude"<100 in both channels) or inconsistent fluorescence patterns ("confidence" < 0.5 or "quality" = 0) was excluded from further analysis.
• Log2 ratio values were then normalised by median block values, still using Bluefuse capabilities.

Raw images green/red

For each individual there are 2 files : one per intensity signal ( red, green ).

These images are the raw output from the laser scanner (Agilent Technologies) after the experiment.

Examples of raw image files raw scanner WGTP image files:

Sample	raw scanner images				directory
NA07019	sample_green	reference_red	sample_red	reference_green	FTP
NA07022	sample_green	reference_red	sample_red	reference_green	FTP
NA07029	sample_green	reference_red	sample_red	reference_green	FTP
NA12057	reference_red	sample_green	reference_green	sample_red	FTP
NA18500	reference_red	sample_green	reference_green	sample_red	FTP
NA18501	reference_red	sample_green	reference_green	sample_red	FTP
NA18502	reference_red	sample_green	reference_green	sample_red	FTP
NA18547	reference_red	sample_green	reference_green	sample_red	FTP
NA18558	reference_red	sample_green	reference_green	sample_red	FTP
NA18555	reference_red	sample_green	reference_green	sample_red	FTP

For any interest in downloading some other image files, please contact Matthew Hurles.

Validation data

All the validation datafiles are in the same format as the one provided for the WGTP Array.

Contact

This project was a collaborative effort of the groups of:

• Nigel Carter
• Matthew Hurles
• Chris Tyler-Smith
• Charles Lee, Harvard Medical School
• Steve Scherer, Hospital for Sick Children

Acknowledgements

Nigel Carter, Richard Redon, Heike Fiegler, Lyndal Montgomery, Matthew Hurles, Chris Tyler-Smith, Tatiana Zerjal, Daniel Andrews, Armand Valsesia, Fengtang Yang, Dimitrios Kalaitzopoulos, Charles Lee, Steve Scherer

Funding was provided by the Wellcome Trust.

Publication

• Global variation in copy number in the human genome.

  Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW and Hurles ME

  Nature 2006;444;7118;444-54

  PUBMED: 17122850; PMC: 2669898; DOI: 10.1038/nature05329