Description
This track shows copy number variation (CNV) in the ENCODE Tier 1 and Tier 2
human cell lines GM12878, HepG2, and K562 as determined by Illumina's Human
1M-Duo Infinium HD BeadChip assay and CNV analysis by circular binary segmentation (CBS).
Two biological replicates were generated for each cell line.
Because biological replicates gave very similar results,
the replicates were averaged to provide a single genotyping
dataset in order to apply these data to other ENCODE experiments.
Possible uses of this data are for correction of copy number in
peak-calling for interactome,
transcriptome, DNase hypersensitivity, and methylome determinations.
Display Conventions and Configuration
This track is a multi-view composite track that contains multiple data types
(views). For each view, there are multiple subtracks that display
individually on the browser. Instructions for configuring multi-view tracks are
here.
- Regions
- Regions of the genome where copy number variation has been assesed.
CNV regions are colored by type:
- blue = amplified
- black = normal
- orange = heterozygous deletion
- red = homozygous deletion
- Signal
- Mean log R ratio for each region. See Methods below.
Signals are colored by cell type, not by copy number variation.
To show only selected subtracks, uncheck the boxes next to the tracks that
you wish to hide.
Methods
Cells were grown according to the approved
ENCODE cell culture protocols.
Isolation of genomic DNA and hybridization
Genomic DNA was extracted using the QIAGEN DNeasy Blood & Tissue Kit according
to the instructions provided by the manufacturer.
For each biological replicate of each cell line, DNA concentrations and
a level of quality were determined by UV absorbance.
Genotypes were determined from 400 nanograms of each sample at 1 million loci
using Illumina Human 1M-Duo arrays and standard Illumina protocols.
Processing and Analysis
Genotypes were ascertained from the 1M-Duo Arrays with BeadStudio using
default settings and formatting with the A/B genotype designation for each SNP
(see 1M-Duo manifest file for specific nucleotide).
Copy Number Variation (CNV) analysis was performed using circular binary
segmentation (DNAcopy) of the log R ratio values at each probe
(Olshen et al., 2004).
The parameters used were alpha=0.001, nperm=5000, sd.undo=1.
Copy number segments are reported with the mean log R ratio for each
chromosomal segment called by CBS.
Log ratios of ~-0.2 to -1.5 can be considered heterozygous deletions,
< -1.5 homozygous deletions, and > 0.2 amplifications.
The coordinates for the genotypes and copy number calls are from Human Genome Build 36.
Release Notes
Release 2 (April 2011) of this track updates the colors used in the Regions view subtracks (the
data remains unchanged). The colors now adhere to the color standards determined at the first annual
International Standards for Cytogenomic Arrays (ISCA) Scientific Conference.
Credits
Tim Reddy, Rebekka Sprouse, Richard Myers, Devin Absher from HudsonAlpha Institute.
Contact:
Flo Pauli.
References
Olshen AB, Venkatraman ES, Lucito R, Wigler M.
Circular binary segmentation for the analysis of array-based DNA copy number
data. Biostatistics. 2004 Oct;5(4)557-572.
Data Release Policy
Data users may freely use ENCODE data, but may not, without prior
consent, submit publications that use an unpublished ENCODE dataset until
nine months following the release of the dataset. This date is listed in
the Restricted Until column on the track configuration page and
the download page. The full data release policy for ENCODE is available
here.
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