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SNP 6.0 Array Launched
The new Affymetrix® Genome-Wide Human SNP Array 6.0 features
1.8 million genetic markers, including more than 906,600 single nucleotide
polymorphisms (SNPs) and more than 946,000 probes for the detection of
copy number variation. Please visit the SNP
6.0 product page for more information. Links to sample data and
annotations are listed below.
Genotyping Console Now Available
Affymetrix
Genotyping Console is a new genotyping analysis software package
designed to streamline whole-genome genotyping analysis and quality
control for the Genome-Wide SNP Arrays 5.0 and 6.0. Genotyping
Console's QC and visualization tools easily identify and
segregate sample outliers. SNP cluster visualization provides a
detailed look at the performance of SNPs of interest. Reporting
of seventy-two signature SNPs enable verification of a sample’s
identity if compared to known genotypes for
that sample. In addition, flexible SNP filtering,
data management and visualization export features make it easy to share
data with collaborators and downstream application
software.
SNP 6.0 Probe Level Access Tool
The SNP 6.0 Probe Level Access Tool (SPLAT) is a research tool
for customers who are investigating the use of SNP 6.0 for genome-wide
copy number. SPLAT extracts probe intensities for collections of Genome-Wide
SNP Array 6.0 CEL files. The software tool writes output files that
contain normalized probe intensities and genomic position information in
tabular format for more than 1.8 million genetic markers from both SNP and
copy number probes on the SNP Array 6.0. DevNet
Tools SPLAT
Download
Command Console Beta 5 is Now Available
Affymetrix has released the final beta version of the Command
Console software. The user interface has substantially changed from
previous beta versions based on your
feedback.
Affymetrix Power Tools (APT), Release 1.8.0
APT 1.8.0 is now available for download. The main addition in version 1.8.0 is
implementation of the BRLMM-P and Birdseed methods and support for
genotype calling from Genome Wide SNP 5.0 and Genome Wide SNP 6.0 chips. A
new application apt-geno-qc
enables computing single chip QC metrics for SNP probe sets on 500k, SNP
5.0, and SNP 6.0 genotyping chips. See the APT
Product Page for downloads and further details.
SNP 6.0 Sample Data and Annotations
Available
Please visit the SNP
6.0 page of the Affymetrix Data Resource Center for information on
ordering SNP 6.0 Sample Data via delivery on DVD. Due to its size, data is
not available for direct download.
HapMap Data
Set
This dataset contains the 270
samples from the International HapMap Project run on the Affymetrix Genome
Wide Human SNP Array 6.0. The 270 samples are comprised of 30 CEPH
trios, 30 Yoruban trios, 45 unrelated Han Chinese samples and 45 unrelated
Japanese samples.
Chromosome X Titration
The copy number variation
dataset consists of 5 replicates each of 5 samples. Three of the
samples have abnormal copies of the X chromosome, having 3, 4 and 5 copies
respectively. The remaining two are a normal male and a normal
female, but are of special interest as the female is the sample studied by
fosmid paired end sequencing in Tuzun et al (N at Gen 2005) and much work
has been done on this sample (Redon et al, Nature 2006) relative to the
included male HapMap sample NA10851.
Annotation
Files
There are several different
annotation files for the Genome Wide SNP 6.0 array. Please visit the SNP
6 .0 Support Page for links to download these data.
-
GenomeWidsSNP_6.cn.na22.annot.csv
- This file contains the copy number probe
annotations
- GenomeWideSNP_6.na22.annot.csv
- This file contains the SNP probe
annotations
- GenomeWideSNP_6.CN_probe_tab
- This file contains the CN probe
sequences
- GenomeWideSNP_6.probe_tab -
This file contains the SNP probe
sequences
Human Gene ST 1.0 Sample Data
AGCC formatted CEL and CHP files with matched Sample files
(*.ARR) are now available at the Human
Gene ST 1.0 page of the Data Resource
Center.
Tissue Panel Mixture Data Set on Human Exon, Gene and
U133
Available from the Human
Gene ST 1.0 Sample Data Page, Affymetrix has released a set of tissue
mixture data run on the Human
Exon 1.0 ST Array, Human
Gene 1.0 ST Array and the Human
U133 Plus 2.0 Array. AGCC formatted data are now available at the data
resource center with richly annotated sample files (*.ARR) grouped with
either CEL or CHP files.
Human Genome U133 Array Plate Set
Data presented in the performance Whitepaper comparing U133 plate versus cartridge
performance are now available for download from the Data
Resource Center.
Interested in Integrating Gene Expression and Regulation
Data from Chip-chip experiments?
Data is available from the Carroll et al. Nature
Genetics 38(11):1289, Nov 2006. Genome-wide analysis of estrogen
receptor binding sites. The data is hosted on the Affymetrix Secure File
Exchange due to its size. Please email mike_lelivelt@affymetrix.com
for access to this data set. Affymetrix thanks the laboratories of Shirley
Liu and Myles Brown for permission to redistribute these
data.
2007 Low Level Analysis Workshop Preceding
RECOMB
Affymetrix hosted another well attended Low Level Analysis
Workshop on 21 April 2007. The event preceded the annual RECOMB meeting.
Abstracts and slides are now available at the Low
Level Event Archive.
Sample Registration in a Mixed GCOS/AGCC Environment
Programmatic methods for registering samples into both GCOS and
the new Command Console (AGCC) software are presented. Available online
are the archived
WebTalk recording and
DTT command line and array
registration tools that were demonstrated during the talk. Please
email mailto:devnet@affymetrix.com with
any questions on the materials or methods.
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