Frequency of exome-chip
variants in samples from UK
Version 1.0, 19th November 2013
WeÕve compiled the frequencies
of variants genotyped on Illumina
HumanExome-12v1_A Beadchip (247,870 markers) in 55,726
European individuals from UK, provided in the enclosed file.
Download the latest copy of the data here.
Genotype calling at each centre was carried out using Illumina's
GenTrain clustering algorithm in GenomeStudio and zCall
was run as a post-processing step.
This information was generated
using summary statistics shared by UK exome chip
consortium members in December 2012. For calculating overall frequencies, we
have considered only quality control passed variants from each cohort/study.
Content Contributors
|
Contributor |
N |
Contact |
|
1958
Birth Cohort |
5963
controls |
Panos Deloukas |
|
BRIGHT |
1364
cases |
Patricia Munroe |
|
BHF- FHS |
2991
cases |
Nilesh Samani |
|
CAMCANCER |
3598
controls and 4348 cases of various cancers |
Deborah Thompson |
|
Cambridge
BioResource |
2646
controls |
Panos Deloukas |
|
CLOZUK |
1937
schizophrenia cases |
Michael
O'Donovan |
|
Dunlop
|
1843
cases |
Richard Houlston |
|
EPIC CAD
Norfolk |
1396
cases |
Nick Wareham/Panos
Deloukas |
|
EPIC T2D
Norfolk |
681
cases |
Nick Wareham |
|
Exeter |
1415
T2D cases and 1538 controls |
Tim Frayling |
|
Fenland
|
1028
controls |
Nick Wareham |
|
GoDARTS CAD |
1424
cases |
Colin Palmer/Panos Deloukas |
|
GoDARTS T2D |
1715
T2D cases and 1719 controls |
Colin Palmer |
|
GRAPHIC
|
969
controls |
Nilesh Samani |
|
Houlston |
1209
cases |
Richard Houlston |
|
Moorfields |
1953
cases |
Gerome Breen |
|
Oxford BioBank |
4522
controls |
Fredrik Karpe |
|
TwinsUK |
1185
controls |
Timothy Spector |
|
UK COPD exome chip consortium |
3735
COPD cases and 976 controls |
Martin Tobin |
|
UK MS |
1661
multiple sclerosis cases |
Stephen Sawcer |
|
WTCCC/UKT2D |
3910
T2D cases |
Mark McCarthy |
Please
note that some of this data will be available from EGA controlled data access
in due course.
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File header description:
The
enclosed file FrequencyVariantsUK.ExomechipConsortium.Nov2013.txt is a
tab-separated text file with three columns:
variantID: Illumina
SNP ID
N: Number
of samples contributing to the counts
MAF:
Minor allele frequency
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For any queries please contact:
Mark McCarthy <mark.mccarthy@drl.ox.ac.uk>
Panos Deloukas
<p.deloukas@qmul.ac.uk>
Anubha Mahajan <anubha@well.ox.ac.uk>
Neil Robertson <neil.robertson@well.ox.ac.uk>
###################################################################################
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Please acknowledge UK exome chip consortium if you use this information in your
research.
AM20131119