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This dataset is expected to be useful for the development and evaluation of low-level analysis methods for making genotype calls from probe intensity data. It consists of 30 trios each analyzed on both the Xba and Hind array (so a total of 30x3x2=180 hybridizations). The trios are CEPH trios also used in the International HapMap Project.

Of particular use is the fact that the HapMap Project has made available a large number of reference genotypes which can be used in conjunction with this dataset. The HapMap data access policy limits redistribution rights on these genotypes so they cannot be made available directly by Affymetrix, but the reference data can be downloaded directly from the HapMap Project. As of HapMap release 16c1, a total of 30,000 SNPs have reference genotypes available for the samples shared here. These numbers are steadily increasing with each HapMap update.

The details of the analysis method used by GDAS to determine genotype calls based on probe intensity data have been published in Bioinformatics.

The dataset has been split into 11 parts for convenient download. These can be unzipped on top of one another. The file with the word 'base' in the filename is required, the other 10 zip files each contain distinct collections of chip data and users wanting to download only a subset of the data may pick a subset of these zips.

The data is provided in two versions. Each version contains the same data but in different file formats. Version 1 (in table 1) contains raw CEL, CHP and EXP files and is suitable for use outside of the GCOS/GTYPE framework. It is expected to be mainly of interest for users interested in low-level probe analysis. Version 2 (in table 2) contains DTT format files for integration with the GCOS/GTYPE framework and is expected to be mainly of interest for users wishing to integrate the data with these applications.

In either case there is a file named README.txt provided in the 'base' file with detailed instructions on how to use the data. Md5 checksums are provided in the tables below for verification of the integrity of downloaded data.

Version 1 release of data: CEL,CHP and EXP format

(Suitable for use outside of GCOS/GTYPE framework)

File	Size	md5 Checksum	Description
100K_trios.base.zip	37MB	f70cb636002b4ac8bc807f0639dae691	Documentation and library files for entire dataset
100K_trios.hind.1.zip	229MB	6d593c94260804ada939952ac4df2503	Probe intensities and genotype calls for 18 samples on Hind Array
100K_trios.hind.2.zip	228MB	84691de89bff1aa38704f41682c85940	Probe intensities and genotype calls for 18 samples on Hind Array
100K_trios.hind.3.zip	230MB	fb1efb1ed2f713c7b077b57146880903	Probe intensities and genotype calls for 18 samples on Hind Array
100K_trios.hind.4.zip	228MB	e0aeaada50ec4dc23ed75b2154f3de75	Probe intensities and genotype calls for 18 samples on Hind Array
100K_trios.hind.5.zip	230MB	a29dcc1780ba66ebdd8342faa01c46fa	Probe intensities and genotype calls for 18 samples on Hind Array
100K_trios.xba.1.zip	245MB	941c0e36785440b85b2e9127ae91c26d	Probe intensities and genotype calls for 18 samples on Xba Array
100K_trios.xba.2.zip	232MB	4ff4aecb882b9e30c6fbebff84080489	Probe intensities and genotype calls for 18 samples on Xba Array
100K_trios.xba.3.zip	228MB	71dc53123fd26d5da441d48c2dd21e6c	Probe intensities and genotype calls for 18 samples on Xba Array
100K_trios.xba.4.zip	228MB	34b85d8188276f529a2ad3e273c8dce9	Probe intensities and genotype calls for 18 samples on Xba Array
100K_trios.xba.5.zip	230MB	4f48983e00f4940ab77cf4c6ec46a75e	Probe intensities and genotype calls for 18 samples on Xba Array

Version 2 release of data: DTT format

(Intended for use within GCOS/GTYPE framework)

File	Size	md5 Checksum	Description
100K_trios.base.zip	38MB	f70cb636002b4ac8bc807f0639dae691	Documentation and library files for entire dataset
100K_trios.hind.dtt.1.zip	229MB	8a28150d937fa81f29431b71da36706b	Archived DTT files for 18 samples on Hind Array
100K_trios.hind.dtt.2.zip	215MB	705be96f555a85bdc38d5a24c7c8b15b	Archived DTT files for 18 samples on Hind Array
100K_trios.hind.dtt.3.zip	203MB	19ddd1744b6f12b3b20c2401295858b2	Archived DTT files for 18 samples on Hind Array
100K_trios.hind.dtt.4.zip	228MB	d9ba75c0ae6de144738ffa683e9e9f34	Archived DTT files for 18 samples on Hind Array
100K_trios.hind.dtt.5.zip	230MB	746aeec3022a632c516883d3f021e33d	Archived DTT files for 18 samples on Hind Array
100K_trios.xba.dtt.1.zip	245MB	a0f8b6af3a21243f816e6bad2a5e94a9	Archived DTT files for 18 samples on Xba Array
100K_trios.xba.dtt.2.zip	232MB	51fd6cffda8856d21718372dd04cf137	Archived DTT files for 18 samples on Xba Array
100K_trios.xba.dtt.3.zip	228MB	cf717614f6e708b81ab1e8f01577aa9d	Archived DTT files for 18 samples on Xba Array
100K_trios.xba.dtt.4.zip	228MB	e04f50ec919854b86b9c87fe0cb037d6	Archived DTT files for 18 samples on Xba Array
100K_trios.xba.dtt.5.zip	230MB	ad1dfa43fee7766625930e01334fc229	Archived DTT files for 18 samples on Xba Array

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