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Series GSE10668 Query DataSets for GSE10668
Status Public on Feb 29, 2008
Title The Complete Genome of a Single Individual by Massively Parallel DNA Sequencing
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary The association of genetic variation with disease and drug response, together with improvements in nucleic acids technologies, has given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome has prevented the routine application of sequencing methods to deciphering complete individual human genomes, and has so far limited the realization of the full potential of genomics for science and human health. Working towards the goal of harnessing the power of genomics, we sequenced the diploid genome of a single individual, Dr. James D. Watson, using a massively-parallel method of sequencing in picoliter size reaction vessels. Here we report the results of genotyping the subject's DNA using an Affymetrix 500k GeneChip as well as copy number variations as reported by Agilent 244k comparative genomic hybridization arrays.
Keywords: Genotyping, copy number variation (CNV), aCGH
Overall design Affymetrix Gene Chip 500: Duplicate genomic DNA samples from JW's lymphocytes, 250 ng each, were annealed to the Affymetrix 250K NspI and 250K StyI arrays according to the manufacturer's protocol. Genotypes were determined using the Bayesian Robust Linear Model with Mahalanobis distance classifier (BRLMM) algorithm provided by Affymetrix in the GeneChip Genotyping Analysis software v. 4.0.
Agilent 244k Whole Human Genome Oligo Microarray: 2 ug of DNA from experimental (JW) and reference samples were processed according to Agilent protocols with some modification. Reference samples were procured from the standard reference Caucasian male, Kleberg Cytogenetics Laboratory, Baylor College of Medicine (Chip 1) and Coriell number NA10851 (Chip 2).
Contributor(s) Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen Y, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song X, Liu Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM
Citation(s) 18421352
Submission date Feb 28, 2008
Last update date May 17, 2017
Contact name Omar Alvi
Organization name Baylor College of Medicine
Department Human Genome Sequencing Center
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (3)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
GPL4544 Agilent-014584 Human Genome 244K CGH Microarray (Alpha Test)
Samples (6)
GSM261478 Affymetrix 250k NspI, JW S1
GSM261479 Affymetrix 250k NspI, JW S2
GSM261480 Affymetrix 250k StyI, JW S1
BioProject PRJNA107641

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10668_RAW.tar 249.8 Mb (http)(custom) TAR (of CEL, TXT)
Processed data included within Sample table

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