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Systems epidemiology of blood transcriptome variability in a representative sample of postmenopausal women

ABSTRACT: Using a large representative sample of postmenopausal women in the Norwegian Women and Cancer (NOWAC) postgenome study, we investigated blood gene expression changes due to intra-technical variability, normal inter-individuality (age, body mass index, fasting status), and exposure variables (smoking, hormone therapy and medication use) at proportion and level of real life situation revealing mechanistic insights of these effects mirrored in blood. We used a representative sample of postmenopausal women (N=286) in the NOWAC postgenome study. We investigated blood gene expression changes due to intra-technical variability, normal inter-individuality (age, body mass index, fasting status), and exposure variables (smoking, hormone therapy and medication use). A total of 304 arrays, including 18 technical replicates, were analyzed. We filtered out samples which had less than 40% probes with a signal to noise ratio (S/N) greater than or equal to 3. When a technical replicate was conducted, the array with the least number of probes with S/N greater than or equal to 3 was excluded. After samples filtration, a total of 286 arrays were analyzed. The following samples were filtered out; they were not used in the normalization processing, and none of the study conclusions are based on these samples. NWbAB_ 1 NWbAB_ 2 NWbAB_ 3 NWbAB_ 4 NWbAB_ 5 NWbAB_ 7 NWbAB_ 8 NWbAB_ 61 NWbAB_ 63 NWbAB_ 116 NWbAB_ 120 NWbAB_ 121 NWbAB_ 180 NWbAB_ 183 NWbAB_ 214 NWbAB_ 249 NWbAB_ 254 NWbAB_ 299 Sample records (GSMxxxx) are not provided for the filtered-out samples. However, the metadata for the filtered-out samples is included in the Series supplementary file GSE15289_filtered_metadata.txt. The raw data for both the filtered-out samples and non-filtered-out samples (GSM381832-GSM382117) are included in the Series supplementary file GSE15289_raw.txt.

ORGANISM(S): Homo sapiens

SUBMITTER: Vanessa Dumeaux 

PROVIDER: E-GEOD-15289 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Deciphering normal blood gene expression variation--The NOWAC postgenome study.

Dumeaux Vanessa V   Olsen Karina S KS   Nuel Gregory G   Paulssen Ruth H RH   Børresen-Dale Anne-Lise AL   Lund Eiliv E  

PLoS genetics 20100312 3

There is growing evidence that gene expression profiling of peripheral blood cells is a valuable tool for assessing gene signatures related to exposure, drug-response, or disease. However, the true promise of this approach can not be estimated until the scientific community has robust baseline data describing variation in gene expression patterns in normal individuals. Using a large representative sample set of postmenopausal women (N = 286) in the Norwegian Women and Cancer (NOWAC) postgenome s  ...[more]

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