 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 02, 2021 |
| Title |
Genetic variants associated with development of colorectal cancer, type 1 diabetes, Hodgkin lymphoma and Diffuse large B-cell lymphoma |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
|
| Summary |
In our genome-wide association study, we searched for an association of genetic variants with colorectal cancer, type 1 diabetes, Hodgkin lymphoma and Diffuse large B-cell lymphoma among Polish population.
|
| |
|
| Overall design |
A total of 72 of 24-DNA sample pools from gender-matched individuals (18 colorectal cancer, 9 Hodgkin lymphoma, 8 Diffuse large B-cell lymphoma, 9 type 1 diabetes and 28 controls) were included in the study. Genomic DNA was extracted from whole blood treated with EDTA. Aliquots of DNA samples that passed quality control tests were combined according to diagnosis and gender in equimolar concentrations to obtain pools of DNA samples, adjusted to a final concentration of 50 ng/ml in Tris-EDTA buffer (pH 8).
Please note that no data processing was applied and thus only theta values from unprocessed file were used as a signal.
The main reason for not normalizing the data was that it was derived from pooled samples. Data normalization algorithms were in general optimized for genotype calling (which is impossible for these samples), and thus may introduce possible artifact introduction. Thus "the less the better" approach was made with the data analysis. PCA hasn't revealed any considerable stratification. Raw theta values were used as an input for Student's t-test. Clusters of significant probes were selected for validation in individual patients.
|
| |
|
| Contributor(s) |
Ambrożkiewicz F, Bałabas A, Cybula P, Dąbrowska M, Goryca K, Hennig E, Karczmarski J, Kluska A, Kulecka M, Mikula M, Ostrowski J, Paziewska A, Piątkowska M, Skubisz K, Żeber-Lubecka N, Cukrowska B, Paszkiewicz E, Olesiński T |
| Citation(s) |
34070617 |
| Submission date |
Aug 18, 2020 |
| Last update date |
Jul 03, 2021 |
| Contact name |
Krzysztof Goryca |
| Organization name |
Uniwersytet Warszawski
|
| Department |
CeNT
|
| Street address |
Banacha 2c
|
| City |
Warszawa |
| ZIP/Postal code |
02-097 |
| Country |
Poland |
| |
|
| Platforms (1) |
| GPL16104 |
Illumina HumanOmni2.5-8 BeadChip |
|
| Samples (72)
|
|
| Relations |
| BioProject |
PRJNA657851 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156411_RAW.tar |
2.5 Gb |
(http)(custom) |
TAR (of IDAT) |
| GSE156411_geo.processed.20_08_06.txt.gz |
1.6 Gb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...