 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 04, 2024 |
| Title |
DNA methylation profiles of lymph node tissue of head and neck cancer of unknown primary |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
|
| Summary |
Background. The unknown tissue of origin in head and neck cancer of unknown primary (hnCUP) leads to invasive diagnostic procedures and unspecific and potentially inefficient treatment options for patients. The most common histological subtype, squamous cell carcinoma, can stem from various tumor primary sites, including the oral cavity, oropharynx, larynx, head and neck skin, lungs, and esophagus. DNA methylation profiles are highly tissue-specific and have been successfully used to classify tissue origin. We therefore developed a support vector machine (SVM) classifier trained with publicly available DNA methylation profiles of commonly cervically metastasizing squamous cell carcinomas (n = 1,103) in order to identify the primary tissue of origin of our own cohort of squamous cell hnCUP patient’s samples (n = 28). Methylation analysis was performed with Infinium MethylationEPIC v1.0 BeadChip by Illumina. Results. The SVM algorithm achieved the highest overall accuracy of tested classifiers, with 87%. Squamous cell hnCUP samples on DNA methylation level resembled squamous cell carcinomas commonly metastasizing into cervical lymph nodes. The most frequently predicted cancer localization was the oral cavity in 11 cases (39%), followed by the oropharynx and larynx (both 7, 25%), skin (2, 7%), and esophagus (1, 4%). These frequencies concord with the expected distribution of lymph node metastases in epidemiological studies. Conclusions. On DNA methylation level, hnCUP is comparable to primary tumor tissue cancer types that commonly metastasize to cervical lymph nodes. Our SVM-based classifier can accurately predict these cancers’ tissues of origin and could significantly reduce the invasiveness of hnCUP diagnostics and enable a more precise therapy after clinical validation.
|
| |
|
| Overall design |
Bisulphite treated genomic DNA from 28 lymph nodes (FFPE) and 28 patients, one lymph node per patient, were hybridised to an Illumina Infinium MethylationEPIC v1.0 Array. One array per sample, no replicates, no control samples.
|
| |
|
| Contributor(s) |
Stark L, Winter C, Wirth M |
| Citation(s) |
38528631 |
| Submission date |
Feb 22, 2024 |
| Last update date |
Apr 05, 2024 |
| Contact name |
Christof Winter |
| Organization name |
Technical University of Munich
|
| Street address |
Ismaninger Str. 22
|
| City |
Munich |
| ZIP/Postal code |
81675 |
| Country |
Germany |
| |
|
| Platforms (1) |
|
| Samples (28)
|
| GSM8098170 |
lymph node tissue (FFPE) from patient C05 |
| GSM8098171 |
lymph node tissue (FFPE) from patient C06 |
| GSM8098172 |
lymph node tissue (FFPE) from patient C08 |
| GSM8098173 |
lymph node tissue (FFPE) from patient C09 |
| GSM8098174 |
lymph node tissue (FFPE) from patient C10 |
| GSM8098175 |
lymph node tissue (FFPE) from patient C11 |
| GSM8098176 |
lymph node tissue (FFPE) from patient C12 |
| GSM8098177 |
lymph node tissue (FFPE) from patient C01 |
| GSM8098178 |
lymph node tissue (FFPE) from patient C02 |
| GSM8098179 |
lymph node tissue (FFPE) from patient C03 |
| GSM8098180 |
lymph node tissue (FFPE) from patient C15 |
| GSM8098181 |
lymph node tissue (FFPE) from patient C16 |
| GSM8098182 |
lymph node tissue (FFPE) from patient C17 |
| GSM8098183 |
lymph node tissue (FFPE) from patient C18 |
| GSM8098184 |
lymph node tissue (FFPE) from patient C19 |
| GSM8098185 |
lymph node tissue (FFPE) from patient C20 |
| GSM8098186 |
lymph node tissue (FFPE) from patient C21 |
| GSM8098187 |
lymph node tissue (FFPE) from patient C22 |
| GSM8098188 |
lymph node tissue (FFPE) from patient C23 |
| GSM8098189 |
lymph node tissue (FFPE) from patient C24 |
| GSM8098190 |
lymph node tissue (FFPE) from patient C25 |
| GSM8098191 |
lymph node tissue (FFPE) from patient C26 |
| GSM8098192 |
lymph node tissue (FFPE) from patient C27 |
| GSM8098193 |
lymph node tissue (FFPE) from patient C28 |
| GSM8098194 |
lymph node tissue (FFPE) from patient C30 |
| GSM8098195 |
lymph node tissue (FFPE) from patient C31 |
| GSM8098196 |
lymph node tissue (FFPE) from patient C32 |
| GSM8098197 |
lymph node tissue (FFPE) from patient C33 |
|
| Relations |
| BioProject |
PRJNA1079373 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE256413_RAW.tar |
548.4 Mb |
(http)(custom) |
TAR (of IDAT) |
|
|
|
|
 |
Less...
More...