PXD000622-1
PXD000622 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Biomarker discovery for lung nodules |
Description | Each year millions of pulmonary nodules are discovered by computed tomography and subsequently biopsied. As the majority of these nodules are benign, many patients undergo unnecessary and costly invasive procedures. We present a 13-protein blood-based classifier that differentiates malignant and benign nodules with high confidence, thereby providing a diagnostic tool to avoid invasive biopsy on benign nodules. Using a systems biology strategy, 371 protein candidates were identified and a multiple reaction monitoring (MRM) assay was developed for each. The MRM assays were applied in a three-site discovery study (n = 143) on plasma samples from patients with benign and Stage IA cancer matched on nodule size, age, gender and clinical site, producing a 13-protein classifier. The classifier was validated on an independent set of plasma samples (n = 104), exhibiting a high negative predictive value (NPV) of 90%. Validation performance on samples from a non-discovery clinical site showed NPV of 94%, indicating the general effectiveness of the classifier. A pathway analysis demonstrated that the classifier proteins are likely modulated by a few transcription regulators (NF2L2, AHR, MYC, FOS) that are associated with lung cancer, lung inflammation and oxidative stress networks. The classifier score was independent of patient nodule size, smoking history and age, which are risk factors used for clinical management of pulmonary nodules. Thus this molecular test can provide a powerful complementary tool for physicians in lung cancer diagnosis. |
HostingRepository | PeptideAtlas |
AnnounceDate | 2013-12-05 |
AnnouncementXML | Submission_2013-12-05_12:40:13.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by respository |
PrimarySubmitter | Paul Kearney |
SpeciesList | scientific name: Homo sapiens; NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | AB SCIEX 5500 QTrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2013-12-05 11:20:50 | ID requested | |
⏵ 1 | 2013-12-05 12:40:26 | announced | |
2 | 2013-12-16 15:34:10 | announced | Fixed Dataset Link URIs and cvParams |
3 | 2013-12-17 14:36:56 | announced | Updated to XML 1.2 |
Publication List
Keyword List
curator keyword: selected reaction monitoring, SRM, targeted |
Contact List
Lik Wee Lee | |
---|---|
contact email | llee@indidx.com |
role type | Data submitter |
contact organization | Integrated Diagnostics |
Paul Kearney | |
contact email | pkearney@indidx.com |
role type | Lab head |
contact organization | Integrated Diagnostics |
Full Dataset Link List
PeptideAtlas dataset URI |
PASSEL experiment browser URI |
PASSEL transition group browser URI |