PXD000622

PXD000622 is an original dataset announced via ProteomeXchange.

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	2013-12-17
AnnouncementXML	Submission_2013-12-17_14:36:39.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Lik Wee Lee
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	QTRAP 5500

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

Li et al., submitted

curator keyword: selected reaction monitoring, SRM, targeted

Lik Wee Lee
contact affiliation	Integrated Diagnostics
contact email	llee@indidx.com
dataset submitter
Paul Kearney
contact affiliation	Integrated Diagnostics
contact email	pkearney@indidx.com
lab head

PeptideAtlas dataset URI

PASSEL experiment URI

PASSEL transition group browser URI