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Author:

Wang, Xuedong (Wang, Xuedong.) | Wang, Xiaoxi (Wang, Xiaoxi.) | Li, Xiaoqin (Li, Xiaoqin.) | Chang, Yu (Chang, Yu.) (Scholars:常宇)

Indexed by:

Scopus SCIE PubMed

Abstract:

DNA methylation abnormalities are frequent events in early tumors. DNA methylation is relatively stable over time and can be detected in blood. Therefore, DNA methylation has a great potential to become an early diagnostic biomarker of cancers. To find potential diagnostic markers for lung squamous cell carcinoma (LUSC), a method for identifying LUSC-specific candidate diagnostic markers was proposed. We screened 6 LUSC-specific CpGs by comparing the methylation profiles of 172 samples from LUSC patients, 42 normal lung samples, 1306 samples from patients with other cancers, which was collected from The Cancer Genome Atlas (TCGA) database, and 184 normal blood samples, which was collected from Gene Expression Omnibus (GEO) database. A support vector machine model was built based on the methylation levels of the candidate diagnostic biomarkers, and we optimized the model by sixfold cross-validation. The combination of six sites achieved 93%-99% sensitivity in predicting LUSC, 100% specificity in excluding normal samples, and 99.55% specificity in excluding non-LUSC samples. In addition, a diagnostic model was established by using six LUSC-specific biomarkers, and the sensitivity and specificity of LUSC stage I samples were 95.2% and 99.4%. At the same time, genes for six LUSC-specific CpGs localization are closely related to cancer occurrence, which indicates that six LUSC-specific CpGs can be used as candidate biomarkers for LUSC diagnosis. Overall, our study provides promising biomarkers for the diagnosis of LUSC.

Keyword:

lung squamous cell carcinoma specific biomarkers early diagnosis DNA methylation

Author Community:

  • [ 1 ] [Wang, Xuedong]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China
  • [ 2 ] [Wang, Xiaoxi]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China
  • [ 3 ] [Li, Xiaoqin]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China
  • [ 4 ] [Chang, Yu]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China

Reprint Author's Address:

  • [Li, Xiaoqin]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100124, Peoples R China

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Source :

JOURNAL OF COMPUTATIONAL BIOLOGY

ISSN: 1066-5277

Year: 2019

Issue: 5

Volume: 27

Page: 825-833

1 . 7 0 0

JCR@2022

ESI Discipline: BIOLOGY & BIOCHEMISTRY;

ESI HC Threshold:169

JCR Journal Grade:4

Cited Count:

WoS CC Cited Count: 1

SCOPUS Cited Count: 1

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 5

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