Program Official

Principal Investigator

James G.
Awardee Organization

University Of Pittsburgh At Pittsburgh
United States

Fiscal Year
Activity Code
Early Stage Investigator Grants (ESI)
Not Applicable
Project End Date

Ultrasensitive Detection of Tumor Specific DNA Methylation Changes for the Early Detection of Lung Cancer

Ultrasensitive Detection of Tumor Specific DNA Methylation Changes for the Early Detection of Lung Cancer  ABSTRACT  This proposal seeks to improve upon the management of lung cancer through detection of tumor specific abnormal DNA methylation. Despite highly publicized advances in genomics and proteomics, the promise of non-invasive diagnostics and personalized medicine remains largely unrealized. Recently, comprehensive determination of genetic and epigenetic aberrations has become a major activity in cancer research since it is well understood that these aberrations provide clues to the process of tumorigenesis. The applicants have developed extremely sensitive assays for the detection of hypermethylated DNA sequences. They have also optimized the isolation and processing of circulating cell free DNA from tumors for these sensitive methods. The comprehensive genome wide analysis of molecular changes in cancer completed by The Cancer Genome Atlas (TCGA) has been used to identify many highly frequent cancer specific methylation events in lung cancer that will be combined with an integrated approach to sample processing and preparation and novel sensitive detection strategies to provide utrasensitive detection of tumor specific changes in DNA methylation in blood and sputum samples. With a large population based screening cohort, the Pittsburgh Lung Screening Study, they will develop and characterize the performance of sensitive methods for detecting cancer specific changes in DNA methylation. This molecular detection will compliment CT screening to address the important issue of early detection of lung cancer.


  • O'Keefe CM, Kaushik AM, Wang TH. Highly Efficient Real-Time Droplet Analysis Platform for High-Throughput Interrogation of DNA Sequences by Melt. Analytical chemistry. 2019 Sep 3;91(17):11275-11282. Epub 2019 Aug 19. PMID: 31356737
  • Stark A, Pisanic TR 2nd, Herman JG, Wang TH. High-throughput sample processing for methylation analysis in an automated, enclosed environment. SLAS technology. 2022 Jun;27(3):172-179. Epub 2021 Dec 17. PMID: 35058199
  • Miller BF, Pisanic Ii TR, Margolin G, Petrykowska HM, Athamanolap P, Goncearenco A, Osei-Tutu A, Annunziata CM, Wang TH, Elnitski L. Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers. Clinical epigenetics. 2020 Oct 20;12(1):154. PMID: 33081832
  • Li S, Li A, Hsieh K, Friedrich SM, Wang TH. Electrode-Free Concentration and Recovery of DNA at Physiologically Relevant Ionic Concentrations. Analytical chemistry. 2020 Apr 21;92(8):6150-6157. Epub 2020 Apr 13. PMID: 32249576
  • Kammer MN, Lakhani DA, Balar AB, Antic SL, Kussrow AK, Webster RL, Mahapatra S, Barad U, Shah C, Atwater T, Diergaarde B, Qian J, Kaizer A, New M, Hirsch E, Feser WJ, Strong J, Rioth M, Miller YE, Balagurunathan Y, Rowe DJ, Helmey S, Chen SC, Bauza J, Deppen SA, Sandler K, Maldonado F, Spira A, Billatos E, Schabath MB, Gillies RJ, Wilson DO, Walker RC, Landman B, Chen H, Grogan EL, Barón AE, Bornhop DJ, Massion PP. Integrated Biomarkers for the Management of Indeterminate Pulmonary Nodules. American journal of respiratory and critical care medicine. 2021 Dec 1;204(11):1306-1316. PMID: 34464235
  • Liu B, Ricarte Filho J, Mallisetty A, Villani C, Kottorou A, Rodgers K, Chen C, Ito T, Holmes K, Gastala N, Valyi-Nagy K, David O, Gaba RC, Ascoli C, Pasquinelli M, Feldman LE, Massad MG, Wang TH, Jusue-Torres I, Benedetti E, Winn RA, Brock MV, Herman JG, Hulbert A. Detection of Promoter DNA Methylation in Urine and Plasma Aids the Detection of Non-Small Cell Lung Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research. 2020 Aug 15;26(16):4339-4348. Epub 2020 May 19. PMID: 32430478
  • Hsieh K, Zhao G, Wang TH. Applying biosensor development concepts to improve preamplification-free CRISPR/Cas12a-Dx. The Analyst. 2020 Jul 13;145(14):4880-4888. PMID: 32478351
  • Chen C, Huang X, Yin W, Peng M, Wu F, Wu X, Tang J, Chen M, Wang X, Hulbert A, Brock MV, Liu W, Herman JG, Yu F. Ultrasensitive DNA hypermethylation detection using plasma for early detection of NSCLC: a study in Chinese patients with very small nodules. Clinical epigenetics. 2020 Mar 5;12(1):39. PMID: 32138766
  • Park JS, Pisanic T, Zhang Y, Wang TH. Ligation-Enabled Fluorescence-Coding PCR for High-Dimensional Fluorescence-Based Nucleic Acid Detection. Analytical chemistry. 2021 Feb 2;93(4):2351-2358. Epub 2021 Jan 11. PMID: 33427441
  • O'Keefe CM, Wang TJ. Fabrication of Multilayer Microfluidic Arrays for Passive, Efficient DNA Trapping and Profiling. Methods in molecular biology (Clifton, N.J.). 2023;2679:315-322. PMID: 37300626
  • O'Keefe CM, Giammanco D, Li S, Pisanic TR, Wang TJ. Multilayer microfluidic array for highly efficient sample loading and digital melt analysis of DNA methylation. Lab on a chip. 2019 Jan 29;19(3):444-451. PMID: 30623957
  • Danilova L, Wrangle J, Herman JG, Cope L. DNA-methylation for the detection and distinction of 19 human malignancies. Epigenetics. 2022 Jan-Feb;17(2):191-201. Epub 2021 Mar 5. PMID: 33666134
  • Farooq M, Herman JG. Noninvasive Diagnostics for Early Detection of Lung Cancer: Challenges and Potential with a Focus on Changes in DNA Methylation. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2020 Dec;29(12):2416-2422. Epub 2020 Nov 4. PMID: 33148791
  • Zhao Y, O'Keefe CM, Hsieh K, Cope L, Joyce SC, Pisanic TR, Herman JG, Wang TH. Multiplex Digital Methylation-Specific PCR for Noninvasive Screening of Lung Cancer. Advanced science (Weinheim, Baden-Wurttemberg, Germany). 2023 Jun;10(16):e2206518. Epub 2023 Apr 11. PMID: 37039321
  • Stark A, Trick A, Pisanic TR 2nd, Wang TH. Droplet Magnetofluidic Assay Platform for Quantitative Methylation-Specific PCR. Methods in molecular biology (Clifton, N.J.). 2022;2394:199-209. PMID: 35094330