Geneseeq Publications

Explore selected peer-reviewed publications from Geneseeq team across precision oncology and cancer genomics, including research in cell-free DNA (cfDNA), liquid biopsy, cancer early detection, molecular residual disease (MRD), genomic profiling, AI-driven genomic analysis, and related research areas.

1. Fragmentia-AI lymphoma: a cfDNA language model for lymphoma detection using ultra-low-pass WGS. Cell Communication and Signaling. 2026 Aug 19. doi: 10.1186/s12964-026-03115-4.
2. Generalizable cancer detection from ultra-low-pass WGS via deep contextual modeling of cfDNA sequences. Molecular Biomedicine. 2026 Aug 12;7:136. doi: 10.1186/s43556-026-00538-w.
3. Toward generalizable prediction of cancer signal using a cell-free DNA language model. Cell Reports Medicine. 2026 Jul 21;7(7):102866. doi: 10.1016/j.xcrm.2026.102866.

1. Noninvasive detection and prognostic stratification of biliary tract cancer using cell-free DNA fragmentomics: a model development and validation study. Molecular Biomedicine. 2026 May 21;7:72. doi: 10.1186/s43556-026-00468-7.
2. Development and prospective validation of a cell-free DNA–based model for the early detection of pancreatic cancer. Cancer Discovery. 2026 Jan 12;16(1):66–80. doi: 10.1158/2159-8290.CD-25-0323.
3. Noninvasive detection and differentiation of gastric malignancy using cell-free DNA biomarkers. Journal of Advanced Research. 2025 Dec 9. doi: 10.1016/j.jare.2025.12.005.
4. Development and validation of a cell-free DNA fragmentomics–based model for early detection of pancreatic cancer. Journal of Clinical Oncology. 2025 Sept 10;43(26):2863-2874. doi: 10.1200/JCO.24.00287
5. Early detection of multiple cancer types using multidimensional cell-free DNA fragmentomics. Nature Medicine. 2025 Aug;31(8):2737–2745. doi: 10.1038/s41591-025-03735-2.
6. Leveraging cfDNA fragmentomic features in a stacked ensemble model for early detection of esophageal squamous cell carcinoma. Cell Report Medicine. 2024 Aug 20;5(8):101664. doi: 10.1016/j.xcrm.2024.101664. 
7. Multidimensional Fragmentomics Enables Early and Accurate Detection of Colorectal Cancer. Cancer Research. 2024 Oct 1;84(19):3286–3295. doi: 10.1158/0008-5472.CAN-23-3486.
8. Multidimensional cell-free DNA-based liquid biopsy for sensitive early detection of gastric cancer. Genome Medicine. 2024 Jun 7;16(1):79. doi: 10.1186/s13073-024-01352-1.
9. Multidimensional cell-free DNA fragmentomic assay for detection of early-stage lung cancer. American Journal of Respiratory and Critical Care Medicine. 2023 May 1;207(9):1203-1213. doi: 10.1164/rccm.202109-2019OC.

1. MRDadaptis: self-adaptive parameter configuration enhances minimal residual disease detection in heterogeneous ctDNA samples. Briefings in Bioinformatics. 2025 Aug 31;26(5):bbaf529. doi: 10.1093/bib/bbaf529.
2. Dynamic circulating tumor DNA indicates pathological benefits of additional neoadjuvant chemoimmunotherapy courses for locally advanced non-small-cell lung cancer patients. Frontiers in Oncology. 2025 Jul 24;15:1563315. doi: 10.3389/fonc.2025.1563315.
3. Enhanced detection of landmark minimal residual disease in lung cancer using cell-free DNA fragmentomics. Cancer Research Communications. 2023 May 30;3(5):933–942. doi: 10.1158/2767-9764.CRC-22-0363.
4. Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer. Journal of Hematology & Oncology. 2022 Oct 1;15(1):137. doi: 10.1186/s13045-022-01355-8.
5. The clinical utility of dynamic ctDNA monitoring in inoperable localized NSCLC patients. Molecular Cancer. 2022 May 19;21(1):117. doi: 10.1186/s12943-022-01590-0.
6. Dynamic recurrence risk and adjuvant chemotherapy benefit prediction by ctDNA in resected NSCLC. Nature Communications. 2021 Nov 19;12(1):6770. doi: 10.1038/s41467-021-27022-z.
7. Utility of ctDNA in predicting response to neoadjuvant chemoradiotherapy and prognosis assessment in locally advanced rectal cancer: A prospective cohort study. PLoS Medicine. 2021 Aug 31;18(8):e1003741. doi: 10.1371/journal.pmed.1003741.
8. Postoperative circulating tumor DNA as markers of recurrence risk in stages II to III colorectal cancer. Journal of Hematology & Oncology. 2021 May 17;14(1):80. doi: 10.1186/s13045-021-01089-z.

1. BRAF fusions define therapeutic vulnerability and tyrosine kinase inhibitor resistance in non-small cell lung cancer. Lung Cancer. 2026 Sep;219:109556. doi: 10.1016/j.lungcan.2026.109556.
2. Integrative cfDNA profiling from low-pass whole-genome sequencing enables tissue-of-origin prediction in cancer. Molecular Biomedicine. 2026 Aug 5;7(1):125. doi: 10.1186/s43556-026-00497-2.
3. Comprehensive characterization of MET exon 14 skipping mutations in non-small cell lung cancer. Respiratory Research. 2026 May 23. doi: 10.1186/s12931-026-03626-1.
4. Functional characterization and a real-world clinical laboratory pilot of the Foundation for the National Institutes of Health circulating tumor DNA quality control materials. JCO Precision Oncology. 2025 Nov;9:e2500245. doi: 10.1200/PO-25-00245.
5. Tumor-naïve circulating tumor DNA as an early response biomarker for patients treated with immunotherapy in early phase clinical trials. JCO Precision Oncology. 2023 Apr;7:e2200509. doi: 10.1200/PO.22.00509.
6. Genomic signatures define three subtypes of EGFR-mutant stage II–III non-small-cell lung cancer with distinct adjuvant therapy outcomes. Nature Communications. 2021 Nov 8;12(1):6450. doi: 10.1038/s41467-021-26806-7.
7. Timing and origins of local and distant metastases in lung cancer. Journal of Thoracic Oncology. 2021 Jul;16(7):1136–1148. doi: 10.1016/j.jtho.2021.02.023.
8. Biomarkers of osimertinib response in patients with refractory, EGFR-T790M-positive non-small cell lung cancer and central nervous system metastases: the Apollo study. Clinical Cancer Research. 2020 Dec 1;26(23):6168-6175. doi: 10.1158/1078-0432.CCR-20-2081.
9. Developing more sensitive genomic approaches to detect radioresponse in precision radiation oncology: From tissue DNA analysis to circulating tumor DNA. Cancer Letters. 2020 Mar 1;472:108-118. doi: 10.1016/j.canlet.2019.12.004.
10. Distribution of NRG1 gene fusions in a large population of Chinese patients with NSCLC. Journal of Thoracic Oncology. 2019 Dec;14(12):e263-e266. doi: 10.1016/j.jtho.2019.07.012.
11. Comprehensive genomic profiling identifies novel genetic predictors of response to anti-PD-(L)1 therapies in non-small-cell lung cancer. Clinical Cancer Research. 2019 Aug 15;25(16):5015-5026. doi: 10.1158/1078-0432.CCR-19-0585.
12. Tumor-derived DNA from pleural effusion supernatant as a promising alternative to tumor tissue in genomic profiling of advanced lung cancer. Theranostics. 2019 Jul 28;9(19):5532-5541. doi: 10.7150/thno.34070.
13. Liquid biopsies to track trastuzumab resistance in metastatic HER2-positive gastric cancer. Gut. 2019 Jul;68(7):1152-1161. doi: 10.1136/gutjnl-2018-316522.
14. Clinical and molecular features of acute promyelocytic leukemia with variant retinoid acid receptor fusions. Haematologica. 2019 May;104(5):e195-e199. doi: 10.3324/haematol.2018.205369.
15. Widespread and functional RNA circularization in localized prostate cancer. Cell. 2019 Feb 7;176(4):831-843.e22. doi: 10.1016/j.cell.2019.01.025.
16. High prevalence of KRAS/BRAF somatic mutations in brain and spinal cord arteriovenous malformations. Brain. 2019 Jan 1;142(1):23-34. doi: 10.1093/brain/awy307
17. Investigating novel resistance mechanisms to third-generation EGFR tyrosine kinase inhibitor osimertinib in non-small cell lung cancer patients. Clinical Cancer Research. 2018 Jul 1;24(13):3097–3107. doi: 10.1158/1078-0432.CCR-17-2310.
18. Circulating tumor DNA mutation profiling by targeted next generation sequencing provides guidance for personalized treatments in multiple cancer types. Scientific Reports. 2017 Apr 3;7(1):583. doi: 10.1038/s41598-017-00520-1.
19. The unique characteristics of MET Exon 14 mutation in Chinese patients with NSCLC. Journal of Thoracic Oncology. 2016 Sep;11(9):1503–1510. doi: 10.1016/j.jtho.2016.05.016.