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Article Open Access

Comprehensive genomic profiling of Taiwanese triple‑negative breast cancer samples with medium‑ and large‑sized sequencing panels: A comparative study implicating treatment allocations

  • Authors:
    • Chi-Cheng Huang
    • Yi-Chen Yeh
    • Yi-Fang Tsai
    • Yen-Shu Lin
    • Ta-Chung Chao
    • Chun-Yu Liu
    • Hsiang-Ling Ho
    • Ling-Ming Tseng
  • View Affiliations / Copyright

    Affiliations: Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan, R.O.C., Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan, R.O.C., School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan, R.O.C.
    Copyright: © Huang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Article Number: 162
    |
    Published online on: August 5, 2025
       https://doi.org/10.3892/br.2025.2040
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Abstract

Comprehensive genomic profiling (CGP) is a molecular diagnostic tool with increasing use in cancer research and treatment. There are several commercialized CGP assays with variable targeted genes, while the differences between medium‑ and large‑sized panels in refining genomic profiling strategies, optimizing resource allocation and enhancing clinical applications require evaluation. In the present study, patients with triple‑negative breast cancer (TNBC) from the Veterans General Hospital TAipei‑Yung‑Ling foundation sinO‑canceR study were initially assayed using a medium‑sized CGP panel (Oncomine comprehensive panel), and the remaining nucleic acid specimens were re‑sequenced with a large‑sized panel (TruSight Oncology 500). The molecular profiling between the two sequencing panels was compared. A total of 108 breast cancer samples were successfully assayed using both platforms and 272 variants were reported at least once by either type of CGP. The reported variants were among actionable genes (AKT1, BRCA1/2, PALB2, ERBB2, PIK3CA and PTEN), which can be acted upon or have clinical relevance for therapeutic intervention and TP53. The concordance rate between the medium‑ and large‑sized panels was 34.6%, which was enhanced to 58.9% after excluding polymorphisms, out‑of‑targeted region variants and those with low variant allele frequency (<10%), with variants of TP53, ERBB2 and PTEN being mostly enhanced. A majority of discordance came from TruSight Oncology 500‑detected only variants, especially BRCA1, BRCA2 and PALB2. In conclusion, the results indicated that only one‑third of actionable mutations could be detected consistently between the medium‑ and large‑sized CGP panels using the default analytical pipelines, while extensive bioinformatics analyses improved concordance substantially. The large‑sized panel detected more variants, thereby enhancing clinical actionability. With more therapeutic targets revealed in the future, CGP may be particularly impactful in refining strategies for TNBC management.
View Figures

Figure 1

Mutational landscape of 108 Taiwanese
patients with breast cancer assayed with (A) the TruSight Oncology
500 and (B) the Oncomine Comprehensive Assay Panel v3 for
actionable genes. HER2, human epidermal growth factor receptor 2;
ER, estrogen receptor; PR, progesterone receptor.

Figure 2

Interpretation categories of 272
variants called at least once by either TSO500, OCP or both.
TSO500, TruSight Oncology 500; OCP, Oncomine Comprehensive Assay
Panel v3; VAF, variant allele frequency.

Figure 3

(A) Concordance and (B) discordance
distributions among variants of actionable genes and TP53
between the TSO500 and the Oncomine Comprehensive Assay Panel v3.
TSO500, TruSight Oncology 500; VAF, variant allele frequency.
View References

1 

Huang CC, Yeh YC, Ho HL, Liu CY, Tsai YF and Tseng LM: Comprehensive genomic profiling of Taiwanese patients with breast cancer using a novel targeted panel: Preliminary analyses from a prospective triple-negative cohort. J Clin Oncol. 41 (Suppl 16)(e12553)2023.

2 

Wang L, Zhai Q, Lu Q, Lee K, Zheng Q, Hong R and Wang S: Clinical genomic profiling to identify actionable alterations for very early relapsed triple-negative breast cancer patients in the Chinese population. Ann Med. 53:1358–1369. 2021.PubMed/NCBI View Article : Google Scholar

3 

Tierno D, Grassi G, Scomersi S, Bortul M, Generali D, Zanconati F and Scaggiante B: Next-generation sequencing and triple-negative breast cancer: Insights and applications. Int J Mol Sci. 24(9688)2023.PubMed/NCBI View Article : Google Scholar

4 

O'Haire S, Degeling K, Franchini F, Tran B, Luen SJ, Gaff C, Smith K, Fox S, Desai J and IJzerman M: Comparing survival outcomes for advanced cancer patients who received complex genomic profiling using a synthetic control arm. Target Oncol. 17:539–548. 2022.PubMed/NCBI View Article : Google Scholar

5 

Cifuentes C, Lombana M, Vargas H, Laguado P, Ruiz-Patiño A, Rojas L, Navarro U, Vargas C, Ricaurte L, Arrieta O, et al: Application of comprehensive genomic profiling-based next-generation sequencing assay to improve cancer care in a developing country. Cancer Control. 30(10732748231175256)2023.PubMed/NCBI View Article : Google Scholar

6 

Almansour NM: Triple-negative breast cancer: A brief review about epidemiology, risk factors, signaling pathways, treatment and role of artificial intelligence. Front Mol Biosci. 9(836417)2022.PubMed/NCBI View Article : Google Scholar

7 

Dent R, Trudeau M, Pritchard KI, Hanna WM, Kahn HK, Sawka CA, Lickley LA, Rawlinson E, Sun P and Narod SA: Triple-negative breast cancer: Clinical features and patterns of recurrence. Clin Cancer Res. 13:4429–4434. 2007.PubMed/NCBI View Article : Google Scholar

8 

Foulkes WD, Smith IE and Reis-Filho JS: Triple-negative breast cancer. N Engl J Med. 363:1938–1948. 2010.PubMed/NCBI View Article : Google Scholar

9 

Stewart RL, Updike KL, Factor RE, Henry NL, Boucher KM, Bernard PS and Varley KE: A multigene assay determines risk of recurrence in patients with triple-negative breast cancer. Cancer Res. 79:3466–3478. 2019.PubMed/NCBI View Article : Google Scholar

10 

Jie H, Ma W and Huang C: Diagnosis, prognosis, and treatment of triple-negative breast cancer: A review. Breast Cancer (Dove Med Press). 17:265–274. 2025.PubMed/NCBI View Article : Google Scholar

11 

Mateo J, Chakravarty D, Dienstmann R, Jezdic S, Gonzalez-Perez A, Lopez-Bigas N, Ng CKY, Bedard PL, Tortora G, Douillard JY, et al: A framework to rank genomic alterations as targets for cancer precision medicine: The ESMO scale for clinical actionability of molecular targets (ESCAT). Ann Oncol. 29:1895–1902. 2018.PubMed/NCBI View Article : Google Scholar

12 

Condorelli R, Mosele F, Verret B, Bachelot T, Bedard PL, Cortes J, Hyman DM, Juric D, Krop I, Bieche I, et al: Genomic alterations in breast cancer: Level of evidence for actionability according to ESMO scale for clinical actionability of molecular targets (ESCAT). Ann Oncol. 30:365–373. 2019.PubMed/NCBI View Article : Google Scholar

13 

Bianchini G, Balko JM, Mayer IA, Sanders ME and Gianni L: Triple-negative breast cancer: Challenges and opportunities of a heterogeneous disease. Nat Rev Clin Oncol. 13:674–690. 2016.PubMed/NCBI View Article : Google Scholar

14 

Masci D, Naro C, Puxeddu M, Urbani A, Sette C, La Regina G and Silvestri R: Recent advances in drug discovery for triple-negative breast cancer treatment. Molecules. 28(7513)2023.PubMed/NCBI View Article : Google Scholar

15 

Baden J, Zhao C, Pratt J, Kirov S, Pant A, Seminara A, Green G, Bilke S, Deras I, Fabrizio DA and Pawlowski T: 90PD-Comparison of platforms for determining tumour mutational burden (TMB) in patients with non-small cell lung cancer (NSCLC). Ann Oncol. 30 (Suppl 5)(v25)2019.

16 

Wei B, Kang J, Kibukawa M, Arreaza G, Maguire M, Chen L, Qiu P, Lang L, Aurora-Garg D, Cristescu R and Levitan D: Evaluation of the TruSight oncology 500 assay for routine clinical testing of tumor mutational burden and clinical utility for predicting response to pembrolizumab. J Mol Diagn. 24:600–608. 2022.PubMed/NCBI View Article : Google Scholar

17 

Liu CY, Huang CC, Tsai YF, Chao TC, Lien PJ, Lin YS, Feng CJ, Chen JL, Chen YJ, Chiu JH, et al: VGH-TAYLOR: Comprehensive precision medicine study protocol on the heterogeneity of Taiwanese breast cancer patients. Future Oncol: Oct 19, 2021 (Epub ahead of print).

18 

Huang CC, Tsai YF, Liu CY, Chao TC, Lien PJ, Lin YS, Feng CJ, Chiu JH, Hsu CY and Tseng LM: Comprehensive molecular profiling of Taiwanese breast cancers revealed potential therapeutic targets: prevalence of actionable mutations among 380 targeted sequencing analyses. BMC Cancer. 21(199)2021.PubMed/NCBI View Article : Google Scholar

19 

Huang CC, Tsai YF, Liu CY, Lien PJ, Lin YS, Chao TC, Feng CJ, Chen YJ, Lai JI, Phan NN, et al: Prevalence of tumor genomic alterations in homologous recombination repair genes among taiwanese breast cancers. Ann Surg Oncol. 29:3578–3590. 2022.PubMed/NCBI View Article : Google Scholar

20 

Huang CC, Tsai YF, Liu CY, Lien PJ, Lin YS, Chao TC, Feng CJ, Chen YJ, Lai JI, Cheng HF, et al: Concordance of targeted sequencing from circulating tumor DNA and paired tumor tissue for early breast cancer. Cancers (Basel). 15(4475)2023.PubMed/NCBI View Article : Google Scholar

21 

Chao TC, Tsai YF, Liu CY, Lien PJ, Lin YS, Feng CJ, Chen YJ, Lai JI, Hsu CY, Lynn JJ, et al: Prevalence of PIK3CA mutations in Taiwanese patients with breast cancer: A retrospective next-generation sequencing database analysis. Front Oncol. 13(1192946)2023.PubMed/NCBI View Article : Google Scholar

22 

Gradishar WJ, Moran MS, Abraham J, Abramson V, Aft R, Agnese D, Allison KH, Anderson B, Burstein HJ, Chew H, et al: NCCN guidelines® insights: Breast cancer, version 4.2023. J Natl Compr Canc Netw. 21:594–608. 2023.PubMed/NCBI View Article : Google Scholar

23 

Gennari A, André F, Barrios CH, Cortés J, de Azambuja E, DeMichele A, Dent R, Fenlon D, Gligorov J, Hurvitz SA, et al: ESMO clinical practice guideline for the diagnosis, staging and treatment of patients with metastatic breast cancer. Ann Oncol. 32:1475–1495. 2021.PubMed/NCBI View Article : Google Scholar

24 

No authors listed. Pathologists' guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer. Breast Care (Basel). 5:185–187. 2010.PubMed/NCBI View Article : Google Scholar

25 

Wolff AC, Somerfield MR, Dowsett M, Hammond MEH, Hayes DF, McShane LM, Saphner TJ, Spears PA and Allison KH: Human epidermal growth factor receptor 2 testing in breast cancer: ASCO-college of american pathologists guideline update. J Clin Oncol. 41:3867–3872. 2023.PubMed/NCBI View Article : Google Scholar

26 

Schirmer M, Ijaz UZ, D'Amore R, Hall N, Sloan WT and Quince C: Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 43(e37)2015.PubMed/NCBI View Article : Google Scholar

27 

Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A and Nikiforova MN: Standards and guidelines for the interpretation and reporting of sequence variants in cancer: A joint consensus recommendation of the association for molecular pathology, American society of clinical oncology, and college of American pathologists. J Mol Diagn. 19:4–23. 2017.PubMed/NCBI View Article : Google Scholar

28 

Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, et al: Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 6(pl1)2013.PubMed/NCBI View Article : Google Scholar

29 

Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, et al: The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2:401–404. 2012.PubMed/NCBI View Article : Google Scholar

30 

Chakravarty D, Gao J, Phillips SM, Kundra R, Zhang H, Wang J, Rudolph JE, Yaeger R, Soumerai T, Nissan MH, et al: OncoKB: A precision oncology knowledge base. JCO Precis Oncol. 2017(PO.17.00011)2017.PubMed/NCBI View Article : Google Scholar

31 

Phan L, Zhang H, Wang Q, Villamarin R, Hefferon T, Ramanathan A and Kattman B: The evolution of dbSNP: 25 Years of impact in genomic research. Nucleic Acids Res. 53:D925–D931. 2025.PubMed/NCBI View Article : Google Scholar

32 

Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C, Gauthier LD, et al: A genomic mutational constraint map using variation in 76,156 human genomes. Nature. 625:92–100. 2024.PubMed/NCBI View Article : Google Scholar

33 

Karczewski KJ, Weisburd B, Thomas B, Solomonson M, Ruderfer DM, Kavanagh D, Hamamsy T, Lek M, Samocha KE, Cummings BB, et al: The ExAC browser: Displaying reference data information from over 60 000 exomes. Nucleic Acids Res. 45:D840–D845. 2017.PubMed/NCBI View Article : Google Scholar

34 

Robinson JT, Thorvaldsdottir H, Turner D and Mesirov JP: igv.js: An embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics. 39(btac830)2023.PubMed/NCBI View Article : Google Scholar

35 

Wolff L and Kiesewetter B: Applicability of ESMO-MCBS and ESCAT for molecular tumor boards. Memo. 15:190–195. 2022.

36 

Huang CC, Yeh YC, Cheng HF, Chen BF, Liu CY, Tsai YF, Ho HL and Tseng LM: Comprehensive genomic profiling of Taiwanese triple-negative breast cancer with a large targeted sequencing panel. J Chin Med Assoc: Jun 20, 2025 (Epub ahead of print).

37 

Loderer D, Hornáková A, Tobiášová K, Lešková K, Halašová E, Danková Z, Biringer K, Kúdela E, Rokos T, Dzian A, et al: Comparison of next-generation sequencing quality metrics and concordance in the detection of cancer-specific molecular alterations between formalin-fixed paraffin-embedded and fresh-frozen samples in comprehensive genomic profiling with the Illumina® TruSight oncology 500 assay. Exp Ther Med. 29(64)2025.

38 

Carpten JD, Faber AL, Horn C, Donoho GP, Briggs SL, Robbins CM, Hostetter G, Boguslawski S, Moses TY, Savage S, et al: A transforming mutation in the pleckstrin homology domain of AKT1 in cancer. Nature. 448:439–444. 2007.PubMed/NCBI View Article : Google Scholar

39 

Kalinsky K, Hong F, McCourt CK, Sachdev JC, Mitchell EP, Zwiebel JA, Doyle LA, McShane LM, Li S, Gray RJ, et al: Effect of capivasertib in patients with an AKT1 E17K-mutated tumor: NCI-MATCH subprotocol EAY131-Y nonrandomized trial. JAMA Oncol. 7:271–278. 2021.PubMed/NCBI View Article : Google Scholar

40 

Turner NC, Oliveira M, Howell SJ, Dalenc F, Cortes J, Gomez Moreno HL, Hu X, Jhaveri K, Krivorotko P, Loibl S, et al: Capivasertib in hormone receptor-positive advanced breast cancer. N Engl J Med. 388:2058–2070. 2023.PubMed/NCBI View Article : Google Scholar

41 

Daly GR, AlRawashdeh MM, McGrath J, Dowling GP, Cox L, Naidoo S, Vareslija D, Hill ADK and Young L: PARP inhibitors in breast cancer: A short communication. Curr Oncol Rep. 26:103–113. 2024.PubMed/NCBI View Article : Google Scholar

42 

Szabo C, Masiello A, Ryan JF and Brody LC: The breast cancer information core: Database design, structure, and scope. Hum Mutat. 16:123–131. 2000.PubMed/NCBI View Article : Google Scholar

43 

Chenevix-Trench G, Milne RL, Antoniou AC, Couch FJ, Easton DF and Goldgar DE: CIMBA. An international initiative to identify genetic modifiers of cancer risk in BRCA1 and BRCA2 mutation carriers: The consortium of investigators of modifiers of BRCA1 and BRCA2 (CIMBA). Breast Cancer Res. 9(104)2007.PubMed/NCBI View Article : Google Scholar

44 

Spain BH, Larson CJ, Shihabuddin LS, Gage FH and Verma IM: Truncated BRCA2 is cytoplasmic: Implications for cancer-linked mutations. Proc Natl Acad Sci USA. 96:13920–13925. 1999.PubMed/NCBI View Article : Google Scholar

45 

Tung NM, Robson ME, Ventz S, Santa-Maria CA, Nanda R, Marcom PK, Shah PD, Ballinger TJ, Yang ES, Vinayak S, et al: TBCRC 048: Phase II study of olaparib for metastatic breast cancer and mutations in homologous recombination-related genes. J Clin Oncol. 38:4274–4282. 2020.PubMed/NCBI View Article : Google Scholar

46 

Cheng HF, Tsai YF, Liu CY, Hsu CY, Lien PJ, Lin YS, Chao TC, Lai JI, Feng CJ, Chen YJ, et al: Prevalence of BRCA1, BRCA2, and PALB2 genomic alterations among 924 Taiwanese breast cancer assays with tumor-only targeted sequencing: Extended data analysis from the VGH-TAYLOR study. Breast Cancer Res. 25(152)2023.PubMed/NCBI View Article : Google Scholar

47 

Hyman DM, Piha-Paul SA, Won H, Rodon J, Saura C, Shapiro GI, Juric D, Quinn DI, Moreno V, Doger B, et al: HER kinase inhibition in patients with HER2- and HER3-mutant cancers. Nature. 554:189–194. 2018.PubMed/NCBI View Article : Google Scholar

48 

André F, Ciruelos EM, Juric D, Loibl S, Campone M, Mayer IA, Rubovszky G, Yamashita T, Kaufman B, Lu YS, et al: Alpelisib plus fulvestrant for PIK3CA-mutated, hormone receptor-positive, human epidermal growth factor receptor-2-negative advanced breast cancer: Final overall survival results from SOLAR-1. Ann Oncol. 32:208–217. 2021.PubMed/NCBI View Article : Google Scholar

49 

Choudhury AD, Higano CS, de Bono JS, Cook N, Rathkopf DE, Wisinski KB, Martin-Liberal J, Linch M, Heath EI, Baird RD, et al: A phase I study investigating AZD8186, a potent and selective inhibitor of PI3Kβ/δ, in patients with advanced solid tumors. Clin Cancer Res. 28:2257–2269. 2022.PubMed/NCBI View Article : Google Scholar

50 

Chen HJ, Romigh T, Sesock K and Eng C: Characterization of cryptic splicing in germline PTEN intronic variants in Cowden syndrome. Hum Mutat. 38:1372–1377. 2017.PubMed/NCBI View Article : Google Scholar

51 

Mester JL, Ghosh R, Pesaran T, Huether R, Karam R, Hruska KS, Costa HA, Lachlan K, Ngeow J, Barnholtz-Sloan J, et al: Gene-specific criteria for PTEN variant curation: Recommendations from the ClinGen PTEN expert panel. Hum Mutat. 39:1581–1592. 2018.PubMed/NCBI View Article : Google Scholar

52 

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M, et al: Sherloc: A comprehensive refinement of the ACMG-AMP variant classification criteria. Genet Med. 19:1105–1117. 2017.PubMed/NCBI View Article : Google Scholar

53 

Garrido-Navas MC, García-Díaz A, Molina-Vallejo MP, González-Martínez C, Alcaide Lucena M, Cañas-García I, Bayarri C, Delgado JR, González E, Lorente JA and Serrano MJ: The polemic diagnostic role of TP53 mutations in liquid biopsies from breast, colon and lung cancers. Cancers (Basel). 12(3343)2020.PubMed/NCBI View Article : Google Scholar

54 

Zhou W, Chen T, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB and Chen K: TransVar: A multilevel variant annotator for precision genomics. Nat Methods. 12:1002–1003. 2015.PubMed/NCBI View Article : Google Scholar

55 

Mosteiro M, Azuara D, Villatoro S, Alay A, Gausachs M, Varela M, Baixeras N, Pijuan L, Ajenjo-Bauza M, Lopez-Doriga A, et al: Molecular profiling and feasibility using a comprehensive hybrid capture panel on a consecutive series of non-small-cell lung cancer patients from a single centre. ESMO Open. 8(102197)2023.PubMed/NCBI View Article : Google Scholar

56 

Fox EJ, Reid-Bayliss KS, Emond MJ and Loeb LA: Accuracy of Next generation sequencing platforms. Next Gener Seq Appl. 1(1000106)2014.PubMed/NCBI View Article : Google Scholar

57 

Song P, Chen SX, Yan YH, Pinto A, Cheng LY, Dai P, Patel AA and Zhang DY: Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing. Nat Biomed Eng. 5:690–701. 2021.PubMed/NCBI View Article : Google Scholar

58 

Apostoli AJ and Ailles L: Clonal evolution and tumor-initiating cells: New dimensions in cancer patient treatment. Crit Rev Clin Lab Sci. 53:40–51. 2016.PubMed/NCBI View Article : Google Scholar

59 

Edsjö A, Gisselsson D, Staaf J, Holmquist L, Fioretos T, Cavelier L and Rosenquist R: Current and emerging sequencing-based tools for precision cancer medicine. Mol Aspects Med. 96(101250)2024.PubMed/NCBI View Article : Google Scholar

60 

Cocco E, Scaltriti M and Drilon A: NTRK fusion-positive cancers and TRK inhibitor therapy. Nat Rev Clin Oncol. 15:731–747. 2018.PubMed/NCBI View Article : Google Scholar

61 

Mosele MF, Westphalen CB, Stenzinger A, Barlesi F, Bayle A, Bièche I, Bonastre J, Castro E, Dienstmann R, Krämer A, et al: Recommendations for the use of next-generation sequencing (NGS) for patients with advanced cancer in 2024: A report from the ESMO precision medicine working group. Ann Oncol. 35:588–606. 2024.PubMed/NCBI View Article : Google Scholar

62 

Gradishar WJ, Moran MS, Abraham J, Abramson V, Aft R, Agnese D, Allison KH, Anderson B, Bailey J, Burstein HJ, et al: Breast cancer, version 3.2024, NCCN clinical practice guidelines in oncology. J Natl Compr Canc Netw. 22:331–357. 2024.PubMed/NCBI View Article : Google Scholar

63 

Kang J, Na K, Kang H, Cho U, Kwon SY, Hwang S and Lee A: Prediction of homologous recombination deficiency from oncomine comprehensive assay plus correlating with SOPHiA DDM HRD solution. PLoS One. 19(e0298128)2024.PubMed/NCBI View Article : Google Scholar

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Copy and paste a formatted citation
Spandidos Publications style
Huang C, Yeh Y, Tsai Y, Lin Y, Chao T, Liu C, Ho H and Tseng L: Comprehensive genomic profiling of Taiwanese triple‑negative breast cancer samples with medium‑ and large‑sized sequencing panels: A comparative study implicating treatment allocations. Biomed Rep 23: 162, 2025.
APA
Huang, C., Yeh, Y., Tsai, Y., Lin, Y., Chao, T., Liu, C. ... Tseng, L. (2025). Comprehensive genomic profiling of Taiwanese triple‑negative breast cancer samples with medium‑ and large‑sized sequencing panels: A comparative study implicating treatment allocations. Biomedical Reports, 23, 162. https://doi.org/10.3892/br.2025.2040
MLA
Huang, C., Yeh, Y., Tsai, Y., Lin, Y., Chao, T., Liu, C., Ho, H., Tseng, L."Comprehensive genomic profiling of Taiwanese triple‑negative breast cancer samples with medium‑ and large‑sized sequencing panels: A comparative study implicating treatment allocations". Biomedical Reports 23.4 (2025): 162.
Chicago
Huang, C., Yeh, Y., Tsai, Y., Lin, Y., Chao, T., Liu, C., Ho, H., Tseng, L."Comprehensive genomic profiling of Taiwanese triple‑negative breast cancer samples with medium‑ and large‑sized sequencing panels: A comparative study implicating treatment allocations". Biomedical Reports 23, no. 4 (2025): 162. https://doi.org/10.3892/br.2025.2040
Copy and paste a formatted citation
x
Spandidos Publications style
Huang C, Yeh Y, Tsai Y, Lin Y, Chao T, Liu C, Ho H and Tseng L: Comprehensive genomic profiling of Taiwanese triple‑negative breast cancer samples with medium‑ and large‑sized sequencing panels: A comparative study implicating treatment allocations. Biomed Rep 23: 162, 2025.
APA
Huang, C., Yeh, Y., Tsai, Y., Lin, Y., Chao, T., Liu, C. ... Tseng, L. (2025). Comprehensive genomic profiling of Taiwanese triple‑negative breast cancer samples with medium‑ and large‑sized sequencing panels: A comparative study implicating treatment allocations. Biomedical Reports, 23, 162. https://doi.org/10.3892/br.2025.2040
MLA
Huang, C., Yeh, Y., Tsai, Y., Lin, Y., Chao, T., Liu, C., Ho, H., Tseng, L."Comprehensive genomic profiling of Taiwanese triple‑negative breast cancer samples with medium‑ and large‑sized sequencing panels: A comparative study implicating treatment allocations". Biomedical Reports 23.4 (2025): 162.
Chicago
Huang, C., Yeh, Y., Tsai, Y., Lin, Y., Chao, T., Liu, C., Ho, H., Tseng, L."Comprehensive genomic profiling of Taiwanese triple‑negative breast cancer samples with medium‑ and large‑sized sequencing panels: A comparative study implicating treatment allocations". Biomedical Reports 23, no. 4 (2025): 162. https://doi.org/10.3892/br.2025.2040
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