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Optimizing spin‑column elution parameters for efficient HPV DNA recovery from preservative liquid‑based cytology cervical scrape samples

  • Authors:
    • Nilamsari Kurniasih Indrawan
    • Wuri Handayani
    • Henny Meitri Andrie R. Putri
    • Kartika Hapsari
    • Paramita Sudirman
    • Nur Al Faizah
    • Innas Widiasti
    • Muhammad Al‑Haddad P. Iko
    • Ajeng Kusumaningtyas Pramono
    • Pertho Rinaldi Marpaung
    • Nabila Tsoerayya Gustia Pudjas
    • Vincentius Simeon Weo Budhyanto
    • Putri Wikie Novianti
  • View Affiliations / Copyright

    Affiliations: Laboratory Optimization Team, Yayasan Satriabudi Dharma Setia, Tangerang 15345, Indonesia, Department of Obstetrics and Gynecology, Indonesia Army Hospital, Jakarta 10410, Indonesia, Department of Obstetrics and Gynecology, Rumah Sakit Umum Pusat Nasional Dr. Cipto Mangunkusumo, Jakarta 10430, Indonesia, Siena Clinical, Siena Sains Medika, Jakarta 10340, Indonesia, GENEPICA, London, HA4 7AE, UK, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
    Copyright: © Indrawan et al. This is an open access article distributed under the terms of Creative Commons Attribution License [CC BY 4.0].
  • Article Number: 89
    |
    Published online on: August 28, 2026
       https://doi.org/10.3892/wasj.2026.504
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Abstract

Optimizing DNA extraction protocols is critical for improving downstream molecular analyses, particularly for low‑cellularity clinical samples, such as HPV ThinPrep liquid‑based cytology specimens. Variations in pre‑analytical extraction parameters substantially influence DNA yield, purity and integrity; yet, these factors remain underexplored beyond default manufacturer guidelines. The present study systematically evaluated the effects of lysis incubation duration (30, 40, 50, 60 and 80 min), elution volume (ranging from 30 to 75 µl) and the number of elution cycles on DNA recovery using a silica spin‑column extraction method. The extraction performance was assessed using fluorometry and spectrophotometry, alongside DNA integrity number (DIN) evaluation using a TapeStation. To account for between‑sample biological variations and storage temperature confounders, a linear mixed‑effects model (LMM) was employed for DNA yield, while a generalized linear mixed model (GLMM) evaluated purity. Response surface methodology was subsequently applied to determine non‑linear parameter effects and global optima. The LMM identified the number of elution cycles and its interaction with incubation duration as critical determinants of DNA yield. Response surface methodology optimization identified an individual optimum for maximizing yield, and for optimal purity. A compromise operational point was established to simultaneously satisfy both responses. Furthermore, the first elution cycle consistently recovered the vast majority of DNA mass, rendering a second cycle largely redundant. Quality control analysis demonstrated that an elevated DNA yield does not inherently guarantee a high DNA integrity, emphasizing the compounding impact of storage temperature. On the whole, these findings demonstrate that tailoring extraction parameters and utilizing a single‑elution workflow can significantly enhance the quality and quantity of DNA recovered from low‑biomass clinical specimens for advanced molecular diagnostics.
View Figures

Figure 1

Visualization of response surface
methodology results. Columns represent the visualization type: 2D
contour plots (left panels) and 3D response surface plots (right
panels). Rows represent the optimized parameters: (A) ‘Yield’ and
(B) ‘Purity’. The green dotted lines indicate the predicted optimum
values for each response variable.
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Copy and paste a formatted citation
Spandidos Publications style
Indrawan N, Handayani W, Putri HM, Hapsari K, Sudirman P, Faizah NA, Widiasti I, Iko MA, Pramono AK, Marpaung PR, Marpaung PR, et al: Optimizing spin‑column elution parameters for efficient HPV DNA recovery from preservative liquid‑based cytology cervical scrape samples. World Acad Sci J 8: 89, 2026.
APA
Indrawan, N., Handayani, W., Putri, H.M., Hapsari, K., Sudirman, P., Faizah, N.A. ... Novianti, P.W. (2026). Optimizing spin‑column elution parameters for efficient HPV DNA recovery from preservative liquid‑based cytology cervical scrape samples. World Academy of Sciences Journal, 8, 89. https://doi.org/10.3892/wasj.2026.504
MLA
Indrawan, N., Handayani, W., Putri, H. M., Hapsari, K., Sudirman, P., Faizah, N. A., Widiasti, I., Iko, M. A., Pramono, A. K., Marpaung, P. R., Pudjas, N. T., Budhyanto, V. S., Novianti, P. W."Optimizing spin‑column elution parameters for efficient HPV DNA recovery from preservative liquid‑based cytology cervical scrape samples". World Academy of Sciences Journal 8.5 (2026): 89.
Chicago
Indrawan, N., Handayani, W., Putri, H. M., Hapsari, K., Sudirman, P., Faizah, N. A., Widiasti, I., Iko, M. A., Pramono, A. K., Marpaung, P. R., Pudjas, N. T., Budhyanto, V. S., Novianti, P. W."Optimizing spin‑column elution parameters for efficient HPV DNA recovery from preservative liquid‑based cytology cervical scrape samples". World Academy of Sciences Journal 8, no. 5 (2026): 89. https://doi.org/10.3892/wasj.2026.504
Copy and paste a formatted citation
x
Spandidos Publications style
Indrawan N, Handayani W, Putri HM, Hapsari K, Sudirman P, Faizah NA, Widiasti I, Iko MA, Pramono AK, Marpaung PR, Marpaung PR, et al: Optimizing spin‑column elution parameters for efficient HPV DNA recovery from preservative liquid‑based cytology cervical scrape samples. World Acad Sci J 8: 89, 2026.
APA
Indrawan, N., Handayani, W., Putri, H.M., Hapsari, K., Sudirman, P., Faizah, N.A. ... Novianti, P.W. (2026). Optimizing spin‑column elution parameters for efficient HPV DNA recovery from preservative liquid‑based cytology cervical scrape samples. World Academy of Sciences Journal, 8, 89. https://doi.org/10.3892/wasj.2026.504
MLA
Indrawan, N., Handayani, W., Putri, H. M., Hapsari, K., Sudirman, P., Faizah, N. A., Widiasti, I., Iko, M. A., Pramono, A. K., Marpaung, P. R., Pudjas, N. T., Budhyanto, V. S., Novianti, P. W."Optimizing spin‑column elution parameters for efficient HPV DNA recovery from preservative liquid‑based cytology cervical scrape samples". World Academy of Sciences Journal 8.5 (2026): 89.
Chicago
Indrawan, N., Handayani, W., Putri, H. M., Hapsari, K., Sudirman, P., Faizah, N. A., Widiasti, I., Iko, M. A., Pramono, A. K., Marpaung, P. R., Pudjas, N. T., Budhyanto, V. S., Novianti, P. W."Optimizing spin‑column elution parameters for efficient HPV DNA recovery from preservative liquid‑based cytology cervical scrape samples". World Academy of Sciences Journal 8, no. 5 (2026): 89. https://doi.org/10.3892/wasj.2026.504
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