Evaluation of the Roche MagNA Pure 96 nucleic acid extraction platform for the Seegene Anyplex II HPV28 detection assay

Atchison, Steph; Shilling, Hannah; Balgovind, Prisha; Machalek, Dorothy A; Hawkes, David; Garland, Suzanne M.; Saville, Marion; Murray, Gerald L; Molano, Mónica; Danielewski, Jennifer; Phillips, Samuel

doi:10.1111/jam.15126

Cited by 6 publications

(7 citation statements)

References 22 publications

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“…Total nucleic acids were extracted from FFPE tissue samples using the MagNA Pure 96 DNA and Viral and NA Small Volume Kit, eluted in 100 μL of Roche elution buffer 7,8 . Detection of host β-globin gene was used as quality control for the nucleic acid extraction process 7 .…”

Section: Methodsmentioning

confidence: 99%

“…Total nucleic acids were extracted from FFPE tissue samples using the MagNA Pure 96 DNA and Viral and NA Small Volume Kit, eluted in 100 μL of Roche elution buffer. 7,8 Detection of host β-globin gene was used as quality control for the nucleic acid extraction process. 7 Two reactions with 5 μL each of DNA extracts were tested on Seegene Anyplex II 28HPV (Seegene, Seoul, South Korea), which detects 28 HPV genotypes including 14 high risk (16,18,31,33,35,39,45,51,52,56,58,59, 66, and 68) and 14 lower risk types (6,11,26,40,42,43,44,53,54,61,69,70,73,82).…”

Section: Methodsmentioning

confidence: 99%

“…7 Two reactions with 5 μL each of DNA extracts were tested on Seegene Anyplex II 28HPV (Seegene, Seoul, South Korea), which detects 28 HPV genotypes including 14 high risk (16,18,31,33,35,39,45,51,52,56,58,59, 66, and 68) and 14 lower risk types (6,11,26,40,42,43,44,53,54,61,69,70,73,82). 7,8 Nucleic acids were extracted and tested in duplicate or triplicate to increase the chance of HPV DNA detection. Samples were deemed unassessable if they had a negative β-globin test and an invalid Anyplex II internal control.…”

Section: Methodsmentioning

confidence: 99%

“…Detection of host β-globin gene was used as quality control for the nucleic acid extraction process 7 . Two reactions with 5 μL each of DNA extracts were tested on Seegene Anyplex II 28HPV (Seegene, Seoul, South Korea), which detects 28 HPV genotypes including 14 high risk (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) and 14 lower risk types (6, 11, 26, 40, 42, 43, 44, 53, 54, 61, 69, 70, 73, 82) 7,8 . Nucleic acids were extracted and tested in duplicate or triplicate to increase the chance of HPV DNA detection.…”

Section: Methodsmentioning

confidence: 99%

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The Clinicopathologic Challenge of Nonneoplastic Vulvar Acanthosis

Day

Scurry

Haqshenas

et al. 2022

J Low Genit Tract Dis

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The aim of the study was to evaluate clinicopathologic features of cases demonstrating an acanthotic tissue reaction not clearly consistent with psoriasis, lichen simplex chronicus, mycosis, or condyloma.Materials and Methods: This is a retrospective pathologic case series of biopsies reported as "benign acanthotic lesion" and "acanthotic tissue reaction" that lacked a clear diagnosis on expert review. Cases with nuclear atypia were excluded. Clinical and histopathologic data were collected, immunohistochemistry for p16 and p53 were obtained, and molecular testing for 28 common anogenital human papillomavirus (HPV) genotypes was undertaken.Results: There were 17 cases with a median age of 47 years. Unilaterality and medial location were clinical reasons for diagnostic difficulty. Histopathologic uncertainty often related to lack of papillary dermal fibrosis to support lichen simplex chronicus or psoriasiform lesions without parakeratosis, subcorneal pustules, and/or mycotic elements. Firm pathologic diagnoses were not possible, but 3 groups emerged: favoring chronic dermatitis, favoring psoriasis, and unusual morphologies. p16 results were negative or nonblock positive while p53 was normal or basal overexpressed. Human papillomavirus testing was negative in 12, low positive for HPV 16 in 1, unassessable in 3, and not requested in 1. Conclusions:There is a group of acanthotic tissue reactions that cannot be classified with standard histopathologic assessment. Further clinicopathologic research into unilateral acanthotic lesions may provide insight into separation of psoriasis and mycosis when organisms are absent. Once nuclear atypia is excluded, immunohistochemistry for p16 and p53 and HPV molecular testing do not assist in diagnostic identification.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

The Clinicopathologic Challenge of Nonneoplastic Vulvar Acanthosis

Day

Scurry

Haqshenas

et al. 2022

J Low Genit Tract Dis

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“…Hence, clinical management decisions depend on the reliable detection and genotyping of HPV in cervical swab samples properly taken and evaluated 22 . Besides these preanalytical procedures, aspects of the actual analytical procedure are likely to influence the results and include the amount and volume of swab sample, the extraction method or the actual amount of DNA, and the signal intensity raising questions about the significance of weaker signals and the co‐detection of multiple HPV genotypes 22–25 . These issues let us to prospectively compare automated routine DNA extraction on routine HPV genotyping using nucleic acid testing (NAT) and provide a summary over 314 samples with the newly established procedure.…”

Section: Introductionmentioning

confidence: 99%

Impact of nucleic acid extraction procedures on human papillomavirus (HPV) detection and genotyping

Naegele

Weissbach

Leuzinger

et al. 2023

Journal of Medical Virology

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Human papillomavirus (HPV) infections are often asymptomatic, but some of the >200 HPV genotypes confer a high risk for precancerous cervical lesions and cervical cancer. Current clinical management of HPV infections relies on reliable nucleic acid testing detection and genotyping. We prospectively compared nucleic acid extraction without and with prior centrifugation enrichment for detecting and genotyping HPV in cervical swabs with atypical squamous or glandular cells. Consecutive swabs were analyzed from 45 patients with atypical squamous or glandular cells. Nucleic acids were extracted in parallel using three procedures, Abbott‐M2000, Roche‐MagNA‐Pure‐96 Large‐Volume Kit without (Roche‐MP‐large) and with prior centrifugation (Roche‐MP‐large/spin) and tested using Seegene‐Anyplex‐II HPV28. In total, 54 HPV‐genotypes were detected in 45 samples, 51 by Roche‐MP‐large/spin, 48 by Abbott‐M2000 and 42 by Roche‐MP‐large. The overall concordance was 80% for detecting any HPV and 74% for specific HPV‐genotypes. Roche‐MP‐large/spin and Abbott‐M2000 showed the highest concordance for HPV detection (88.9%; kappa 0.78), and genotyping (88.5%). Two and more HPV‐genotypes were detected in 15 samples, often with one HPV being more abundant. Dilution series confirmed the specific detection of multiple HPV‐genotypes and their relative abundance. In 285 consecutive follow‐up samples extracted by Roche‐MP‐large/spin, the top three detected genotypes were the high‐risk HPV16, HPV53, HPV56 and the low‐risk HPV42, HPV54 and HPV61. Rate and breadth of HPV detection in cervical swabs depends on extraction protocols being highest after centrifugation/enrichment. As multivalent HPV‐vaccine coverage increases, detecting the evolving HPV virome depends on improved extraction and broader genotype coverage.

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Evaluation of the Roche MagNA Pure 96 nucleic acid extraction platform for the SPF10 line probe assay system

Peng

Yin

Liu

et al. 2023

Journal of Applied Microbiology

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Objective To evaluate the MagNA Pure 96 (MP96) nucleic acid extraction system as an alternative for cervical specimen processing for HPV genotyping detection by reverse hybridization line probe assay (LiPA-25), compared to the well-established extraction system MagNA Pure LC 2.0 (MPLC). Methods and results A total of 200 cervical samples preserved in ThinPrepCyt® solution were extracted by MP96 and MPLC, respectively, and then purified nucleic acids were amplified using the SPF10 PCR primer set. Amplification products were subjected to SPF10-DNA enzyme immunoassay (DEIA) and LiPA-25. The concordance between different extraction methods in this study was reflected in the comparison of the results of the DEIA and LiPA-25. Agreement of HPV-positive results (DEIA) was 97.5% (Kappa = 0.932). Pair-wise analyses of either HPV grouping (any HPV genotypes, any high-risk HPV genotypes, any low-risk HPV genotypes, any nonavalent vaccine-targeted HPV, and any non-vaccine-targeted oncogenic HPV genotypes) identified over 95% agreement (all Kappa > 0.900). For the two extraction methods, there was no statistical difference (chi-square test: P = 0.690) for single versus multiple genotypes, and concordant, compatible and discordant genotypes were observed in 87.0%, 9.5% and 3.5% of 200 samples, respectively. Conclusion HPV genotyping results of the MPLC system and the MP96 system showed a high degree of concordance. Combined with the advantages of high-throughput and anti-contamination of MP96, the MP96 extraction system could more suitable for testing of samples in future studies.

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Evaluation of the Roche MagNA Pure 96 nucleic acid extraction platform for the Seegene Anyplex II HPV28 detection assay

Cited by 6 publications

References 22 publications

The Clinicopathologic Challenge of Nonneoplastic Vulvar Acanthosis

The Clinicopathologic Challenge of Nonneoplastic Vulvar Acanthosis

Impact of nucleic acid extraction procedures on human papillomavirus (HPV) detection and genotyping

Evaluation of the Roche MagNA Pure 96 nucleic acid extraction platform for the SPF10 line probe assay system

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