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Maxwell rsc ffpe plus dna purification kit

Manufactured by Promega
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The Maxwell RSC FFPE Plus DNA Purification Kit is a laboratory equipment product designed for the extraction and purification of genomic DNA from formalin-fixed, paraffin-embedded (FFPE) tissue samples. The kit utilizes an automated magnetic bead-based technology to facilitate the DNA extraction process.

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Lab products found in correlation

Qubit dna hs assay, by Thermo Fisher Scientific (5 mentions) Iscan system, by Illumina (2 mentions) Zymo ez methylation kit, by Zymo Research (2 mentions) Infinium hd ffpe dna restore kit, by Zymo Research (2 mentions) Fluorescent labeled primers, by Merck Group (1 mentions) Sample loading solution, by Beckman Coulter (1 mentions) Maxwell 16 instrument, by Promega (1 mentions) Genomelab gexp genetic analysis system, by Beckman Coulter (1 mentions) Amplitaq gold dna polymerase, by Thermo Fisher Scientific (1 mentions) Infinium methylation 450k, by Illumina (1 mentions) Epic beadchip array, by Illumina (1 mentions) Pyromark q24, by Qiagen (1 mentions) Infinium hd ffpe dna restore kit, by Illumina (1 mentions) Infinium methylationepic beadchip, by Illumina (1 mentions) Quantifluor one dsdna kit, by Promega (1 mentions) Maxwell rsc blood dna kit, by Promega (1 mentions) Quantus fluorometer, by Promega (1 mentions) Maxwell rsc instrument, by Promega (1 mentions) Maxwell rsc 16 instrument, by Promega (1 mentions) Epitect fast dna bisulfite kit, by Qiagen (1 mentions)

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Maxwell RSC Maxwell kits

11 protocols using maxwell rsc ffpe plus dna purification kit

1

Microsatellite Analysis of FFPE Samples

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Genomic DNA was extracted from macrodissected paraffin sections using the Maxwell® RSC FFPE Plus DNA Purification Kit and the Maxwell® 16 Instrument (Promega, Madison, WI), according to the manufacturer's instructions. Microsatellite PCR in duplicates was performed using genomic DNA and AmpliTaq Gold DNA Polymerase (ThermoFisher) as well-fluorescent labeled primers (Sigma-Aldrich). For GeneScan analysis PCR products were mixed with sample loading solution (Beckman Coulter). The products were separated by capillary electrophoresis on the GenomeLab GeXP Genetic Analysis System and analyzed by the GenomeLab GeXP software 10.2 (Beckman Coulter).
Löffler M.W., Nussbaum B., Jäger G., Jurmeister P.S., Budczies J., Pereira P.L., Clasen S., Kowalewski D.J., Mühlenbruch L., Königsrainer I., Beckert S., Ladurner R., Wagner S., Bullinger F., Gross T.H., Schroeder C., Sipos B., Königsrainer A., Stevanović S., Denkert C., Rammensee H.G., Gouttefangeas C, & Haen S.P. (2019). A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Frontiers in Immunology, 10, 2526.
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2

Extracting DNA from FFPE Tumour Samples

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For samples of the clinical test sets, tumour areas with the highest tumour cell content were identified using a light microscope (Olympus, BX46). From the tumour region of interest, the FFPE block was punched for DNA extraction. Semi-automated DNA extraction was performed according to the manufacturer's instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, Promega). DNA quantities were measured using Qubit HS DNA assay (Thermo Fisher Scientific).
Dragomir M.P., Calina T.G., Perez E., Schallenberg S., Chen M., Albrecht T., Koch I., Wolkenstein P., Goeppert B., Roessler S., Calin G.A., Sers C., Horst D., Roßner F, & Capper D. (2023). DNA methylation-based classifier differentiates intrahepatic pancreato-biliary tumours. eBioMedicine, 93, 104657.
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3

DNA Methylation and Copy Number Analysis of FFPE Tumor Samples

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DNA methylation and copy number analyses were performed using the Infinium Methylation450k and EPIC BeadChip array platforms (Illumina, USA). All analyses were performed according to the manufacturer’s instructions. In brief, DNA was extracted from FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA). After bisulfite conversion using the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. The beadchips were scanned on the iScan system (Illumina, USA). The unprocessed output data (.idat files) from the iScan reader were checked for general quality measures as indicated by the manufacturer. DNA methylation based classification was performed for both 450 k and 850 k data using the publically available “brain tumor classifier”, version v11b4 (https://www.molecularneuropathology.org/mnp) [7 (link)].
Schmid S., Solomon D.A., Perez E., Thieme A., Kleinschmidt-DeMasters B.K., Giannini C., Reinhardt A., Asa S.L., Mete O., Stichel D., Siewert C., Dittmayer C., Hasselblatt M., Paulus W., Nagel C., Harter P.N., Schittenhelm J., Honegger J., Rushing E., Coras R., Pfister S.M., Buslei R., Koch A., Perry A., Jones D.T., von Deimling A., Capper D, & Lopes M.B. (2021). Genetic and epigenetic characterization of posterior pituitary tumors. Acta Neuropathologica, 142(6), 1025-1043.
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4

FFPE DNA Extraction and IDH2 Mutation Detection

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DNA was extracted from FFPE tumor sections using Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) according to the manufacturer’s instructions. Pyrosequencing analysis to detect IDH2 R172 mutations was performed by PyroMark Q24 (Qiagen) according to the manufacturer’s instructions.
Glöss S., Jurmeister P., Thieme A., Schmid S., Cai W.Y., Serrette R.N., Perner S P.r.o.f., Ribbat-Idel J., Pagenstecher A P.r.o.f., Bläker H P.r.o.f., Keber U., Stadelmann C P.r.o.f., Zechel S., Johann P.D., Hasselblatt M P.r.o.f., Paulus W P.r.o.f., Thomas C., Dohmen H., Baumhoer D P.r.o.f., Frank S P.r.o.f., Agaimy A P.r.o.f., Schüller U P.r.o.f., Vasudevaraja V., Snuderl M., Liu C.Z., Pfister D.G., Jungbluth A.A., Ghossein R.A., Xu B., Capper D P.r.o.f, & Dogan S. (2021). IDH2 R172 Mutations Across Poorly Differentiated Sinonasal Tract Malignancies: 40 Molecularly Homogenous and Histologically Variable Cases with Favorable Outcome. The American journal of surgical pathology, 45(9), 1190-1204.
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5

DNA Methylation and Copy Number Analysis

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For all tumors, DNA methylation and copy number analyses were performed using the EPIC (850k) Bead-Chip array platform (Illumina, USA).133 (link) All analyses were carried out according to the manufacturer's instructions. DNA was extracted from FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA). After bisulfite conversion with the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. The beadchips were scanned on the iScan system (Illumina USA).
Bader J.M., Deigendesch N., Misch M., Mann M., Koch A, & Meissner F. (2022). Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status. Cell Reports Medicine, 4(1), 100877.
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6

Genome-wide Methylation Analysis of AHRR and SFRP2 in HGSOC

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For 16 randomly selected HGSOC samples from the survival cohort, for which IHC data for AHRR and SFRP2 were available, a genome-wide methylation analysis was performed as previously described [18 (link)]. Briefly, tumour areas were punched out from the FFPE block for DNA extraction. Semi-automated DNA extraction was performed according to the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, Promega). DNA quantities were measured using Qubit HS DNA assay (Thermo Fisher Scientific). DNA restoration was performed using the Infinium HD FFPE DNA Restore Kit and methylation analysis was performed using the Illumina Infinium MethylationEPIC BeadChip. All methylation data pre-processing was conducted in R using various methods as implemented in the ChAMP package. Raw signals were loaded from the IDAT files using the minfi package [19 (link), 20 (link)]. A number of CpG sites were filtered out: all SNP-related sites; multi-hit sites; and CpGs located on chromosomes X and Y. Lastly, the beta values of the remaining CpG sites were normalised using FunNorm [21 (link)] followed by BMIQ [22 (link)]. Next, we selected the normalised beta values for CpGs that passed the above filters and extracted from the annotated file provided by the Illumina the CpGs mapped to AHRR (138 CpGs) and SFRP2 (41 CpGs) genes.
Monjé N., Dragomir M.P., Sinn B.V., Hoffmann I., Makhmut A., Simon T., Kunze C.A., Ihlow J., Schmitt W.D., Pohl J., Piwonski I., Marchenko S., Keunecke C., Calina T.G., Tiso F., Kulbe H., Kreuzinger C., Cacsire Castillo-Tong D., Sehouli J., Braicu E.I., Denkert C., Darb-Esfahani S., Kübler K., Capper D., Coscia F., Morkel M., Horst D., Sers C, & Taube E.T. (2024). AHRR and SFRP2 in primary versus recurrent high-grade serous ovarian carcinoma and their prognostic implication. British Journal of Cancer, 130(8), 1249-1260.
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7

Tumor DNA Extraction from FFPE

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We identified representative tumor areas using light microscopy of hematoxylin and eosin stained sections. If necessary, macrodissection was performed to reach a tumor cell content of at least 70%. Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions. Extracted total DNA quantities were measured using the Qubit™ HS DNA Assay (Thermo Fisher Scientific).
Jurmeister P., Weber K., Villegas S., Karn T., Untch M., Thieme A., Müller V., Taube E., Fasching P., Schmitt W.D., Marmé F., Stickeler E., Sinn B.V., Jank P., Schem C., Klauschen F., van Mackelenbergh M., Denkert C., Loibl S, & Capper D. (2021). DNA methylation profiling identifies two distinct subgroups in breast cancers with low hormone receptor expression, mainly associated with HER2 amplification status. Clinical Epigenetics, 13, 184.
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8

DNA Extraction from FFPE Samples

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Representative tumor areas were identified using light microscopy of hematoxylin and eosin-stained sections. Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega). Extracted total DNA quantities were measured using the Qubit™ HS DNA Assay (Thermo Fisher Scientific).
Jurmeister P., Glöß S., Roller R., Leitheiser M., Schmid S., Mochmann L.H., Payá Capilla E., Fritz R., Dittmayer C., Friedrich C., Thieme A., Keyl P., Jarosch A., Schallenberg S., Bläker H., Hoffmann I., Vollbrecht C., Lehmann A., Hummel M., Heim D., Haji M., Harter P., Englert B., Frank S., Hench J., Paulus W., Hasselblatt M., Hartmann W., Dohmen H., Keber U., Jank P., Denkert C., Stadelmann C., Bremmer F., Richter A., Wefers A., Ribbat-Idel J., Perner S., Idel C., Chiariotti L., Della Monica R., Marinelli A., Schüller U., Bockmayr M., Liu J., Lund V.J., Forster M., Lechner M., Lorenzo-Guerra S.L., Hermsen M., Johann P.D., Agaimy A., Seegerer P., Koch A., Heppner F., Pfister S.M., Jones D.T., Sill M., von Deimling A., Snuderl M., Müller K.R., Forgó E., Howitt B.E., Mertins P., Klauschen F, & Capper D. (2022). DNA methylation-based classification of sinonasal tumors. Nature Communications, 13, 7148.
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9

Tumor DNA Extraction Protocol

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Representative tumor areas were identified using light microscopy of H&E-stained sections. If necessary, macrodissection was performed to reach a tumor cell content of at least 60%. Semi-automated DNA extraction was performed on the Maxwell RSC Instrument (Promega, Madison, WI, USA) using the Maxwell RSC FFPE Plus DNA Purification Kit (AS1720; Promega) for FFPE samples and the Maxwell RSC Blood DNA Kit (AS1400; Promega) for melanocyte specimens, each according to the manufacturer's instructions. Extracted total DNA quantities were measured with a Quantus Fluorometer (Promega) using the QuantiFluor ONE dsDNA Kit (Promega).
Jurmeister P., Wrede N., Hoffmann I., Vollbrecht C., Heim D., Hummel M., Wolkenstein P., Koch I., Heynol V., Schmitt W.D., Thieme A., Teichmann D., Sers C., von Deimling A., Thierauf J.C., von Laffert M., Klauschen F, & Capper D. (2022). Mucosal melanomas of different anatomic sites share a common global DNA methylation profile with cutaneous melanoma but show location-dependent patterns of genetic and epigenetic alterations. The Journal of pathology, 256(1).
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10

FFPE DNA Methylation Analysis

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For samples from the study dataset, DNA methylation analysis was performed on FFPE tissue with a tumor cell content of at least 60%. Semi-automated DNA extraction was performed using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, Fitchburg, WI, USA) on a Maxwell RSC 16 instrument (Promega) according to protocols supplied by the manufacturer. DNA quantities were measured using the Qubit HS DNA assay (Thermo Fisher Scientific, Waltham, MA, USA). The EpiTect Fast DNA Bisulfite Kit (Qiagen, Venlo, The Netherlands) was used to perform DNA bisulfite
Leitheiser M., Capper D., Seegerer P., Lehmann A., Schüller U., Müller K.R., Klauschen F., Jurmeister P, & Bockmayr M. (2022). Machine learning models predict the primary sites of head and neck squamous cell carcinoma metastases based on DNA methylation. The Journal of pathology, 256(4).
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