Biostic ffpe tissue dna isolation kit

Manufactured by Qiagen

Sourced in United States

The BiOstic FFPE Tissue DNA Isolation Kit is a laboratory product designed to extract and purify DNA from formalin-fixed, paraffin-embedded (FFPE) tissue samples. The kit provides a standardized and efficient method for isolating high-quality DNA from these types of samples, which are commonly used in clinical and research applications.

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DNA isolation kit (207 citations) FFPE Tissue Kit (21 citations) FFPE DNA Kit (17 citations) DNA kits (7 citations) FFPE DNA isolation kit (4 citations) FFPE Kits (2 citations)

15 protocols using biostic ffpe tissue dna isolation kit

FFPE Tissue DNA Extraction for Genomic Sequencing

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Formalin-fixed, paraffin embedded (FFPE) cancer tissue from surgical specimens was used for analysis. An independent pathologist evaluated the tumor content using H&E slides. Where applicable, unstained slides were macro-dissected to enrich for tumor content and genomic DNA was extracted using the BiOstic FFPE Tissue DNA Isolation Kit (Mo Bio Laboratories, Inc; Carlsbad, CA). Sample preparation, genomic sequencing and subsequent analyses were all performed in a CLIA/CAP-accredited laboratory (KEW Inc.; Cambridge, MA).

Sato S., Nagahashi M., Koike T., Ichikawa H., Shimada Y., Watanabe S., Kikuchi T., Takada K., Nakanishi R., Oki E., Okamoto T., Akazawa K., Lyle S., Ling Y., Takabe K., Okuda S., Wakai T, & Tsuchida M. (2018). Impact of Concurrent Genomic Alterations Detected by Comprehensive Genomic Sequencing on Clinical Outcomes in East-Asian Patients with EGFR-Mutated Lung Adenocarcinoma. Scientific Reports, 8, 1005.

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FFPE Tumor Analysis for Genomic Profiling

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For Japanese and US patient samples, archival tissue in the form of formalin-fixed, paraffin embedded (FFPE) tumor or unstained tissue sections obtained during routine biopsy and/or resection were used for analysis. An independent pathologist evaluated tumor content on H&E stained slides for each study sample to ensure > 50% tumor content was present. Where applicable, unstained slides were macro-dissected to enrich for tumor content and genomic DNA (gDNA) was extracted using BiOstic FFPE Tissue DNA Isolation Kit (Mo Bio Laboratories, Inc.). All sample prep, CGS, and analytics were performed in a CLIA/CAP-accredited laboratory (KEW Inc; Cambridge, MA, USA).

Nagahashi M., Wakai T., Shimada Y., Ichikawa H., Kameyama H., Kobayashi T., Sakata J., Yagi R., Sato N., Kitagawa Y., Uetake H., Yoshida K., Oki E., Kudo S.E., Izutsu H., Kodama K., Nakada M., Tse J., Russell M., Heyer J., Powers W., Sun R., Ring J.E., Takabe K., Protopopov A., Ling Y., Okuda S, & Lyle S. (2016). Genomic landscape of colorectal cancer in Japan: clinical implications of comprehensive genomic sequencing for precision medicine. Genome Medicine, 8, 136.

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Evaluating FFPE Tumor Samples for NGS

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We analyzed archival tissues of primary cancer from surgical specimens that were confirmed to be of high quality in the form of formalin-fixed, paraffin-embedded (FFPE) slides.^{18 (link)} An independent pathologist evaluated the tumor content on H&E stained slides for each study sample to ensure that > 20% tumor content was present. Where applicable, unstained slides were macro-dissected to enrich for tumor content, and genomic DNA was extracted using the BiOstic FFPE Tissue DNA Isolation Kit (Mo Bio Laboratories, Inc; Carlsbad, CA). DNA quality of the samples was confirmed by QC ratio as previously described.^{18 (link)} Briefly, the quality of an adequate quantity of DNA was assessed by determining the Q-ratio, in which 41 bp and 129 bp targets were amplified by qPCR and compared using a KAPA Human Genomic DNA Quantification and QC Kit (KAPA Biosystems). The 41 bp assay was used for absolute quantification of DNA samples. DNA with a Q-ratio (129 bp/41 bp) > 0.1 was designated as being of high enough quality for NGS analysis based on our previous results.^{18 (link)} All sample preparation, NGS, and analytics were performed in a CLIA/CAP-accredited laboratory (KEW Inc; Cambridge, MA).

Kelly J.M., Miles M.A, & Skinner A.C. (1999). The Anti-Influenza Virus Drug Rimantadine Has Trypanocidal Activity. Antimicrobial Agents and Chemotherapy, 43(4), 985-987.

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Genomic Profiling of MCT-SCC Tumors

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Six FFPE MCT-SCC samples (samples #6, #7, #8, #23, #24, and #25) obtained by surgical resection at the Niigata Cancer Center were analyzed by a gene panel containing 435 cancer-associated genes (CANCERPLEX®). The details of the 435 genes are shown in https://kewinc.com/wp-content/uploads/2017/07/Full-gene-list.pdf. An independent pathologist evaluated tumor content, and over 20% of tumor content was confirmed in all samples. DNA was extracted using the BioStic FFPE Tissue DNA Isolation Kit (MO BIO Laboratories, Carlsbad, CA, USA). Three FFPE samples (samples #23, #24, and #25) were excluded because of poor DNA quality. All sample preparation and genomic sequencing and analysis were performed in a CLIA/CAP-accredited laboratory (KEW, Cambridge, MA, USA). The details of experimental methods for next-generation sequencing and computational analyses are the same as previously described [41 (link)].

Tamura R., Yoshihara K., Nakaoka H., Yachida N., Yamaguchi M., Suda K., Ishiguro T., Nishino K., Ichikawa H., Homma K., Kikuchi A., Ueda Y., Takei Y., Fujiwara H., Motoyama T., Okuda S., Wakai T., Inoue I, & Enomoto T. (2020). XCL1 expression correlates with CD8-positive T cells infiltration and PD-L1 expression in squamous cell carcinoma arising from mature cystic teratoma of the ovary. Oncogene, 39(17), 3541-3554.

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Comprehensive Tissue DNA/RNA/Protein Extraction

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Frozen tissues were first homogenized using the QIAShredder (Qiagen, 79656). Tumor DNA, RNA and protein samples were subsequently extracted using the AllPrep DNA/RNA/Protein Mini kit (Qiagen, 80004). For formalin-fixed, paraffin-embedded tissues, tumor DNA was extracted using the BiOstic FFPE Tissue DNA Isolation kit (MO BIO Laboratories, 12250-50). Extracted DNA was repaired using BioLabs PreCR Repair Mix (New England BioLabs, M0309S) with human alkyladenine DNA glycosylase (hAAG) (New England BioLabs, M0313S). Repaired DNA was subsequently purified using the QIAquick Nucleotide Removal kit (Qiagen, 28304). Normal blood DNA samples were extracted from patient-matched peripheral blood mononuclear cells using the QIAamp DNA Blood Mini kit (Qiagen, 51104).

Bai H., Harmanci A.S., Erson-Omay E.Z., Li J., Coşkun S., Simon M., Krischek B., Özduman K., Omay S.B., Sorensen E.A., Turcan Ş., Bakırcığlu M., Carrión-Grant G., Murray P.B., Clark V.E., Ercan-Sencicek A.G., Knight J., Sencar L., Altınok S., Kaulen L.D., Gülez B., Timmer M., Schramm J., Mishra-Gorur K., Henegariu O., Moliterno J., Louvi A., Chan T.A., Tannheimer S.L., Pamir M.N., Vortmeyer A.O., Bilguvar K., Yasuno K, & Günel M. (2015). Integrated genomic characterization of IDH1-mutant glioma malignant progression. Nature genetics, 48(1), 59-66.

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DNA Extraction from Various Samples

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Genomic DNA was extracted from PBLs and buccal swabs using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions.
Urine samples were centrifuged at 3500 rpm for 10 minutes, genomic DNA was obtained from the pellet using the QIAmp DNA Micro Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.
Tumor DNA was isolated from paraffin-embedded tissue fragments using the Biostic FFPE tissue DNA isolation Kit (MO BIO Laboratories, Carlsbad, CA, U.S.A.), following manufacturer’s instructions. The DNAs were quantified by a spectrophotometer and stored at -20°C.

Azzollini J., Pesenti C., Ferrari L., Fontana L., Calvello M., Peissel B., Portera G., Tabano S., Carcangiu M.L., Riva P., Miozzo M, & Manoukian S. (2017). Revertant mosaicism for family mutations is not observed in BRCA1/2 phenocopies. PLoS ONE, 12(2), e0171663.

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FFPE Tumor DNA Isolation and GSC DNA Extraction

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DNA from the FFPE tumour samples was obtained using a Biostic FFPE tissue DNA isolation kit (MO BIO Laboratories, Carlsbad, CA, USA), following manufacturer's instructions. DNA extraction was performed from FFPE tissue sections with at least 70% of tumour content, assessed by hematoxylin/eosin staining. DNA was extracted from GSCs, at a passage ranging from P4 and P10, using the QIAamp DNA Micro Kit (Qiagen, Hilden, Germany), according to manufacturer's protocol.

Pesenti C., Navone S.E., Guarnaccia L., Terrasi A., Costanza J., Silipigni R., Guarneri S., Fusco N., Fontana L., Locatelli M., Rampini P., Campanella R., Tabano S., Miozzo M, & Marfia G. (2019). The Genetic Landscape of Human Glioblastoma and Matched Primary Cancer Stem Cells Reveals Intratumour Similarity and Intertumour Heterogeneity. Stem Cells International, 2019, 2617030.

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Exome Capture and Sequencing from FFPE

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Briefly, DNA was extracted from FFPE samples using a BiOstic® FFPE Tissue DNA Isolation Kit (MO BIO Laboratories #12250-50) with a modified protocol. Genomic DNA was captured on the NimbleGen 2.1M human exome array and subjected to 74 base paired-end reads on the Illumina HiSeq 2000 instrument as described (2 (link)). Sequence reads were mapped to the reference genome (hg19) using the ELAND program. Reads outside the targeted sequences were discarded and statistics on coverage were collected from the remaining reads using in-house Perl scripts as previously described (2 (link)).

Santin A.D., Bellone S., Buza N., Choi J., Schwartz P.E., Schlessinger J, & Lifton R.P. (2016). Regression of chemotherapy-resistant Polymerase ε (POLE) ultra-mutated and MSH6 hyper-mutated endometrial tumors with nivolumab. Clinical cancer research : an official journal of the American Association for Cancer Research, 22(23), 5682-5687.

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Tumor DNA Extraction from FFPE Samples

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Tumor DNA was extracted from FFPE sections using a Biostic FFPE tissue DNA isolation kit (MO BIO Laboratories, Carlsbad, CA, USA), following the manufacturer's instructions. FFPE tissue samples had previously been stained using hematoxylin and eosin and analyzed independently by two pathologists. The tumor cell content in all samples was at least 70%.
DNA from PBLs was isolated using the QiAMP DNA Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer's protocol and used to test for the 1p/19q codeletion.

Pesenti C., Paganini L., Fontana L., Veniani E., Runza L., Ferrero S., Bosari S., Menghi M., Marfia G., Caroli M., Silipigni R., Guerneri S., Tabano S, & Miozzo M. (2017). Mass spectrometry-based assay for the molecular diagnosis of glioma: concomitant detection of chromosome 1p/19q codeletion, and IDH1, IDH2, and TERT mutation status. Oncotarget, 8(34), 57134-57148.

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DNA Extraction and Exome Sequencing from Blood and Tumor Samples

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Briefly, DNA was extracted from patient’s peripheral blood as source of germinal DNA and FFPE tumor samples using a BiOstic® FFPE Tissue DNA Isolation Kit (MO BIO Laboratories #12250-50) with a modified protocol. Genomic DNA was captured on the NimbleGen 2.1M human exome array and subjected to 74 base paired-end reads on the Illumina HiSeq 2000 instrument as described (17 (link)). Sequence reads were mapped to the reference genome (hg19) using the ELAND program. Reads outside the targeted sequences were discarded and statistics on coverage were collected from the remaining reads using in-house Perl scripts as previously described (17 (link)).

Bellone S., Buza N., Choi J., Zammataro L., Gay L., Elvin J., Rimm D.L., Liu Y., Ratner E.S., Schwartz P.E, & Santin A.D. (2018). Exceptional response to pembrolizumab in a metastatic, chemotherapy/radiation-resistant ovarian cancer patient harboring a PD-L1-genetic rearrangement. Clinical cancer research : an official journal of the American Association for Cancer Research, 24(14), 3282-3291.

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