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Ampfistr identifiler

Manufactured by Thermo Fisher Scientific
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The AmpFISTR Identifiler is a short tandem repeat (STR) multiplex assay used for human DNA identification and profiling. It amplifies 15 STR loci and the gender-determining locus, Amelogenin, in a single PCR reaction. The assay is designed for use in forensic, paternity, and human identification applications.

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Lab products found in correlation

Rna 6000 nano assay, by Agilent Technologies (5 mentions) Mirvana mirna isolation kit, by Thermo Fisher Scientific (5 mentions) Allprep dna rna kit, by Qiagen (5 mentions) Qiaamp blood midi kit, by Qiagen (3 mentions) Qiaamp dna blood midi kit, by Qiagen (2 mentions) Hct116, by Thermo Fisher Scientific (2 mentions) Ht 29, by Thermo Fisher Scientific (2 mentions) Cellcheck, by IDEXX (2 mentions) Hop 92, by Thermo Fisher Scientific (2 mentions) Genescan 500 liz internal size standard, by Thermo Fisher Scientific (1 mentions) Abi 3130xl genetic analyser, by Thermo Fisher Scientific (1 mentions)

Close spelling variants of this product

AmpFISTR Identifiler PCR amplification kit (33 citations) AmpFISTR® Identifiler® Plus PCR Amplification Kit (2 citations)

8 protocols using ampfistr identifiler

1

Molecular Profiling of Tumor and Normal Tissues

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RNA and DNA were extracted from tumor and adjacent normal tissue specimens using a modification of the DNA/RNA AllPrep kit (QIAGEN). The flow-through from the QIAGEN DNA column was processed using a mirVana miRNA Isolation Kit (Ambion). This latter step generated RNA preparations that included RNA < 200 nt suitable for miRNA analysis. DNA was extracted from blood using the QiaAmp Blood Midi Kit (QIAGEN). Each specimen was quantified by measuring Abs260 with a UV spectrophotometer or by PicoGreen assay. DNA specimens were resolved by 1% agarose gel electrophoresis to confirm high molecular weight fragments. A custom Sequenom SNP panel or the AmpFISTR Identifiler (Applied Biosystems) was utilized to verify that tumor DNA and germline DNA were derived from the same patient. Five hundred nanograms of each tumor and normal DNA were sent to QIAGEN for REPLI-g whole genome amplification using a 100 µg reaction scale. Only specimens yielding a minimum of 6.9 µg of tumor DNA, 5.15 µg RNA, and 4.9 µg of germline DNA were included in this study. RNA was analyzed via the RNA6000 Nano assay (Agilent) for determination of an RNA Integrity Number (RIN), and only the cases with RIN > 7.0 were included in this study.
Hoadley K.A., Yau C., Hinoue T., Wolf D.M., Lazar A.J., Drill E., Shen R., Taylor A.M., Cherniack A.D., Thorsson V., Akbani R., Bowlby R., Wong C.K., Wiznerowicz M., Sanchez-Vega F., Robertson A.G., Schneider B.G., Lawrence M.S., Noushmehr H., Malta T.M., Stuart J.M., Benz C.C, & Laird P.W. (2018). Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell, 173(2), 291-304.e6.
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2

Comprehensive Biospecimen Processing Protocol

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DNA and RNA were extracted and quality was assessed at the central BCR. RNA and DNA were extracted from tumor and adjacent non-tumor tissue specimens using a modification of the DNA/RNA AllPrep kit (Qiagen). The flow-through from the Qiagen DNA column was processed using a mirVana miRNA Isolation Kit (Ambion). This latter step generated RNA preparations that included RNA < 200 nt suitable for miRNA analysis. DNA was extracted from blood using the QiaAmp DNA Blood Midi kit (Qiagen).
RNA samples were quantified by measuring Abs260 with a UV spectrophotometer and DNA quantified by PicoGreen assay. DNA specimens were resolved by 1% agarose gel electrophoresis to confirm high molecular weight fragments. A custom Sequenom SNP panel or the AmpFISTR Identifiler (Applied Biosystems) was utilized to verify that tumor DNA and germline DNA representing a case were derived from the same patient. Five hundred nanograms of each tumor and germline DNA were sent to Qiagen (Hilden, Germany) for REPLI-g whole genome amplification using a 100 μg reaction scale. RNA was analyzed via the RNA6000 Nano assay (Agilent) for determination of an RNA Integrity Number (RIN), and only analytes with a RIN ≥ 7.0 were included in this study. Only cases yielding a minimum of 6.9 μg of tumor DNA, 5.15 μg RNA, and 4.9 μg of germline DNA were included in this study.
Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. (2017). Cancer cell, 32(2), 185-203.e13.
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3

Comprehensive Cancer Cell Line Characterization

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CRC cell lines HCT-116 (obtained 2018), HT-29 (obtained 2018), and LoVo (obtained 2018), lung cancer cell line HOP-92 (obtained 2017), breast cancer cell line MCF7 (obtained 2021) and melanoma cell line RPMI-7951 (obtained 2021) were obtained through the NCI Cell Line Repository (Division of Cancer Treatment and Diagnosis (DCTD) Tumor Repository, NCI at Frederick, Frederick, MD). The prostate cancer cell line PC-3 were provided by Dr. Esta Sterneck (NCI-Frederick, obtained 2019). HCT-116, HT-29, LoVo, HOP-92, MCF7, RPMI-7951, and PC-3 cells were cultured in RPMI 1640 Medium supplemented with 10% FBS, 1% P/S, and 2mM L-Glutamine. All cells were incubated at 5% CO2 at 37⁰C. Cell lines were tested for mycoplasma contamination by PPLO culture under aerobic and anaerobic conditions and orcein staining of Fogh or by PCR-based assay. Cell lines obtained from the NCI DCTD Tumor Respository (HCT-116, HT-29, LoVo, HOP-92, MCF7, RPMI-7951) were authenticated using Applied Biosystems AmpFISTR® Identifiler with PCR amplification prior to cell line receipt. PC-3 cells were authenticated using CellCheck, (IDEXX BioAnalytics, Columbia, MO) a comprehensive cell line authentication service that utilizes STR-based DNA profiling and multiplex PCR to detect both contamination and misidentification of cell lines.
Loomans-Kropp H.A., Song Y., Gala M., Parikh A.R., Van Seventer E.E., Alvarez R., Hitchins M.P., Shoemaker R.H, & Umar A. (2022). Methylated Septin9 (mSEPT9): A Promising Blood-Based Biomarker for the Detection and Screening of Early-Onset Colorectal Cancer. Cancer Research Communications, 2(2), 90-98.
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4

Authenticated Cell Lines for Cancer Research

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Colorectal cancer cell lines HCT-116 (obtained 2018), HT-29 (obtained 2018), and LoVo (obtained 2018), lung cancer cell line HOP-92 (obtained 2017), breast cancer cell line MCF7 (obtained 2021), and melanoma cell line RPMI-7951 (obtained 2021) were obtained through the NCI Cell Line Repository [Division of Cancer Treatment and Diagnosis (DCTD) Tumor Repository, NCI at Frederick, Frederick, MD]. The prostate cancer cell line PC-3 was provided by Dr. Esta Sterneck (NCI-Frederick, obtained 2019). HCT-116, HT-29, LoVo, HOP-92, MCF7, RPMI-7951, and PC-3 cells were cultured in RPMI1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, and 2 mmol/L l-glutamine. All cells were incubated at 5% CO2 at 37°C. Cell lines were tested for Mycoplasma contamination by PPLO culture under aerobic and anaerobic conditions and orcein staining of Fogh or by PCR-based assay. Cell lines obtained from the NCI DCTD Tumor Repository (HCT-116, HT-29, LoVo, HOP-92, MCF7, RPMI-7951) were authenticated using Applied Biosystems AmpFISTR Identifiler with PCR amplification prior to cell line receipt. PC-3 cells were authenticated using CellCheck (IDEXX BioAnalytics), a comprehensive cell line authentication service that utilizes STR-based DNA profiling and multiplex PCR to detect both contamination and misidentification of cell lines.
Loomans-Kropp H.A., Song Y., Gala M., Parikh A.R., Van Seventer E.E., Alvarez R., Hitchins M.P., Shoemaker R.H, & Umar A. (2022). Methylated Septin9 (mSEPT9): A Promising Blood-Based Biomarker for the Detection and Screening of Early-Onset Colorectal Cancer. Cancer Research Communications, 2(2), 90-98.
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5

Comprehensive Tumor Genomic Profiling

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DNA and RNA were extracted and quality was assessed at the central BCR. RNA and DNA were extracted from tumor using a
modification of the DNA/RNA AllPrep kit (Qiagen). The flow-through from the Qiagen DNA column was processed using a mirVana
miRNA Isolation Kit (Ambion). This latter step generated RNA preparations that included RNA <200 nt suitable for miRNA
analysis. DNA was extracted from blood using the QiaAmp DNA Blood Midi kit (Qiagen).
RNA samples were quantified by measuring Abs260 with a UV spectrophotometer and DNA quantified by PicoGreen assay. DNA
specimens were resolved by 1% agarose gel electrophoresis to confirm high molecular weight fragments. A custom
Sequenom SNP panel or the AmpFISTR Identifiler (Applied Biosystems) was utilized to verify that tumor DNA and germline DNA
representing a case were derived from the same patient. Five hundred nanograms of each tumor and germline DNA were sent to
Qiagen (Hilden, Germany) for REPLI-g whole genome amplification using a 100 μg reaction scale. RNA was analyzed via
the RNA6000 Nano assay (Agilent) for determination of an RNA Integrity Number (RIN), and only analytes with a RIN≥7.0
were included in this study. Only cases yielding a minimum of 6.9 μg of tumor DNA, 5.15 μg RNA, and 4.9
μg of germline DNA were included in this study.
Radovich M., Pickering C.R., Felau I., Ha G., Zhang H., Jo H., Hoadley K.A., Anur P., Zhang J., McLellan M., Bowlby R., Matthew T., Danilova L., Hegde A.M., Kim J., Leiserson M.D., Sethi G., Lu C., Ryan M., Su X., Cherniack A.D., Robertson G., Akbani R., Spellman P., Weinstein J.N., Hayes D.N., Raphael B., Lichtenberg T., Leraas K., Zenklusen J.C., Fujimoto J., Scapulatempo-Neto C., Moreira A.L., Hwang D., Huang J., Marino M., Korst R., Giaccone G., Gokmen-Polar Y., Badve S., Rajan A., Ströbel P., Girard N., Tsao M.S., Marx A., Tsao A.S, & Loehrer P.J. (2018). The integrated genomic landscape of thymic epithelial tumors. Cancer cell, 33(2), 244-258.e10.
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6

Comprehensive Tissue DNA and RNA Extraction

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RNA and DNA were extracted from tumor and adjacent normal tissue
specimens using a modification of the DNA/RNA AllPrep kit (Qiagen). The
flow-through from the Qiagen DNA column was processed using a mirVana miRNA
Isolation Kit (Ambion). This latter step generated RNA preparations that
included RNA <200 nt suitable for miRNA analysis. DNA was extracted from
blood using the QiaAmp blood midi kit (Qiagen). Each specimen was quantified
by measuring Abs260 with a UV spectrophotometer or by PicoGreen assay. DNA
specimens were resolved by 1% agarose gel electrophoresis to confirm
high molecular weight fragments. A custom Sequenom SNP panel or the AmpFISTR
Identifiler (Applied Biosystems) was utilized to verify tumor DNA and
germline DNA were derived from the same patient. Five hundred nanograms of
each tumor and normal DNA were sent to Qiagen for REPLI-g whole genome
amplification using a 100 μg reaction scale. Only specimens yielding
a minimum of 6.9 μg of tumor DNA, 5.15 μg RNA, and 4.9
μg of germline DNA were included in this study. RNA was analyzed via
the RNA6000 Nano assay (Agilent) for determination of an RNA Integrity
Number (RIN), and only the cases with RIN >7.0 were included in this
study.
Liu Y., Sethi N.S., Hinoue T., Schneider B.G., Cherniack A.D., Sanchez-Vega F., Seoane J.A., Farshidfar F., Bowlby R., Islam M., Kim J., Chatila W., Akbani R., Kanchi R.S., Rabkin C.S., Willis J.E., Wang K.K., McCall S.J., Mishra L., Ojesina A.I., Bullman S., Pedamallu C.S., Lazar A.J., Sakai R., Thorsson V., Bass A.J, & Laird P.W. (2018). Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer cell, 33(4), 721-735.e8.
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7

Molecular Profiling of Tumor and Normal Tissues

Check if the same lab product or an alternative is used in the 5 most similar protocols
RNA and DNA were extracted from tumor and adjacent normal tissue specimens using a modification of the DNA/RNA AllPrep kit (QIAGEN). The flow-through from the QIAGEN DNA column was processed using a mirVana miRNA Isolation Kit (Ambion). This latter step generated RNA preparations that included RNA < 200 nt suitable for miRNA analysis. DNA was extracted from blood using the QiaAmp Blood Midi Kit (QIAGEN). Each specimen was quantified by measuring Abs260 with a UV spectrophotometer or by PicoGreen assay. DNA specimens were resolved by 1% agarose gel electrophoresis to confirm high molecular weight fragments. A custom Sequenom SNP panel or the AmpFISTR Identifiler (Applied Biosystems) was utilized to verify that tumor DNA and germline DNA were derived from the same patient. Five hundred nanograms of each tumor and normal DNA were sent to QIAGEN for REPLI-g whole genome amplification using a 100 µg reaction scale. Only specimens yielding a minimum of 6.9 µg of tumor DNA, 5.15 µg RNA, and 4.9 µg of germline DNA were included in this study. RNA was analyzed via the RNA6000 Nano assay (Agilent) for determination of an RNA Integrity Number (RIN), and only the cases with RIN > 7.0 were included in this study.
Hoadley K.A., Yau C., Hinoue T., Wolf D.M., Lazar A.J., Drill E., Shen R., Taylor A.M., Cherniack A.D., Thorsson V., Akbani R., Bowlby R., Wong C.K., Wiznerowicz M., Sanchez-Vega F., Robertson A.G., Schneider B.G., Lawrence M.S., Noushmehr H., Malta T.M., Stuart J.M., Benz C.C, & Laird P.W. (2018). Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell, 173(2), 291-304.e6.
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8

Tumor DNA Profiling using Identifiler

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All biopsied tumour regions were amplified using AmpFISTR® Identifiler® (polymerase-chain reaction amplification kit, Applied Biosystems, Waltham, MA, USA), containing loci D8S1179, D21S11, D7S820, CSF1P0, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, and the Amelogenin locus for sex determination, according to the manufacturer’s recommendations. Fragment size was detected using Applied Biosystems ABI 3130XL genetic analyser and sized with GeneScan500-LIZ internal size standard (Applied Biosystems, Waltham, MA, USA) following the manufacturer’s protocols. Allele calling was performed using GeneMapper ID (v1.1) software (Thermofisher Scientific, Waltham, MA, USA).
Siraj S., Masoodi T., Siraj A.K., Azam S., Qadri Z., Ahmed S.O., AlBalawy W.N., Al-Obaisi K.A., Parvathareddy S.K., AlManea H.M., AlHussaini H.F., Abduljabbar A., Alhomoud S., Al-Dayel F.H., Alkuraya F.S, & Al-Kuraya K.S. (2020). Clonal Evolution and Timing of Metastatic Colorectal Cancer. Cancers, 12(10), 2938.
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