Human comprehensive cancer panel

Manufactured by Qiagen

Sourced in Belgium

The Human Comprehensive Cancer Panel is a targeted next-generation sequencing (NGS) solution that analyzes multiple genes associated with various types of cancer. The panel is designed to detect genetic variants that may be relevant for cancer diagnosis, prognosis, and treatment selection.

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Lab products found in correlation

Ngs data analysis web portal, by Qiagen (2 mentions) Ion ampliseq cancer hotspot panel, by Thermo Fisher Scientific (1 mentions) Generead dna library 1 core kit, by Qiagen (1 mentions) Generead dnaseq panel pcr kit v2, by Qiagen (1 mentions) Miseq ngs platform, by Illumina (1 mentions) Gene read dna seq panel pcr regent v2, by Qiagen (1 mentions) Miseq reporter, by Illumina (1 mentions)

5 protocols using human comprehensive cancer panel

Cancer Gene Re-Sequencing Panel Comparison

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In order to select the most relevant cancer-related genes, we focused on 5 different companies releasing commercial re-sequencing panels. The selected 21 panels are the following: Ion AmpliSeq™ Cancer Hotspot Panel v.2, Ion AmpliSeq™ Colon and Lung Research Panel v.2, Ion AmpliSeq™ Comprehensive Cancer Panel, Ion AmpliSeq™ Cancer Panel Primer Pool (Thermo Fisher Scientific); TruSeq™ Amplicon Cancer Panel, TruSight™ Tumor Panel (llumina Inc); Human Breast Cancer Panel, Human Colorectal Cancer Panel, Human Liver Cancer Panel, Human Lung Cancer Panel, Human Ovarian Cancer Panel, Human Prostate Cancer Panel, Human Gastric Cancer Panel, Human Cancer Predisposition Panel, Human Clinically Relevant Tumor Panel, Human Tumor Actionable Mutations Panel, Human Comprehensive Cancer Panel (Qiagen), Somatic 1 MASTR v.2, Somatic 2 MASTR Plus (Multiplicom, Niel, Belgium); Clear Seq Comprehensive Cancer and Clear Seq Cancer (Agilent Technologies).

Bonfiglio S., Vanni I., Rossella V., Truini A., Lazarevic D., Dal Bello M.G., Alama A., Mora M., Rijavec E., Genova C., Cittaro D., Grossi F, & Coco S. (2016). Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples. BMC Cancer, 16(1), 692.

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Comprehensive Genomic Profiling of Cancers

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Multiplex PCR was performed using a GeneReadDNAseq Panel PCR Kit V2 (Qiagen) and Human Comprehensive Cancer Panel (Qiagen), which included 160 cancer‐related genes. Finally, an optimized library was constructed using a Gene Read DNA Library I Core Kit (Qiagen). The library was analyzed using an Agilent DNA 1000 Kit Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Library preparation was achieved within two working days. The enriched libraries were sequenced to obtain paired‐end reads (2 × 150 bp) using the MiSeq NGS platform (Illumina, San Diego, CA, USA), resulting in a mean depth of >500×. The sequencing data were analyzed using an original bioinformatics pipeline, GenomeJack, tuned for clinical sequence examination, “CLUHRC” (Mitsubishi Space Software Co., Ltd., Tokyo, Japan).¹⁷ (link)

Miyamoto S., Suda G., Ishikawa M., Hayashi H., Nimura S., Matsuno Y., Mori R., Tanishima S., Kudo T., Takagi T., Yamamoto Y., Ono S., Shimizu Y, & Sakamoto N. (2021). Genomic profiling of intestinal/mixed‐type superficial non‐ampullary duodenal epithelial tumors. JGH Open: An Open Access Journal of Gastroenterology and Hepatology, 5(9), 1071-1077.

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Comprehensive Cancer Panel DNA Sequencing

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DNA from patient tumor or early passage (P2) PDX tumor (PDX1577, 1668, 2316, and 2552) and from leukocytes isolated from peripheral blood from the PDX donor were submitted for QC and DNAseq using the Human Comprehensive Cancer Panel (QIAGEN Sciences, Frederick, MD). Identification of tumor-associated somatic mutations and copy number alterations was performed using the QIAGEN NGS Data Analysis Web Portal. A color-coded map of genetic alterations in PDXs was constructed using OncoPrinter available through cBioPortal (35 (link),36 (link))

Shattuck-Brandt R.L., Chen S.C., Murray E., Johnson C.A., Crandall H., O’Neal J.F., Al-rohil R.N., Nebhan C.A., Bharti V., Dahlman K.B., Ayers G.D., Kelley M., Kauffmann R.M., Hooks M., Grau A., Johnson D.B., Vilgelm A.E, & Richmond A. (2020). Metastatic Melanoma Patient-derived Xenografts Respond to MDM2 Inhibition as a Single Agent or in Combination with BRAF/MEK Inhibition. Clinical cancer research : an official journal of the American Association for Cancer Research, 26(14), 3803-3818.

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Comprehensive Cancer Genetic Profiling

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DNA from tumor and peripheral blood derived from PDX donor was submitted to VANTAGE core for QC and DNAseq using Human Comprehensive Cancer Panel (Qiagen). Identification of tumor-associated somatic mutations and copy number alterations was performed using QIAGEN NGS Data Analysis Web Portal. Color-coded map of genetic alterations in PDXs was constructed using OncoPrinter available through cBioPortal (75 ).

Vilgelm A.E., Saleh N., Shattuck-Brandt R., Riemenschneider K., Slesur L., Chen S.C., Johnson C.A., Yang J., Blevins A., Yan C., Johnson D.B., Al-Rohil R.N., Halilovic E., Kauffmann R.M., Kelley M., Ayers G.D, & Richmond A. (2019). MDM2 Antagonists Overcome Intrinsic Resistance to CDK4/6 Inhibition by Inducing p21. Science translational medicine, 11(505), eaav7171.

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Comprehensive Cancer Gene Profiling

Cited 2 times

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Using the obtained genomic DNA, we then amplified the target genes by a polymerase chain reaction (PCR) method with Gene Read DNA seq Panel PCR Regent V2 (Qiagen) and Human Comprehensive Cancer Panel (Qiagen). We performed targeted amplicon exome sequencing for 160 cancer-related genes based on the Illumina MiSeq sequencing platform (Illumina, San Diego, USA) with an average depth of coverage of approximately 500 × with at least 80% of bases covered >50 × [[16] (link), [17] (link), [18] (link), [19] (link), [20] (link), [21] (link)]. Sequencing (paired-end, 150 bp) of samples and demultiplexing of libraries was performed by Illumina MiSeq Reporter. The list of 160 genes is shown in Supplementary Table 1 [19 (link),20 (link)]. Details of data analysis are described in Supplementary Methods. Germline variants were classified according to the American College of Medical Genetics and Genomics (ACMG) guidelines [22 (link)], and retained as pathogenic based on the recommendations of ACMG and ClinVar [23 (link)]. Germline secondary findings were disclosed only to those patients who agreed to receive this information.

Hagio K., Hatanaka K.C., Amano T., Matsuno Y., Hatanaka Y, & Yamashita H. (2021). Genetic heterogeneity during breast cancer progression in young patients. The Breast : Official Journal of the European Society of Mastology, 60, 206-213.

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