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qBiomarker™ Somatic Mutation PCR Arrays: Data

qBiomarker Somatic Mutation Assay Detection Limit

Assay detection limit test for qBiomarker Somatic Mutation BRaf V600E assay. A series of 10ng genomic DNA samples, which contain genomic DNA from A375 cell line (mutant harboring the BRaf V600E mutation) mixed with genomic DNA from the Coriell GM00131 cell line (wild type) at different ratios, were tested on qBiomarker Somatic Mutation Assay for BRaf V600E with or without whole genome amplification (WGA) using the QIAGEN Repli-g UltraFast Kit. Mutation detection limit for this assay is determined to be <=1%.

qBiomarker Somatic Mutation - Pathway-Focused Cancer Cell Profiling

Mutation profiling of cancer cell line DNAs on the qBiomarker Somatic Mutation EGFR Pathway PCR array.

200ng each of genomic DNA from a wildtype control cell line (WT) and 7 well characterized cancer cell lines were subject to profiling on the qBiomarker Somatic Mutation EGFR Pathway PCR array on an ABI 7900HT sequence detection system. Raw Ct data were analyzed with the qBiomarker Somatic Mutation PCR Array Data Analysis template using DDCt method. Each spike represents the presence of a mutation at each locus (x-axis) in each sample (y-axis).

Somatic Mutation Profiling of Cancer - Correlation with PyroSequencing

(A) Human lung cancer FFPE samples profiled on qBiomarker Somatic Mutation EGFR Pathway PCR array. Genomic DNA from 10 FFPE tissue samples (adenocarcinoma) were subject to profiling on the qBiomarker Somatic Mutation EGFR Pathway PCR Array on an ABI 7900HT sequence detection system. Raw Ct data were analyzed with the qBiomarker Somatic Mutation PCR Array Data Analysis template using average Ct method. Each spike represents the presence of a mutation at each locus (x-axis) in each sample (y-axis).

(B) PyroMark pyrosequencing verifies the deletion and mutations identified by mutation PCR array. Two QIAGEN PyroMark pyrosequencing assays (one for EGFR c.2236_2250del15, one for KRas codon 12 and 13) confirmed the identities of the following mutant alleles in remaining DNA samples: samples 266-1 and 3237-1: EGFR c2236-2250del15 deletion; samples 276-2 and 296-1: KRas c.35G>T mutation. The pyrosequencing results further confirmed that the mutant alleles occur in only a fraction of the cells. A KRas c.37G>C (p.13G>R) mutation was detected by mutation profiler PCR array in sample 264-4, but the percentage of the mutation in this sample appears to be below the detection limit of the pyrosequencing method.

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