cfDNA Extraction Controls

The Extraction Controls are contrived human plasma cfDNA samples with a series of dilutions of cfDNA.

The members of Panel 1 have different Allele Frequency (AF%), from 0 to 3%, quantified with ddPCR.  To best mimic the patient ctDNA sample, both the variant and the wild-type cfDNAs are nucleosomally-fragmentated gDNA derived from cell lines. The cfDNA was spiked into human DNA-free plasma. These make them the ideal patient-like reference material. They can be used to estimate the sensitivity of ctDNA detection throughout the entire assay, including especially the extraction step. They can be used to calculate a particular variant detection’s Limit of Detection (LOD). Individual members can be used as quality control.

The members of Panel 2 have different total cfDNA mass (ng/ml). They can help monitor plasma cfDNA loss, determine how low the absolute cfDNA number of copies can be reliably extracted, and standardize QC workflow for plasma cfDNA extraction process.

Individual panel members can be separately purchased for assay quality control purposes. Customized panels and controls can be built per requirements of the customer. For the price and availability of catalog and customized products, please send an email inquiry to info@anchormolecular.com.

Characterization of our cfDNA can be found here: Characterization of the fragmented cfDNA

Extraction Panel 1 

• DNA-free plasma spiked with cell-derived DNA fragment containing 23 variants at 0, 0.1, 0.3, 1, and 3% average AF in a constant 20 ng/ml fragmented total gDNA background. The list of 23 variants is below. Each member of the panel can be separately purchased.
  

  Variant Name	Cosmic ID
  KRAS G12C	COSV55497469
  KRAS G12D	COSV55497369
  KRAS G12V	COSV55497419
  TP53 R248Q	COSV52661580
  PIK3CA E545K	COSV55873239
  PIK3CA H1047R	COSV55873195
  EGFR T790M	COSV51765492
  EGFR C797S	COSV51766493
  EGFR D770_N771insG	COSV51769298
  EGFR L858R	COSV51765161
  BRAF V600E	COSV56056643
  NRAS Q61R	COSV54736340
  PTEN R130G	COSV64288384
  TP53 R175H	COSV52661038
  IDH1 R132H	COSV61615239
  CTNNB1 T41A	COSV62687862
  CTNNB1 S33C	COSV62687839
  FGFR3 S249C	COSV53390026
  APC Q1429*	COSV57322632
  APC R1450*	COSV57321313
  EGFR E746-A750del v1	COSV51765119
  EGFR E746-A750del v2	COSV51765066
  KIT D816V	COSV55386424

Extraction Panel 2 

• DNA-free plasma spiked with increasing concentration of total gDNA fragments at 0, 0.3, 1, 3, and 10 ng/ml. Customized controls at specific ng/ml can be ordered.
  

  Product Description	Cat. No.	Buffer
  Extraction Panel 1, Variants at 0.1, 0.3, 1, and 3% AF, 20ng/ml total gDNA	60100545	Plasma
  Extraction Panel 3% Member, 20ng/ml total gDNA	60100540	Plasma
  Extraction Panel 0% Member, 20ng/ml total gDNA	60100544	Plasma
  Extraction Panel 2, gDNA at a series concentration: 0, 0.3, 1, 3, 10 ng/ml	60100555	Plasma
  gDNA Positive Control (gDNA at 3ng/ml)	60100551	Plasma