Real-time PCR-based assay to quantify the relative amount of human and mouse tissue present in tumor xenografts

BMC Biotechnology

Table 1 Species quantification results from a survey of selected xenografts.

Xenograft Name	Tumor Type	in vivo Passage	Initial DNA (ng)	Average % Human ± SD	Average % Mouse	Calculated Human DNA	Calculated Mouse DNA	Sum DNA (ng)	% of Initial DNA
HL-60(TB)	Leukemia	P01	27.6	100.0 ± 0.00	0.0	26.96	0.00	27.0	97.7
MDA-MB-361	Breast	P01	48.8	12.8 ± 1.84	87.2	4.80	31.20	36.0	73.7
NCI-H157	Lung	P01	72.4	98.9 ± 1.50	1.1	97.83	1.29	99.1	136.8
RXF-631	Renal	P01	23.2	43.2 ± 0.06	56.8	9.90	11.34	21.2	91.5
SK-MEL-2	Melanoma	P01	29.2	81.8 ± 1.42	18.2	38.63	7.66	46.3	158.4
UACC-257	Melanoma	P01	53.7	99.9 ± 0.08	0.1	49.49	0.04	49.5	92.3
LOX IMVI	Melanoma	P01-a	50.6	48.4 ± 7.26	51.6	16.15	17.54	33.7	66.6
LOX IMVI	Melanoma	P01-b	52.8	55.1 ± 6.38	45.0	19.30	16.77	36.1	68.3
LOX IMVI	Melanoma	P01-c	55.5	39.6 ± 7.99	60.4	17.13	27.34	44.5	80.2
LOX IMVI	Melanoma	P01-d	52.1	53.1 ± 6.56	46.9	24.81	35.35	60.2	115.4
LOX IMVI	Melanoma	P01-e	53.5	33.9 ± 7.76	66.1	20.15	45.56	65.7	122.9
AS283	Lymphoma	P04-a	56.9	83.5 ± 5.89	16.5	37.12	7.39	44.5	78.3
AS283	Lymphoma	P04-b	71.6	83.6 ± 4.90	16.4	86.85	13.31	100.2	139.8
CA46	Lymphoma	P04	43.4	99.9 ± 0.09	0.1	47.76	0.04	47.8	110.2
CP70	Ovarian	P04	61.4	83.5 ± 3.23	16.6	59.56	9.87	69.4	113.0
Daudi	Lymphoma	P04	56.5	100.0 ± 0.02	0.0	49.03	0.01	49.0	86.7
GTL-16	Gastric	P04	42.3	100.0 ± 0.00	0.0	39.92	0.00	39.9	94.4
OVCAR-5	Ovarian	P04	53	88.8 ± 0.31	11.2	63.11	6.98	70.1	132.1
AS283	Lymphoma	P10	49.2	99.3 ± 0.82	0.7	48.04	0.22	48.3	98.1
HuH-7	Liver	P10	55.2	90.1 ± 4.26	9.9	52.24	4.36	56.6	102.5
NCI-H1975-Luc-GFP	Lung	P10	56.4	34.9 ± 6.18	65.1	18.67	29.45	48.1	85.4
NCI-H209-Luc-GFP	Lung	P10	61.7	81.0 ± 2.00	19.0	79.70	15.83	95.5	154.8

The xenograft names, tumor types, and number of in vivo passages a sample has progressed through are given for each sample at the time of sample collection. Letters following the passage number signify independent tumor samples derived from tumors grown on different mice of the same cohort. After DNA extraction and purification, samples were diluted between 25 ng/μl and 75 ng/μl; one microliter of this dilution serves as the initial DNA (ng) template in the qPCR reactions. The CT value for each sample was derived from standard curves and converted to a log genomes value, which can be converted to the number of measured haploid genomes present. Percent Human and Percent Mouse values were derived by dividing # human genomes by total genomes present or # mouse genomes divided by total genomes present, respectively. Genome numbers for each species are back-calculated into DNA (ng), the sum of which should be equal to the initial DNA used in the qPCR sample. The far right column lists the percentage of the initial sample calculated from the qPCR assay and gives a measure of quality assurance.

ISSN: 1472-6750