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. 2011 Dec;85(23):12830-4.
doi: 10.1128/JVI.05624-11. Epub 2011 Sep 21.

Analysis of single-nucleotide polymorphisms in patient-derived retrovirus integration sites reveals contamination from cell lines acutely infected by xenotropic murine leukemia virus-related virus

Alice Rusmevichientong  1 , Jaydip Das Gupta, Petra S Elias, Robert H Silverman, Samson A Chow
Affiliations

Analysis of single-nucleotide polymorphisms in patient-derived retrovirus integration sites reveals contamination from cell lines acutely infected by xenotropic murine leukemia virus-related virus

Alice Rusmevichientong et al. J Virol. 2011 Dec.

Abstract

We analyzed xenotropic murine leukemia virus-related virus (XMRV) integration site sequences previously identified from human prostate tissues for single-nucleotide polymorphisms (SNPs) to discriminate between patient and potential cell line sources of the proviruses. The SNPs of two integration sites were identical to those in cell lines but not the patients, whereas the data on the remaining 12 integration sites were inconclusive. Our results provide direct evidence for contamination during analysis of XMRV integration sites.

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Figures

Fig. 1.
Fig. 1.
Alignment of EU981808 with VP363 patient and prostate cancer cell line genomic DNA. The genomic sequence of EU981808 (patient-derived integration site) is compared to that of GU816103 (DU145-derived integration site), the patient VP363, and the cell lines DU145, LNCaP, and 22Rv1. The locations of this sequence in the human genome build hg19 are shown at the beginning and the end of the sequence as the chromosome number followed by the nucleotide position.
Fig. 2.
Fig. 2.
Alignment of EU981801 with VP432 patient and prostate cancer cell line genomic DNA. The genomic sequence of EU981801 (patient-derived integration site) is compared to that of patient VP432 and the cell lines DU145 and LNCaP. The annotations are identical to those in Fig. 1.
Fig. 3.
Fig. 3.
Alignment of EU981800 with VP432 patient and prostate cancer cell line genomic DNA. The genomic sequence of EU981800 (patient-derived integration site) is compared to that of patient VP432 and the cell lines DU145 and LNCaP. The annotations are identical to those in Fig. 1.
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