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Using Quantitative Pcr For Hiv Viral Load Control

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An HIV GWAS SNP marks expression of a long non-coding RNA (lncRNA).
Human chromosome 3p21–22 harbors a cluster of chemokine receptor genes, several of which serve as major or minor co-receptors of HIV-1 [1]. The genetic associations of CCR5 and CCR2 gene polymorphisms with HIV-1 pathogenesis are well known [2-5], but any potential role of variation in other regions of the cluster is largely unknown. An intergenic SNP (rs1015164 A/G) downstream of the CCRL2 gene was shown to associate with HIV viral load control [6] and progression to AIDS [7] in two independent cohorts of HIV-infected patients. Importantly, the SNP showed genome-wide significant association with HIV outcomes in meta-analyses that collectively examined genotyping data from 6,315 HIV-infected patients [8]. The SNP is in close genomic proximity to a non-coding RNA gene RP-11-24F11.2 (Fig. S1). We were able to detect and quantify the polyadenylated lncRNA transcript in the total RNA from peripheral blood lymphocytes (PBLs) using quantitative PCR (qPCR). Specificity of the primers was confirmed by sequencing of the amplicons. We designated this lncRNA as Lnc11.2. The rs1015164A allele, which associated with higher viral loads (OR=1.4, p=3.3 ×10-5) [6] and more rapid disease progression (HR=1.4, p=8.6 ×10-6) [7] correlated with higher expression levels of Lnc11.2 in PBLs (Fig. 1).

Characterization of the Lnc11.2 transcript Amplification of the 3’and 5’ends of the Lnc11.2 transcript uncovered the

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