title: Lipid levels in HIV-positive men receiving anti-retroviral therapy are not associated with copy number variation of reverse cholesterol transport pathway genes.
abstract: BACKGROUND
  The exacerbation of HIV-1 associated dyslipidemia seen in a subset of patients receiving anti-retroviral therapy suggests that genetic factors put these individuals at greater risk of cardiovascular disease. Single nucleotide polymorphisms (SNPs) within genes of and influencing the reverse cholesterol transport (RCT) pathway are associated with lipid levels but little is known regarding their copy number variation (CNV). This form of quantitative genetic variation has the potential to alter the amount of gene product made, thereby also influencing lipid metabolism.
  
  
  RESULTS
  To examine if CNV in RCT pathway genes was associated with altered serum lipid profiles in HIV-positive individuals receiving therapy, we designed a custom multiplex ligation-dependent probe amplification assay to screen 16 RCT genes within a subset of individuals from the Multicenter AIDS Cohort Study who show extreme lipid phenotypes. Verification of CNV was performed using a custom NanoString assay, and the Illumina HT-12 mRNA expression microarray was used to determine the influence of copy number on gene expression. Among the RCT genes, CNV was observed to be extremely rare. The only CNV seen was in the CETP gene, which showed a loss of copy in 1 of the 320 samples (0.3%) in our study. The genes in our study showed little variation in expression between individuals, and the variation seen was not related to any detected CNV.
  
  
  CONCLUSIONS
  Whole gene CNV is uncommon in RCT pathway genes, and not a major factor in the development of highly active antiretroviral therapy (HAART) associated dyslipidemia.
authors.affiliation: Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 130 De Soto St, Pittsburgh, PA, 15261, USA. rsbmarino@gmail.com.
authors.forename: Rebecca B
authors.initials: RB
authors.lastname: Marino
authors.affiliation: Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 130 De Soto St, Pittsburgh, PA, 15261, USA. kingsey@pitt.edu.
authors.forename: Lawrence A
authors.initials: LA
authors.lastname: Kingsley
authors.affiliation: Division of Hematology/Oncology, Department of Medicine, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. skhussain@ucla.edu.
authors.forename: Shehnaz K
authors.initials: SK
authors.lastname: Hussain
authors.affiliation: Bloomberg School of Public Health, Johns Hopkins University, 615 Wolfe St, Baltimore, MD, 21205, USA. jbream1@jhu.edu.
authors.forename: Jay H
authors.initials: JH
authors.lastname: Bream
authors.affiliation: Feinberg School of Medicine, Northwestern University, 645 N Michigan Avenue, Chicago, IL, 60611, USA. s-penugonda@md.northwestern.edu.
authors.forename: Sudhir
authors.initials: S
authors.lastname: Penogonda
authors.affiliation: Bloomberg School of Public Health, Johns Hopkins University, 615 Wolfe St, Baltimore, MD, 21205, USA. pduggal@jhu.edu.
authors.forename: Priya
authors.initials: P
authors.lastname: Duggal
authors.affiliation: Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 130 De Soto St, Pittsburgh, PA, 15261, USA. jmartins@pitt.edu.
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Martinson
mesh_terms: D000328:Adult; D023241:Antiretroviral Therapy, Highly Active / Q000009:adverse effects*; D002784:Cholesterol / Q000378:metabolism*; D053480:Cholesterol Ester Transfer Proteins / Q000235:genetics; D056915:DNA Copy Number Variations; D050171:Dyslipidemias / Q000097:blood / Q000139:chemically induced / Q000235:genetics; D006679:HIV Seropositivity / Q000097:blood / Q000188:drug therapy / Q000235:genetics; D006801:Humans; D008297:Male; D008875:Middle Aged
chemical_list: C506642:CETP protein, human; D053480:Cholesterol Ester Transfer Proteins; D002784:Cholesterol