| Literature DB >> 26367535 |
Jean-Louis Spadoni1, Pierre Rucart1, Sigrid Le Clerc1, Daniëlle van Manen2, Cédric Coulonges1, Damien Ulveling1, Vincent Laville1, Taoufik Labib1, Lieng Taing1, Olivier Delaneau3, Matthieu Montes1, Hanneke Schuitemaker2, Josselin Noirel1, Jean-François Zagury1.
Abstract
BACKGROUND: Many genome-wide association studies have been performed on progression towards the acquired immune deficiency syndrome (AIDS) and they mainly identified associations within the HLA loci. In this study, we demonstrate that the integration of biological information, namely gene expression data, can enhance the sensitivity of genetic studies to unravel new genetic associations relevant to AIDS.Entities:
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Year: 2015 PMID: 26367535 PMCID: PMC4569262 DOI: 10.1371/journal.pone.0136989
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Fig 1Schematic summary of our methodology.
The data from three databases are integrated to provide us with functional SNPs likely to be associated with changes in gene transcription in the tissue of interest. Using the SNAP Pairwise LD server, we only kept independent SNPs by removing superfluous SNPs that were in linkage disequilibrium (r 2 ≥ 0.2). Among those SNPs, associations with slow and non-progression towards AIDS are sought and replicated. Randomisations are carried out in order to evaluate the statistical robustness of our results. Finally, the genetic associations are used to link progression to AIDS and gene expression in candidate genes.
List of the significant associations (p ≤ 0.05) with slow and non-progression.
Alleles, allele frequencies (AF), positional data and genetic modes are provided with the results of the statistical inferences. Opposite signs for the β coefficients are required for an association to be replicated in the GRIV (non-progression) and ACS cohorts (time to AIDS93).
| SNP | Alleles Ref/Alt | AF (Alt) | Chromosome/position | Mode |
|
|
|
| Allele associated with non-progression | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
|
| T | C | 53% | 8 | 23,488,013 | additive | -0.23 | 0.029 | 0.21 | 0.029 | T |
|
| T | C | 53% | 8 | 23,488,013 | recessive | -0.41 | 0.024 | 0.40 | 0.007 | T |
|
| T | C | 12% | 21 | 28,657,885 | recessive | -2.24 | 0.038 | 2.81 | 1.5·10–4 | T |
|
| C | T | 45% | 7 | 134,294,616 | dominant | 0.44 | 0.015 | -0.34 | 0.034 | T |
|
| G | T | 78% | 17 | 75,246,420 | recessive | 0.49 | 0.003 | -0.33 | 0.025 | T |
|
| C | A | 66% | 10 | 72,691,727 | dominant | 0.53 | 0.037 | -0.48 | 0.024 | A |
|
| G | T | 7% | 6 | 30,360,062 | additive | -0.66 | 0.019 | 0.51 | 0.001 | G |
|
| G | T | 7% | 6 | 30,360,062 | dominant | -0.73 | 0.015 | 0.42 | 0.010 | G |
|
| A | G | 77% | 6 | 31,168,676 | dominant | -0.78 | 0.021 | 0.81 | 0.038 | A |
|
| G | A | 6% | 6 | 29,374,998 | dominant | -0.67 | 0.036 | 0.37 | 0.031 | G |
|
| A | G | 83% | 6 | 42,206,820 | recessive | -0.32 | 0.049 | 0.33 | 0.045 | A |
(*) Note that rs3749971 is in linkage disequilibrium with rs3130350 and is therefore not considered an independent finding in our statistics (see text).
Fig 2Statistical significance of our associations.
Histogram of the number of SNPs that pass the significance criterion for this study using phenotype and SNP randomisations. These results provide us with a way to estimate the sensitivity of our study (diamond): it would be extremely unlikely for our eight independent findings to arise by chance alone (p = 0.001).
List of SNP/gene pairs associated with AIDS progression.
The genetic association is linked back to its association with gene expression levels to provide an association between transcription levels (we use the word ‘regulation’ for convenience’s sake) and AIDS progression.
| SNP | Chromosome | Gene | Gene function | Association with non-progression |
|---|---|---|---|---|
|
| 8 |
| ectonucleoside triphosphate diphosphohydrolase 4 | Down-regulation |
|
| 21 |
| chaperonin containing TCP1, subunit 8 (theta) | Down-regulation |
|
| 7 |
| solute carrier family 35 (UDP-xylose/UDP-N-acetylglucosamine transporter), member B4 | Up-regulation |
|
| 17 |
| mitochondrial ribosomal protein S7 | Up-regulation |
|
| 10 |
| DnaJ (Hsp40) homolog, subfamily B, member 12 | Down-regulation |
|
| 6 |
| ZFP57 zinc finger protein | Down-regulation |
|
| 6 |
| HLA complex group 27 (non-protein coding) | Down-regulation |
|
| 6 |
| guanylate cyclase activator 1B (retina) | Down-regulation |
|
|
|
| mitochondrial ribosomal protein S10 | Down-regulation |
(*) Note that rs3749971 is in linkage disequilibrium with rs3130350 and is therefore not considered an independent finding (see text).