Limits...
Two loci control tuberculin skin test reactivity in an area hyperendemic for tuberculosis.

Cobat A, Gallant CJ, Simkin L, Black GF, Stanley K, Hughes J, Doherty TM, Hanekom WA, Eley B, Jaïs JP, Boland-Auge A, van Helden P, Casanova JL, Abel L, Hoal EG, Schurr E, Alcaïs A - J. Exp. Med. (2009)

Bottom Line: The genetic basis of TST reactivity is not known.We also detected a second major locus (TST2) on chromosomal region 5p15 (P < 10(-5)), which controls TST-QTL or the intensity of T cell-mediated delayed type hypersensitivity (DTH) to tuberculin.Fine mapping of this region identified SLC6A3, encoding the dopamine transporter DAT1, as a promising gene for further studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de Santé et de Recherche Médicale, Paris 75015, France.

ABSTRACT
Approximately 20% of persons living in areas hyperendemic for tuberculosis (TB) display persistent lack of tuberculin skin test (TST) reactivity and appear to be naturally resistant to infection by Mycobacterium tuberculosis. Among those with a positive response, the intensity of TST reactivity varies greatly. The genetic basis of TST reactivity is not known. We report on a genome-wide linkage search for loci that have an impact on TST reactivity, which is defined either as zero versus nonzero (TST-BINa) or as extent of TST in millimeters (TST-quantitative trait locus [QTL]) in a panel of 128 families, including 350 siblings, from an area of South Africa hyperendemic for TB. We detected a major locus (TST1) on chromosomal region 11p14 (P = 1.4 x 10(-5)), which controls TST-BINa, with a lack of responsiveness indicating T cell-independent resistance to M. tuberculosis. We also detected a second major locus (TST2) on chromosomal region 5p15 (P < 10(-5)), which controls TST-QTL or the intensity of T cell-mediated delayed type hypersensitivity (DTH) to tuberculin. Fine mapping of this region identified SLC6A3, encoding the dopamine transporter DAT1, as a promising gene for further studies. Our results pave the way for the understanding of the molecular mechanisms involved in resistance to M. tuberculosis infection in endemic areas (TST1) and for the identification of critical regulators of T cell-dependent DTH to tuberculin (TST2).

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Fine mapping of the 90% confidence interval for the location of TST2 locus in a panel of 128 families including 350 siblings. Evidence for association with TST-QTL of 113 SNPs located in the 90% confidence linkage interval is given as −log10P and plotted against SNP position (blue diamonds). The locations of the 13 genes of this region are provided. Two intervals with no annotated genes (2–2.7 Mb and 2.9–3.2 Mb) are not shown (//). The red lines indicate the P = 0.05 and P = 0.01 significance thresholds.
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fig4: Fine mapping of the 90% confidence interval for the location of TST2 locus in a panel of 128 families including 350 siblings. Evidence for association with TST-QTL of 113 SNPs located in the 90% confidence linkage interval is given as −log10P and plotted against SNP position (blue diamonds). The locations of the 13 genes of this region are provided. Two intervals with no annotated genes (2–2.7 Mb and 2.9–3.2 Mb) are not shown (//). The red lines indicate the P = 0.05 and P = 0.01 significance thresholds.

Mentions: Encouraged by the narrow linkage peak, we decided to fine map the TST2 locus. Based on the 1-LOD confidence interval for the location of the underlying QTL for TST2, we selected a chromosomal region extending from 1.1 to 3.2 Mb on the physical map of chromosome 5 (Fig. 4) for association studies of TST-QTL in a familial sample including the 128 nuclear families used in the linkage study and two additional trios (one child and her/his two parents). This interval contains 13 genes (NKD2→C5orf38; National Center for Biotechnology Information build 36 [http://www.ncbi.nlm.nih.gov]). We genotyped 133 SNPs in the targeted interval, 113 of which were considered suitable for association analysis (Fig. 4 and Table S2). To optimize gene coverage, we used a genocentric strategy for SNPs selection. Tag SNPs were identified for each known gene including 2 kb of their 5′ and 3′ regulatory regions. To capture most genetic variation, a very stringent tag-SNP selection scheme was used (r2 = 0.8 with all tagged SNPs and minor allele frequency > 5%). Because no genes have been annotated on chromosomal intervals 2–2.7 Mb and 2.9–3.2 Mb, few SNPs were genotyped in these chromosomal segments and none were significant. In univariate analysis, nine SNPs (rs4975579, rs6554677, rs1801075, rs250682, rs10475030, rs11747565, rs2922061, rs1018120, and rs2232376) were significantly associated with TST-QTL at the 0.05 level (Fig. 4). Analysis of the linkage disequilibrium (LD) patterns between these nine SNPs showed no LD, supporting the hypothesis of independent effects even though it is likely that some of these signals are false positives (unpublished data). Out of these nine SNPs, rs250682 located in SLC6A3 (solute carrier family 6 member 3) displayed the strongest association with TST-QTL (P = 0.001). Allele G of rs250682 (q = 0.36) has a dominant effect and is associated with lower values of the TST-QTL. To ensure that SNP rs250682 was responsible for the observed association, we screened the Yoruba sample of the HapMap database (www.hapmap.org) in a region spanning 5 Mb around rs250682. Only four SNPs (rs250681, rs40358, rs403636, and rs464049) were correlated with an r2 > 0.5 with rs250682. All of these four SNPs are located in the SLC6A3 gene. These results identified SLCA63 as a promising target for further study on the intensity of T cell–mediated DTH to tuberculin.


Two loci control tuberculin skin test reactivity in an area hyperendemic for tuberculosis.

Cobat A, Gallant CJ, Simkin L, Black GF, Stanley K, Hughes J, Doherty TM, Hanekom WA, Eley B, Jaïs JP, Boland-Auge A, van Helden P, Casanova JL, Abel L, Hoal EG, Schurr E, Alcaïs A - J. Exp. Med. (2009)

Fine mapping of the 90% confidence interval for the location of TST2 locus in a panel of 128 families including 350 siblings. Evidence for association with TST-QTL of 113 SNPs located in the 90% confidence linkage interval is given as −log10P and plotted against SNP position (blue diamonds). The locations of the 13 genes of this region are provided. Two intervals with no annotated genes (2–2.7 Mb and 2.9–3.2 Mb) are not shown (//). The red lines indicate the P = 0.05 and P = 0.01 significance thresholds.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2806605&req=5

fig4: Fine mapping of the 90% confidence interval for the location of TST2 locus in a panel of 128 families including 350 siblings. Evidence for association with TST-QTL of 113 SNPs located in the 90% confidence linkage interval is given as −log10P and plotted against SNP position (blue diamonds). The locations of the 13 genes of this region are provided. Two intervals with no annotated genes (2–2.7 Mb and 2.9–3.2 Mb) are not shown (//). The red lines indicate the P = 0.05 and P = 0.01 significance thresholds.
Mentions: Encouraged by the narrow linkage peak, we decided to fine map the TST2 locus. Based on the 1-LOD confidence interval for the location of the underlying QTL for TST2, we selected a chromosomal region extending from 1.1 to 3.2 Mb on the physical map of chromosome 5 (Fig. 4) for association studies of TST-QTL in a familial sample including the 128 nuclear families used in the linkage study and two additional trios (one child and her/his two parents). This interval contains 13 genes (NKD2→C5orf38; National Center for Biotechnology Information build 36 [http://www.ncbi.nlm.nih.gov]). We genotyped 133 SNPs in the targeted interval, 113 of which were considered suitable for association analysis (Fig. 4 and Table S2). To optimize gene coverage, we used a genocentric strategy for SNPs selection. Tag SNPs were identified for each known gene including 2 kb of their 5′ and 3′ regulatory regions. To capture most genetic variation, a very stringent tag-SNP selection scheme was used (r2 = 0.8 with all tagged SNPs and minor allele frequency > 5%). Because no genes have been annotated on chromosomal intervals 2–2.7 Mb and 2.9–3.2 Mb, few SNPs were genotyped in these chromosomal segments and none were significant. In univariate analysis, nine SNPs (rs4975579, rs6554677, rs1801075, rs250682, rs10475030, rs11747565, rs2922061, rs1018120, and rs2232376) were significantly associated with TST-QTL at the 0.05 level (Fig. 4). Analysis of the linkage disequilibrium (LD) patterns between these nine SNPs showed no LD, supporting the hypothesis of independent effects even though it is likely that some of these signals are false positives (unpublished data). Out of these nine SNPs, rs250682 located in SLC6A3 (solute carrier family 6 member 3) displayed the strongest association with TST-QTL (P = 0.001). Allele G of rs250682 (q = 0.36) has a dominant effect and is associated with lower values of the TST-QTL. To ensure that SNP rs250682 was responsible for the observed association, we screened the Yoruba sample of the HapMap database (www.hapmap.org) in a region spanning 5 Mb around rs250682. Only four SNPs (rs250681, rs40358, rs403636, and rs464049) were correlated with an r2 > 0.5 with rs250682. All of these four SNPs are located in the SLC6A3 gene. These results identified SLCA63 as a promising target for further study on the intensity of T cell–mediated DTH to tuberculin.

Bottom Line: The genetic basis of TST reactivity is not known.We also detected a second major locus (TST2) on chromosomal region 5p15 (P < 10(-5)), which controls TST-QTL or the intensity of T cell-mediated delayed type hypersensitivity (DTH) to tuberculin.Fine mapping of this region identified SLC6A3, encoding the dopamine transporter DAT1, as a promising gene for further studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de Santé et de Recherche Médicale, Paris 75015, France.

ABSTRACT
Approximately 20% of persons living in areas hyperendemic for tuberculosis (TB) display persistent lack of tuberculin skin test (TST) reactivity and appear to be naturally resistant to infection by Mycobacterium tuberculosis. Among those with a positive response, the intensity of TST reactivity varies greatly. The genetic basis of TST reactivity is not known. We report on a genome-wide linkage search for loci that have an impact on TST reactivity, which is defined either as zero versus nonzero (TST-BINa) or as extent of TST in millimeters (TST-quantitative trait locus [QTL]) in a panel of 128 families, including 350 siblings, from an area of South Africa hyperendemic for TB. We detected a major locus (TST1) on chromosomal region 11p14 (P = 1.4 x 10(-5)), which controls TST-BINa, with a lack of responsiveness indicating T cell-independent resistance to M. tuberculosis. We also detected a second major locus (TST2) on chromosomal region 5p15 (P < 10(-5)), which controls TST-QTL or the intensity of T cell-mediated delayed type hypersensitivity (DTH) to tuberculin. Fine mapping of this region identified SLC6A3, encoding the dopamine transporter DAT1, as a promising gene for further studies. Our results pave the way for the understanding of the molecular mechanisms involved in resistance to M. tuberculosis infection in endemic areas (TST1) and for the identification of critical regulators of T cell-dependent DTH to tuberculin (TST2).

Show MeSH
Related in: MedlinePlus