| Literature DB >> 23437094 |
Katariina Hannula-Jouppi1, Satu Massinen, Tuula Siljander, Siru Mäkelä, Katja Kivinen, Rasko Leinonen, Hong Jiao, Päivi Aitos, Matti Karppelin, Jaana Vuopio, Jaana Syrjänen, Juha Kere.
Abstract
BACKGROUND: Bacterial non-necrotizing erysipelas and cellulitis are often recurring, diffusely spreading infections of the skin and subcutaneous tissues caused most commonly by streptococci. Host genetic factors influence infection susceptibility but no extensive studies on the genetic determinants of human erysipelas exist.Entities:
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Year: 2013 PMID: 23437094 PMCID: PMC3577772 DOI: 10.1371/journal.pone.0056225
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Figure 1The six most representative families used for initial linkage analysis.
Arrows indicate probands and asterisks other family members studied.
Non-parametric linkage results from using additional microsatellite markers surrounding the suggested linkage peaks.
| Chromosomal locus | Marker | Genetic locus (cM) | Physical locus (bp) | Configuration 0 | Configuration 0 | Configuration 2 | Mb between markers (total area on Chr) |
| NPLall | Genome-wide p-value | NPLall | |||||
| 3q22-24 | D3S1238 | 142.60 | 133915404 | 0.98 | 0.692 | 1.10 | |
| D3S1576 | 144.46 | 137420009 | 1.04 | 0.660 | 1.16 | 3.50 | |
| D3S1309 | 146.63 | 140726546 | 0.96 | 0.703 | 1.05 | 3.31 | |
| D3S3694 | 148.82 | 142190878 | 0.95 | 0.708 | 1.04 | 1.46 | |
| D3S1569 | 150.58 | 143371594 | 0.85 | 0.762 | 0.94 | 1.18 | |
| D3S1593 | 152.31 | 145328023 | 0.86 | 0.761 | 0.96 | 1.96 | |
| D3S1306 | 154.18 | 147801038 | 1.06 | 0.651 | 1.04 | 2.47 | |
| D3S1555 | 156.59 | 148807201 | 1.11 | 0.629 | 0.94 | 1.01 | |
| D3S1299 | 158.56 | 150183860 | 1.02 | 0.669 | 0.72 | 1.38 | |
| D3S1279 | 160.19 | 151025260 | 0.91 | 0.732 | 0.61 | 0.84 | |
| D3S3531 | 162.79 | 154213366 | 0.75 | 0.803 | 0.46 | 3.19 | |
| D3S1607 | 164.61 | 156964125 | 0.43 | 0.921 | 0.14 | 2.75 | |
| D3S3579 | 166.45 | 160580277 | 0.29 | 0.959 | 0.00 | 3.62 (26.66) | |
| 9q34 | D9S290 | 136.40 | 131527468 | 2.31 | 0.074 | 2.26 | |
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| D9S1863 | 140.35 | 133499845 | 2.67 | 0.034 | 2.62 | 1.08 | |
| D9S313 | 141.04 | 133887414 | 2.66 | 0.035 | 2.60 | 0.39 | |
| D9S179 | 143.19 | 135091628 | 2.42 | 0.063 | 2.36 | 1.20 | |
| D9S1199 | 144.51 | 135831155 | 2.18 | 0.104 | 2.14 | 0.74 (4.25) | |
| 21q22 | D21S262 | 35.68 | 33816306 | 1.20 | 0.560 | 1.34 | |
| D21S1898 | 37.68 | 34609231 | 1.32 | 0.491 | 1.47 | 0.79 | |
| D21S1445 | 38.48 | 35375662 | 1.33 | 0.482 | 1.48 | 0.77 | |
| D21S1920 | 38.82 | 35697192 | 1.31 | 0.497 | 1.46 | 0.32 | |
| D21S1895 | 39.51 | 36351059 | 0.92 | 0.723 | 1.01 | 0.65 (2.53) | |
| 22q13 | D22S1171 | 53.45 | 44417584 | 0.44 | 0.914 | 0.49 | |
| D22S1159 | 54.62 | 44750615 | 0.39 | 0.933 | 0.48 | 0.33 | |
| D22S274 | 56.47 | 45269152 | 0.51 | 0.889 | 0.66 | 0.52 | |
| D22S1141 | 58.59 | 45718900 | 0.37 | 0.938 | 0.52 | 0.45 | |
| D22S1153 | 61.82 | 46404511 | 0.84 | 0.766 | 0.98 | 0.69 | |
| D22S1161 | 67.43 | 47596331 | 0.29 | 0.959 | 0.38 | 1.19 | |
| D22S1170 | 70.98 | 48350736 | 0.22 | 0.967 | 0.29 | 0.75 (3.93) |
The most significant locus is highlighted in bold. Physical coordinates were mapped against the GRCh37.2 human genome assembly. The deCODE genetic map was used for genetic locations [22] and for markers absent on the deCODE map, genetic coordinates were estimated with linear interpolation using the markers’ physical coordinates. cM = centiMorgan.
NPLall = non-parametric linkage score when testing for allele sharing among affected individuals.
Finemapping of the 9q34 linkage peak region with microsatellite markers.
| Marker | Physicallocus (bp) | Candidategenes | Mouse GASgenes |
| 130026756–130155828 |
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| 130882972–130890712 |
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| D9S918 | 130457260 | ||
| 130500596–130541048 |
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| D9S1827 | 131001749 | ||
| D9S290* | 131527468 | ||
| 131873228–131911225 |
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| D9S752* | 131951047 | ||
| D9S972* | 132051085 | ||
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| D9S115* | 132248174 | ||
| D9S1795* | 132306492 | ||
| D9S159* | 132369694 | ||
| D9S1831* | 132421728 | ||
| 132427920–132484953 |
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| D9S62* | 132461670 | ||
| 132500615–132515344 |
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| D9S1861* | 133370746 | ||
| D9S118* | 133419164 | ||
| D9S1863* | 133499845 | ||
| 133589268–133763062 |
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| 133777825–133814455 |
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| 133884504–133968446 |
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| D9S313* | 133887414 | ||
| D9S903* | 133935886 | ||
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| D9S179* | 135091628 | ||
| D9S1847* | 135436949 | ||
| D9S1830* | 135715761 | ||
| D9S1199* | 135831155 | ||
| D9S2157 | 136035489 | ||
| 139743256–139745490 |
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| 139756571–139760738 |
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| 139942553–139948505 |
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| 140069236–140083057 |
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The linkage area is marked by asterisks and the highest linkage peaks are highlighted in bold.
Genes in the mouse quantitative trait locus for susceptibility to group A streptococcal (GAS) infections on chromosome 2 [18]. (↑) Genes up regulated and, (↓) down regulated in GAS susceptible mouse strains.
Non-parametric genome-wide linkage analysis results with MERLIN.
| Chromosomal locus | Max NPLall | Genome-wide p-value | Marker(s) | Physical locus (bp) |
| 3q22 | 3.25 | 0.64 | rs361239-rs1429759 | 136701295–137656598 |
| 3p24 | 2.53 | 0.97 | rs1994987 | 30456489 |
| 3p22 | 2.64 | 0.94 | rs2167176 | 35383108 |
| 9q34 | 3.84 | 0.24 | rs578802-rs708616 | 135453277–135564946 |
| 10q25 | 2.40 | 0.98 | rs1337987-rs959127 | 113538188–113611569 |
| 11q24 | 2.27 | 1.00 | rs1940007-rs1940006 | 126754451–126754515 |
| 21q22 | 3.24 | 0.64 | rs743337-rs717205 | 35265524–35310905 |
| 22q13 | 2.83 | 0.83 | rs719925-rs136578 | 45758758–45770619 |
Max NPLall = maximum non-parametric linkage score when testing for allele sharing among affected individuals.
Figure 2The NPLall scores from initial non-parametric linkage analysis for the chromosomes showing suggestive linkage.
Allele frequencies for the Affymetrix HMA10K Array were estimated using 20 affected individuals from six families and MERLIN was used for multipoint NPL analysis.
Affymetrix HMA250K results for 3q22.
| SNP | Physicallocus (bp) | Gene; position | Haploview | Haploview | Shared heterozygosity | Haplotype pattern mining | Haplotype pattern mining |
| Associated allele | p-value | p-value | Score | ||||
| rs2091023 | 148265311 | G | 0.787 | 0.460 | 16 | ||
| rs12490567 | 148274505 | G | 0.775 | 0.336 | 32 | ||
| rs1522940 | 148315687 | G | 0.389 | 0.169 | 59 | ||
| rs2687661 | 148319233 | T | 0.795 |
| 101 | ||
| rs6803324 | 148335030 | A | 0.313 | x |
| 142 | |
| rs6440561 | 148358582 | C |
| x |
| 194 | |
| rs6440562 | 148358705 | x |
| 218 | |||
| rs9862062* | 148359724 |
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| x |
| 259 | |
| rs9811115* | 148360046 |
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| x |
| 263 | |
| rs275679 | 148368303 |
| 0.129 | x |
| 231 | |
| rs10513336 | 148368387 | x | 0.078 | 188 | |||
| rs275711 | 148374631 |
| 0.230 | x | 0.084 | 163 | |
| rs718424 | 148380543 |
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| x | 0.082 | 164 | |
| rs2087737 | 148381522 |
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| x | 0.092 | 140 | |
| rs16860674 | 148382002 | x | 0.108 | 90 | |||
| rs872212 | 148386747 |
| 0.166 | x | 0.108 | 55 | |
| rs2012052 | 148386856 |
| 0.166 | x | 0.113 | 36 | |
| rs454530 | 148400657 |
| 0.228 | x | 0.113 | 25 | |
| rs2638359 | 148406383 |
| 0.228 | x | 0.086 | 19 | |
| rs2638358 | 148406537 |
| 0.228 | x | 0.119 | 18 | |
| rs2638357 | 148406619 |
| 0.228 | x | 0.119 | 22 | |
| rs2933251 | 148406799 |
| 0.228 | x | 0.096 | 39 | |
| rs409742 | 148412365 |
| 0.228 | x | 0.091 | 59 | |
| rs4681157 | 148412408 |
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| x | 0.080 | 80 | |
| rs12721267 | 148416327 |
| x | 0.082 | 76 | ||
| rs12695877 | 148427034 |
| 0.105 | 74 | |||
| rs1492103 | 148432964 |
| G | 0.129 | 0.113 | 68 | |
| rs12695918 | 148456627 |
| 0.123 | 58 | |||
| rs13097326 | 148468746 | C | 0.197 | 0.126 | 50 |
The haplotype that was significantly associated to erysipelas in Haploview is marked with bold letters in the “Associated allele” column. Significant p-values in Haploview or Haplotype pattern mining (HPM) for individual SNPs are also highlighted in bold. SNPs belonging to the associated haplotype and a significant p-value in Haploview, and with a significant p-value in HPM, and that showed shared heterozygosity among cases are marked with an asterisk.