| Literature DB >> 28104671 |
Kathrin Schuldt1, Christa Ehmen2, Juergen Sievertsen2, Jennifer Evans2, Juergen May3, Daniel Ansong4, Birgit Muntau2, Gerd Ruge2, Christian Timmann2, Tsiri Agbenyega4, Rolf D Horstmann2, Thorsten Thye2.
Abstract
In a recent report, the cellular receptor CD55 was identified as a molecule essential for the invasion of human erythrocytes by Plasmodium falciparum, the causal agent of the most severe form of malaria. As this invasion process represents a critical step during infection with the parasite, it was hypothesized that genetic variants in the gene could affect severe malaria (SM) susceptibility. We performed high-resolution variant discovery of rare and common genetic variants in the human CD55 gene. Association testing of these variants in over 1700 SM cases and unaffected control individuals from the malaria-endemic Ashanti Region in Ghana, West Africa, were performed on the basis of single variants, combined rare variant analyses, and reconstructed haplotypes. A total of 26 genetic variants were detected in coding and regulatory regions of CD55 Five variants were previously unknown. None of the single variants, rare variants, or haplotypes showed evidence for association with SM or P. falciparum density. Here, we present the first comprehensive analysis of variation in the CD55 gene in the context of SM and show that genetic variants present in a Ghanaian study group appear not to influence susceptibility to the disease.Entities:
Keywords: CD55; DAF; genetic association study; high-resolution screen; malaria
Mesh:
Substances:
Year: 2017 PMID: 28104671 PMCID: PMC5345716 DOI: 10.1534/g3.116.036475
Source DB: PubMed Journal: G3 (Bethesda) ISSN: 2160-1836 Impact factor: 3.154
Characteristics of severe malaria case-control study
| Median Age (Range in Months) | Ethnic Group (%) | ||||
|---|---|---|---|---|---|
| Akan | Northerner | Ewe | |||
| Case-control study | |||||
| Severe malaria | 831 | 18 (3–147) | 68.3 | 29.5 | 2.2 |
| Controls | 903 | 27 (4–161) | 84.1 | 14.2 | 1.7 |
| Cases stratified by major phenotypes | |||||
| Severe anemia | 506 | 13 (3–132) | 69.7 | 28.2 | 2.1 |
| Cerebral malaria | 166 | 24 (3–147) | 66.9 | 30.7 | 2.4 |
Severe malaria anemia (hemoglobin level < 5 g/dl) with or without additional complications including cerebral malaria.
Cerebral malaria (Blantyre Coma Score [BCS] < 3) with or without additional complications including severe anemia.
Genetic variants in the CD55 gene detected in 1734 Ghanaian children
| SNP ID | Position Chr1 (Build 37) | Relative Position | Amino Acid Exchange | Novel | MAF Cases ( | MAF Controls ( | Polyphen2 Prediction | SIFT Prediction | |
|---|---|---|---|---|---|---|---|---|---|
| 1 | rs6685886 | 207,494,218 | −893C > A | 0.27 | 0.23 | ||||
| 2 | rs28371586 | 207,494,913 | −198C > G | 0.02 | 0.03 | ||||
| 3 | rs879066510 | 207,495,089 | −21C > G | Yes | - | 0.0006 | |||
| 4 | rs7542430 | 207,495,116 | c.6C > G | T2T | 0.01 | 0.02 | |||
| 5 | rs28371587 | 207,495,224 | c.100 + 14C > T | 0.002 | 0.002 | ||||
| 6 | rs28371588 | 207,495,781 | c.155G > T | R52H | 0.04 | 0.04 | Benign | Tolerated | |
| 7 | rs147474393 | 207,495,871 | c.245T > G | L82R | 0.008 | 0.01 | Benign | Tolerated | |
| 8 | rs28371603 | 207,497,911 | c.294C > T | C98C | 0.005 | 0.007 | |||
| 9 | rs2564979 | 207,498,939 | c.479-28T > A | 0.03 | 0.04 | ||||
| 10 | rs150286783 | 207,500,169 | c.651G > A | L217L | - | 0.0005 | Tolerated | ||
| 11 | rs878953964 | 207,504,465 | c.677C > T | P226L | Yes | — | Singleton | Probably damaging | Tolerated |
| 12 | rs60822373 | 207,504,467 | c.679G > C | A227P | — | Singleton | Probably damaging | Tolerated | |
| 13 | rs566298946 | 207,504,537 | c.749C > T | T250M | — | Singleton | Probably damaging | Damaging | |
| 14 | rs756597715 | 207,510,066 | c.882A > G | P294P | — | Singleton | |||
| 15 | rs779822800 | 207,510,067 | c.883A > G | T295A | Singleton | — | Possibly damaging | Tolerated | |
| 16 | rs879028717 | 207,510,084 | c.900 | T300T | Yes | — | Singleton | ||
| 17 | rs774684822 | 207,510,665 | c.980-9A > G | Singleton | — | ||||
| 18 | rs116473488 | 207,510,691 | c.997G > A | V333I | 0.02 | 0.02 | Benign | Tolerated | |
| 19 | rs550337244 | 207,510,708 | c.1014G > A | K338K | 0.001 | 0.002 | |||
| 20 | rs150172588 | 207,510,725 | c.1031C > T | T344I | 0.003 | 0.003 | Possibly damaging | Tolerated | |
| 21 | rs28371628 | 207,512,734 | c.1081-8G > A | 0.08 | 0.07 | ||||
| 22 | rs542054808 | 207,513,741 | c.1081 + 979C > T | Singleton | — | ||||
| 23 | rs879071049 | 207,513,772 | c.1081 + 1010G > A | Yes | Singleton | — | |||
| 24 | rs138016651 | 207,513,861 | c.1081 + 1099C > T | 0.005 | 0.007 | ||||
| 25 | rs375489214 | 207,532,908 | c.1099T > C | V406A | — | Singleton | n.a. | Tolerated | |
| 26 | rs878906671 | 207,532,925 | c.1117G > T | D412Y | YES | Singleton | — | n.a. | Damaging |
SNP ID, single nucleotide polymorphism identifier; Chr1, chromosome 1; MAF, minor allele frequency; n.a., not applicable.
Reference sequence NCBI NM_000574.4.
URL: http://genetics.bwh.harvard.edu/pph2.
URL: http://sift.jcvi.org/www/SIFT_chr_coords_submit.html.
Association tests of CD55 SNPs (MAF > 1%) with severe malaria phenotypes
| Severe Malaria ( | Severe Malaria Anemia ( | Cerebral Malaria ( | Parasite Density (Log) ( | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| No. | SNP ID | Maj/Min Allele | MAF (Aff/Unaff) | OR (95% C.I.) | p-Value | OR (95% C.I.) | p-Value | OR (95% C.I.) | p-Value | β (SE) | p-Value |
| 1 | rs6685886 | C/A | 0.27/0.23 | 1.12 (0.95–1.31) | 0.181 | 1.15 (0.95–1.39) | 0.144 | 1.01 (0.83–1.44) | 0.525 | −0.09 (0.12) | 0.476 |
| 2 | rs28371586 | C/G | 0.02/0.03 | 0.84 (0.54–1.32) | 0.457 | 0.73 (0.41–1.20) | 0.229 | 1.21 (0.61–2.40) | 0.587 | 0.54 (0.37) | 0.147 |
| 3 | rs7542430 | C/G | 0.01/0.02 | 0.44 (0.25–0.79) | 0.006 | 0.40 (0.20–0.81) | 0.011 | 0.84 (0.36–1.97) | 0.681 | −0.69 (0.48) | 0.158 |
| 4 | rs28371588 | G/T | 0.04/0.04 | 0.88 (0.61–1.25) | 0.469 | 0.83 (0.54–1.28) | 0.393 | 1.07 (0.59–1.94) | 0.829 | 0.03 (0.30) | 0.910 |
| 5 | rs2564979 | T/A | 0.03/0.04 | 0.82 (0.55–1.21) | 0.312 | 0.85 (0.55–1.33) | 0.488 | 0.57 (0.25–1.29) | 0.176 | 0.11 (0.32) | 0.740 |
| 6 | rs116473488 | G/A | 0.02/0.02 | 0.86 (0.52–1.41) | 0.556 | 0.86 (0.48–1.53) | 0.599 | 0.56 (0.20–1.60) | 0.278 | 0.02 (0.42) | 0.967 |
| 7 | rs28371628 | G/A | 0.08/0.07 | 1.24 (0.93–1.64) | 0.141 | 1.14 (0.82–1.59) | 0.436 | 1.33 (0.84–2.01) | 0.228 | −0.04 (0.22) | 0.849 |
Severe malaria, severe malaria anemia, cerebral malaria, and parasite density results of logistic regression analyses (linear regression for parasite density) are presented, assuming an additive mode of inheritance adjusted for gender, age, and ethnicity. No., number; SNP ID, single nucleotide polymorphism identifier; Maj, major; Min, minor; MAF, minor allele frequency; Aff, affected individuals; Unaff, unaffected individuals; OR, odds ratio.
Association tests of CD55 haplotypes of ≥ 1% frequencies with severe malaria
| Severe Malaria | Severe Malaria Anemia | Cerebral Malaria | Parasite Density (Log) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Haplotype | 1-2-3-4-5-6-7 | Frequency (Aff/Unaff) | p-Value | Simulated p-Value | p-Value | Simulated p-Value | p-Value | Simulated p-Value | p-Value | Simulated p-Value |
| CD55-1 | 0.55/0.57 | 0.475 | 0.487 | 0.673 | 0.665 | 0.325 | 0.342 | 0.428 | 0.423 | |
| CD55-2 | 0.25/0.21 | 0.031 | 0.036 | 0.027 | 0.024 | 0.100 | 0.108 | 0.298 | 0.265 | |
| CD55-3 | 0.08/0.07 | 0.133 | 0.116 | 0.509 | 0.507 | 0.112 | 0.111 | 0.820 | 0.821 | |
| CD55-4 | 0.04/0.04 | 0.403 | 0.414 | 0.361 | 0.347 | 0.951 | 0.941 | 0.689 | 0.729 | |
| CD55-5 | 0.03/0.03 | 0.255 | 0.265 | 0.368 | 0.346 | 0.087 | 0.084 | 0.796 | 0.802 | |
| CD55-6 | 0.02/0.03 | 0.484 | 0.489 | 0.372 | 0.375 | 0.969 | 0.968 | 0.629 | 0.630 | |
| CD55-7 | 0.02/0.02 | 0.524 | 0.534 | 0.630 | 0.639 | 0.232 | 0.255 | 0.894 | 0.889 | |
| CD55-8 | 0.01/0.02 | 0.011 | 0.007 | 0.024 | 0.031 | 0.659 | 0.646 | 0.124 | 0.120 | |
Aff, affected individuals; Unaff, unaffected individuals; SNP, single nucleotide polymorphism.
Refers to SNP number as designated in Table 2.
Results of haplotypic-specific score tests adjusted for gender, age, and ethnicity assuming an additive mode of inheritance.
Simulation p-values are computed based on a permuted reordering of the trait and covariates in HaploStats (Schaid ).
CD55 rare variant analyses including eight SNPs with MAF ≤ 1%
| Severe Malaria | Severe Malaria Anemia | Cerebral Malaria | Hyperparasitemia (> 200,000/µl) | |
|---|---|---|---|---|
|
| ||||
| p-Value | p-Value | p-Value | p-Value | |
| Univariate tests | ||||
| CMC | 0.952 | 0.979 | 0.890 | 0.507 |
| WSS | 0.954 | 0.976 | 0.835 | 0.451 |
| C(α) | 0.400 | 0.412 | 0.777 | 0.641 |
| Multivariate tests | ||||
| CMC | 0.935 | 0.963 | 0.904 | 0.423 |
| WSS | 0.972 | 0.970 | 0.907 | 0.491 |
| VT test (13 variants) | 0.966 | 0.982 | 0.829 | 0.896 |
CMC, combined and multivariate collapsing; WSS, weighted sum statistic; VT, variable-thresholds methods.
Adjusted for age, gender, and ethnic group.