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Multiallelic copy number variation in the complement component 4A (C4A) gene is associated with late-stage age-related macular degeneration (AMD).

Grassmann F, Cantsilieris S, Schulz-Kuhnt AS, White SJ, Richardson AJ, Hewitt AW, Vote BJ, Schmied D, Guymer RH, Weber BH, Baird PN - J Neuroinflammation (2016)

Bottom Line: We find strong statistical significance for association of increased copy number of C4A (OR 0.81 (0.73; 0.89);P = 4.4 × 10(-5)), with the effect most pronounced in individuals over 78 years (OR 0.67 (0.55; 0.81)) and females (OR 0.77 (0.68; 0.87)).Furthermore, this association is independent of known AMD-associated risk variants in the nearby CFB/C2 locus, particularly in females and in individuals over 78 years.In addition, for the first time, we provide evidence that multiallelic CNVs are associated with AMD pathology.

View Article: PubMed Central - PubMed

Affiliation: Institute of Human Genetics, University of Regensburg, Regensburg, 93053, Germany.

ABSTRACT

Background: Age-related macular degeneration (AMD) is the leading cause of vision loss in Western societies with a strong genetic component. Candidate gene studies as well as genome-wide association studies strongly implicated genetic variations in complement genes to be involved in disease risk. So far, no association of AMD with complement component 4 (C4) was reported probably due to the complex nature of the C4 locus on chromosome 6.

Methods: We used multiplex ligation-dependent probe amplification (MLPA) to determine the copy number of the C4 gene as well as of both relevant isoforms, C4A and C4B, and assessed their association with AMD using logistic regression models.

Results: Here, we report on the analysis of 2645 individuals (1536 probands and 1109 unaffected controls), across three different centers, for multiallelic copy number variation (CNV) at the C4 locus. We find strong statistical significance for association of increased copy number of C4A (OR 0.81 (0.73; 0.89);P = 4.4 × 10(-5)), with the effect most pronounced in individuals over 78 years (OR 0.67 (0.55; 0.81)) and females (OR 0.77 (0.68; 0.87)). Furthermore, this association is independent of known AMD-associated risk variants in the nearby CFB/C2 locus, particularly in females and in individuals over 78 years.

Conclusions: Our data strengthen the notion that complement dysregulation plays a crucial role in AMD etiology, an important finding for early intervention strategies and future therapeutics. In addition, for the first time, we provide evidence that multiallelic CNVs are associated with AMD pathology.

No MeSH data available.


Related in: MedlinePlus

Normalized probe dosage quality control of complement C4A (a),C4B (b), and total C4 (c) in three independent studies. Distribution of unrounded MLPA-based dosage estimates for 2645 individuals from three studies (AUS, WUE, and MUE/TUE) are shown. Distinct peaks corresponding to integer copy numbers are demonstrated for C4A, C4B, and total C4. There is no obvious discrepancy in the distribution of the normalized dosages between studies
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Fig1: Normalized probe dosage quality control of complement C4A (a),C4B (b), and total C4 (c) in three independent studies. Distribution of unrounded MLPA-based dosage estimates for 2645 individuals from three studies (AUS, WUE, and MUE/TUE) are shown. Distinct peaks corresponding to integer copy numbers are demonstrated for C4A, C4B, and total C4. There is no obvious discrepancy in the distribution of the normalized dosages between studies

Mentions: The multiallelic CNV at theC4locus was assessed by MLPA in three independent studies totalling 1536 late-stage AMD cases of European descent and 1109 age and ethnicity-matched AMD-free controls (Table 1). The published MLPA probe sequences [24] were adapted to facilitate the parallel assessment of the multiallelic CNV forC4and its two isoforms C4A and C4B, despite the two isoforms sharing >99 % sequence identity [25, 26] (Additional file 1: Table S1). We observed that the range of copy numbers in control individuals was comparable to distributions observed in previous studies of European descent (Additional file 3: Table S2) [27, 28] and that the distribution of copy number integers matched those reported previously (C4A between 0 and 5 and C4B between 0 and 4) [29]. A comparison between cohorts revealed a distinct clustering of results around several maxima, corresponding to integer copy numbers (Fig. 1). As homozygous deletions can be miscalled due to unexpected polymorphism at the site of ligation between two MLPA probes [16], we confirmed all suspected homozygous deletions by direct isotype PCR as previously described [21] and achieved 100 % concordance. It has been suggested that batch effects could result in differential bias leading to false-positive associations in quantitative data sets seeking to measure complex multiallelic CNVs [13]. We therefore examined the distribution of raw unrounded probe dosages for diploid copy number carriers for both C4A and C4B or tetraploid copy number carriers for total C4 in cases and controls (Additional file 8: Table S5 and Fig. 1). We found no evidence that mean distributions were significantly different between cases and controls, indicating that association results should represent true biological signals.Fig. 1


Multiallelic copy number variation in the complement component 4A (C4A) gene is associated with late-stage age-related macular degeneration (AMD).

Grassmann F, Cantsilieris S, Schulz-Kuhnt AS, White SJ, Richardson AJ, Hewitt AW, Vote BJ, Schmied D, Guymer RH, Weber BH, Baird PN - J Neuroinflammation (2016)

Normalized probe dosage quality control of complement C4A (a),C4B (b), and total C4 (c) in three independent studies. Distribution of unrounded MLPA-based dosage estimates for 2645 individuals from three studies (AUS, WUE, and MUE/TUE) are shown. Distinct peaks corresponding to integer copy numbers are demonstrated for C4A, C4B, and total C4. There is no obvious discrepancy in the distribution of the normalized dosages between studies
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4835888&req=5

Fig1: Normalized probe dosage quality control of complement C4A (a),C4B (b), and total C4 (c) in three independent studies. Distribution of unrounded MLPA-based dosage estimates for 2645 individuals from three studies (AUS, WUE, and MUE/TUE) are shown. Distinct peaks corresponding to integer copy numbers are demonstrated for C4A, C4B, and total C4. There is no obvious discrepancy in the distribution of the normalized dosages between studies
Mentions: The multiallelic CNV at theC4locus was assessed by MLPA in three independent studies totalling 1536 late-stage AMD cases of European descent and 1109 age and ethnicity-matched AMD-free controls (Table 1). The published MLPA probe sequences [24] were adapted to facilitate the parallel assessment of the multiallelic CNV forC4and its two isoforms C4A and C4B, despite the two isoforms sharing >99 % sequence identity [25, 26] (Additional file 1: Table S1). We observed that the range of copy numbers in control individuals was comparable to distributions observed in previous studies of European descent (Additional file 3: Table S2) [27, 28] and that the distribution of copy number integers matched those reported previously (C4A between 0 and 5 and C4B between 0 and 4) [29]. A comparison between cohorts revealed a distinct clustering of results around several maxima, corresponding to integer copy numbers (Fig. 1). As homozygous deletions can be miscalled due to unexpected polymorphism at the site of ligation between two MLPA probes [16], we confirmed all suspected homozygous deletions by direct isotype PCR as previously described [21] and achieved 100 % concordance. It has been suggested that batch effects could result in differential bias leading to false-positive associations in quantitative data sets seeking to measure complex multiallelic CNVs [13]. We therefore examined the distribution of raw unrounded probe dosages for diploid copy number carriers for both C4A and C4B or tetraploid copy number carriers for total C4 in cases and controls (Additional file 8: Table S5 and Fig. 1). We found no evidence that mean distributions were significantly different between cases and controls, indicating that association results should represent true biological signals.Fig. 1

Bottom Line: We find strong statistical significance for association of increased copy number of C4A (OR 0.81 (0.73; 0.89);P = 4.4 × 10(-5)), with the effect most pronounced in individuals over 78 years (OR 0.67 (0.55; 0.81)) and females (OR 0.77 (0.68; 0.87)).Furthermore, this association is independent of known AMD-associated risk variants in the nearby CFB/C2 locus, particularly in females and in individuals over 78 years.In addition, for the first time, we provide evidence that multiallelic CNVs are associated with AMD pathology.

View Article: PubMed Central - PubMed

Affiliation: Institute of Human Genetics, University of Regensburg, Regensburg, 93053, Germany.

ABSTRACT

Background: Age-related macular degeneration (AMD) is the leading cause of vision loss in Western societies with a strong genetic component. Candidate gene studies as well as genome-wide association studies strongly implicated genetic variations in complement genes to be involved in disease risk. So far, no association of AMD with complement component 4 (C4) was reported probably due to the complex nature of the C4 locus on chromosome 6.

Methods: We used multiplex ligation-dependent probe amplification (MLPA) to determine the copy number of the C4 gene as well as of both relevant isoforms, C4A and C4B, and assessed their association with AMD using logistic regression models.

Results: Here, we report on the analysis of 2645 individuals (1536 probands and 1109 unaffected controls), across three different centers, for multiallelic copy number variation (CNV) at the C4 locus. We find strong statistical significance for association of increased copy number of C4A (OR 0.81 (0.73; 0.89);P = 4.4 × 10(-5)), with the effect most pronounced in individuals over 78 years (OR 0.67 (0.55; 0.81)) and females (OR 0.77 (0.68; 0.87)). Furthermore, this association is independent of known AMD-associated risk variants in the nearby CFB/C2 locus, particularly in females and in individuals over 78 years.

Conclusions: Our data strengthen the notion that complement dysregulation plays a crucial role in AMD etiology, an important finding for early intervention strategies and future therapeutics. In addition, for the first time, we provide evidence that multiallelic CNVs are associated with AMD pathology.

No MeSH data available.


Related in: MedlinePlus