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Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus.

Black HA, Khan FF, Tyson J, Al Armour J - BMC Genomics (2014)

Bottom Line: Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry.The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus.The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK. john.armour@nottingham.ac.uk.

ABSTRACT

Background: The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3-16); hence, the mechanisms responsible for changes in copy number at this locus are unclear.

Results: In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure.

Conclusions: Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.

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Structure of theDEFA1A3locus. A) The DEFA1A3 locus consists of two single-copy partial repeats surrounding a variable number of full repeats. Each of the full repeats and the centromeric partial repeat contain a gene locus occupied by either DEFA1 or DEFA3. Symbols show the positions of the variant distinguishing DEFA1 from DEFA3, a 7 bp duplication in intron 1 of each copy of DEFA1A3 and a 5 bp Indel located upstream of each copy of DEFA1A3. The positions of the four SNPs tagging DEFA1A3 haplotype class are shown. Adapted from Khan et al.[18]. B) There are SNPs either side of the DEFA1A3 locus displaying high levels of linkage disequilibrium (D’ = 1), as shown by phased SNP genotype data for the HapMap CEU1 individuals, downloaded from the HapMap project (release #24, phase 1 and 2)[35, 54]. D’ values are shown.
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Fig1: Structure of theDEFA1A3locus. A) The DEFA1A3 locus consists of two single-copy partial repeats surrounding a variable number of full repeats. Each of the full repeats and the centromeric partial repeat contain a gene locus occupied by either DEFA1 or DEFA3. Symbols show the positions of the variant distinguishing DEFA1 from DEFA3, a 7 bp duplication in intron 1 of each copy of DEFA1A3 and a 5 bp Indel located upstream of each copy of DEFA1A3. The positions of the four SNPs tagging DEFA1A3 haplotype class are shown. Adapted from Khan et al.[18]. B) There are SNPs either side of the DEFA1A3 locus displaying high levels of linkage disequilibrium (D’ = 1), as shown by phased SNP genotype data for the HapMap CEU1 individuals, downloaded from the HapMap project (release #24, phase 1 and 2)[35, 54]. D’ values are shown.

Mentions: One locus exhibiting multiallelic CNV is the α-defensin DEFA1A3 locus on human chromosome 8p23.1 (Figure 1A)[15–18], with individuals having between 3–16 copies of DEFA1A3[17–20]. SNPs are usually poor tags of copy number at multiallelic loci, due to the limited ability of a biallelic SNP to tag multiple different copy number states[21]. However, the SNP rs4300027 has been identified as a tag of DEFA1A3 copy number in populations with European ancestry, an association which has not been shown in other populations[18]. At the locus, each DEFA1A3 repeat unit can be occupied by one of two α-defensin genes, either DEFA1 or DEFA3, adding additional complexity. The two genes encode the human neutrophil peptides (HNP) 1–3; these are antimicrobial peptides involved in the innate immune response[22–25]. A recent GWAS found the SNP rs2738048, which falls within the same linkage disequilibrium block as DEFA1A3, to be associated with risk of IgA nephropathy in the Han Chinese population[26]. The basis of this association is unknown, but highlights a need to understand how variation at the DEFA1A3 locus influences HNP1-3 expression. There has only been a single small-scale study comparing DEFA1A3 copy number with HNP1-3 expression, which identified a positive correlation[19]. However, the spatial arrangement of the locus may influence expression.Figure 1


Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus.

Black HA, Khan FF, Tyson J, Al Armour J - BMC Genomics (2014)

Structure of theDEFA1A3locus. A) The DEFA1A3 locus consists of two single-copy partial repeats surrounding a variable number of full repeats. Each of the full repeats and the centromeric partial repeat contain a gene locus occupied by either DEFA1 or DEFA3. Symbols show the positions of the variant distinguishing DEFA1 from DEFA3, a 7 bp duplication in intron 1 of each copy of DEFA1A3 and a 5 bp Indel located upstream of each copy of DEFA1A3. The positions of the four SNPs tagging DEFA1A3 haplotype class are shown. Adapted from Khan et al.[18]. B) There are SNPs either side of the DEFA1A3 locus displaying high levels of linkage disequilibrium (D’ = 1), as shown by phased SNP genotype data for the HapMap CEU1 individuals, downloaded from the HapMap project (release #24, phase 1 and 2)[35, 54]. D’ values are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4117965&req=5

Fig1: Structure of theDEFA1A3locus. A) The DEFA1A3 locus consists of two single-copy partial repeats surrounding a variable number of full repeats. Each of the full repeats and the centromeric partial repeat contain a gene locus occupied by either DEFA1 or DEFA3. Symbols show the positions of the variant distinguishing DEFA1 from DEFA3, a 7 bp duplication in intron 1 of each copy of DEFA1A3 and a 5 bp Indel located upstream of each copy of DEFA1A3. The positions of the four SNPs tagging DEFA1A3 haplotype class are shown. Adapted from Khan et al.[18]. B) There are SNPs either side of the DEFA1A3 locus displaying high levels of linkage disequilibrium (D’ = 1), as shown by phased SNP genotype data for the HapMap CEU1 individuals, downloaded from the HapMap project (release #24, phase 1 and 2)[35, 54]. D’ values are shown.
Mentions: One locus exhibiting multiallelic CNV is the α-defensin DEFA1A3 locus on human chromosome 8p23.1 (Figure 1A)[15–18], with individuals having between 3–16 copies of DEFA1A3[17–20]. SNPs are usually poor tags of copy number at multiallelic loci, due to the limited ability of a biallelic SNP to tag multiple different copy number states[21]. However, the SNP rs4300027 has been identified as a tag of DEFA1A3 copy number in populations with European ancestry, an association which has not been shown in other populations[18]. At the locus, each DEFA1A3 repeat unit can be occupied by one of two α-defensin genes, either DEFA1 or DEFA3, adding additional complexity. The two genes encode the human neutrophil peptides (HNP) 1–3; these are antimicrobial peptides involved in the innate immune response[22–25]. A recent GWAS found the SNP rs2738048, which falls within the same linkage disequilibrium block as DEFA1A3, to be associated with risk of IgA nephropathy in the Han Chinese population[26]. The basis of this association is unknown, but highlights a need to understand how variation at the DEFA1A3 locus influences HNP1-3 expression. There has only been a single small-scale study comparing DEFA1A3 copy number with HNP1-3 expression, which identified a positive correlation[19]. However, the spatial arrangement of the locus may influence expression.Figure 1

Bottom Line: Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry.The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus.The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK. john.armour@nottingham.ac.uk.

ABSTRACT

Background: The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3-16); hence, the mechanisms responsible for changes in copy number at this locus are unclear.

Results: In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure.

Conclusions: Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.

Show MeSH