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Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes

Carpenter, D., Dhar, S., Mitchell, L. M., Fu, B., Tyson, J., Shwan, N. A. A., Yang, F., Thomas, M. G., Armour, J. A. L.·2015·Human Molecular Genetics
DOI 10.1093/hmg/ddv098PMC PMC4498156
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Figure 1. General overview of the human amylase gene region, showing the positions of assays used. The corresponding region of the human reference (hg19) assembly shown includes three copies of AMY1 (AMY1A/1B/1C) and one copy each of AMY2A and AMY2B. In each case, the broad arrow indicates the position and orientation of the gene, and the more extensive region of near-perfect sequence identity around each copy of AMY1 is shown as a narrower red rectangle. Exons 4–10 of AMY2A are repeated in the truncated pseudogene AMYP1 between AMY1B and AMY1C. The black ‘18 kb’ rectangles indicate two near-identical regions with multiple sequence similarity to other parts of the locus. The ‘read-depth’ annotation shows the regions used for read-depth analysis of AMY2B (dark blue), AMY2A (light blue) and AMY1 (red), indicating coherent intervals not compromised by high-sequence identity to other locations. The ‘PRT_ref12’, ‘PRT_ref1’ and ‘microsatellite’ annotations indicate the predicted positions of PCR products used in our copy number measurements at this locus.
Figure 1. General overview of the human amylase gene region, showing the positions of assays used. The corresponding region of the human reference (hg19) assembly shown includes three copies of AMY1 (AMY1A/1B/1C) and one copy each of AMY2A and AMY2B. In each case, the broad arrow indicates the position and orientation of the gene, and the more extensive region of near-perfect sequence identity around each copy of AMY1 is shown as a narrower red rectangle. Exons 4–10 of AMY2A are repeated in the truncated pseudogene AMYP1 between AMY1B and AMY1C. The black ‘18 kb’ rectangles indicate two near-identical regions with multiple sequence similarity to other parts of the locus. The ‘read-depth’ annotation shows the regions used for read-depth analysis of AMY2B (dark blue), AMY2A (light blue) and AMY1 (red), indicating coherent intervals not compromised by high-sequence identity to other locations. The ‘PRT_ref12’, ‘PRT_ref1’ and ‘microsatellite’ annotations indicate the predicted positions of PCR products used in our copy number measurements at this locus.CC BY · PubMed Central
Figure 2. Most people have an even number of AMY1; odd numbers are associated with AMY2A CNV. (A) Integer AMY1 maximum-likelihood copy number (MLCN) measured by PRT and microsatellite methods for 209 unrelated Eurasian individuals from the HapMap project. (B) AMY2A copy number (CN) for the same individuals, with pie charts illustrating the significant association between even numbers of AMY1 and an AMY2A CN of 2 (P ≈ 5.3 × 10−7). (C) Estimates of read-depth-derived copy number estimates for AMY2A versus AMY1 for 644 Eurasian samples from the 1000 Genomes Project; the association between (integer-rounded) even numbers of AMY1 and an AMY2A copy number of 2 is significant (P ≈ 1.5 × 10−24).
Figure 2. Most people have an even number of AMY1; odd numbers are associated with AMY2A CNV. (A) Integer AMY1 maximum-likelihood copy number (MLCN) measured by PRT and microsatellite methods for 209 unrelated Eurasian individuals from the HapMap project. (B) AMY2A copy number (CN) for the same individuals, with pie charts illustrating the significant association between even numbers of AMY1 and an AMY2A CN of 2 (P ≈ 5.3 × 10−7). (C) Estimates of read-depth-derived copy number estimates for AMY2A versus AMY1 for 644 Eurasian samples from the 1000 Genomes Project; the association between (integer-rounded) even numbers of AMY1 and an AMY2A copy number of 2 is significant (P ≈ 1.5 × 10−24).CC BY · PubMed Central
Figure 3. 1000 Genomes read-depth demonstrates CNVs at AMY2A and AMY2B. Estimates of read-depth-derived copy number estimates for AMY2B versus AMY2A in 1047 samples from the 1000 Genomes Project, showing variant clusters corresponding to carriers of the AMY2A deletion (one copy of AMY2A, two copies of AMY2B), the AMY2A/2B duplication (three copies of AMY2A, three copies of AMY2B) and the AMY2A-only duplication (three copies of AMY2A, two copies of AMY2B). Eight samples have two copies of AMY2A and three copies of AMY2B, and this composition has been verified by segregation and other analyses in the case of NA11933.
Figure 3. 1000 Genomes read-depth demonstrates CNVs at AMY2A and AMY2B. Estimates of read-depth-derived copy number estimates for AMY2B versus AMY2A in 1047 samples from the 1000 Genomes Project, showing variant clusters corresponding to carriers of the AMY2A deletion (one copy of AMY2A, two copies of AMY2B), the AMY2A/2B duplication (three copies of AMY2A, three copies of AMY2B) and the AMY2A-only duplication (three copies of AMY2A, two copies of AMY2B). Eight samples have two copies of AMY2A and three copies of AMY2B, and this composition has been verified by segregation and other analyses in the case of NA11933.CC BY · PubMed Central
Figure 4. Inferred structures of AMY1/AMY2 variants found commonly in European and Asian populations. The coordinates of the 3-copy haplotype in the hg19 reference assembly are shown at the top. Most haplotypes contain an odd number of AMY1 and conform to the general structure shown in (A), containing one copy each of AMY2A and AMY2B, and variable numbers of a 95 kb variable-copy DNA unit containing two inverted copies of AMY1 (bracketed) between exons 4–10 of AMY2A and the corresponding part of its pseudogene. The AMY2A deletion haplotype shown in (B) results from deletion of 75 kb containing both AMY2A and one copy of AMY1, thereby generating haplotypes carrying even numbers of AMY1, with a 2-copy example shown here. The haplotype in (C) shows the structure in which the AMY2A and AMY2B genes plus a copy of AMY1 are included in a duplication unit of about 116 kb. The involvement of one copy of AMY1 in the rearrangement again leads to haplotypes containing even numbers of the AMY1 gene. Genes (and the pseudogene) are represented as arrows, with the extended region of sequence identity around AMY1 shown as a narrow red rectangle. The black rectangles indicate two regions of about 18 kb between AMY2A and AMY2B, and between inverted copies of AMY1, that show high-sequence similarity. The position-specific nomenclature of AMY1A/AMY1B/AMY1C of Groot et al. (4) is adopted in this figure for clarity.
Figure 4. Inferred structures of AMY1/AMY2 variants found commonly in European and Asian populations. The coordinates of the 3-copy haplotype in the hg19 reference assembly are shown at the top. Most haplotypes contain an odd number of AMY1 and conform to the general structure shown in (A), containing one copy each of AMY2A and AMY2B, and variable numbers of a 95 kb variable-copy DNA unit containing two inverted copies of AMY1 (bracketed) between exons 4–10 of AMY2A and the corresponding part of its pseudogene. The AMY2A deletion haplotype shown in (B) results from deletion of 75 kb containing both AMY2A and one copy of AMY1, thereby generating haplotypes carrying even numbers of AMY1, with a 2-copy example shown here. The haplotype in (C) shows the structure in which the AMY2A and AMY2B genes plus a copy of AMY1 are included in a duplication unit of about 116 kb. The involvement of one copy of AMY1 in the rearrangement again leads to haplotypes containing even numbers of the AMY1 gene. Genes (and the pseudogene) are represented as arrows, with the extended region of sequence identity around AMY1 shown as a narrow red rectangle. The black rectangles indicate two regions of about 18 kb between AMY2A and AMY2B, and between inverted copies of AMY1, that show high-sequence similarity. The position-specific nomenclature of AMY1A/AMY1B/AMY1C of Groot et al. (4) is adopted in this figure for clarity.CC BY · PubMed Central
Figure 5. Haplotype copy numbers of AMY1 inferred from pedigree segregation. Distribution of AMY1 copy numbers in 123 haplotypes from 16 three-generation CEPH pedigrees. Colours distinguish haplotypes containing CNVs (2 or 0 copies) of AMY2A (all associated with even numbers of AMY1) from haplotypes containing one copy of AMY2A (the majority with an odd number of copies of AMY1).
Figure 5. Haplotype copy numbers of AMY1 inferred from pedigree segregation. Distribution of AMY1 copy numbers in 123 haplotypes from 16 three-generation CEPH pedigrees. Colours distinguish haplotypes containing CNVs (2 or 0 copies) of AMY2A (all associated with even numbers of AMY1) from haplotypes containing one copy of AMY2A (the majority with an odd number of copies of AMY1).CC BY · PubMed Central
Figure 6. Fibre-FISH confirmation of 18 copies of AMY1 in sample NA18972, with 13-copy and 5-copy haplotypes. The probes are identical to those used by Perry et al. (11) with the upstream (ERV) probe shown in green and the AMY1 gene probe in red. Other sequences in the region which have >90% sequence identity to the AMY1 gene probe hybridize more faintly and less reliably, interpreted here as AMY2A, AMY2B and the AMY2A pseudogene. (A) Two images of the 5-copy haplotype are interpreted using the diagrammatic representation shown in Figure 4. Note the faint and inconsistent cross-hybridization of the (red) AMY1 gene probe to AMY2B, AMY2A and pseudogene sequences (circled). (B) For simplicity, the annotation of the 13-copy haplotype shows only sequentially numbered AMY1 gene copies as paired red + green signals, with indication of the cross-hybridizing AMY2B, AMY2A and pseudogene (P) sequences circled in red. We estimate that the 13-copy haplotype, here presented as two overlapping images from the same molecule, spans about 670 kb between AMY2B and the last (13th) copy of AMY1. The overlap between images A and B is indicated by the horizontal blue line spanning AMY1 repeats 5 and 6.
Figure 6. Fibre-FISH confirmation of 18 copies of AMY1 in sample NA18972, with 13-copy and 5-copy haplotypes. The probes are identical to those used by Perry et al. (11) with the upstream (ERV) probe shown in green and the AMY1 gene probe in red. Other sequences in the region which have >90% sequence identity to the AMY1 gene probe hybridize more faintly and less reliably, interpreted here as AMY2A, AMY2B and the AMY2A pseudogene. (A) Two images of the 5-copy haplotype are interpreted using the diagrammatic representation shown in Figure 4. Note the faint and inconsistent cross-hybridization of the (red) AMY1 gene probe to AMY2B, AMY2A and pseudogene sequences (circled). (B) For simplicity, the annotation of the 13-copy haplotype shows only sequentially numbered AMY1 gene copies as paired red + green signals, with indication of the cross-hybridizing AMY2B, AMY2A and pseudogene (P) sequences circled in red. We estimate that the 13-copy haplotype, here presented as two overlapping images from the same molecule, spans about 670 kb between AMY2B and the last (13th) copy of AMY1. The overlap between images A and B is indicated by the horizontal blue line spanning AMY1 repeats 5 and 6.CC BY · PubMed Central

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Metadata

Authors
Carpenter, D., Dhar, S., Mitchell, L. M., Fu, B., Tyson, J., Shwan, N. A. A., Yang, F., Thomas, M. G., & Armour, J. A. L.
Venue
Human Molecular Genetics
Publisher
Oxford University Press (OUP)
Published
2015-03-18
Volume
24
Issue
12
Pages
3472-3480
ISSN
  • 0964-6906
  • 1460-2083
DOI
10.1093/hmg/ddv098
PMC
PMC4498156
Cited by
128
References
9
Language
en

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CoChat. (2026). Citation check: Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes. https://app.cochat.ai/papers/10.1093/hmg/ddv098
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Carpenter, D., Dhar, S., Mitchell, L. M., Fu, B., Tyson, J., Shwan, N. A. A., Yang, F., Thomas, M. G., & Armour, J. A. L. (2015). Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes. Human Molecular Genetics. https://doi.org/10.1093/hmg/ddv098