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Shwan NAA, Moise EC, Necsoiu PE, Farr AJ, Gale DP, Barratt J, Armour JAL. Segregation analysis identifies specific alpha-defensin (DEFA1A3) SNP-CNV haplotypes in predisposition to IgA nephropathy. Ann Hum Genet 2023; 87:1-8. [PMID: 36214424 DOI: 10.1111/ahg.12481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Immunoglobulin A (IgA) nephropathy is a disorder of the immune system affecting kidney function, and genome-wide association studies (GWAS) have defined numerous loci with associated variation, all implicating components of innate or adaptive immunity. Among these, single nucleotide polymorphisms (SNPs) in a region including the multiallelic copy number variation (CNV) of DEFA1A3 are associated with IgA nephropathy in both European and Asian populations. At present, the precise factors underlying the observed associations at DEFA1A3 have not been defined, although the key alleles differ between Asian and European populations, and multiple independent factors may be involved even within a single population. METHODS In this study, we measured DEFA1A3 copy number in UK family trios with an offspring affected by IgA nephropathy, used the population distributions of joint SNP-CNV haplotypes to infer the likely segregation in trios, and applied transmission disequilibrium tests (TDT) to examine joint SNP-CNV haplotypes for over- or undertransmission into affected offspring from heterozygous parents. RESULTS AND CONCLUSIONS We observed overtransmission of 3-copy class 2 haplotypes (raw p = 0.029) and some evidence for under-transmission of 3-copy class 1 haplotypes (raw p = 0.051), although these apparent effects were not statistically significant after correction for testing of multiple haplotypes.
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Affiliation(s)
- Nzar A A Shwan
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Erbil Technical Health and Medical College, Erbil Polytechnic University, Erbil, Kurdistan Region, Iraq
| | - Eric C Moise
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Paula E Necsoiu
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Amy J Farr
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Daniel P Gale
- Department of Renal Medicine, Division of Medicine, University College London, London, UK
| | - Jonathan Barratt
- Department of Cardiovascular Medicine, University of Leicester, Leicester, UK
| | - John A L Armour
- School of Life Sciences, University of Nottingham, Nottingham, UK
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Shwan NAA, Armour JAL. No Evidence for Association of BMI with Salivary Amylase Gene Copy Number in the UK 1958 Birth Cohort. Obesity (Silver Spring) 2019; 27:1533-1538. [PMID: 31441234 DOI: 10.1002/oby.22565] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 05/28/2019] [Indexed: 01/08/2023]
Abstract
OBJECTIVE In a 2014 publication, evidence was presented supporting the association of BMI with the copy number of the salivary amylase 1 (AMY1) gene, with an unprecedented effect size of -0.15 kg/m2 (SE 0.02) per copy of AMY1. Most well-powered attempts to reproduce these findings have not been successful. However, because of different study designs, a significant association may still apply under restricted conditions such as in particular age groups. This study specifically tested the BMI-AMY1 association at different age points in the same individuals using longitudinal BMI information from participants in the UK 1958 Birth Cohort study. METHODS This study measured the AMY1 copy number by paralogue ratio tests in genomic DNA and by using array comparative genomic hybridization data. BMI data from 1958 Birth Cohort participants were available from eight different age points between 7 and 50 years. RESULTS No evidence, even at nominal significance, was found for association of the AMY1 copy number with BMI at any age point in approximately 1,400 members of the 1958 Birth Cohort or in 2,835 people from two disease cohorts from the Wellcome Trust Case Control Consortium. CONCLUSIONS The results do not support an association between BMI and AMY1 copy number at any age point.
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Affiliation(s)
- Nzar A A Shwan
- School of Life Sciences, Queen's Medical Centre, The University of Nottingham, Nottingham, UK
- Erbil Technical Health College, Erbil Polytechnic University, Erbil, Iraq
| | - John A L Armour
- School of Life Sciences, Queen's Medical Centre, The University of Nottingham, Nottingham, UK
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Shwan NAA, Louzada S, Yang F, Armour JAL. Recurrent Rearrangements of Human Amylase Genes Create Multiple Independent CNV Series. Hum Mutat 2017; 38:532-539. [PMID: 28101908 DOI: 10.1002/humu.23182] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/16/2017] [Indexed: 01/17/2023]
Abstract
The human amylase gene cluster includes the human salivary (AMY1) and pancreatic amylase genes (AMY2A and AMY2B), and is a highly variable and dynamic region of the genome. Copy number variation (CNV) of AMY1 has been implicated in human dietary adaptation, and in population association with obesity, but neither of these findings has been independently replicated. Despite these functional implications, the structural genomic basis of CNV has only been defined in detail very recently. In this work, we use high-resolution analysis of copy number, and analysis of segregation in trios, to define new, independent allelic series of amylase CNVs in sub-Saharan Africans, including a series of higher-order expansions of a unit consisting of one copy each of AMY1, AMY2A, and AMY2B. We use fiber-FISH (fluorescence in situ hybridization) to define unexpected complexity in the accompanying rearrangements. These findings demonstrate recurrent involvement of the amylase gene region in genomic instability, involving at least five independent rearrangements of the pancreatic amylase genes (AMY2A and AMY2B). Structural features shared by fundamentally distinct lineages strongly suggest that the common ancestral state for the human amylase cluster contained more than one, and probably three, copies of AMY1.
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Affiliation(s)
- Nzar A A Shwan
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK.,Scientific Research Centre, University of Salahaddin, Erbil, Kurdistan, Iraq
| | - Sandra Louzada
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Fengtang Yang
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - John A L Armour
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK
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Inchley CE, Larbey CDA, Shwan NAA, Pagani L, Saag L, Antão T, Jacobs G, Hudjashov G, Metspalu E, Mitt M, Eichstaedt CA, Malyarchuk B, Derenko M, Wee J, Abdullah S, Ricaut FX, Mormina M, Mägi R, Villems R, Metspalu M, Jones MK, Armour JAL, Kivisild T. Selective sweep on human amylase genes postdates the split with Neanderthals. Sci Rep 2016; 6:37198. [PMID: 27853181 PMCID: PMC5112570 DOI: 10.1038/srep37198] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 11/24/2022] Open
Abstract
Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.
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Affiliation(s)
- Charlotte E Inchley
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK
| | - Cynthia D A Larbey
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK
| | - Nzar A A Shwan
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.,Scientific Research Centre, University of Salahaddin, Erbil, Kurdistan, Iraq
| | - Luca Pagani
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Estonian Biocentre, Tartu, 51010, Estonia
| | - Lauri Saag
- Estonian Biocentre, Tartu, 51010, Estonia
| | - Tiago Antão
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Guy Jacobs
- Complexity Institute, Nanyang Technological University, Singapore
| | - Georgi Hudjashov
- Estonian Biocentre, Tartu, 51010, Estonia.,Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Mario Mitt
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Christina A Eichstaedt
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Thoraxclinic at the University Hospital Heidelberg, 69126 Heidelberg, Germany
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Joseph Wee
- Division of Radiation Oncology, National Cancer Centre, Singapore
| | | | - François-Xavier Ricaut
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Maru Mormina
- Department of Applied Social Sciences, University of Winchester, Sparkford Road, Winchester SO22 4NR, UK
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Richard Villems
- Estonian Biocentre, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Estonia.,Estonian Academy of Sciences, 10130 Tallinn, Estonia
| | | | - Martin K Jones
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK
| | - John A L Armour
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Toomas Kivisild
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Estonian Biocentre, Tartu, 51010, Estonia
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Carpenter D, Dhar S, Mitchell LM, Fu B, Tyson J, Shwan NAA, Yang F, Thomas MG, Armour JAL. Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes. Hum Mol Genet 2015; 24:3472-80. [PMID: 25788522 PMCID: PMC4498156 DOI: 10.1093/hmg/ddv098] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/13/2015] [Indexed: 12/16/2022] Open
Abstract
The human salivary amylase genes display extensive copy number variation (CNV), and recent work has implicated this variation in adaptation to starch-rich diets, and in association with body mass index. In this work, we use paralogue ratio tests, microsatellite analysis, read depth and fibre-FISH to demonstrate that human amylase CNV is not a smooth continuum, but is instead partitioned into distinct haplotype classes. There is a fundamental structural distinction between haplotypes containing odd or even numbers of AMY1 gene units, in turn coupled to CNV in pancreatic amylase genes AMY2A and AMY2B. Most haplotypes have one copy each of AMY2A and AMY2B and contain an odd number of copies of AMY1; consequently, most individuals have an even total number of AMY1. In contrast, haplotypes carrying an even number of AMY1 genes have rearrangements leading to CNVs of AMY2A/AMY2B. Read-depth and experimental data show that different populations harbour different proportions of these basic haplotype classes. In Europeans, the copy numbers of AMY1 and AMY2A are correlated, so that phenotypic associations caused by variation in pancreatic amylase copy number could be detected indirectly as weak association with AMY1 copy number. We show that the quantitative polymerase chain reaction (qPCR) assay previously applied to the high-throughput measurement of AMY1 copy number is less accurate than the measures we use and that qPCR data in other studies have been further compromised by systematic miscalibration. Our results uncover new patterns in human amylase variation and imply a potential role for AMY2 CNV in functional associations.
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Affiliation(s)
- Danielle Carpenter
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Sugandha Dhar
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Laura M Mitchell
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and
| | - Jess Tyson
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Nzar A A Shwan
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - John A L Armour
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK,
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