Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity.

ABSTRACT: Salivary amylase in humans is encoded by the copy variable gene AMY1 in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number variation (CNV) at AMY1 on salivary amylase protein production are less well understood. The amylase gene cluster is highly structured with a fundamental difference between odd and even AMY1 copy number haplotypes. In this study, we aimed to explore, in samples from 119 unrelated individuals, not only the effects of AMY1 CNV on salivary amylase protein expression and amylase enzyme activity but also whether there is any evidence for underlying difference between the common haplotypes containing odd numbers of AMY1 and even copy number haplotypes.AMY1 copy number was significantly correlated with the variation observed in salivary amylase production (11.7% of variance, P?

SUBMITTER: Carpenter D

PROVIDER: S-EPMC5319014 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity.

Carpenter Danielle D Mitchell Laura M LM Armour John A L JA

Human genomics 20170220 1

<h4>Background</h4>Salivary amylase in humans is encoded by the copy variable gene AMY1 in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number variation (CNV) at AMY1 on salivary amylase protein production are less well understood. The amylase gene cluster is highly structured with a fundamental difference between odd and even AMY1 copy number haplotypes. In this study, we aimed to explore, in samples from 119 u ...[more]

PMID: 28219410

Similar Datasets

Association of Salivary Amylase (AMY1) Gene Copy Number with Obesity in Alabama Elementary School Children.

Project description:Salivary amylase (AMY1) is the most abundant enzyme in human saliva, responsible for the hydrolysis of α-1,4 glycosidic linkages that aids in the digestion of starch. Recently studies have shown that the copy number of AMY1 is associated with obesity; however, the data varies with location. One-third of children are overweight/obese in Alabama. In this study, we aim to determine the relationship between the copy number of AMY1 gene and obesity measurements in children from Alabama. One hundred twenty-seven children aged between 6 to 10 years participated in this study. Anthropometric measurements were measured using WHO recommendations. Genomic DNA was extracted from saliva, and the copy number of the AMY1 gene was estimated by digital PCR. The association between AMY1 copy number and obesity measurements was analyzed by linear regression. The mean AMY1 copy number significantly decreased in overweight/obese (6.21 ± 1.48) compared to normal weight (7.97 ± 2.35) children. AMY1 copy number inversely associated with the obesity measurements. African Americans had a stronger association between low AMY1 copy number and obesity compared to white/European Americans. Our findings suggest that overweight/obese children have a low AMY1 copy number and the effect is more prominent in African Americans.

| S-EPMC6627241 | biostudies-literature

Salivary AMY1 Copy Number Variation Modifies Age-Related Type 2 Diabetes Risk.

Project description:BackgroundCopy number variation (CNV) in the salivary amylase gene (AMY1) modulates salivary α-amylase levels and is associated with postprandial glycemic traits. Whether AMY1-CNV plays a role in age-mediated change in insulin resistance (IR) is uncertain.MethodsWe measured AMY1-CNV using duplex quantitative real-time polymerase chain reaction in two studies, the Boston Puerto Rican Health Study (BPRHS, n = 749) and the Genetics of Lipid-Lowering Drug and Diet Network study (GOLDN, n = 980), and plasma metabolomic profiles in the BPRHS. We examined the interaction between AMY1-CNV and age by assessing the relationship between age with glycemic traits and type 2 diabetes (T2D) according to high or low copy numbers of the AMY1 gene. Furthermore, we investigated associations between metabolites and interacting effects of AMY1-CNV and age on T2D risk.ResultsWe found positive associations of IR with age among subjects with low AMY1-copy-numbers in both studies. T2D was marginally correlated with age in participants with low AMY1-copy-numbers but not with high AMY1-copy-numbers in the BPRHS. Metabolic pathway enrichment analysis identified the pentose metabolic pathway based on metabolites that were associated with both IR and the interactions between AMY1-CNV and age. Moreover, in older participants, high AMY1-copy-numbers tended to be associated with lower levels of ribonic acid, erythronic acid, and arabinonic acid, all of which were positively associated with IR.ConclusionsWe found evidence supporting a role of AMY1-CNV in modifying the relationship between age and IR. Individuals with low AMY1-copy-numbers tend to have increased IR with advancing age.

| S-EPMC7192522 | biostudies-literature

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

Project description: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.

| S-EPMC4498156 | biostudies-literature

Individual differences in AMY1 gene copy number, salivary ?-amylase levels, and the perception of oral starch.

Project description:The digestion of dietary starch in humans is initiated by salivary ?-amylase, an endo-enzyme that hydrolyzes starch into maltose, maltotriose and larger oligosaccharides. Salivary amylase accounts for 40 to 50% of protein in human saliva and rapidly alters the physical properties of starch. Importantly, the quantity and enzymatic activity of salivary amylase show significant individual variation. However, linking variation in salivary amylase levels with the oral perception of starch has proven difficult. Furthermore, the relationship between copy number variations (CNVs) in the AMY1 gene, which influence salivary amylase levels, and starch viscosity perception has not been explored.Here we demonstrate that saliva containing high levels of amylase has sufficient activity to rapidly hydrolyze a viscous starch solution in vitro. Furthermore, we show with time-intensity ratings, which track the digestion of starch during oral manipulation, that individuals with high amylase levels report faster and more significant decreases in perceived starch viscosity than people with low salivary amylase levels. Finally, we demonstrate that AMY1 CNVs predict an individual's amount and activity of salivary amylase and thereby, ultimately determine their perceived rate of oral starch viscosity thinning.By linking genetic variation and its consequent salivary enzymatic differences to the perceptual sequellae of these variations, we show that AMY1 copy number relates to salivary amylase concentration and enzymatic activity level, which, in turn, account for individual variation in the oral perception of starch viscosity. The profound individual differences in salivary amylase levels and salivary activity may contribute significantly to individual differences in dietary starch intake and, consequently, to overall nutritional status.

| S-EPMC2954178 | biostudies-literature

Low Salivary Amylase Gene (AMY1) Copy Number Is Associated with Obesity and Gut Prevotella Abundance in Mexican Children and Adults.

Project description:Genome-wide association studies (GWAS) have identified copy number variants (CNVs) associated with obesity in chromosomal regions 1p31.1, 10q11.22, 11q11, 16p12.3, and recently 1p21.1, which contains the salivary amylase gene (AMY1). Recent evidence suggests this enzyme may influence gut microbiota composition through carbohydrate (mainly starch) degradation. The role of these CNVs in obesity has been scarcely explored in the Latino population, and thus the aim of our study was to evaluate the association of 1p31.1, 10q11.22, 11q11, 16p12.3 and 1p21.1 CNVs with obesity in 921 Mexican children, to replicate significant associations in 920 Mexican adults, and to analyze the association of AMY1 copy number with gut microbiota in 75 children and 45 adults. Of the five CNVs analyzed, 1q11 CNV was significantly associated with obesity in children, but not in adults. Only AMY1 CNV was significantly associated with obesity in both age groups. Moreover, gut microbiota analyses revealed a positive correlation between AMY1 copy number and Prevotella abundance. This genus has enzymes and gene clusters essential for complex polysaccharide degradation and utilization. To our knowledge, this is the first study to analyze the association of these five CNVs in the Mexican population and to report a correlation between AMY1 CN and gut microbiota in humans.

| S-EPMC6266693 | biostudies-literature

Association of Serum Amylase Activity and the Copy Number Variation of <i>AMY1/2A/2B</i> with Metabolic Syndrome in Chinese Adults.

Project description:PurposeLow serum amylase activity and copy number (CN) variation (CNV) of the salivary amylase gene (AMY1) are reportedly associated with obesity and abnormal glucose metabolism; however, this association remains controversial. We aimed to clarify the relationship between serum amylase activity and the CNV of AMY1/2A/2B with the occurrence of metabolic syndrome (MetS) in Chinese adults.Patients and methodsAnthropometry, metabolic risk factors, and serum amylase activity were assessed in 560 subjects (260 MetS patients; 300 healthy controls). AMY1/2A/2B CNs were evaluated using the highly sensitive droplet digital PCR.ResultsThe serum total, pancreatic, and salivary amylase activity, but not the AMY1/2A/2B CNs, was significantly lower in MetS patients than that in the control subjects. Patients <45 y had a lower AMY1 CN, compared to that in healthy controls. Low serum amylase activity was significantly associated with high MetS prevalence (p < 0.001). In the receiver operating characteristic curve analysis, serum amylase activity was a significant diagnostic indicator for MetS. The diagnostic value of total amylase was second only to that of γ-glutamyl transpeptidase; it was higher than that of alanine aminotransferase and uric acid.ConclusionLow serum amylase activity was significantly associated with increased risk of MetS in Chinese adults. Therefore, amylase could be a potential biomarker for predicting MetS.

| S-EPMC8648087 | biostudies-literature

High plasma salivary α-amylase, but not high AMY1 copy number, associated with low obesity rate in Qatari adults: cross-sectional study.

Project description:The relationship between salivary α-amylase activity (psAAa) or AMY1 copy number and the risk of obesity remains controversial. We aimed to assess this relationship in a cohort from Qatar, where obesity affects 43% of adults. The relationship was investigated cross-sectionally in 923 Qatari adults from the Qatar biobank cohort. AMY1 CN was estimated form whole genome sequencing data. The associations with obesity prevalence were assessed by linear and logistic regressions. We found no difference in AMY1 CN between obese and normal-weight individuals. However, the psAAa was significantly lower in obese individuals. Significant inverse correlations were found between adiposity markers and psAAa in both sexes, but were marginally stronger in men. A significant effect of high psAAa, but not AMY1 CN, on reduced obesity rates was identified in men (OR per psAAa unit 0.957 [95% CI 0.937-0.977], p < 0.001, with psAAa ranging between 5 to 66 U/L). A significantly higher prevalence of obesity was observed in the lowest quartile of psAAa in men (75% (Q1) vs. 36% (Q4), p < 0.001) and women (74% (Q1) vs 56% (Q4), p = 0.009). Our findings suggest that high psAAa, but not AMY1 CN, has a potential positive benefit against obesity in the Qatari population.

| S-EPMC7578794 | biostudies-literature

Low copy number of the salivary amylase gene predisposes to obesity.

Project description:Common multi-allelic copy number variants (CNVs) appear enriched for phenotypic associations compared to their biallelic counterparts. Here we investigated the influence of gene dosage effects on adiposity through a CNV association study of gene expression levels in adipose tissue. We identified significant association of a multi-allelic CNV encompassing the salivary amylase gene (AMY1) with body mass index (BMI) and obesity, and we replicated this finding in 6,200 subjects. Increased AMY1 copy number was positively associated with both amylase gene expression (P = 2.31 × 10(-14)) and serum enzyme levels (P < 2.20 × 10(-16)), whereas reduced AMY1 copy number was associated with increased BMI (change in BMI per estimated copy = -0.15 (0.02) kg/m(2); P = 6.93 × 10(-10)) and obesity risk (odds ratio (OR) per estimated copy = 1.19, 95% confidence interval (CI) = 1.13-1.26; P = 1.46 × 10(-10)). The OR value of 1.19 per copy of AMY1 translates into about an eightfold difference in risk of obesity between subjects in the top (copy number > 9) and bottom (copy number < 4) 10% of the copy number distribution. Our study provides a first genetic link between carbohydrate metabolism and BMI and demonstrates the power of integrated genomic approaches beyond genome-wide association studies.

| S-EPMC6485469 | biostudies-literature

Diet and the evolution of human amylase gene copy number variation.

Project description:Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch. This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis. We found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number-variable gene is, to our knowledge, one of the first discovered in the human genome. Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease.

| S-EPMC2377015 | biostudies-literature

CYP1B1 copy number variation is not a major contributor to primary congenital glaucoma.

Project description:PURPOSE: To evaluate the prevalence and the diagnostic utility of testing for CYP1B1 copy number variation (CNV) in primary congenital glaucoma (PCG) cases unexplained by CYP1B1 point mutations in The Australian and New Zealand Registry of Advanced Glaucoma. METHODS: In total, 50 PCG cases either heterozygous for disease-causing variants or with no CYP1B1 sequence variants were included in the study. CYP1B1 CNV was analyzed by Multiplex Ligation-dependent Probe Amplification (MLPA). RESULTS: No deletions or duplications were found in any of the cases. CONCLUSION: This is the first study to report on CYP1B1 CNV in PCG cases. Our findings show that this mechanism is not a major contributor to the phenotype and is of limited diagnostic utility.

| S-EPMC4333725 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data