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

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.

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Abstract 4908: Deep sequence analysis of the relationship between gene expression, CpG island methylation, and gene copy number in breast cancer cells

10.1158/1538-7445.am2011-4908 ◽

2011 ◽

Author(s):

Zhifu Sun ◽

Yan W Asmann ◽

Krishna R Kalari ◽

Brian Bot ◽

Jeanette E Eckel-Passow ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Copy Number ◽

Breast Cancer Cells ◽

Cpg Island ◽

Gene Copy Number ◽

Gene Copy ◽

Cpg Island Methylation ◽

The Relationship ◽

Deep Sequence Analysis

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Pretreatment Prevotella-to-Bacteroides ratio and salivary amylase gene copy number as prognostic markers for dietary weight loss

American Journal of Clinical Nutrition ◽

10.1093/ajcn/nqaa007 ◽

2020 ◽

Vol 111 (5) ◽

pp. 1079-1086 ◽

Cited By ~ 5

Author(s):

Mads F Hjorth ◽

Lars Christensen ◽

Thomas M Larsen ◽

Henrik M Roager ◽

Lukasz Krych ◽

...

Keyword(s):

Weight Loss ◽

Weight Change ◽

Copy Number ◽

Gene Copy Number ◽

Diet Group ◽

Gene Copy ◽

Whole Grain ◽

Amylase Gene ◽

Salivary Amylase ◽

To Receive

ABSTRACT Background The inconsistent link observed between salivary amylase gene copy number (AMY1 CN) and weight management is likely modified by diet and microbiome. Objective Based on analysis of a previously published study, we investigated the hypothesis that interaction between diet, Prevotella-to-Bacteriodes ratio (P/B ratio), and AMY1 CN influence weight change. Methods Sixty-two people with increased waist circumference were randomly assigned to receive an ad libitum New Nordic Diet (NND) high in dietary fiber, whole grain, intrinsic sugars, and starch or an Average Danish (Western) Diet (ADD) for 26 weeks. All foods were provided free of charge. Before subjects were randomly assigned to receive the NND or ADD diet, blood and fecal samples were collected, from which AMY1 CN and P/B ratio, respectively, were determined. Body weight change was described by using linear mixed models, including biomarker [log10(P/B ratio) and/or AMY1 CN] diet-group interactions. Results Baseline means ± SDs of log10(P/B ratio) and AMY1 CN were −2.1 ± 1.8 and 6.6 ± 2.4, respectively. Baseline P/B ratio predicted a 0.99-kg/unit (95% CI: 0.40, 1.57; n = 54; P < 0.001) higher weight loss for those subjects on the NND compared with those on the ADD diet, whereas AMY1 CN was not found to predict weight loss differences between the NND and ADD groups [0.05 kg/CN (95% CI: −0.40, 0.51; n = 54; P = 0.83)]. However, among subjects with low AMY1 CN (<6.5 copies), baseline P/B ratio predicted a 2.12-kg/unit (95% CI: 1.37, 2.88; n = 30; P < 0.001) higher weight loss for the NND group than the ADD group. No such differences in weight loss were found among subjects in both groups with high AMY1 CN [−0.17 kg/unit (95% CI: −1.01, 0.66; n = 24; P = 0.68)]. Conclusions The combined use of low AMY1 CN and pretreatment P/B ratio for weight loss prediction led to highly individualized weight loss results with the introduction of more fiber, whole grain, intrinsic sugars, and starch in the diet. These preliminary observations suggest that more undigested starch reaches the colon in individuals with low AMY1 CN, and that the fate of this starch depends on the gut microbiota composition. This trial was registered at clinicaltrials.gov as NCT01195610.

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Gene Copy-Number Variation and Associated Polymorphisms of Complement Component C4 in Human Systemic Lupus Erythematosus (SLE): Low Copy Number Is a Risk Factor for and High Copy Number Is a Protective Factor against SLE Susceptibility in European Americans

The American Journal of Human Genetics ◽

10.1086/518257 ◽

2007 ◽

Vol 80 (6) ◽

pp. 1037-1054 ◽

Cited By ~ 314

Author(s):

Yan Yang ◽

Erwin K. Chung ◽

Yee Ling Wu ◽

Stephanie L. Savelli ◽

Haikady N. Nagaraja ◽

...

Keyword(s):

Lupus Erythematosus ◽

Copy Number ◽

Protective Factor ◽

Gene Copy Number ◽

Gene Copy ◽

Human Systemic Lupus Erythematosus ◽

Gene Copy Number Variation ◽

European Americans ◽

Low Copy Number ◽

Number Variation

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The relationship between EGFR gene copy number and EGFR mutation and clinical predicting significance in the Chinese patients with advanced non-small cell lung cancer patients.

Journal of Clinical Oncology ◽

10.1200/jco.2010.28.15_suppl.e18082 ◽

2010 ◽

Vol 28 (15_suppl) ◽

pp. e18082-e18082

Author(s):

L. Zhao ◽

H. Bai ◽

M. Zhuo ◽

J. Zhao ◽

J. Duan ◽

...

Keyword(s):

Copy Number ◽

Egfr Mutation ◽

Gene Copy Number ◽

Small Cell ◽

Chinese Patients ◽

Gene Copy ◽

Small Cell Lung ◽

Egfr Gene ◽

Lung Cancer Patients ◽

The Relationship

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Measurement of gene amplifications related to drug resistance in Plasmodium falciparum using droplet digital PCR

10.21203/rs.3.rs-103611/v2 ◽

2021 ◽

Author(s):

Suttipat Srisut ◽

Kanokon Suwannasin ◽

Rungirun Sugaram ◽

Arjen M. Dondorp ◽

Mallika Imwong

Keyword(s):

Drug Resistance ◽

Copy Number ◽

Gene Copy Number ◽

Digital Pcr ◽

Droplet Digital Pcr ◽

Gene Copy ◽

Antimalarial Drug Resistance ◽

Quantification Limit ◽

Field Samples ◽

The Cost

Abstract Background: Copy number variations (CNVs) of the Plasmodium falciparum multidrug resistance 1 (pfmdr1), P. falciparum pfplasmepsin2 (pfplasmepsin2) and P. falciparum GTP cyclohydrolase 1 (pfgch1) genes are associated with antimalarial drug resistance in P. falciparum malaria. Droplet digital PCR (ddPCR) assays have been developed for accurate assessment of CNVs in several human genes. The aim of the present study was to develop and validate ddPCR assays for detection of the CNVs of P. falciparum genes associated with resistance to antimalarial drugs.Methods: A multiplex ddPCR assay was developed to detect the CNVs in the pfmdr1 and pfplasmepsin2 genes, while a duplex ddPCR assay was developed to detect CNV in the pfgch1 gene. The gene copy number (GCN) quantification limit, as well as the accuracy and precision of the ddPCR assays were determined and compared to conventional quantitative PCR (qPCR). In order to reduce the cost of testing, a multiplex ddPCR assay of two target genes, pfmdr1 and pfplasmepsin2, was validated. In addition, the CNVs of genes of field samples collected from Thailand from 2015 to 2019 (n = 84) were assessed by ddPCR and results were compared to qPCR as the reference assay.Results: There were no significant differences between the GCN results obtained from uniplex andmultiplex ddPCR assays for detection of CNVs in the pfmdr1 and pfplasmepsin2 genes (p = 0.363 and 0.330, respectively). Based on the obtained gene copy number quantification limit, the accuracy and percent relative standard deviation (%RSD) value of the multiplex ddPCR assay were 95% and 5%, respectively, for detection of the CNV of the pfmdr1 gene, and 91% and 5% for detection of the CNV of the pfplasmepsin2 gene. There was no significant difference in gene copy numbers assessed by uniplex or duplex ddPCR assays regarding CNV in the pfgch1 gene (p = 0.276). The accuracy and %RSD value of the duplex ddPCR assay were 95% and 4, respectively, regarding pfgch1 GCN. In the P. falciparum field samples, pfmdr1 and pfplasmepsin2 GCNs were amplified in 15% and 27% of samples from Ubon Ratchathani, Thailand, while pfgch1 GCN was amplified in 50% of samples from Yala, Thailand. There was 100% agreement between the GCN results obtained from the ddPCR and qPCR assays (κ = 1.00). The results suggested that multiplex ddPCR assay is the optional assay for the accurate detection of gene copy number without requiring calibration standards, while the cost and required time are reduced. Based on the results of this study, criteria for GCN detection by ddPCR analysis were generated.Conclusions: The developed ddPCR assays are simple, accurate, precise and cost-effective tools for detection of the CNVs in the pfmdr1, pfplasmepsin2 and pfgch1 genes of P. falciparum. The ddPCR assay is a useful additional tool for the surveillance of antimalarial drug resistance.

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High levels of copy number variation of ampliconic genes across major human Y haplogroups

10.1101/230342 ◽

2017 ◽

Author(s):

Danling Ye ◽

Arslan Zaidi ◽

Marta Tomaszkiewicz ◽

Corey Liebowitz ◽

Michael DeGiorgio ◽

...

Keyword(s):

Copy Number Variation ◽

Y Chromosome ◽

Copy Number ◽

Gene Copy Number ◽

Gene Families ◽

Digital Pcr ◽

Gene Copy ◽

Copy Numbers ◽

Number Variation ◽

Gene Copy Numbers

AbstractDue to its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared by males from very different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according to major Y haplogroups. Overall, only three gene families (DATZ, RBMY, TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of an individual could not be predicted based on his ampliconic gene copy numbers. Finally, we found a significant correlation between copy number variation and individual’s height (for three gene families), but not between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.

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