Related Experiment Video
Updated: Mar 8, 2026
09:16
Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
20.6K
Genome-Wide Association of Copy Number Polymorphisms and Kidney Function
Man Li1,2, Jacob Carey1, Stephen Cristiano3
1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America.
Plos One
|January 31, 2017
Summary
Copy number variations (CNVs) were investigated for their association with kidney function, measured by estimated glomerular filtration rate (eGFR). This study found limited evidence that CNVs explain significant eGFR variability in European and African ancestry cohorts.
Area of Science:
- Genetics
- Nephrology
- Genomics
Background:
- Genome-wide association studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs) linked to estimated glomerular filtration rate (eGFR), a key indicator of kidney function.
- However, identified SNPs explain only a small fraction of the variability in eGFR, suggesting other genetic factors contribute to kidney function differences.
- The role of germline DNA copy number variations (CNVs) in eGFR variability remains largely unevaluated.
Purpose of the Study:
- To investigate the association between germline DNA copy number variations (CNVs) and estimated glomerular filtration rate (eGFRcrea).
- To identify copy number polymorphic regions (CNPs) associated with eGFR in European ancestry (EA) and African ancestry (AA) populations.
Main Methods:
- Utilized hidden Markov models (HMMs) to detect copy number polymorphic regions (CNPs) from SNP array data in 2,514 AA and 8,645 EA participants from the Atherosclerosis Risk in Communities (ARIC) study.
- Employed Bayesian Gaussian mixture models to estimate copy number at identified CNPs and previously reported regions (HapMap Project) separately for EA and AA cohorts.
- Applied multivariate models, adjusting for population structure covariates derived from SNPs, to assess CNP associations with eGFR.
Main Results:
- Identified 312 autosomal CNPs in the EA cohort and 464 autosomal CNPs in the AA cohort.
- One CNP on chromosome 5 (876-880kb) in the EA cohort approached genome-wide statistical significance (Bonferroni-adjusted p = 0.067) after adjusting for population structure.
- The overall contribution of identified CNPs to eGFR variability was found to be limited.
Conclusions:
- Germline DNA copy number variations (CNVs) appear to play a minor role in the variability of estimated glomerular filtration rate (eGFR).
- Further research may be needed to explore other genetic architectures or larger sample sizes to fully elucidate the contribution of CNVs to kidney function.
- The findings suggest that genetic factors beyond common SNPs and the identified CNPs are likely responsible for the majority of eGFR variability.
Related Concept Videos
02:26Comparing Copy Number Variations and SNPs
18.9K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.9K
01:11Genome-wide Association Studies-GWAS
16.2K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
16.2K
01:05Single Nucleotide Polymorphisms-SNPs
19.2K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
19.2K
01:27Principles of Pharmacogenetics: Types of Genetic Variants
67
The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
67
01:28Drug Dosing in Renal Diseases: Estimation of Glomerular Filtration Rate Based on Serum Creatinine Concentration
285
Glomerular filtration rate (GFR) can be estimated from serum creatinine using the modification of diet in renal disease (MDRD) formula or the chronic kidney disease–epidemiology collaboration (CKD–EPI) equation. Both methods are widely used in clinical practice to assess kidney function and guide treatment decisions.The MDRD equation does not require weight or height measurements and is normalized to the body surface area of 1.73 m², considered the average adult surface area.
285
01:28Imaging Studies I: Kidney, Ureter, and Bladder Studies
538
Kidney, Ureter, and Bladder (KUB) StudiesKidney, Ureter, and Bladder (KUB) studies are standard diagnostic imaging procedures used to assess the anatomy of the urinary system. They are commonly utilized for patients experiencing abdominal pain or urinary symptoms. By using a simple X-ray of the abdomen, KUB studies can reveal structural and pathological abnormalities within the kidneys, ureters, and bladder. These studies are particularly valuable in diagnosing kidney stones, urinary...
538