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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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%...

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

UPD detection using homozygosity profiling with a SNP genotyping microarray.

Peter Papenhausen1, Stuart Schwartz, Hiba Risheg

  • 1Laboratory Corporation of Cytogenetics Triangle Park, North Carolina, USA. papenhp@labcorp.com

American Journal of Medical Genetics. Part A
|May 20, 2011
PubMed
Summary
This summary is machine-generated.

Single nucleotide polymorphism (SNP) arrays detect uniparental disomy (UPD) by identifying long contiguous stretches of homozygosity (LCSH). This method successfully identified UPD in 29 out of 46 tested cases, correlating LCSH with UPD presence.

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Infinium Assay for Large-scale SNP Genotyping Applications
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Infinium Assay for Large-scale SNP Genotyping Applications

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Single nucleotide polymorphism (SNP) based chromosome microarrays offer high-density, whole-genome analysis of copy number and genotype.
  • Uniparental disomy (UPD) is associated with regions of isoallelism, detectable through allele homozygosity (HZ).

Purpose of the Study:

  • To determine if a long contiguous stretch of homozygosity (LCSH) above a specific threshold correlates with UPD.
  • To establish a reliable method for identifying UPD using SNP array data.

Main Methods:

  • Analysis of over 13,000 samples using Affymetrix SNP/CN 6.0 array platform.
  • Focus on the distribution of allele homozygosity (HZ) to identify LCSH.
  • Retrospective and prospective analysis of cases with confirmed UPD and control patients.

Main Results:

  • Nine confirmed UPD cases showed LCSH, with the smallest at 13.5 Mb, establishing a prospective threshold.
  • Ninety-two cases met the LCSH threshold; 29 of 46 tested cases were positive for UPD.
  • Sixteen cases showed complete HZ (isoUPD), and 19 cases had segmental UPD with an average LCSH of 46.3 Mb.

Conclusions:

  • LCSH detected by SNP arrays is a strong indicator of UPD.
  • Both the size and location of LCSH are relevant for UPD correlation.
  • Further research is needed to optimize the LCSH threshold for UPD detection.