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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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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.
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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,...
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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.
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Related Experiment Video

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Comparative Lesions Analysis Through a Targeted Sequencing Approach
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SNP Array in Hematopoietic Neoplasms: A Review.

Jinming Song1, Haipeng Shao2

  • 1Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA. Jinming.Song@moffitt.org.

Microarrays (Basel, Switzerland)
|September 8, 2016
PubMed
Summary

Single nucleotide polymorphism (SNP) arrays enhance the diagnosis of hematopoietic neoplasms by identifying genetic abnormalities missed by traditional methods. These arrays reveal copy number variants (CNVs) and uniparental disomy (UPD) with prognostic significance.

Keywords:
SNP arrayhematopoieticleukemialymphomamyelodysplastic syndrome

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Area of Science:

  • Genetics and Genomics
  • Hematology
  • Oncology

Background:

  • Cytogenetic analysis is crucial for diagnosing and predicting the course of hematopoietic neoplasms.
  • Conventional methods like karyotyping and FISH identify structural and numerical chromosomal abnormalities.
  • Limitations exist in detecting subtle genetic changes with traditional cytogenetics.

Purpose of the Study:

  • To review the application of Single Nucleotide Polymorphism (SNP) arrays in identifying clinically significant genetic abnormalities in hematopoietic neoplasms.
  • To highlight the role of SNP arrays in detecting copy number variants (CNVs) and copy-neutral loss of heterozygosity (LOH)/uniparental disomy (UPD).
  • To emphasize the prognostic significance of genetic variants identified by SNP arrays.

Main Methods:

  • Review of current literature on the application of SNP arrays in hematopoietic malignancies.
  • Focus on high-resolution identification of copy number variants (CNVs) and uniparental disomy (UPD).
  • Comparison of SNP array findings with conventional cytogenetic and FISH studies.

Main Results:

  • SNP arrays provide high-resolution detection of CNVs and UPDs, often missed by conventional methods.
  • Numerous CNVs and UPDs have been identified across various hematopoietic neoplasms.
  • CNVs detected by SNP arrays demonstrate prognostic significance in certain hematopoietic malignancies.

Conclusions:

  • SNP arrays are increasingly valuable tools for comprehensive genetic analysis in hematopoietic neoplasms.
  • Identified genetic variants, including CNVs and UPDs, have clinical implications for prognosis.
  • Further research may identify specific genes targeted for future therapeutic interventions.