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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Single nucleotide polymorphism microarray analysis of genetic alterations in cancer
1Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA. charles.mullighan@stjude.org
Methods in Molecular Biology (Clifton, N.J.)
|March 25, 2011
Summary
Single nucleotide polymorphism (SNP) microarrays identify genetic alterations in hematologic malignancies. This chapter details methods for accurate DNA copy number and loss of heterozygosity detection using SNP arrays, crucial for understanding disease pathogenesis.
Area of Science:
- Genomics
- Molecular Biology
- Oncology
Background:
- Single nucleotide polymorphism (SNP) microarrays are powerful tools for identifying structural genetic alterations like amplifications, deletions, and loss of heterozygosity (LOH).
- These alterations are key to understanding the pathogenesis of hematologic malignancies.
- Current SNP arrays offer high resolution, interrogating the genome with over a million probes.
Purpose of the Study:
- To provide comprehensive methods and guidelines for the accurate detection of DNA copy number abnormalities and LOH using SNP microarrays.
- To outline best practices for sample preparation, data processing, and analysis.
- To ensure robust validation of newly identified genetic lesions in hematologic cancers.
Main Methods:
- Utilizing high-quality DNA and matched reference samples for optimal accuracy.
- Implementing optimal normalization techniques for raw microarray data.
- Employing sophisticated computational algorithms for sensitive and robust detection of copy number alterations and LOH.
- Specific application demonstrated using Affymetrix SNP arrays in acute lymphoblastic leukemia.
Main Results:
- Established protocols for reliable identification of DNA amplifications, deletions, and LOH.
- Demonstrated the critical dependence of accurate detection on DNA quality, reference samples, data normalization, and algorithms.
- Provided practical examples for the application of SNP arrays in a specific hematologic malignancy.
Conclusions:
- SNP microarrays are essential for elucidating genetic alterations in hematologic malignancies.
- Adherence to rigorous methods in sample preparation, data analysis, and validation is paramount for accurate results.
- The guidelines presented facilitate the advancement of research and clinical applications of SNP array technology in hematologic oncology.
Related Concept Videos
02:34DNA 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...
01:05Single 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,...
02:26Comparing 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%...
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%...