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Single nucleotide polymorphism microarrays in the analysis of cancer

Published on March 30, 2009 Updated on August 14, 2020   35 min

A selection of talks on Oncology

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Hello, this is Rameen Beroukhim. I will be speaking about Single Nucleotide Polymorphism Microarrays
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in the analysis of cancer. I will start by describing these arrays and how they are capable of simultaneously interrogating thousands to millions of single nucleotide polymorphisms throughout the genome. I will then move on to describe how they're used in cancer, including in the mapping of somatic genetic events such as loss of heterozygosity, and changes in copy-number, and also how they're used to identify germline inherited alleles that lead to increased susceptibility to cancer.
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As their name implies, single nucleotide polymorphism arrays interrogate single nucleotide polymorphisms or SNPs. SNPs are single bases within the genome that differ between individuals or between chromosomes within an individual. In the examples shown, a SNP resides in the central position. Here, the majority of individuals carry a G representing the A allele. A minority of individuals carry a C representing the B allele. Typically, there are only two alleles at a SNP locus. To be called a SNP the minor or less prevelant allele must be present in at least 1% of the population, here the population may refer to a single geographic or ethnic group. It is estimated that approximately 10 million SNPs exist in the human genome
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representing 1 SNP for every four hundred to one thousand base pairs. As of the fall of 2008 the central SNP database dbSNP contained aproximately 6 million SNPs aproximately half of these have minor allele frequencies of greater than 10%. SNPs are thought to account for much if not most of the inherited differences between individuals, these inherited differences include predisposition to certain diseases. Therefore SNPs are increasingly being studied as inherited risk factors for a variety of diseases. Any one or more of these 10 million SNPs may predispose an individual to
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Single nucleotide polymorphism microarrays in the analysis of cancer

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