Hello, this is Rameen Beroukhim.
I will be speaking about
Single Nucleotide Polymorphism Microarrays
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.
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
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