The ability to analyze data obtained from the entire human
genome (genomics) is having a significant impact on hematology and
on medicine in general. This chapter provides a basic description
of microarray technology and how this technology can be used to study
disease-associated genetic variation, copy number variation, gene
expression, and patterns of epigenetic modification. In addition,
the principles of epigenetics, in which the expression of genes
is altered by chemical modifications such as methylation, are reviewed.
Several disease examples are given in which epigenetic modifications
have significant clinical effects.
Acronyms and Abbreviations
Acronyms and abbreviations
that occur in this chapter include: DMR, differentially methylated
region; IGF2, insulin-like growth factor 2; mRNA, messenger ribonucleic
acid; SNP, single nucleotide polymorphism.
Increasingly, genetic variation is being assessed at the level
of the entire genome. Studies of genome-wide variation are part
of the now well-known science of genomics.1 During
the past decade, several important tools have emerged that allow
investigators to collect and analyze genomic data.
The most widely used of these tools is the microarray (Fig. 10–1).2,3 To
make a DNA microarray, single-stranded DNA sequences consisting
of about 20 bases (oligonucleotides, from “a few” nucleotides)
are robotically placed on a small glass slide. A single slide (1
cm2) can contain millions of different oligonucleotides. These
oligonucleotides correspond to different alleles (DNA sequences
at a specific chromosome location) in populations. Typically these
alleles are single-nucleotide polymorphisms (SNPs).
Some of the oligonucleotides may contain known disease-causing mutations.
Fluorescently labeled single-stranded DNA from a subject is hybridized
with the oligonucleotides on the slide to determine, for a specific
region in the genome, which DNA sequence undergoes complementary
base pairing with that of the subject. The pattern of hybridization signals
is analyzed by a computer, providing a detailed profile of genetic
variation specific to an individual’s DNA. With current
technology, enough probes can be placed on a single microarray to
analyze variation in one million SNPs in an individual.
Schematic of a microarray, in which oligonucleotides are
placed or synthesized on a glass slide and then hybridized with
labeled single-stranded DNA from a subject. Complementary base pairing
will occur between the subject DNA fragment and the oligonucleotide
on the slide only if the sequences are complementary to one another.
A fluorescent label on the subject’s DNA marks the location
on the microarray at which the subject’s DNA undergoes
hybridization, thus indicating the DNA sequence of the subject at
a specific location in the genome.
(From Jorde LB, Carey JC, Bamshad MJ: Medical Genetics,
4th ed. Mosby/Elsevier, Philadelphia, 2010. With permission.)
SNP microarrays are now used routinely to perform genome-wide
association studies, in which the frequencies of each SNP
are compared in disease cases and unaffected controls.4 SNPs
that show ...