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CHaPTEr 33 Human Genomics in Immunology 467

(i) segments of DNA located in chromatin loops that allow
chromatin–chromatin interaction; (ii) regions of open chromatin,
which are accessible to transcription; (iii) motifs that bind
transcription factors; (iv) regions that are associated with histones A A a
that have been modified to either promote or suppress transcrip- b Y b B
tion; and (v) regions with differential methylation of cytosine
residues in different tissues, with methylation being associated
with inactivity. *
Now, approximately 15 years into the project, ENCODE has * *
created a large database of more than 4 million functional regions
of the genome. Mostly on the basis of biochemical evidence, it
has been estimated that 80% of the genome may be of functional a A A A a A A A a a A A
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significance, but this estimate is probably too high and has b Y b b b B B Y b Y b b B Y b b
been strongly criticized. For example, evidence of transcription FIG 33.3 An Example of Family-Based Linkage Analysis as
of a segment does not necessarily mean that the transcript plays a Means to Identify a Disease Gene. The pedigree of a family
any functional role, nor is it likely to be true that the millions with X-linked severe combined immunodeficiency (SCID) caused
of vestigial repetitive DNA sequences that are undergoing muta- by an IL2RG mutation in the proximal long arm of the X chromo-
tion without any apparent selection could have important some (marked with black bar) is shown. Affected males have
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functional roles. A more stringent threshold for ascribing a filled in square; female carriers are designated by dot in the
functional role to DNA segments (i.e., direct effect on gene center of their symbols. Two loci, one with alleles A and a, and
expression and phenotype of at least one human cell type) reduces the other with alleles B and b, are shown in the proximal and
that fraction to the range of 10–20%. Much more research will distal long arm of the X (Xq). There are no recombinations during
be needed before the ENCODE project delivers its final assessment female meiosis between allele a and the IL2RG mutation in any
of the fraction of the human genome that plays a role in gene of the eight children, while three children (marked with asterisk)
regulation—that is, in how different cells use their genomes. 22
show a recombination with the locus on the distal Xq. The
father’s X chromosome is passed on without any recombinations
APPLYING HUMAN GENOMICS TO to each of his daughters and is shown on the left of each pair
of X chromosomes in the daughters.
UNDERSTANDING DISORDERS OF
THE HUMAN IMMUNE SYSTEM

Genome research has provided geneticists with a catalogue responsible for association to have been carried along, on the
of all known human genes, knowledge of their location and same chromosome in a haplotype block, through many genera-
structure, and an ever-growing list of variants in DNA sequences tions (Fig. 33.4). Association analysis does not require pedigrees
found among individuals in different populations. In the past, and is particularly useful for complex diseases that do not show
geneticists followed two approaches to identifying the genetic strict mendelian inheritance.
basis for human disorders. The first approach, linkage analysis, Linkage analysis and association studies have limitations in
is family based (Fig. 33.3). Linkage analysis takes advantage of investigating the genetic basis for human immunological disorders.
family pedigrees to follow the inheritance of a disease among Linkage analysis is problematic if the disorder is a rare autosomal
family members and test a few hundred DNA variants distributed recessive condition such that there are not enough families with
throughout the genome for consistent, repeated coinheritance, two carrier parents to enable such a study; nonetheless, the
or segregation, with the disease. A demonstration of significant increased frequency of consanguineous matings in some popula-
coinheritance with a variant or variants located in a particular tions has been utilized to overcome this limitation. 23,24 Another
region of the genome indicates that the disease-causing mutation challenge with linkage analysis is if the disorder is genetically
is also located in a gene within or near this region. The variants lethal so that it is never inherited and always occurs sporadically
showing coinheritance with the disease are usually not the variants as a result of a new mutation. Detecting an association in a
responsible for the disorder. Marker variants need, however, to case-control study is also a problem when the frequency of any
be located close enough that recombination between the marker particular allele associated with the disease is too low among
and the gene mutation responsible for the disease is sufficiently the cases to give a detectable association. For example, if the
rare that cosegregation is observed over a few generations. disorder arises from different, independent mutations and if
The second approach, genome-wide association analysis these mutations are found on many different haplotypes in
(GWAS), is population based. A sample of affected individuals, affected individuals, it may be very difficult to establish a sig-
or “cases,” taken from the population, is chosen along with a nificant association with any one variant.
matched set of unaffected “control” individuals from the same When linkage and association studies are not possible, as in
population. Then, a large number, in the order of a million or very rare mendelian disorders, a third approach is now available—
more, variants are examined individually for an increased or genome sequencing. Vastly improved methods of DNA sequencing
decreased frequency of cases compared with controls. The alleles have cut the cost of sequencing six orders of magnitude over
used to test for association need not be the actual variants what was spent generating the Human Genome Project’s reference
functionally responsible for the disease association—in fact, it is sequence, opening up new possibilities to discover the genes and
highly unlikely this would be the case. Instead, GWAS, like linkage, mutations responsible for rare mendelian disorders. One can
depends on the vast number of marker alleles that can be tested generate a whole-genome sequence (WGS) or, in what has often
for association to be located close enough to the alleles functionally proven a cost-effective compromise, a sequence of only about