Page 484 - Clinical Immunology_ Principles and Practice ( PDFDrive )

CHaPTEr 33 Human Genomics in Immunology 465

individuals in the general population, whereas variants encom- of DNA in the offspring of inversion carriers because of aberrant
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passing more than a million bases (1 Mb) are found in 1–2%. recombination during meiosis, leading to serious syndromes
Smaller CNVs, in particular, may have only two alleles (i.e., the brought about by chromosomal imbalance. Furthermore, if
presence or absence of a segment), similar to indels. Larger CNVs inversions interfere with normal gene expression by disrupting
tend to have multiple alleles because of the presence of different a gene or altering the physical relationship between a gene and
numbers of copies of a segment of DNA in tandem. The content its regulatory elements, it may be detrimental to health. 9,10
of any two human genomes can differ by as much as 50–100 Mb
as a result of copy number differences at CNV loci, compared CLINICAL IMPACT OF HUMAN VARIATION
with some 3–4 Mb of differences because of SNVs and indels.
Thus simply on the basis of the number of nucleotides involved One of the greatest challenges facing human geneticists is linking
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in the variation, CNVs represent vastly more human variation variation to phenotype. The significance for the health of the
than do SNVs or indels. vast majority of variants of any type is unknown, and yet this
Not only are CNVs a very significant contributor to human knowledge is essential if we are to apply genomics to clinical
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variation and disease, the areas of the genome where they are care. The impact of variants ranges from completely benign to
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found are often the sites of segmental duplications, some of the highly pathogenic, the latter causing devastating disorders of
most difficult regions in which to develop an accurate reference the immune system that may occur as new mutation dominants
sequence. Segmental duplications are ubiquitous throughout the or as autosomal recessively inherited syndromes. Even common
genome. It is difficult to construct an accurate contiguous genome polymorphic variants may affect health or longevity, although
sequence in regions of segmental duplications because the most their being common means that they are likely to produce a
widely used massively parallel sequencing technologies generate relatively subtle alteration of disease susceptibility rather than
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only short reads of a few hundred base pairs and therefore may not directly cause a serious illness. Working out the functional
be able to differentiate between the sequences of nearly identical impact of human variation will occupy genomics researchers
DNA segments using unique DNA that flanks them. The assembly for many years to come. An essential component of this work
algorithms, which always try to create the simplest assembly is to make databases of genetic variants and their impact on
possible, may consider two nearly identical segments of DNA that human health available to the research and clinical communities,
have been duplicated in the genome, but differ at a few locations as is being done with the ClinVar database hosted by the National
in their sequence, to be the same sequence and collapse them Library of Medicine in the United States and the Leiden Open-
into a single segment of DNA. The fixed sequence differences source Variation Database (LOVD). 13-15
between the duplicated segments are incorrectly interpreted as
polymorphic differences between two alleles of a nonduplicated COMPARATIVE GENOMICS
locus instead of being real sequence differences between different
copies of duplicated DNA. The fact that there is a segmental Evolution at work is nowhere better illustrated than in the field
duplication is therefore overlooked. Conversely, the sequence of comparative genomics, which deals with similarities in the
of a unique DNA segment with many SNVs compared with the sequence, structure, and chromosomal location of genes between
reference may be incorrectly interpreted as having come from different species whose evolutionary paths diverged from a few
distinct but highly similar duplicated segments, leading to the years ago to many hundreds of millions of years ago. Direct
supposition that there are paralogues or duplicated segments. As sequence comparison has revealed that an enormous number of
a result, segmental duplications are liable to both false-negative human proteins have orthologues (genes derived from a common
and false-positive representations in the human genome assembly. ancestor) in other organisms, ranging from 87% in chimps to
CNVs are particularly difficult to detect and interpret if the 79% in mice, 63% in zebrafish, 39% in the fruit fly (Drosophila
number of segments in the reference is incorrect or ambiguous. melanogaster), and 31% in the nematode (Caenorhabditis elegans)
Many CNVs include genes, from one up to several dozens; (Fig. 33.1). The study of the human genome and the genomic
thus CNVs are frequently implicated in diseases that result from basis for human disease has benefited from studies done in other
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altered gene dosage. One well-known human immunological organisms, particularly mice, in which many decades of inbreeding
multisystem disorder, DiGeorge syndrome, is caused by a deletion and gene manipulation have permitted study of the genes and
CNV that occurs de novo in about 1 in 5000 individuals. When underlying mechanisms by which mutations responsible for
a CNV is more frequent, it represents a background of common immune defects lead to phenotypes. Mouse models of immunity
polymorphism that must be understood if to properly interpret have been highly relevant and informative for humans.
alterations in copy number observed in patients. As with all DNA However, orthologous genes may serve different functions in
variations, the significance of different CNV alleles in health and different species; therefore one cannot assume that a disease-
in disease susceptibility is the subject of intensive investigation. causing mutation in humans will cause a similar defect when
The most common SVs in the human genome sequence are its orthologue is similarly mutated in mice, and vice versa. For
inversions, which differ in size from a few base pairs to large example, the V(D)J recombination activating genes RAG1 and
regions of the genome (up to several Mb) that can be present RAG2 in humans and Rag1 and Rag2 in mice appear to have
in either of two orientations in the genomes of different individu- identical functions, with knockout mice showing the same inability
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als. As with CNVs, inversions are usually flanked by regions of to recombine T- and B-lymphocyte antigen receptor genes as
sequence homology, which indicates that recombination of these humans with RAG1 or RAG2 deficient severe combined immu-
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homologous regions is likely involved in the origin of the inver- nodeficiency (SCID; Ch. 35). As a result, the lymphocyte profile
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sions. Most inversions do not involve gain or loss of DNA; in in both species is absent T and B cells with normal natural killer
− −
+
this case, the two alleles corresponding to the two orientations (NK) cells, referred to as T B NK SCID. A contrasting situation
can achieve substantial frequencies in the general population. occurs in other SCID genotypes. For example, humans lacking
Such inversions can, however, cause significant gains or losses the common γ chain (γc) of receptors for interleukin-2 (IL-2)