Page 96 - Genetics_From_Genes_to_Genomes_6th_FULL_Part3

390 Chapter 11 Analyzing Genomic Variation

TABLE 11.2 Finding the Disease-Causing Mutation in Nic Volker’s Genome
Analysis Step Candidate Variants Remaining
Sequence of Nic’s exome 16,124
Filter for missense mutations changing an amino acid 7,157
Filter for novel variants not previously reported in databases 878
Filter for variants that are X-linked or display a recessive pattern in Nic’s exome 136
Filter for variants that change evolutionarily conserved amino acids 35
Filter for variants in genes that are not frequently mutated in the general population 5
Filter for variants in genes known to be mutated in other genetic diseases of some relevance 1 (XIAP)

candidates for disease-causative mutations. In contrast, it is in databases previously, in this way ignoring common
possible that different patients suffering from similar, or at variants known to exist in the genomes of normal indi-
least vaguely related symptoms, may share either the same viduals. The following step was to filter the list for muta-
rare mutation or they may have different rare mutations in tions consistent with X-linked or recessive inheritance, as
the same gene. these were the most likely scenarios for a disease that af-
Even genomes of other organisms can point genetic fected Nic but not his parents or other relatives.
sleuths in the proper direction. For example, consider a At this point, the list of good candidates for the cause
gene that has been closely conserved during evolution so of Nic’s condition had been narrowed to 136 variants
that some of the amino acids in the protein product are (Table 11.2). The researchers now took an evolutionary
identical in diverse organisms, such as humans and fruit approach and asked whether any of these changes might
flies. Conservation suggests that these particular amino ac- have altered the identity of an amino acid that was tightly
ids play crucial roles in the protein’s function. If you now conserved in many diverse species. The next-to-last step of
find a rare variant in a patient that changed such a highly the analysis was to examine the remaining candidates for
conserved amino acid to a different one, this mutation those that were in genes known from databases to be never
would be a strong candidate because of the likelihood it or only infrequently inactivated (for example, by nonsense
would affect phenotype. or frameshift mutations) in the general population. The idea
behind this step was to ignore genes that are defective in
many normal individuals and are thus unlikely to influence
Pinpointing a Disease Gene Requires a disease phenotypes.
Combination of Approaches Five candidate variants remained in the investigators’
target list. The researchers realized that one of these candi-
The beginning of this chapter introduced the case of Nic date mutations was in a gene called XIAP. Other mutations
Volker, one of the first patients to be treated successfully in XIAP were known to cause a serious condition called
for a genetic disease based on identification of the caus- X-linked lymphoproliferative disease (XLPD), in which the
ative gene through sequencing of his personal exome. blood contains too many lymphocytes (white blood cells of
When Nic’s DNA was characterized in 2009, sequencing the immune system), crowding out the oxygen-carrying red
was still relatively expensive, so investigators sequenced blood cells and damaging the liver. These symptoms were
only Nic’s exome, rather than his whole genome or the very different from Nic’s, but XLPD had some vague rele-
exomes/genomes of his parents or siblings. Table 11.2 ex- vance to Nic’s case because the immune system is clearly
amines how geneticists analyzed Nic’s exome, using many involved in gastrointestinal inflammation.
sources of information to narrow down the candidate vari- The researchers became particularly excited when
ants to the single responsible mutation. they noticed that the variation in Nic’s XIAP gene was a
Nic’s exome contained about 16,000 variants relative missense mutation changing in the protein product the
to the human standard RefSeq (Table 11.2). These variants identity of a single amino acid that is completely con-
were mostly SNPs, but some DIPs and SSRs were also served among humans, frogs, flies, and many other spe-
found. Researchers started to winnow this list by exclud- cies (Fig. 11.27). XLPD-causing mutations in the same
ing likely anonymous variants in the exons (that is, silent gene are instead nonsense and frameshift mutations that
mutations in codons, or mutations in the sequences encod- would prevent synthesis of full-length protein, potentially
ing the 5′ and 3′ UTRs of mRNAs). They next focused explaining the difference in Nic’s symptoms and in those
their attention on novel variants that had not been recorded of XLPD patients.