Biomedical Engineering Reference
In-Depth Information
the
SLC29A1
gene encoding ENT1,
ABCC1
encoding MRP1, and
SLC22A3
encoding
OCT3.
60
Amino acid diversity was also much lower in the transmembrane regions
of the transporters compared to the loops (Figure 21.1
b
). This was particularly true
for the ABC transporters, with calculated
values for nonsynonymous sites varying
more than 13-fold between loops and transmembrane domains. In the loop regions,
nonsynonymous SNPs were much more common at evolutionarily unconserved sites
than at conserved sites. A similar relationship held for the transmembrane domains of
the SLC, but not the ABC transporters. Of the five ABC transporters analyzed in this
study, average heterozygosity in the transmembrane regions was extremely low at all
sites, irrespective of sequence conservation across species.
60
A number of algorithms
were evaluated that parsed nonsynonymous SNPs into various categories based on
chemical similarities and evolutionary relatedness. Assuming that deleterious amino
acid changes would be selected against and thus found at low frequency, consideration
of conservation at the variant site across orthologous species is predicted to be the
best indicator of a detrimental effect on transporter function.
51
,
60
In fact, functional
analysis of 15 amino acid variants of OCT1 revealed that evolutionary conservation
is a strong predictor of function, although consideration of the degree of chemical
change is also informative.
51
In general, insertion and deletion (indel) mutations are relatively rare.
61
-
63
In the 24
membrane transporter genes that were studied by Leabman and colleagues, a total of
29 indels were found, including eight that affected the coding region.
60
The majority
of these coding indels resulted in the addition or deletion of a single amino acid with
no disruption of the reading frame. A common insertion of a Leu at position 140 in
CNT1 is found at a frequency of
30% in Caucasians and African Americans, and
a frameshift deletion at codon 385 in this same transporter occurs at a frequency of
3% in African Americans.
24
Haplotypes define the combination of genotypes across a given gene or a multi-
genic region and are expected to more accurately predict functional consequences
of genetic variation than is consideration of single SNPs. The near completion of
the HapMap project to define haplotype blocks across all human genes provides
a wealth of information regarding genetic variation in persons of African, Euro-
pean, and Asian descent, and this information is being used increasingly in the de-
sign of genetic association studies.
64
Haplotype structure has been determined for
several membrane transporter genes based on the variants identified during popu-
lation screening.
9
,
10
,
24
,
41
,
43
,
45
,
46
,
48
In some cases, a relatively low number of haplo-
types describes the genetic variation in a given population; for example, a single
haplotype (
SLC29A1
*1) accounted for more than 90% of the 494 chromosomes
screened in one study.
43
In contrast, almost 60 coding region haplotypes were es-
timated for
SLC28A1.
24
Numerous haplotypes have been estimated for
ABCB1
, al-
though relatively few contain nonsynonymous variants that would result in altered
protein sequence.
9
,
10
Of these,
ABCB1
*13 is the most common haplotype in Cau-
casians and Asian Americans and contains three intronic variants: two synonymous
changes (1236C
∼
T/A,
Ala893Ser).
10
The
SLC22A4
and
SLC22A5
genes are located in tandem on chromo-
some 5q31 and have a functional haplotype that spans both genes and includes a
>
T and 3435C
>
T) and a single nonsynonymous site (2677G
>
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