Page 99 - Genetics_From_Genes_to_Genomes_6th_FULL_Part3

Solved Problems 393

d. You actually knew the location of this locus even be- a. Which SNP loci could be X-linked?
fore starting the experiment. This is because you de- b. Which SNP loci could be on the Y chromosome?
sign the PCR primers from knowledge of the entire c. Which SNP loci must be autosomal?
human genome sequence.
e. The polymorphism involves a difference in the num- d. For any autosomal SNP loci, what is the sperm donor’s
genotype in somatic tissue?
ber of repeat units, and therefore the two alleles
would produce PCR products that differ in length. e. Do any SNP loci appear to be linked to each other?
You could genotype this locus by gel electrophoresis f. What is the distance between any two linked
of the PCR products, as shown in Fig. 11.12. SNP loci?
f. Direct Sanger sequencing of a PCR product from
genomic DNA produces a trace that includes both Answer
alleles. This is not true of single-molecule DNA se-
quencing techniques. You would require enough se- SNP analysis by PCR is so sensitive that the single al-
quence runs from individual genomic DNA molecules leles present within individual sperm cells can be
to ensure that you could see both alleles if the person assayed, providing researchers with considerable infor-
was a heterozygote. mation. You should also remember that a man’s somatic
cells have two copies of each autosome, one X chromo-
some, and one Y chromosome. Individual sperm will
II. It is difficult to obtain accurate recombination fre- have one copy of each autosome and either an X or a
quencies in humans because family sizes are small. Y chromosome.
An interesting way to circumvent this problem is to a. For any X-linked SNP locus, half of the sperm cells
genotype individual sperm cells so as to obtain large will carry the same SNP allele, but the other half of
data sets for linkage studies. The table that follows the sperm would not have an X chromosome and
shows the genotype of four SNP loci from 20 single would thus not yield a PCR product. Locus 3 shows
sperm that one man provided for this research. The this type of pattern.
genotypes were determined by microarray analysis of
four SNP loci amplified from these samples by PCR. b. Similarly, a locus on the Y chromosome would be
In the table, A, C, G, and T are the alleles of the SNPs found in only half the sperm, and all these sperm
(that is, the nucleotides on one strand) and a dash (–) would have the same allele. Again, Locus 3 is a can-
means that no DNA corresponding to the locus was didate for a Y-linked SNP. The data do not allow you
amplified from the sample. to discriminate between an X or a Y chromosome lo-
cation for Locus 3.
c. For an autosomal SNP locus, all the sperm will
have one copy of the locus. Loci 1, 2, and 4 are thus
autosomal.
SNP: Locus 1 Locus 2 Locus 3 Locus 4
Sperm number d. If a man is homozygous for a single allele of an auto-
1 G C — T somal SNP locus, all the sperm he produces will have
2 G A G C this one allele. If he is a heterozgote for two different
3 G C G C alleles, approximately one-half of the sperm will have
4 G C G T one allele and the other half of the samples will carry
5 G A — C the other allele for the locus. The man’s genotypes for
6 G C — T the autosomal genes are SNP Locus 1: GG (homozy-
7 G A G C gous); SNP Locus 2: CA (heterozygous); and SNP
8 G A — C Locus 4: CT (heterozygous).
9 G A G T e. Alleles at linked loci will segregate together (end
10 G C — T up in the same sperm) more than 50% of the time.
11 G C — T This is true of the C allele of SNP Locus 2 and the
12 G C G T T allele of Locus 4. The reciprocal alleles (A for
13 G A — C Locus 2 and C for Locus 4) are also transmitted
14 G A — C together more often than not. SNP Loci 2 and 4
15 G C G T are linked.
16 G A G C f. Sperm 3, 9, and 18 show evidence of recombination
17 G C — T between alleles at Loci 2 and 4. Three out of 20, or
18 G A — T 15%, of the sperm are recombinant. The distance be-
19 G A G C tween Loci 2 and 4 is therefore 15 cM.
20 G C G T