Page 109 - Genetics_From_Genes_to_Genomes_6th_FULL_Part3

Problems 403

CFTR protein fold properly so that it can insert in those of a brother and sister both affected by the dis-
the cell membrane. Why do you think that neither ease, and of both their parents.
lumacaftor nor ivacaftor alone are effective in a. Researchers made the assumption that Miller syn-
treating ΔF508 homozygotes, while the combina- drome is a recessive trait. Could Miller syndrome
tion of both drugs is effective? instead be due to a dominant mutation? If so, what
scenarios would make this possible?
Section 11.5 b. Why is it highly unlikely that Miller syndrome in
36. In the high-throughput DNA sequencing protocol this family is due to de novo mutations that oc-
shown in Fig. 11.24: curred in the germ line of the mother, or of the fa-
a. What is the purpose of adding poly-A to fragments ther, or of both parents? Describe a scenario based
of single-stranded genomic DNA, and why is the on your understanding of cell divisions in human
poly-A added to the 3′ end of these fragments? ovaries or testes (see Figs. 4.18 and 4.19) that
b. Why at the end of every synthesis cycle do you make the de novo mutation hypothesis at least the-
oretically possible even if very unlikely.
need to remove the fluorescent tag on the incorpo-
rated nucleotide? c. On Fig. 11.26b, indicate the location on chromo-
c. Why do the incorporated nucleotides have a block- some 16 closest to the DHOD gene at which re-
combination took place during meiosis in one of
ing group, and why does this blocking group need the parents of the Miller syndrome patients. In
to be removed each cycle? which parent did this recombination occur?
37. A researcher sequences the whole exome of a patient d. Do the number of crossovers you see in Fig. 11.26b
suffering from Usher syndrome, a rare autosomal re- fit previous estimates that in the human genome,
cessive condition that is nonetheless the leading cause 1 centiMorgan corresponds to about 1 Mb?
for simultaneous deafness and blindness. The exome Chromosome 16 is about 90 Mb long; chromo-
sequence does not show homozygosity for any poly- some 17 is about 81 Mb long.
morphisms different from the human RefSeq.
a. How could the researcher examine the data already e. How could researchers use all the sequence data
from this family to estimate the per-nucleotide rate
gathered to try to find the disease gene, assuming of mutation in humans?
the sequence is accurate?
b. If the attempt described in part (a) was unsuccess- 40. A research paper published in the summer of 2012
presented a method to obtain the whole-genome se-
ful, the researcher might contemplate sequencing quence of a fetus without any invasive procedure such
the patient’s whole genome. What are the potential as amniocentesis that could on rare occasions cause
pitfalls of this strategy? miscarriage. This new technique is based on the fact
38. As explained in the text, the cause of many genetic that some fetal cells leak into the mother’s blood-
diseases cannot yet be discerned by analyzing whole- stream and then break down, releasing their DNA.
exome/genome sequences. But in some of these Assume that exactly 10% of the DNA fragments in
seemingly intractable cases, important clues can be the mother’s blood serum come from the fetus, while
obtained by looking at mRNAs or proteins, rather the remaining 90% of the DNA fragments in the se-
than at the DNA. rum come from the mother’s genome.
a. As you will see in more detail in later chapters, it is The investigators collected cell-free DNA from a
possible to use single-molecule methods to se- pregnant woman’s bloodstream and subjected it to an
quence cDNA copies of millions of mRNA mole- advanced high-throughput sequencing method. The
cules from any particular tissue cheaply. How table at the end of this problem looks at seven un-
could you sometimes use such information to find linked loci; the number of reads of particular alleles
a disease gene? When would this information be (identified by Greek letters) are shown. You should
noninformative? assume for the sake of simplicity that all numerical
b. A technique called Western blotting allows you to differences are statistically significant (even though
examine any protein for which you have an anti- actual data are never this clean).
body; it is possible to see differences in size or a. Determine whether each locus is autosomal,
amount of that protein. How could you sometimes X-linked, or Y-linked.
use such information to find a disease gene? When b. Describe the diploid genomes of the mother and
would this information be noninformative? fetus by using Greek letters for the alleles, or a
39. Figure 11.26 portrayed the analysis of Miller syndrome dash (–) if no Greek letter is appropriate.
through the sequencing of four complete genomes: c. Is the fetus male or female?