Chapter 11, Problem 40P

A research paper published in the summer of 2012 presented a method to obtain the whole-genome sequence of a fetus without any invasive procedure such as amniocentesis that could on rare occasions cause miscarriage. This new technique is based on the fact that some fetal cells leak into the mother’s bloodstream and then break down, releasing their DNA. Assume that exactly 10% of the DNA fragments in the mother’s blood serum come from the fetus, while the remaining 90% of the DNA fragments in the serum come from the mother’s genome.

The investigators collected cell-free DNA from a pregnant woman’s bloodstream and subjected it to an advanced high-throughput sequencing method. The table at the end of this problem looks at seven unlinked loci; the number of reads of particular alleles (identified by Greek letters) are shown. You should assume for the sake of simplicity that all numerical differences are statistically significant (even though actual data are never this clean).

a.	Determine whether each locus is autosomal, X-linked, or Y-linked.
b.	Describe the diploid genomes of the mother and fetus by using Greek letters for the alleles, or a dash (–) if no Greek letter is appropriate.
c.	Is the fetus male or female?
d.	At an eighth locus, 1500 reads of a single type of sequence were found. Provide a possible explanation for this result, being as specific as possible.