ND STONY BROOK UNIVERSITY LOOSELEAF GENETICS: FROM GENES TO GENOMES
6th Edition
ISBN: 9781260406092
Author: HARTWELL, Leland, HOOD, Leroy, Goldberg, Michael
Publisher: Mcgraw-hill Education/stony Brook University
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Textbook Question
Chapter 22, Problem 20P
In GWAS analysis, because of the existence of LD blocks (or haplotype blocks), it is not necessary to genotype a person for every one of the 50 million known SNPs. Haplotype blocks are stretches of DNA containing particular SNP variants that tend to be inherited together (as a block) because recombination within the region is rare. In the accompanying figure, three different SNP loci are shown at top (SNP10, SNP11, and SNP12), each with two alleles among the world’s population of humans.
Only four of all the possible combinations of these SNP alleles are found in human genomes, as shown in the four chromosome types pictured. These three SNPs are part of a larger block of 20 SNPs that are usually inherited in one of the four configurations, or haplotypes, shown. Because these 20 SNPs are inherited as haplotype blocks, genotyping any individual for the three so-called Tag SNPs (SNP4, SNP8, and SNP15 shown in bold) should be sufficient to predict that individual’s alleles for the other 17 SNPs.
| a. | How many configurations of the three SNPs shown at the top of the diagram (SNPs 10, 11, and 12) are theoretically possible? |
| b. | How many haplotype variants are theoretically possible considering all 20 SNPs in the haplotype block, and assuming that each of them has two possible alleles? |
| c. | Given that humans are diploid, every individual has two copies of every (autosomal) haplotype block, one on each homolog. Does heterozygosity for the haplotype blocks interfere with genotyping individuals using the Tag SNPs shown in the diagram? Explain? |
| d. | In part (c), you saw that the three Tag SNPs shown in the diagram are sufficient to type any individual for this particular haplotype block. Is this the only set of three Tag SNPs that could be used? |
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A small-scale pedigree study involving 15 families with a total of 50 children was performed to determine whether a SNP
in a candidate gene is linked to a disease. The result showed that among 22 children who developed the disease, 19
belonged to non-recombinants while 3 recombinants. For the remaining 28 children, 21 were non-recombinants and 7
belonged to recombinants. A Lod (Z) score can be calculated and used to determine whether this SNP is linked to the
disease. By using a very stringent threshold, which of the following conclusions is correct?
O A.Z is approximately 4.03, indicating a linkage
O B. Z=0.25, indicating no linkage
OCZ=0.2, indicating no linkage
O D.Z is approximately 4.19, indicating a linkage
A SNP that can exist as a C or G is associated with a human disease. The genotypic odds ratio of the homozygote CC relative to the homozygote GG is 2.2, which indicates that
a)both CC and GG individuals are equally likely to get the disease because 2.2 is not a significant value.
b)heterozygotes are 2.2 times as likely to get the disease as GG homozygotes.
c) CC homozygotes are 2.2 times as likely to get the disease as GG homozygotes.
d) CC homozygotes are 2.2 times less likely to get the disease as GG homozygotes.
24. 23andme is a direct to consumer genotyping company that uses a microarray to genotype people
on 1 million known SNPS in the genome. A man who was adopted wants to know about his ancestry,
and purchases a 23andme kit for himself. He finds that of each autosome pair, exactly one is
classified as 100% Sub-Saharan African, while the other is a mixture of various East Asian and
European components. He also finds that his X chromosome is 100% Sub-Saharan African. What can
this man confidently infer about his recent ancestry?
a. His mother was of Sub-Saharan African descent
b. His father was of Sub-Saharan African descent
c. He has no Neanderthal ancestry
d. He has no mutations relative to his parents
e. 23andme mixed up two samples and he can't infer anything
Chapter 22 Solutions
ND STONY BROOK UNIVERSITY LOOSELEAF GENETICS: FROM GENES TO GENOMES
Ch. 22 - Choose the best matching phrase in the right...Ch. 22 - Suppose you grew genetically identical dandelion...Ch. 22 - How can each of the following be used in...Ch. 22 - Two different groups of scientists studying a rare...Ch. 22 - Which of the following statements would be true of...Ch. 22 - Studies have indicated that for pairs of twins...Ch. 22 - Prob. 7PCh. 22 - Prob. 8PCh. 22 - Table 22.2 lists concordance values for MZ and DZ...Ch. 22 - Prob. 10P
Ch. 22 - Prob. 11PCh. 22 - Two alleles at one locus produce three distinct...Ch. 22 - In a certain plant, leaf size is determined by...Ch. 22 - Compare and contrast the use of SNP genotyping: i...Ch. 22 - Explain the similarities and differences between...Ch. 22 - In Fig. 22.14c, the fw2.2 causal gene was...Ch. 22 - Among the most prevalent pathologies that afflict...Ch. 22 - Human geneticists have found the Finnish...Ch. 22 - Canavan disease, caused by homozygosity for a...Ch. 22 - In GWAS analysis, because of the existence of LD...Ch. 22 - In Fig. 22.15: a. Why do some chromosomes in the...Ch. 22 - Consider the triangle diagram shown in Fig. 22.17....Ch. 22 - Prob. 23PCh. 22 - You conduct a Case/Control study comparing the...Ch. 22 - Prob. 25PCh. 22 - ALS amyotrophic lateral sclerosis is a rare, fatal...Ch. 22 - Through GWAS explorations, scientists have...Ch. 22 - In domesticated dogs, size has a high...Ch. 22 - Suppose a GWAS investigation found a particular LD...Ch. 22 - In 2008, Time magazine named as its invention of...
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