Coursera

Warning: The hard deadline has passed. You can attempt it, but you will not get credit for it. You are welcome to try it as a learning exercise.

The following questions are intended to assess your general knowledge before the course and are NOT being graded (all answers will be marked as correct). This survey assessment can help you preview some of the discussions and learning material we may cover, and can help the course team better understand the general knowledge base of its participants. Correct answers will be discussed at the end of the course if questions remain.

In accordance with the Coursera Honor Code, I (Anonymous Student) certify that the answers here are my own work.

Question 1

Genome-Wide Association Studies (GWAS) are designed to identify genetic variants associated with disease traits (such as having Type 2 Diabetes), physical traits (such as height), or biochemical traits (such as response to medications). Many such variants have been discovered. Which of the following statements about GWAS and these variants are true? Please check all items that are true:

A person can have one of more of these variants significantly associated with a disease and not develop that disease

Individuals with the same genetic variant will have similar risk for developing a disease like Type 2 Diabetes

Case-control GWAS can’t provide direct estimates of the relative risk conferred by genetic variants

The risk models used by genetic testing services, which typically include up to 50 variants, can capture almost all of the variation associated with a disease

Because a person can’t change their genetic variants they can’t change their risk for developing diseases like Type 2 Diabetes

Because of natural selection, very common genetic variants, such as those found in 10% or more of people, can only have very small effects on your health and so are not relevant to clinical care

Question 2

Your 50-year old patient brings you a case-control genome-wide association study (GWAS) showing that their genotype is associated with a complex disease with an odds-ratio (OR) of 2.5. The disease has a prevalence of 25% and can arise from age 10 onwards. Although they do not have disease now, they are concerned that they have a 62.5% chance of developing the disease in the future. Which of the following is an accurate way to communicate your patient’s risk to them given the available information? Please check all items that are true:

You are correct; you have a 62.5% chance of developing the disease in the future.

You are underestimating your risk. Relative risk is usually larger than the odds-ratio.

You are correct; you are at 2.5-fold higher risk for the disease than the general population.

You are overestimating both your relative risk and “pre-test” risk; we would estimate your absolute risk to develop the disease to be below 62.5% and may be below 25%.

You are overestimating your relative risk; your absolute risk to develop the disease will be above 25% but below 62.5%.

Question 3

Which of the following statements are true about the human reference genome, a digital sequence of approximately 3 billion nucleotides that represents the human genome? Please check all items that are true:

Ten years after the completion of the human genome project in 2003, the human reference genome is still incomplete

The human reference genome has multiple distinct copies of certain genomic regions

The human reference genome is scientists’ best representation of an ideal healthy human

There is a European bias to the human reference genome

For consistency, the human reference genome has not been changed since 2003

Question 4

Which of the following statements are true about whole exome sequencing (WES) as performed with a 2nd generation short-read technology, such as the Illumina HiSeq? Please check all items that are true:

WES is a test that can be ordered by a physician to identify a molecular cause for a suspected genetic disease

A typical WES run with 50-fold mean coverage may not produce enough data to detect mutations in highly polymorphic regions, e.g. the HLA, but that can be resolved with rerunning the test to acquire more data

WES can replace all of the disease-focused genetic testing panels a physician might have ordered

The lab performing WES is obligated to report all potentially disease-causing mutations found in the sample

WES can detect certain classes of mutations in most but not all of the regions of the genome that code for proteins

WES is similarly effective at detecting both point mutations and structural variants, but is unable to detect mutations outside of protein coding regions

Question 5

You have a 37-year-old patient who has a family history of breast and ovarian cancer (her mother with bilateral breast cancer at the age of 45 years, her maternal aunt with ovarian cancer at the age of 52 years, and her maternal grandmother with bilateral breast cancer at the age of 50 years) but herself has not been diagnosed with cancer. She participated in a research study offering results from whole genome sequencing. She wants you to help her understand her testing results so that she can undergo any appropriate screening and/or prophylactic surgeries.

As epidemiologic background, 13% of the population develops breast cancer in their lifetime, and 5–10% of cases of breast cancer are estimated to be due to a genetic predisposition.

The study promised to report all discovered pathogenic mutations up to 7 nucleotides in size in the 56 ACMG Incidental Findings genes, which includes BRCA1 and BRCA2 (two of several genes associated with hereditary breast and ovarian cancer). The study did not report any pathogenic mutations to your patient.

Which of the following statements are true about this case based on the available data? Please check all items that are true:

The study results indicate your patient did not inherit the mutation carried by her maternal relatives

Mutations in BRCA1/2 can be ruled out, but there may be pathogenic mutations in other genes associated with breast cancer susceptibility

Since no mutation was found, she should follow the screening guidelines for women at average risk

Patient is a carrier of breast cancer

Patient has higher risk than average

Genetic testing should be ordered for her mother or other affected relative, if possible, before proceeding

Question 6

You are considering obtaining you own whole genome sequence using a 2nd generation short-read sequencing instrument, such as the Illumina HiSeq, in a research study. Which of the following statements are true about the potential results? Please check all items that are true:

My results could include risk assessment for common diseases like Type 2 Diabetes or Age-related macular degeneration, although I won’t learn anything I don’t already know from my family history as my risk is necessarily between that of my parents

My results could include variants of unknown significance, i.e. variants that may be disease causing but for which there is insufficient evidence to determine their effect

As the “whole genome” name suggests, I will learn all known genetic associations with disease and physical traits

My results could include variants that impact the safety or efficacy of certain medications

Even though I already have genetic results, my physician will likely need to confirm those finding through additional clinical testing before taking any action.

My results could include variants that don’t affect my health, but may impact my children’s health

Question 7

You found a variant in a gene associated with a severe child onset disease in a healthy female adult participant in your whole genome sequencing study. The prevalence of this disease is 1 in 10,000. After checking the relevant databases, you found that this specific variant has been reported in both healthy and affected individuals. Which of the following statements about the further investigation of this variant are true given the information provided? Please check all items that are true:

If the case reports showed that the affected individuals had other disease causing alleles on the same chromosome, that would be additional evidence this variant is disease causing

Without knowing how the disease is inherited and how many copies of this variant were detected, I can’t interpret this case

The participant’s sex is not relevant to the interpretation of this variant

If the global frequency of this variant was approximately 1/10,000, that would confirm that this variant is disease causing

The disease might be incompletely penetrant — not everyone who has the variant will develop the disease

Since this gene was previously reported with severe disease and this person is reported to be healthy, this variant can’t be associated with the disease

Question 8

An adult patient of yours was recently diagnosed with cancer. The patient is considering a next-generation sequencing-based test that purports to offer a genomic profile of their solid tumor. Your patient asked you to help explain how this test works. Which of the following statements that you could tell your patient are true? Please check all items that are true:

Tumors in the same organ, e.g. the breast, likely have the same underlying genetic cause across patients. That is why the tumor arose in the same organ.

Unfortunately next generation sequencing can’t be used to detect gene fusions, when two gene sequences are combined together in your tumor, which can cause cancer because the resulting fused sequence isn’t in the human reference genome.

One kind of mutation that the laboratory will particularly be looking for is a loss-of-function or inactivating mutation in a proto-oncogene, i.e. a gene that promotes cell growth.

The testing will be performed on a biopsy sample from your tumor, not on a blood sample, as the mutations that cause your cancer are likely only present in your tumor.

The test will employ the same laboratory and analysis process used to detect inherited cancer susceptibility mutations, just applied to the tumor.

There is a 50% chance you could pass on an acquired mutation that caused your cancer to your child.

In accordance with the Coursera Honor Code, I (Anonymous Student) certify that the answers here are my own work.

You cannot submit your work until you agree to the Honor Code. Thanks!

Genomic and Precision Medicine

Top Navigation Bar

Genomic and Precision Medicine
by Jeanette McCarthy, MPH, PhD, Robert L. Nussbaum, MD

Side Navigation Bar

Start Here

Weekly Information

Course Materials

About the course

Pre-Course Assessment (Ungraded) Help Center

Question 1

Question 2

Question 3

Question 4

Question 5

Question 6

Question 7

Question 8

Genomic and Precision Medicine

Genomic and Precision Medicineby Jeanette McCarthy, MPH, PhD, Robert L. Nussbaum, MD

Pre-Course Assessment (Ungraded) Help Center

Question 1

Question 2

Question 3

Question 4

Question 5

Question 6

Question 7

Question 8

Confirm Navigation

Genomic and Precision Medicine
by Jeanette McCarthy, MPH, PhD, Robert L. Nussbaum, MD