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Question 1

A “variant” detected by next-generation sequencing is:

A single nucleotide change in an exon

A common genetic difference compared to a normal person’s genome

Any difference from the reference sequence

A disease-causing mutation

Question 2

Current next-generation sequencing technology is most likely to detect a disease-causing variant caused by:

A heterozygous single exon deletion

A change from A to G in an exon

Gene duplications

A large chromosomal deletion

Question 3

What does “depth of coverage” refer to:

The number of exons sequenced in the genome.

The fraction of the full genome represented by exons.

The number of cells sequenced per patient.

The number of sequencing reads covering the same exact position in the genome.

Question 4

The success rate for using whole genome/exome sequencing for solving diagnostic dilemmas is close to 100%.

True

False

Question 5

Which of the following type of variant is most likely to be damaging:

Synonymous

Intergenic

Splice disruptor

Intronic

Question 6

Which of the following is generally NOT used as a criterion for estimating the likelihood that a variant detected by next-generation sequencing is pathogenic?

In vivo or in vitro experimental evidence that the variant affects the protein or causes a disease

Segregation of that variant in other affected and unaffected family members

Distance of the variant from the chromosomal centromere

Frequency of that variant in the general population

Question 7

Which of the following would be an appropriate component of pre-test counseling before ordering whole-exome or whole-genome sequencing for a patient?

“This test will most likely yield a definitive diagnosis.”

“You may be notified that you carry a disease-risk variant that was not the original purpose for ordering the test.”

“Any genetic change that is uncovered can be interpreted in a straightforward way as it pertains to your health.”

“This test will only evaluate genes that could be involved in the disease in question.”

“Genetic changes that are detected are only relevant for your health and are not relevant to your family.”

Question 8

What is the added value of sequencing the unaffected parents when trying to find variants for an undiagnosed disease in a patient?

The ability to identify variants behaving in a dominant fashion

The ability to uncover de novo genetic variants

There is no added value since the parents do not have the disease

The ability to estimate allele frequency

Question 9

The following is an opinion question to encourage discussion and thought on the intersection of ethics and genetics. There is no single correct answer, and you will receive credit for selecting any answer.

You work for an organization that provides whole-exome sequencing analysis and interpretation. A variant classified as a “variant of unknown significance" in TP53 (often referred to as p53) was detected in a child and his 19-year-old father who underwent testing for an unrelated suspected genetic syndrome. Because the significance was unknown, this variant was not reported. Five years later, a paper is published describing this precise variant as causative of Li-Fraumeni syndrome, a disorder with high risk of several types of cancer for which aggressive screening is recommended. The physician who ordered the test retired four years ago and is no longer in contact with the family, and the family’s address provided on the initial test is also no longer up-to-date. Which option most closely reflects your opinion as to the organization’s obligation to locate the family and alert them to their high risk for cancer and recommended screening precautions?

The organization is obligated to locate and notify this family at any cost.

The organization is obligated to find and notify the patient’s health care provider, but does not need to find the family itself.

The organization is obligated to provide information on its website for patients who receive test results to check back frequently for updates on the status of variants.

The organization has no obligation to contact this family, and the family has the responsibility for following up on their own test.

Question 10

The following is an opinion question to encourage discussion and thought on the intersection of ethics and genetics. There is no single correct answer, and you will receive credit for selecting any answer.

Whole-genome sequencing on a newborn with a suspected genetic disorder, his 15-year-old mother, and her 16-year-old boyfriend is undertaken. The test reveals that the boyfriend is not the father, but the child has extensive regions of homozygosity, strongly suggesting consanguinity. Given the age of the mother, the testing organization is concerned that it has uncovered evidence of rape and/or incest, and is unsure of how to proceed. Which option is closest to how you might proceed?

Disclose all results to local law-enforcement for investigation.

Disclose results privately to the infant’s mother, and leave it to her decision to pursue an investigation.

Disclose results privately to the mother’s parents, and allow them to decide if they wish to pursue an investigation.

Disclose results to the ordering physician and allow him/her to decide if law enforcement should be notified.

Report the false paternity but not the likely consanguinity.

Do not disclose these results, and limit your report to the phenotype for which the test was requested.

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

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Genomic and Precision Medicine

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

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