Mutational Mechanisms and Genetic Testing

Question 1

What 3 conditions are currently (12-09-2015) targeted as Tier I genomic applications by the CD base don evidence supporting potential for positive impact on public health?

Answer 1

HBOC

Lynch syndrome (hereditary cancer syndrome, colorectal, and other tumors, mutations in mismatch repair genes)

Familial hypercholesterolemia

Question 2

What is FH?

Answer 2

FH is a disorder characterized by very high levels of serum cholesterol

Question 3

What is the most common genetic defect leading to FH?

Answer 3

Although mutations in several genes can lead to this phenotype (locus heterogeneity), the most common defect is loss of function mutations in the low-density lipoprotein receptor (LDLR) gene

Question 4

What is the prevalence of FH?

Answer 4

1 in 500

Question 5

What is the MOI of FH?

Answer 5

AD. Note that the vast majority of patients are heterozygous. The presence of two mutant alleles is very severe!!

Heterozygotes (common) are at risk of a coronary event by age 50. People who are homozygous mutant (rare) may be symptomatic in their teens

Question 6

What are some clinical manifestations of FH?

Answer 6

Individuals with FH may have nodular deposits of cholesterol (xanthomas) around the eyelids and on the hands and feet, in addition to atherosclerosis and coronary artery disease

Question 7

Is FH well-diagnosed in the general population?

Answer 7

No, less than 25% diagnosed.

The healthcare gap is that, even when affected individuals are under treatment for their hypercholesterolemia, the hereditary nature of their condition is sadly under-diagnosed. Improved awareness and better diagnosis, followed by cascade screening, has significant public health potential

Question 8

What is cascade screening?

Answer 8

It’s using the index case to systematically track a mutation (hereditary risk) through family members

After you diagnose your patient with this condition, then lipid screening can be offered to first-degree relatives. Since this is an autosomal dominant trait, first-degree relatives (parents, siblings, children) are at 50% risk. Let’s say high LDL-C is found in your patient’s mother, but not in the father. Then, the next step would be to make screening available to the mother’s first-degree relatives, etc

Question 9

What are some other causes of FH besides mutated LDLR?

Answer 9

mutations in APOB and PCSK9

Question 10

How is autism typically tested?

Answer 10

Autism is another example, where a patient with autism may undergo analysis of a large panel of genes in the hopes of identifying a genetic cause.

Question 11

How would CF and DMD be tested?

Answer 11

sequencing a single gene (BRCA uses a gene panel of multiple genes)

Question 12

What is exam sequencing?

Answer 12

Exome sequencing refers to analysis that focuses on all the coding sequences of the human genome, which are only ~1% of the total genome. This is what most patients who undergo genomic sequencing receive at the current time. A common strategy is to sequence parents in addition to the patient, since de novo differences are strong candidates for a pathogenic variant

Question 13

What is expression profiling?

Answer 13

As you might imagine, gene expression in tumor cells is significantly different from normal patterns of gene expression. Extensive work has successfully defined patterns (profiles) of abnormal expression that are characteristic of certain clinical outcomes. Expression profiling takes RNA from the patient’s tumor and applies it to an array-based assay that quantitates the expression of genes that tend to be either upregulated or downregulated in association with specific outcomes. Quantitative measures of the patient’s RNA levels are converted to a numerical score and reported as prognostic indicators. The test does not identify mutations; the molecular phenotype is based on tumor-specific differences in amounts of specific RNAs.


Question 14

What are the applications of expression profiling?

Answer 14

Use of expression profiling in breast cancer helps to determine if a patient is likely to benefit from adjuvant chemotherapy (following surgery).


For example, patient A’s tumor sample had an expression profile consistent with low chance for relapse or metastasis. She probably doesn’t need chemotherapy (and its associated side effects). 
In contrast, the profile from patient B puts her at high risk for relapse or metastasis, and she is a candidate for aggressive therapy.
Expression profiling is used as a decision tool to tailor therapy to a patient’s molecular phenotype.


Question 15

What is companion diagnostics?

Answer 15

In this application, the “companions” are a specific targeted therapy and the diagnostic test that determines if that target is present in a patient (or in the patient’s tumor). As stated under the FDA definition in the center of the slide, use of the targeted drug is indicated ONLY after a genetic test result indicates a high likelihood that its use will be effective

Emphasis is on targeted therapy and personalized diagnosis and treatment, especially in oncology

Question 16

Example of companion diagnostics.

Answer 16

The common BRAF mutation is V600E (missense mutation with normal valine replaced by glutamic acid). The mutation is common in advanced melanomas, also in colorectal tumors and several other tumor types. The drug vemurafenib was developed specifically against BRAF protein containing the V600E mutation. It has no activity against normal BRAF protein. FDA approval of the drug specifies its use only when a positive result is obtained in the genetic test. This was the first official companion diagnostic; the drug and the test were approved concomitantly (2011).

Question 17

What does mutant BRAF cause?

Answer 17

Mutant BRAF is a potent stimulator of cell proliferation. If genetic testing of a patient’s tumor shows presence of the BRAF V600E mutation, then vemurafenib can be administered, and it will inhibit BRAF activity.

Question 18

Vemurafenib is used for what kinds of patients?

Answer 18

patients with late-stage or unresectable melanoma. NOTE: patients are ONLY candidates for vemurafenib therapy if BRAF V6000 is present. It will not act in any form against a normal BRAF protein

Question 19

What percentage of cutaneous melanomas are positive for mutations in the BRAF gene?

Answer 19

40-60%. The BRAF V6000 mutation comprises approximately 90% of BRAF mutations

Question 20

How does Vemurafenib work?

Answer 20

it blocks the mutant BRAF V6000 protein from entering the MEK-ERK pathway of cell proliferation (so it blocks cell growth and division)

It’s cost is roughly $10,000 a month

Question 21

What is direct to consumer testing?

Answer 21

Because genetic testing is an emerging technology, its regulation is still very much in flux. This enabled the emergence of a new model within the last decade, where companies began marketing genetic testing services directly to consumers. Specimen collection kits are sent by mail, and results are generally reported online. Although this system circumvents traditional physician-ordered testing, it has become important to medical training, since many consumers end up in their doctor’s office seeking advice about the test results they receive online

patient just sends saliva in (23andMe is the popular one)

Question 22

What are the up and downsides of DTC testing?

Answer 22

On one side, proponents argue that people have a right to this information, and it is paternalistic to try to restrict its availability. On the other side is the argument that many of the tests for sale have no clinical utility (definitely true), and there is potential harm to consumers who may make decisions that are based on inaccurate or incomplete information (or incomplete understanding of their results)