Familial Variant Targeted Testing (FMTT)

Presentation

Expiration date: 12/04/2026

Presenter

Megan Hoenig, M.S., M.P.H., CGC

Division of Laboratory Genetics and Genomics
Mayo Clinic, Rochester, Minnesota

Transcript

Introduction

Hello and thank you for listening to this Hot Topic on Familial Variant Targeted Testing, or FMTT. My name is Megan Hoenig, and I am a licensed and certified genetic counselor with the Division of Laboratory Genetics and Genomics at Mayo Clinic Laboratories.

Disclosures

I have no disclosures.

Learning Objective

At the end of this Hot Topic, I hope that you are able to describe the principles and benefits of FMTT, compare FMTT to other testing strategies, and identify cases that are appropriate for FMTT.

Overview: Familial Variant Targeted Testing (FMTT)

Familial variant targeted testing, or FMTT, is a test offered at Mayo Clinic Genetics Laboratory. It is a test that looks at a patient sample to specifically determine the presence or absence of a known variant, or variants. This is a single orderable that can be used for targeted testing of most genes currently offered through other Mayo Clinic Laboratory genetic tests, and you can test for two, three, or even four variants in different genes all in one order. Each test undergoes careful, expert review by our genetic counselors and laboratory directors. Of note, this test used to be called familial MUTATION targeted testing; however, the term mutation is out-of-date, and is replaced by pathogenic variant, or just variant, depending on the situation.

Clinical utility of FMTT

FMTT can be used in a variety of settings. Most often, it is used for cascade testing for family members when there is a known familial variant. In these cases, the presence or absence of the variant can guide clinical care in the family members and can inform additional family members about the risk for the familial variant. Similarly, family members may undergo targeted carrier screening based on known familial variants. 

Alternatively, FMTT may be used as a follow-up tool to aid in variant classification. This may involve segregation analysis, where affected and unaffected family members are tested to see if the variant segregates with the phenotype, or phase determination, to see if the variants are in cis (on the same chromosome) or in trans (on different chromosomes). 

FMTT may also be used as follow-up for somatic testing to determine if a variant is germline in origin, as this can have implications on the clinical management for the patient and their family. 

Benefits of FMTT

FMTT is a powerful test that will be able to give clear results, the presence or absence of a specific variant. This allows family members to undergo appropriate clinical care when the variant is detected and also informs family members who do NOT have the variant to NOT undergo additional clinical care. By testing just for the familial variant, testing is generally more affordable. Furthermore, the report is tailored to the patient’s risk based on the presence or absence of the variant. Additionally, FMTT may aid in variant classification, for some variants of uncertain significance. This may contribute to variant reclassification, leading to a molecular diagnosis for a patient, who can then undergo clinical care specific to that condition. 

FMTT algorithm

Here is a helpful testing algorithm for FMTT. FMTT is available when there is provided documentation for a variant of interest. On the other hand, if there is no familial diagnosis, but there is a clear phenotype in the patient or family, multi-gene panel or single-gene testing may be the most appropriate test. If there is a familial diagnosis without a genetic test report, or if the patient does not fully meet testing criteria, you may contact the genetic counselors to discuss the most appropriate testing strategy for your patient.

Required information

In order to do FMTT, we need to know the variant of interest. This can be provided to us in one of two ways. The first is the completion of the patient information sheet. This paperwork includes a section for the familial variant. If it is a single nucleotide substitution or a small insertion/deletion, the top half would need to be completed; this includes the gene, transcript, exon or intron number, the amino acid change, the coding DNA change, and the genomic DNA change. If the familial variant is an exonic deletion or duplication within one gene, the bottom half would need to be completed; this includes if it is a deletion or duplication, the gene, and the involved exons. The paperwork also includes a section for family history and information on individuals who carry the variant. 

The other option for providing the variant information is by including the family member’s lab report. This is strongly encouraged, as the lab report can include other helpful information for the laboratory and can reduce the risk of a typographical error. Alternatively, familial variant details may be included in a family letter written by a genetic counselor or in the family member’s clinical note. 

Finally, FMTT through Mayo Clinic Laboratories is available, even if the proband was originally tested elsewhere.

Limitations

While FMTT can be a very useful test, there are some limitations. First, you need to know and provide the variant for which we are testing. This can be a challenge if the family member was tested a long time ago, if they have a clinical diagnosis of a genetic condition, or if they are not in close contact with family members. Additionally, it is preferred to have a positive control, and without one there may be a false negative result. Relatedly, some genes and variants are not appropriate for FMTT, as full gene, panel testing, or other methodologies may be more appropriate. Finally, because the testing looks at the genomic region encompassing the variant of interest, it is possible to find another, incidental variant.

Case examples

Now, I’d like to walk through examples for which FMTT can be useful.

Cascade testing

In this example, the client initially orders a different test, HBOCZ, which looks at the BRCA1/2 genes, based on a family history of BRCA. If we follow the testing algorithm for FMTT, it brings us to verifying if there is documentation of the family member’s genetic test report. Based on this, the laboratory genetic counselor will contact the client to verify what is known about the familial variant. In this case, the familial report is available, and the relative has a pathogenic variant in PALB2, a different hereditary breast cancer gene. Based on this, FMTT is the most appropriate test. Let’s see how this cascade testing works out.

Filling out the patient information sheet for this familial variant, we start with the gene, in this example, PALB2. Next is the transcript which generally starts with the letters NM and is followed by some numbers. In this case, NM_024675.4. Then the exon or intron number, which is 13 in this example; and finally, the variant details. The amino acid will start with a “p.” followed by some letters (the original amino acid), some numbers (the amino acid position), and more letters (what the amino acid is changed into). For this case, it is p.Tyr1183Ter, or at amino acid residue 1183, the tyrosine is changed into a termination codon. The cDNA, or coding DNA, will start with a “c.” followed by some numbers (the nucleotide position), and some letters (the nucleotide change). For this case, it is c.3549C>A, or at position 3549, a cytosine is replaced by an adenine. 

The gDNA, or genomic DNA, will start with a “g.” followed by some numbers (the genomic position), and some letters (the nucleotide change). For this case, it is g.23614792G>T. The nucleotide change may be the same as the cDNA, or it may be the inverse, like in this case, based on which direction the gene is transcribed. This information is critical in order to ensure we are testing the right part of the gene for the familial variant. Additionally, there is the family history section at the bottom.

Cascade testing: Result

With FMTT, there are generally two testing outcomes, positive or negative. 

For positive results, the familial variant was detected. In this example, it means that this individual has familial cancer syndrome and there are actionable steps to take, such as increased cancer surveillance or surgical intervention. This case also highlights that it is important to obtain information about the reported familial variant, as it was initially thought to be “BRCA” and the original test would have been a false negative, as it would not have looked at the PALB2 gene. 

For negative results, the described familial variant was not detected. In this example, that means that the individual would not have that familial cancer syndrome, and therefore would undergo population-level cancer screening.

Carrier status

Similar to cascade testing, carrier testing via FMTT may be performed based on a family member’s test result. This is often used for reproductive decision-making. In this example, the patient is diagnosed with Wilson’s disease, which is an autosomal recessive condition caused by biallelic pathogenic variants in ATP7B. FMTT may be performed for the parents to confirm carrier status for future family planning, or adult siblings of this patient may undergo FMTT to see if they are a carrier or not. Additional testing, such as pan-ethnic carrier screening may still be pursued to determine carrier status for additional conditions.

VUS resolution

FMTT may also be performed for VUS resolution via segregation analysis or phase determination. Clients should contact the laboratory genetic counselors to confirm for their specific case if testing is available at no charge. Of note, we may not be able to reclassify the variant immediately when doing this type of FMTT, but the evidence gathered will help inform future variant reclassification.

One example of VUS testing in informative family member, would be in a family where only the proband has a phenotype that is consistent with the gene for which a VUS was identified on a Mayo test, and that the gene has a highly specific phenotype and is known to be found de novo. In this example, a VUS was found in FBN1, which is associated with Marfan syndrome, a highly specific and penetrant condition. Neither of the parents have features consistent with this condition, so the client called to verify if FMTT was available at no cost. We tested the parents, and both of them were negative for the familial variant. This de novo occurrence was enough evidence to reclassify the variant to Likely Pathogenic, providing a molecular diagnosis of Marfan syndrome.

Germline confirmation

For our final example, let’s go over germline confirmation. 

If a patient undergoes somatic testing during their cancer workup, a variant detected may be suspicious to be germline in origin. For these cases, a patient may either undergo full germline panel testing in order to rule out additional germline variants that could be missed on somatic testing, or they may undergo FMTT for just the specific variant. If the variant is confirmed to be germline, there may be additional impact to the cancer treatment and management, and there may be an impact on surveillance intervention for other cancer risks. Additionally, family members would be able to undergo cascade testing for the familial variant. On the other hand, if the variant was not detected, then the somatic test results may still impact the cancer treatment and management. Testing negative for that variant would mean that the patient and their family would likely not have to take action specific to that hereditary cancer syndrome, but other testing may be recommended based on personal and/or family history.

Summary

In summary, FMTT is a powerful test that is able to determine the presence or absence of a specific variant and is critical for medical management. FMTT is generally more affordable and targeted compared to other testing strategies, allowing for clear and efficient use of healthcare dollars. FMTT is useful for a variety of clinical situations, and if you have any questions about FMTT for your patients, you can contact the laboratory genetic counselors to discuss in more detail.

Thank you

Thank you for listening.

Questions?

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