HGTD This Week: NEW for the Phenes database - linkage vs direct mutation information

An outcome from the International Dog Health Workshop - Virtual, on Standardizing Genetic Testing, is to improve transparency on how genetic tests are performed - e.g. information on assays or other technical details. The primary focus of this was increasing transparency on where a linkage vs direct variant (mutation) test is being offered. 

New HGTD Phenes resource:

The phenes searchable database in HGTD has always provided genetic test provider (GTP)-specific information on how tests are undertaken, including the specific GTP-reported variants/mutations for each test they offer, especially where their test is different than the variants reported in the literature.

The new option to include Assay/Test Information in the phenes database allows for comment not just specific to individual GTPs, and aims to add clarity where a test is exclusively linkage based, exclusively direct variant, or both. This should also improve transparency where we have reports of tests being performed as a linkage/markers tests by GTPs who are not participants in HGTD or who do not provide linkage/markers information to HGTD.

Why would a linkage test be offered?

A linkage or markers test may be the preferred test performance for a GTP for a number of reasons, including:

• The direct variant(s) are difficult to assay or are part of a panel, and a linkage/markers assay is easier to perform consistently and robustly
• The direct variant isn't known, and only a linkage/marker is available to test
• The direct variant is patented or proprietary, and a linkage test is a way around this

Why is it important to know if a test is a direct mutation or linkage test?

While linkage tests are usually very accurate, generally, direct mutation tests are felt to be more robust so are often the preferred method of test performance by GTPs. Where a linkage test is used (for whatever reason), there may be an increased risk of false-results. This could explain why some owners have experienced different test results for the same genetic test, from different test providers. Knowing whether or not a test is performed as a direct mutation or as a linkage test can be helpful in increasing the confidence of a test result if there are concerns about accuracy. There can be many reasons a test result may appear to differ from the phenotype of a dog, however, so it is valuable to report to a genetic test provider when a test result is in question. It could be a testing error (including owner sampling errors), or that the phenotype is an unknown direct variant, variation on a known direct variant, or something else! In this way, we can work collaboratively to improve the robustness of genetic testing for everyone. It is worth noting that the majority of testing errors across all kinds of genetic tests are due to samples being incorrectly taken or submitted with the wrong dog details, which is why many GTPs offer to re-run a test where there are concerns about the result. 

Additional Information:

This week in HGTD: direct variant/mutation, linkage, and risk tests – what are they?