linkage faq

Fanconi Test FAQ updated July 27, 2007
On July 14, 2007, the Basenji Health Endowment proudly reported that Dr. Gary Johnson of the University of Missouri released the linked marker DNA test for Fanconi Syndrome in Basenjis. As the first predictive test available for Fanconi Syndrome, we are sure you all have many, many concerns and we’ve compiled this list of Frequently Asked Questions to help. This FAQ is a work in progress, so please check back for updates.

Click to Download the FAQ as a PDF
About the Test
What is a linkage test?
Answer: Linkage is the tendency for genes and other genetic markers to be inherited together because they are in close proximity to each on the same chromosome. A linkage or linked marker test selects a segment (or segments) of DNA at a location on the chromosome and tracks their inheritance. Because DNA segments that lie near each other on a chromosome tend to be inherited together, these markers can be used to track the inheritance pattern of a gene that has not yet been identified but whose approximate location is known.
You can read more about genetic linkage at Wikipedia.

How reliable are the results?
Answer: This is a new test. We can report that all of the double-blind samples used for validation fell into one of the four categories (normal, carrier, affected, indeterminate) and that approximately 75% of the samples that tested affected were already known to be affected and none of the samples that tested normal were known to be affected, or had parents that were known to be affected. About 10% of the samples tested returned an indeterminate result.
A significantly larger data set is required to generate meaningful accuracy rates, if you’d like to learn more, read about Bayesian Inference at Wikipedia.

Is it the same as a marker test?
Answer: Yes, a linkage test uses marker(s) to identify conditions caused by an as yet unidentified defective gene. This is not the same as a direct test which identifies the exact gene responsible for a condition.
Why was the linkage test created?
Answer: To reduce the risk of producing Fanconi afflicted puppies now while research continues on locating the actual gene.
Was my dog used to develop the test?
Answer: At this time, we do not have a final list of animals actually used for test development.
My dog was used to develop the test- do I still have to pay $60?
Answer: No. The 48 dogs that were actually used to develop the linked marker test will receive results at no charge. However, these results will not be available until after the breeding season backlog has been cleared and the research team has the manpower available to cross reference their double-blind samples; and if needed, re-run tests if a sample’s results are unavailable.
Why is the test so expensive?
Answer: The $60.00 per dog fee is essentially a time & materials charge covering the cost of reagents used in the test, sequencer time to run the test, OFA recording fee of results, and administrative time to process requests and log results. For comparison, the commercially available Pyruvate Kinase Deficiency (HA) Test for Basenjis costs from $75.00 to $140.00 depending on the testing facility.
Will the direct test be this expensive?
Answer: We cannot predict the cost of the direct test, but our hope is that it will cost no more than the linkage test.
When to Test
To request the Fanconi Test, your dog must first be registered in the Canine Phenome Project (CPP) and complete the breed questionnaires. Print the DNA Sample Submission Form and the Linked Marker Test Form for each dog you are testing and follow the instructions for sample submission.
Dogs that are know to have- or are suspected of having- Fanconi are encouraged to submit samples for the benefit of further research. Please indicate on the dog’s health survey that they are afflicted prior to submitting samples or test requests. There is no charge for testing or recording of results for these dogs.

I want to order a test, whom do I send the form to?
Answer: If submitting a test request when you already have a sample in the CPP, send your Linked Marker Test Form and payment to:
Liz Hansen
321 Connaway Hall
University of Missouri
Columbia, MO 65211
If you are shipping a blood sample at the same time, send your sample, DNA Sample Submission Form, Linked Marker Test Form and payment to:
Dr. Gary Johnson
Basenji DNA Research
320 Connaway Hall
University of Missouri
Columbia, MO 65221
If you have already sent paperwork to Dr. Johnson instead of Liz, don’t be concerned- they’ll figure it out. Don’t forget, all payments should be in US funds payable to the University of Missouri.
I live overseas, can my dogs be tested?
Answer: Any dog registered with the CPP that has submitted a blood sample can be tested. Instructions for shipping samples from outside the United States to the University of Missouri can be found here. We strongly suggest you contact Liz Hansen in Dr. Johnson’s office prior to starting the process.
I already bred this year, should I test the sire & dam? The puppies?
Answer: While the results won’t change the breeding you’ve already done; they will give you information about the parents. Puppies can be tested as soon as they can safely give at least 3mL of blood.
I have a companion dog, should I test? When?
Answer: We ask that people hold off testing dogs that aren’t being considered for breeding in the 2007-2008 season. You may request a test, but it may be delayed until the backlog is cleared. Watch this website for status reports on the backlog.
I have frozen semen from a deceased dog who has blood stored in the CPP, when can I test?
Answer: If you are planning to use the semen this season, by all means request a test now. Otherwise, it is probably best to wait until you are breeding because the direct test may be available.
I have frozen semen from a deceased dog without blood stored in the CPP, can I test?
Answer: We suggest you wait until you are planning to breed as a the direct test may be available. The University of Missouri can extract DNA from semen; however they require 2 straws and they may not get usable DNA. Download this document for instructions. We strongly suggest you contact Liz Hansen in Dr. Johnson’s office prior to starting the process.
Working with the Results
Result emails come from cpp@offa.org
Should carriers only be bred to normals?
Answer: Fanconi can result if a carrier is bred to a carrier and if a carrier is bred to an affected; it is advisable that carriers only be bred to dogs that test normal. If your dog’s result is indeterminate its safest to treat it as a carrier when breeding.
You can read about Punnett Squares, used to determine the probability of an offspring having a particular gene, at Wikipedia.

Should I spay/neuter my dog based on the results?
Answer: No.
My dog came back affected, should I just euthanize it now?
Answer: No.
I’ve tested my puppies and some came back affected. What do I do? What do I tell buyers?
Answer: Explain to buyers that the breeding was done prior to the availability of a Fanconi test. The buyers should be educated in providing a healthy environment for their dog which includes avoiding unnecessary stress, a quality diet and plenty of drinking water. Buyers should be introduced to the Fanconi Protocol developed by Dr. Steve Gonto, taught the early signs of Fanconi, how to monitor urine for sugar, and be referred to a Veterinarian with Fanconi experience.
My dog came back indeterminate, what does that mean? Should I re-test?
Answer: Our linkage test uses 3 markers (for a total of 6 alleles) to predict Fanconi status and requires that all 3 be in agreement. An indeterminate result means the 3 markers are not in agreement (view sample results) and therefore cannot predict Fanconi status. This would not change with a re-test. It is our suggestion that people treat indeterminate results as carriers when making breeding decisions and continue routine strip testing of urine.