Unsure what tests to do next

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monkeyman
Posts: 94
Joined: Wed Jan 28, 2015 1:48 pm

Unsure what tests to do next

Postby monkeyman » Tue Apr 14, 2015 8:07 pm

Hi,

We're still in the early stages of testing with our 19-month old son. I'm going to see our DAN! doctor in a few days, and I'm at a bit of a loss trying to figure out which tests we should be doing next, if any.

I'd appreciate any feedback from the more seasoned forum members.

I'm thinking - Porphyrins, mitochondrial tests (not sure which ones), more extensive genetic testing

Here's what we've done so far. Most have come back within normal limits, none alarmingly high/low. Some I am still awaiting results for.

Fragile X

CGA Microarray

Heavy Metals Screen, blood

Comprehensive Metabolic Panel

Iron, total

Magnesium, Ser/Plas

TSH (thyroid)

Free T4

Hepatic Function Panel

IgG Blood Panel

Magnesium, RBC

Copper/Zinc

Methylmalonic Acid

Homocysteine

MTHFR DNA Mutation

Ammonia, plasma

Coenzyme Q10

Molybdenum

Selenium, RBC

Folates, RBC

Anti-Dnase-B AB

Anti-Streptolysin O (ASO)

Genova ONE (Optimal Nutritional Evaluation) Urine Test
https://www.gdx.net/product/one-fmv-nutritional-test-urine

GI Effects Stool Profile
https://www.gdx.net/product/gi-effects-comprehensive-stool-test

Amino Acids, plasma

Acylcarnitine Profile Quant

Carnitine Level, Free and Total

Lactic Acids

Long-Chain Fatty Acids

Creatine Kinase, Total

CBC with Differential

Ferritin Level

Vitamin D 25 Hydroxy, Serum

C-Reactive Protein

Candida Antibody, blood

Food Allergy IgE Screen
• Chicken
• Corn
• Egg white
• Fish
• Milk
• But
• Oat
• Orange
• Peanut
• Shrimp
• Soy
• Tomato
• Wheat
• Spinach
• Banana
• Strawberry
• Coconut
• Beef

Total IgE

IgG, Serum

IgA, Serum

IgM, Serum

alexsdad
Posts: 134
Joined: Fri Dec 30, 2011 1:31 pm

Re: Unsure what tests to do next

Postby alexsdad » Thu Apr 16, 2015 10:51 am

I would add Whole Exome Sequencing, overnight EEG and MRI. They are all pretty expensive tests so make sure your insurance will cover them. You need to consult your son's Geneticist/Metabolic Specialist for WES and extensive screening for inborn error of metabolism. EEG and MRI will have to be ordered by your son's Neuro.

These tests may sound scary but identifying the cause is always important and should be your top priority. Most of the metabolic issues are actually genetic. A genetic problem doesn't necessarily mean he got it from your or your spouse though. Most of the mutations are spontaneous mutations meaning they came from no where. Many people misunderstand this and decide not to proceed with extensive genetic tests because they don't want to know who to blame in their family. There are quite a few metabolic syndromes (again mostly genetic) that are treatable so if you son has one of them it is important to find it early.

FatherOf2
Posts: 1524
Joined: Mon Mar 11, 2013 1:37 am

Re: Unsure what tests to do next

Postby FatherOf2 » Thu Apr 16, 2015 1:25 pm

The Baylor College of Medicine, which did the whole exome sequencing on my son, only reported mutations that are known to cause autism or other mental disorders and some "uncommon" mutations. According to these mutations, my son should be blind and deaf right now, but he is not. So, obviously not all identified mutations are pathological. Don't expect the whole exome sequencing to tell you MTHFR, CBS, COMT, MAO or other metabolic/methylation/transsulfuration mutations because they are considered "common" even if they are homozygous. For example, the test didn't report the MTHFR homozygous mutation in my son. When I asked BCM to provide a full list of all homozygous mutations, they refused saying that the test was ordered under the diagnosis of "autism". They did give me the file with raw data, but I couldn't find anybody to read the data and identify mutations from it. So, I think the whole exome sequencing is limited in its info. You might as well go with 23&me or Yasko limited genetic tests.

monkeyman
Posts: 94
Joined: Wed Jan 28, 2015 1:48 pm

Re: Unsure what tests to do next

Postby monkeyman » Thu Apr 16, 2015 3:52 pm

Thanks for the replies guys.

Alexsdad, we have done a short 30-45 minute EEG that didn't have any abnormalities. I pushed his neurologist for a 24-hour EEG, but she felt that a 4-hour EEG would be just as beneficial. I would really like to try to capture his entire nights sleep, but she made the point that it would be really hard on him to do the test for the full 24 hours. I don't disagree, but am still interested in doing it. I am going to meet with another neurologist to discuss further.

The MRI would require sedation, which really concerns me. I have read enough accounts of ASD kids having a regression or other bad reaction to the sedatives that I actually cancelled one appointment. We tried to do this at night with no sedation, but didn't even get him on the machine.

Thankfully, my wife and I are not scared of finding out the underlying cause of this. In fact, it's exactly what we're trying to do. We understand that we need to gather as mush information as possible to treat this effectively. What are the benefits to doing the WES as opposed to a Yasko test? We don't have a genetic/metabolic specialist; perhaps we need to see one? I will ask our doctor for a referral.

What are the treatable metabolic syndromes you speak of?

Fatherof2, I'm sorry to hear you had issues with the WES. What seems nice about Yasko's test is that it's fairly easy to interpret, and you don't have to beg for the release of information. It may be prudent to do that first, then consider the WES at a later date.

Thanks,
MM

makingitpossible
Posts: 1260
Joined: Mon Nov 12, 2012 10:25 am

Re: Unsure what tests to do next

Postby makingitpossible » Thu Apr 16, 2015 6:35 pm

I would be interested to know also what metabolic disorders you are referring to? I think tests are important too but it is my understanding that all infants are tested for over 30 metabolic disorders at infancy. When we got the diagnosis of autism I called and confirmed my daughter was tested for several things I suspected.
What other tests are there since most of these are diet related and can be treated with diet.

I would be careful though with the genetic tests. I didn't sleep for like 2 weeks when one of the genetic tests came back with a micro deletion on chromosome 22 I think. There are no known disorders with the location of her microdeletion except if it was a deletion on both chromosomes and then she would be dead by age 7-10. So basically I found out she was a carrier for some rare crazy lethal disease. The doctor finally said we all have these microdeletions and really have no idea if they affect us or not. But it still affected me emotionally for along time and there is no research on her particular deletion other than it being a carrier state so it didn't benefit us in the least.

monkeyman
Posts: 94
Joined: Wed Jan 28, 2015 1:48 pm

Re: Unsure what tests to do next

Postby monkeyman » Thu Apr 16, 2015 8:48 pm

Makingitpossible,

Thanks for the comment. I am with you on this one. I want to know what we're going to do with the information from the genetic testing once we have it.

Is it just going to make my stomach churn with worry and anguish?

If there's something that I can take action on, identifying a flaw in the methylation cycle or something, I want to know.

If it's that crazy gene that you worried about, I'd rather not.

If anyone has a good idea, please fill me in.

Yasko's test makes sense since it seems to focus on methylation, but I am also interested in identifying some condition that can be helped with vitamins/supplementation or something like that. I would hate to miss an opportunity to identify something this early in the process for us.

Thanks,
MM

alexsdad
Posts: 134
Joined: Fri Dec 30, 2011 1:31 pm

Re: Unsure what tests to do next

Postby alexsdad » Fri Apr 17, 2015 12:40 am

I agree WES has many limitations and I didn't think it was very useful when we did it a couple years ago. It only represents 1% of genome anyway. (still contains up to 85% of known disease causing mutations and variants) I have changed my mind to think it is one of the most cost-effective diagnose tools now. It is becoming more and more popular diagnostic tool for the clinical doctors and their database is growing fast. They haven't found anything for us yet but I may get a call from our geneticist one day and finally find out what my son really has. I think it is important to have this data in hand because they continue to find and report the new pathological mutations/variants and relations among different genes everyday. You don't want to waste more time if it turns out to be treatable or manageable one day.

I was recently looking into the possibility of Glut1 DS for my son. One way to diagnose this syndrome is to compare the glucose level in the serum and CSF but the spinal tab is an invasive test and I wouldn't do it unless there is a real good reason. Another way to diagnose Glut1 is to simply look for a mutation on SLC2A1 gene which is part of WES. What complicates the matter is there is about 20% of people with Glut1 DS who don't have SLC2A1 mutation. This is the shortcoming of the current genetics. Maybe there is another gene that causes Glut1 DS but it hasn't reported yet. What complicates even more is that there are some people with SLC2A1 mutation but don't have Glut1 DS. Is it because there is another gene can potentially complement the defective SLC2A1? Maybe. It will be a long process to identify all these relationships among hundred of thousands of genes and map them to the known and unknown syndromes. I spoke with a rep from Balyor recently and she told me they process thousands of WES every month now. Baylor was one of the fist one who offered this test commercially a few years a go but now there are many other labs offer this test. Their data is exponentially growing and with the technology to handle the big data quickly developing WES will be a much better diagnostic tool in the near future. Well, it will be a whole different story when they move to the world of Whole Genome Sequencing but that will be further future. The point is that I could fairly confidently rule out Glut1 DS without doing a spinal tab just because we did WES.

As a side note Glut1 DS is an inborn error or metabolism (definitely not one of the basic metabolic screens done for the new born babies) and until a few years ago there was no treatment other than Ketogenic diet. Now there is a new drug (more like medical food since it is derived from castor bean oil) called Triheptanoin is being tested and it seems very promising.

Here is a link to a story of a recovered girl with Triheptanoin if you are interested:

http://thedoctorstv.com/videos/can-cast ... e-seizures

I know most of us here are dealing with autism not seizure but I'm just trying to say identifying the cause and addressing it scientifically is extremely important. I'm sure a typical American Developmental Pediatrician would give this girl a label of ASD on top of her seizure disorder and recommend ABA, OT, PT etc. which won't hurt but won't address the root of the problem either.

Keep in mind you shouldn't blindly pouring bottles of supplements into son's little body in the hope of hitting a jackpot. That's why often the mainstream doctors look down on biomed. Many DANs orders tests from the labs that will justify the use of their supplements.

Here is another link to a story about the journey of a family who found the right diagnosis through the exome study. They took a real long way because they started it before WES was commercially available. This article would be a good one for someone new to the genetics tests.

http://matt.might.net/articles/my-sons-killer/


Alexsdad, we have done a short 30-45 minute EEG that didn't have any abnormalities. I pushed his neurologist for a 24-hour EEG, but she felt that a 4-hour EEG would be just as beneficial. I would really like to try to capture his entire nights sleep, but she made the point that it would be really hard on him to do the test for the full 24 hours. I don't disagree, but am still interested in doing it. I am going to meet with another neurologist to discuss further.

I would look for another neuro who is willing to do it for you. You need at least 2-3 neuros because you will need to hear 2nd and 3rd opinions often down the road. There are certain types of seizures that show spikes only during sleep - i.e., Landau Klefner Syndrome which is commonly misdiagnosed as ASD.

The MRI would require sedation, which really concerns me. I have read enough accounts of ASD kids having a regression or other bad reaction to the sedatives that I actually cancelled one appointment. We tried to do this at night with no sedation, but didn't even get him on the machine.

Unfortunately sedation is needed in most cases. We had to sedate our son during the both MRIs. Keep in mind even if your son's MRI is normal at this time, it doesn't mean it will be his last MRI. You may want to repeat it in 2-3 years from now depends on his prognosis. If they can do it during night time it will be awesome but I'm not sure if you can arrange it that late unless you are admitted through ER. Often neuros have split opinions on the MRI result. Then you will need to look for a 2nd opinion from a different neuro but you can just bring a copy of the MRI images instead of doing it again.

Thankfully, my wife and I are not scared of finding out the underlying cause of this. In fact, it's exactly what we're trying to do. We understand that we need to gather as mush information as possible to treat this effectively. What are the benefits to doing the WES as opposed to a Yasko test? We don't have a genetic/metabolic specialist; perhaps we need to see one? I will ask our doctor for a referral.

Metabolic specialists are usually geneticists who have specialties metabolic disorder or mitochondrial disorder etc. I would look up the doctor's at the major hospitals in your area and reach out to them directly unless your insurance requires a referral. Often neuros or pediatricians refer their patients to who they know and they are not necessarily the best ones you can access. Don't be afraid of traveling to other states if necessary. Keep in mind not all doctors are the same. You have to look for the best ones you can possibly access.

We did Yasko test too but the ones that are considered 'pathogenical' in the mainstream genetics tests are much more severe than what she looks at. I'm guessing that's why they don't consider the mutations on her panel seriously. Many people have homozygous/heterozygous mutations on the genes on that panel but they are typical and having normal life. It think it can still help with planning the supplements though. I paid $500 to Yasko for that test years ago but you can do the same test at 23andme for much less now.

What are the treatable metabolic syndromes you speak of?

I mentioned Glut1 DS above and KPU you were looking into is another one. Basically if the missing enzyme can be synthesized and supplemented, it should be treatable or manageable in theory. You should be able to find more on google but if you compare to the ones that are not treatable, it will be a small number. Let's look at the brighter side of it though. The first step is to identify what 'it' is then it will be obvious what the next step should be.

I would be interested to know also what metabolic disorders you are referring to? I think tests are important too but it is my understanding that all infants are tested for over 30 metabolic disorders at infancy. When we got the diagnosis of autism I called and confirmed my daughter was tested for several things I suspected.
What other tests are there since most of these are diet related and can be treated with diet.

Makingitpossible - There are many known metabolic disorders and probably more unknown ones and the ones that are done for the newborn babies are the very basic ones. Let me give you an example. We did Purine and Pyramidine panel though a geneticist at NYU in 2011 which is apparently not done as part of basic metabolic screen for newborn babies. They found elevated Uracil level and the geneticist said he wanted to do further testing to rule out Dihydropyrimidine dehydrogenase deficiency. Unfortunately Lab Corp didn't offer that test at that time and only Lab could do this test was Quest Diagnostics which was out of network for our insurance. The out of network test fee was whopping $10,000! Basically all the doctor wanted to know was if my son had a mutation on DPYD gene. WES was not available at that time and doctors had to order a test for single gene each time based on the clinical symptoms or test results. Can you imagine paying $10,000 to rule out an extremely rare metabolic syndrome? I asked the doctor if it's worth it and he said honestly not. Uracil level would have been much higher than my son's level if it was really DPD Deficiency. We would have proceeded with the test if it was covered by insurance but decided to pass on at that time. Later when we did the WES in 2013, DPYD gene was part of it and we knew that our son doesn't have a mutation. If you look up metabolic disease on the internet, you will find that the researchers have already found many associated genes and mutations for the known metabolic disorders. There are still a lot they don't know but for the ones that they already identified, you may be able to save the traditional serum or urine test for diagnosis if you do WES. That's why I think WES is a cost effective diagnostic tool for large screening. In the old days, you really needed a good metabolic specialist who can pick the right set of tests for you based on his or her observation. They could only run limited number of tests and had to make their best guess as part of diagnostic procedure. Nowadays the WES can test the whole 180,000 exons and will screen for every single reported syndrome and you no longer need to depend on your doctor's ability to guess the right tests. Again, it is an expensive test so I wouldn't recommend anyone to it out of pocket but if the insurance covers I don't see why one should hold back on this. More info is always better than less. No matter we want or not, we will eventually have to face the truth one day. It will find us one way or another so I'd rather be prepared. I would advise anyone to get this test done and have the data ready for the immediate and future use. I don't know how long it takes now but it took 6 months for us to get the result when we did it two years ago.

monkeyman - Lastly, I mentioned all the metabolic and genetic things here today but another thing you have to keep in mind is the autoimmune factor of autism. When it is genetic or metabolic cause, it usually starts with the birth or relatively soon in the infancy. Compared to that, immune related autism is more acute. For example, a perfectly normal child suddenly regresses into autism after vaccination is very likely an autoimmune issue in my opinion. In that case, you will more likely find the cause within your son's immune system.

na7222002
Posts: 22
Joined: Thu Feb 06, 2014 11:43 am

Re: Unsure what tests to do next

Postby na7222002 » Sat Apr 18, 2015 4:05 pm

I paid $500 to Yasko for that test years ago but you can do the same test at 23andme for much less now.


We did 23andme instead of Yasko. We got "Assisted Collection Kit" for $25, which comes with sponge swab (looks like giant cotton swab). I used this kit to swab DS's inside cheek and squeeze out the saliva. The good thing when you order this kit is that it requires half the amount of saliva than regular kit. I think the regular kit is about $99 now. ($99 + $25 with 23andme, still cheaper than $495 from Yasko test)

Once you get the raw data, you can get Yasko snp from various site (some free, some with fee). Or, you can enter data into http://www.knowyourgenetics.com/ and get the similar recommendation that you would get from running test from Yasko for free (this site is run by Yasko)

monkeyman
Posts: 94
Joined: Wed Jan 28, 2015 1:48 pm

Re: Unsure what tests to do next

Postby monkeyman » Sat Apr 18, 2015 7:52 pm

Thanks na,

Do you have a link for the assisted collection kit? I can't find it on the 23and me site.

Thanks,
MM

na7222002
Posts: 22
Joined: Thu Feb 06, 2014 11:43 am

Re: Unsure what tests to do next

Postby na7222002 » Sun Apr 19, 2015 9:33 am

Someone from another forum tried to order Assisted Collection Kit beginning of this month, and was told the link isn't working. She was given this instruction and got her order in.

Here is the updated instructions for purchasing a assisted collection kit if you need them:
1) Visit https://www.23andme.com/store/cart/?ack
2) Next to the pink “add to cart” button, click the link “Need an Assisted Collection Kit?”
3) You will see the updated kit price of $124. To add a kit to your cart, click the “add to cart” button.

To purchase additional assisted collection kits, you can continue using the “add to cart” button. To add one or more standard collection kits to your order, click the “← Back” link or “cancel” button. Note that this will not remove any kits from your cart, but will simply navigate you to where you can add standard collection kits to your order.

When you are ready to check out, simply click “Continue” to complete your purchase.


I just tried the steps above and while it's not working quite the same way, I got to the check out process with the price of $133.95 ($124 + $9.95 standard shipping). I didn't want to enter credit card information and check out, so I couldn't confirm.

Hope the website is fixed soon, as most of people wouldn't feel comfortable ordering from broken site. And, I hope they don't stop providing Assisted Collection kit as it helps so many.

ajaxdyn
Posts: 14
Joined: Wed May 06, 2015 1:35 pm

Re: Unsure what tests to do next

Postby ajaxdyn » Tue May 26, 2015 1:47 pm

Just called 23andme.

Assisted Collection Kit - no longer available and not in plans...

concessioner
Posts: 2
Joined: Fri Dec 12, 2014 10:40 pm

Re: Unsure what tests to do next

Postby concessioner » Thu Aug 13, 2015 1:56 am

ajaxdyn wrote:Just called 23andme.

Assisted Collection Kit - no longer available and not in plans...


Hello, any suggestion how to collect the needed amount of saliva without this kit?

appreciate for any help

varen2
Posts: 99
Joined: Mon Mar 30, 2015 11:35 pm

Re: Unsure what tests to do next

Postby varen2 » Sun Aug 23, 2015 4:09 am

My son had an OAT Urine test, Stool test and Hair test for heavy metals from the Great Plains Laboratory.
We had some other tests done but they didn't show anything significant.

An OAT Urine test showed high levels of waste product of Candida yeast overgrowth.
Stool test didn't show Candida yeast , and in most cases stool test doesn't detect yeast.
Hair test for heavy metals didn't show heavy metals.

Yeast overgrowth and bad gut bacteria is a big issue for autistic children. Dr. Bruce Semon, the author of "Feast without Yeast" diet, suggests that Candida (yeast) overgrowth has to be eliminated first, and then other medical interventions can be done.

My son has been on "Feast without Yeast" diet and Nystatin for 5 months now and he is almost free of all autistic symptoms.

For parents considering a diet, "Feast without Yeast" diet is BETTER than GFCFSF, GAPS or SCD diet. Apparently, SCD diet as well as others include foods full of mold and toxins which cause repetitiveness, slow brain function, and promote yeast overgrowth.

"Feast without Yeast" diet can help recover fully from autism if a child is 3 years old or younger and will help get symptoms under control and get a stable recovery for older children.

My son was very autistic and had no speech when he was 2 years old. He was extremely repetitive. He no longer made eye contact, no longer seemed to hear. He started having 5-10 tantrums per day and he would wake up every night screaming and head-banging on the floor. He had dark circles under his eyes, pale skin and a fear of separation with mother. He was lining up cars in a long line, later he was replacing toys from one box to another. He stopped saying "Hi" and "Buy". He stopped pointing at objects.


My son is now 2 years and 9 months old, and he is almost free of any autistic symptoms. He is saying 6-8 word sentences, his eye contact is excellent. He follows my directions, he is curious about everything. Some days he is a bit repetitive (he is not completely free of yeast yet). But most days he is a normal kid, he is progressing, learning, and just being a happy boy. Right now he is learning language just like a normal kid. He is repeating, rephrasing sentences, and asking questions. He has a great sense of humor, he understands emotions. His role play is amazing, he recreates stories from books with toys..

Just a few words about my son's medical history. He was a healthy boy. He never took any antibiotics. He never had any problems with constipation or diarrhea.He was breasfed for 8 months. He reacted badly to MMR vaccine when he was 13 month old. His autistic symptoms started when he was 18 months old.


When my son started a GFDFSF diet, he was getting better. His eye contact got better and he was generally more with us. However, he had some bad days and some good days. Something was setting him off.

We tried multivitamins, probiotics and GFDFSF diet. It helped somehow, but didn't treat autistic symptoms completely.
With "Feast without Yeast" diet and Nystatin, we had immediate and noticeable results. I believe that with this diet my son will be free of all autistic symptoms within a year or so.

Author of this diet, Dr. Bruce Semon has an autistic son. He treated his son and since then many other kids. He says that his diet and treatment worked for every autistic kid he's ever treated.

My post about the diet and additional info here:

viewtopic.php?f=4&t=33403

ajaxdyn
Posts: 14
Joined: Wed May 06, 2015 1:35 pm

Re: Unsure what tests to do next

Postby ajaxdyn » Wed Aug 26, 2015 1:53 pm

concessioner wrote:
ajaxdyn wrote:Just called 23andme.

Assisted Collection Kit - no longer available and not in plans...


Hello, any suggestion how to collect the needed amount of saliva without this kit?

appreciate for any help


We did familytreedna.com. Then converted file and utilized knowyourgenetics.com web site ...


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