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LittleLab4CF

Super Moderator
Cystic Fibrosis (CF) is the result of an error in a particular gene on both chromosomes. One copy of our 23 different chromosomes are inherited from each parent which means all the cells in our body have 23 from mom, 23 from dad for a total of 46. CF is an autosomal recessive genetic disease for the most part.* This means two copies of the same mutation must be present for CF to happen. Germ cells, our sperm and eggs only have one set and that's where the next generation plays dice. People with a single CF mutation each are "Carriers". When two carriers commit parenthood, there is a one in four chance baby will inherit both mutations.

The Cystic Fibrosis Transmembrane electrolyte Conductance Regulation (CFTR) gene regulates the electrolyte balance between the inside of cells and the surrounding environment. In spite of having "Cystic Fibrosis" in the name, it normally is a healthy gene and not doing much for most cells in our bodies. The wet surfaces in our bodies, epithelial mucosa or mucus membranes and our skin especially mucus glands and glands with mucus like the thyroid, pancreas, salivary glands, adrenal glands and our reproductive glands have the gene activated. The lungs are a near perfect models for glands. This is where CF can do quick and lethal damage. When two identical copies of a CFTR gene error like DF508 are present, the regulation of chlorine in and out of the cell membranes fails to work properly, or at all. The CFTR gene sets up electrolyte regulation by sending instruction templates from the cell's nucleus to instruct the cell to make ion channels or selective portals on the cell membrane that allow chloride ions to selectively move in and out of the cells.

If a person has CF as I described above, chloride ion channels are not functional, too low in count or location around the cell membrane or the channels work improperly like transport in but not out of the cell. Other electrolyte channels exist for other electrolytes as well as a number of other chemical channels. Sodium chloride, Potassium chloride, Calcium chloride the importance of proper chloride ion exchange is life and death in the worst case. When the salt balance inside a cell is higher than outside the cell, either the cell needs to gain water through osmosis or lose chloride. Because of CF, all the nice thin mucus our mucus cells makes is coming out thick, sticky and desiccated because the mucus cells are swollen with water in an attempt to equalize the salt concentration. Osmosis is a powerful force even if it takes on impossible tasks.

*CF's definition is a moving target as we learn more about CF's genetics and the genetic database vs patient's presentation. For many, CF's genetics being discovered in 1989 sounds like a long time ago. This was barely a discovery, we initially thought CF was essentially 4 mutations and they HAD to be identical like G551D on both chromosomes. The list of mutations kept growing as Ambry Genetics invested in more refined testing. The list grew from a few to ~1900 plus a list of theoretical mutations now that the gene has been sequenced.

CF can easily be two different mutations where G551D could be on one chromosome copy and DF508 on the other. Since both mutations are known bad genes, CF's definition now includes this type of variation. With 1900 X 1900 possible combinations, the expression of CF symptoms can be from no issues to a life lasting just a few days. Carriers used to be considered perfectly healthy because one chromosome has a perfectly functioning CFTR gene that compensates more than enough to be symptom free. Oops! Not all CFTR mutations cause CF, even in pairs and a number of carriers like me, have CF diagnosis from sweat chloride.

In the final analysis, treatment of the issues is the prize to keep your eyes on. CF is not a disease you wish on anybody, especially your child. Until very recent introduction of Kalydeco, a genetic drug that is mutation specific and similar CF genetic drugs in the pipeline, genetic testing was mostly a novelty. Then again, sometimes a diagnosis is reaffirming.

Not every pulmonary problem is going to be CF. Culturing pseudo or steno frequently comes from a contaminated instrument or oxygen cannula, something "hospital acquired" would be the likely source. Finding 5T polymorphisms is kind of sketchy when it comes to CF. Five T (5T) polymorphisms and higher are common. A contributor who is very knowledgeable about CF genetics is adamant that T polymorphisms do not contribute to the disease. I have a doctorate in genetics and if I know anything it is to avoid absolutes, or rules in mammalian genetics. Every rule in human genetics will have exceptions. High count T polymorphisms are often seen in symptomatic carriers. This is not scientifically valid, it is a general observation.

Best wishes and hopefully Ambry will have some answers,

LL
 

StevenKeiles

New member
Thanks LL for a good background and update for many. Just to clarify about the 5T polymorphism issue. Everyone carries a certain number of T's that are strung together in intron 8 of the CFTR gene. Most people carry 7 or 9, and about 7% of the population carry 5. Right next to this poly T tract is another string of TG's which usually number 10 or 11, and in some cases 12 or 13. When you have 7 or 9 T's the TG number is irrelevant. However, when you have 5T's and it is paired with a higher number of TG's like 12 or 13 this actually acts like another CF mutation. The higher the TG count the more severe the mutation. So if you have a 5T with only 11 is very mild or even asymptomatic. However with 12 or 13 it is more like a moderate CF mutation and when paired with another CF mutation on the other chromosome can actually cause CF. Every body is different and there is variability with all mutation combinations so you can never predict exactly how the disease will be based on the CF mutations.

Steve
 
F

fel

Guest
Hi Steve,

If you are now tracking this thread I would love for you to try to respond to my question above, which I reposted below. The only update I have is my older son is now clearly showing signs of CF (lung and digestive issues, but still pancreatic sufficient), and my younger son is only showing sinus involvement so far. We are taking part in a full genomic study to try to figure this out.




Hi Steve from Ambry,

I am hoping you can help me understand the genetics of my family -- I had two sons dxed with CF in early April.

Both had positive sweat chlorides (initial sweat test 70 and 76, second sweat test a bit lower in each boy, but still on average across arms over 60) They are ages 17 and 14. The 14 year old was tested owing to sinusitis/nasal polyps. The 17-year old has had a dry cough for over a year, but was only tested when brother came out positive. Neither have ever had serious respiratory issues, but both have asthma, and the younger one had more serious asthma as a preschooler (requiring neb treatments). They both have in tact Vas Deferens. Both boys have been tested for other explanations for having a high sweat chloride (e.g. hypothyroid), and this has been ruled out. Their FEV's are in the 80's to 90's.

I (their mother) have a history of unexplained respiratory issues, sinus issues, and adenoid surgery. I am excellent athletic condition but over the past two years have had breathing issues with exertion. I have a sweat chloride of 37 37. Their bio father/my husband does not desire being tested, but is completely asymptomatic.

Both boys had a full genetic sequence from labcorp. I had a full sequence from Ambry. The boys were dxed with CF based on their sweat chloride, and I have been treated like I have CF since April.

Here's the weird part.
My genetics came up with a potentially benign variant: S912L and a bunch of polymorphisms. No CF. Yet I am responding very well to neb treatments with saline, and my fev's shot up by 20 points.
Older son came up with w1282 and a bunch of polymorphisms.
Younger son came up with S912L and a bunch of polymorphisms.

To me the genetics do not add up. Even if I had a secret allele that was not found in your sequence, I could have only donated it to older son, but not younger son, because I gave younger son S912L. Furthermore, for younger son to have the high sweat chloride and symptoms, he would need another mutation from his father that somehow was not caught in his sequencing, because younger son does not have w1282. But, if my husband had an unsequenced disease causing gene, along with his w1282, he should be sick. My husband is in excellent health, in his 50's with no respiratory issues, and fine fertility.

Is there some way to explain this data? It seems to me there are only three possibilities:
A. Both boys are carriers but for some alternative reason have high sweat chloride.
or
B. Both my husband and I carry genes that were not caught in a full sequence -- but for some reason my husband's version does not make him sick even along side of w1282
or
C. the common polymorphisms somehow add up to interfering with sweat chloride in my sons.

Thoughts?

Thanks,
 

StevenKeiles

New member
Fel,

You certainly seem to have a good understanding of the possibilities. There are a lot of families like yours where the genetics doesn't quite add up. It seems like the S912L is definitely not a severe disease causing mutation and may not be a mild one either but it is possible that it may contribute on some unknown level. What is actually more likely is there are other factors, either like the combination of polymorphisms that are significant or other modifiers that are contributing to the symptoms. There is also the possibility that this is something other than CF. My feeling based on the sweats and symptoms is that these findings are at least contributing in some way but probably not totally and there are likely unknown things that are similar for other families sometimes in that we don't always have the exact answers.

Sorry i could not be more helpful and I wish you the best of luck,

steve
 

Mama2Five

New member
Hi there! Steve, I was hoping you could help me out here. Here are the results of my 3 week old daughter's newborn screening-

CFTR DNA sequencing


Mutation 1-delF508
Mutation 2-I1366T-This sequence change was described in an asymptomatic carrier. No reports link this sequence change to CF. This clinical significance of this change in cystic fibrosis is therefore currently unknown.


Poly T/TG-(TG)10-7T/(TG)10-9T


This child carries one severe CF mutation and one sequence change of unknown clinical significance. Clinical followup for potential symptoms is recommended.
Parent studies would be necessary to determine whether the mutation and the sequence change are on the same or on opposite chromosomes.

--------------------------

I see a few posts up that the poly T stuff was touched on, but I'm still uncertain on what it means. The Dr explained it to us based on her results that when run 10 times and it comes back 11 or higher that's indicative of CF, but a 9 or 7 usually isn't seen in CF. Am I misunderstanding and butchering the information I got?

Also, is a sequence change considered a mutation or just a sequence change? Because if it's not actually considered a mutation, wouldn't that mean it doesn't fall into the category of 2 mutations=cf? I just don't understand.

Based off of her screening, they don't know if she does or doesn't have cf. Based on her sweat test (intermediate: 33 and 30), they don't know is she does or doesn't have cf. We're in a "gray" area. She's being classified as CRMS.

Next is genetic testing on my husband and I in a month. Fecal elastase should be in in a couple of days, and waiting on throat swab results. But I have a feeling both will be normal because she doesn't show any symptoms.
 

emason

New member
I see this thread hasn't received a reply in awhile but I'll try anyhow!

My son is in the CRMS classification. He has a copy of DF508 and a mutation of "varying consequence," G1069R.

I read this entire thread (took multiple hours over multiple days).. I've Google searched and checked forums and I can't find anyone out there that has G1069 . According to the John's Hopkins database, there are only 9 people diagnosed with CF that have a copy of G1069 . And the average sweat chloride for someone with this mutation is in the 40s while also being PI, so not exactly following the "typical presentation."

Any information on this mutation would be appreciated. I'm so curious as to whether this mutation may end up being reclassified one way or the other. I don't quite understand how a mutation gets to be classified as "sometimes" disease causing.
 
G

GoryLori

Guest
I am a rare CFer! I have 2 CFTR mutations that are found in LESS than 1% of all carriers. It took a LONG time to figure me out. The GOLD standard for the diagnosis of CF is NOT the DNA test, but having TWO positive sweat chloride tests done on different days. Keep being persistent and hit up all resources you can to get the CFTR screening to include MORE known mutations. I was never caught on the 25 panel, and would never have been found had the NIH not dug in hard to find my mutations. On the www.cff.org website, you CAN have your physician apply to have your blood screened in their mutation analysis at Johns Hopkins. Their goal is to try to ID almost each person with CF as possible to get the mutation data and for "personalized" medicine, like finding CF drugs that work ONLY for certain mutations (think Kalydeco).
 
S

stephen

Guest
GoryLori,

I’m not dismissing the importance of the Sweat Chloride Test, and indeed it used to be the “Gold Standard”. However, I don’t think that’s the case any more. There are many of us here who have had multiple normal, or near normal, Sweat Test numbers but most assuredly have CF - myself included.

If it was not for a CF diagnosis via DNA Testing 10 years ago, thank G-d, I don’t think I would be alive today. Without that diagnosis, I would not have had access to Pulmozyme and Cayston, which slowed the progression of lung damage.

Today, in addition to being a/the key to diagnosing CF, DNA Testing is playing an ever increasing roll in its treatment. Those of us fortunate enough to be benefiting from Kalydeco are doing so only because our mutations were identified by genetic testing.
 

MyBabyCeline

New member
Fel,

You certainly seem to have a good understanding of the possibilities. There are a lot of families like yours where the genetics doesn't quite add up. It seems like the S912L is definitely not a severe disease causing mutation and may not be a mild one either but it is possible that it may contribute on some unknown level. What is actually more likely is there are other factors, either like the combination of polymorphisms that are significant or other modifiers that are contributing to the symptoms. There is also the possibility that this is something other than CF. My feeling based on the sweats and symptoms is that these findings are at least contributing in some way but probably not totally and there are likely unknown things that are similar for other families sometimes in that we don't always have the exact answers.

Sorry i could not be more helpful and I wish you the best of luck,

steve
Hi Steve,

I'm not sure if you are still following this thread but I'm going to post my question in hopes of getting an answer.

My daughter was diagnosed with CF at birth through newborn screening and CFTR genetic analysis was done at Texas Children's Hospital after almost 2 years of her birth with the following outcome:

**CFTR sequence analysis at BCM Genetics Laboratories confirmed that Celine and her mother have one non-working CFTR mutation, specifically c.2051_2052delinsG. In addition, results indicated that Celine and her father each have the c.2909-15T>G variant in the CFTR gene. Celine is negative for the 5T variant. The c.2051_2052delinsG MUTATION and the c.2909-15T>G VARIANT are on separate chromosomes in Celine. Celine is a CARRIER for Cystic Fibrosis. Based on reports from the medical literature and CF databases the classification of (i.e. clinical significance of) the c.2902-15T>G VARIANT is not conclusive; however, as Celine has no clinical findings of cystic fibrosis (i.e. was ascertained by Newborn Screen), the presence of this variant in Celine is judged to be NOT disease-causing in Celine.
Because only one of Celine's parents has an established disease causing change in one of their CFTR genes, their chance of having a child with cystic fibrosis is very low, <1%. While we expect a child with same genotype as Celine would not be affected with cystic fibrosis, there are several other genes which can potentially modify the clinical outcome in an individual who harbors this genotype. Also, a new deletion, or other mutation in CFTR can occur in the next pregnancy; thus the risk of this couple having a child with cystic fibrosis is NOT 0%.**

As you can see it was stated in the genetic report that she is considered as a carrier of CF. I was wondering if you have any more information regarding the c.2909-15T>G variant and its possible outcomes on a patient. Is it true that anyone carrying this variant along with a disease causing mutation is considered a carrier and not affected with CF?

Thank you in advance.
 

A B

New member
Hi. My daughter has df508 and 2789+2insA. I was wondering if anyone could tell me about the second mutation. What type/class is it? I am desperate for any Information. Thank you!
 

CFDAD2018

New member
STEVEN AMBRY


Question on L183i also known as the c.547C>A - Cystic Fibrosis mutation

Hello Steven

Very recently my daughter who will be 8 years of age in June was diagnosed with Cystic Fibrosis at Boston Children Hospital based on the following

1. Sweat test result 62 mmol/L
2. Mild respiratory symptoms

Subsequent to this the doctor ordered a Genetic testing and the result came back as her having a Variant of unknown significance on one of the genes – The other gene had no mutation. the variant identified was p.L183I also known as the c.547C>A. This was very interesting because the mutation was only on one gene and nothing on the other

Apart from the mild respiratory problems my daughter seems to be very healthy – she has a very good height to weight ratio 4 feet 2 inches and a weight of 27.6 kg – also her stool Elastase test came out to be a bit low but not low to require enzymes

As we continue to investigate this further, is any one on this forum aware of this mutation?


The doctor has called for a repeat sweat test on 04/05 for my daughter – it would be nice to hear your thoughts on my questions

Thanks in advance
 
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