Heterozygous / Homozygous

[RoundTheWorld]

The heterozygous / homozygous nature of mutations is sometimes mentioned here. How do you know whether your mutations are one or the other? Is this something that changes over time and/or linked to the percentage allele burden?

Thanks

[TTA_]

Usually you have this information in the genetic testing. The geneticist will write in the report if this is homozygous or heterozygous, what VAF% and how that should be interpreted.

Heterozygous - only one allele of your gene (we inherit 2 copies of a gene, one from each parent) harbours a pathogenic mutation.

Homozygous - both alleles of your gene harbour the same pathogenic mutation.

If you have a very high allele burden (i.e., constantly above 60%), and the only information you have from the genetic testing is the VAF%, then that high VAF% signals the presence of homozygous genotype (both allele of a gene are mutated, the same mutation).

If mutations are heterozygous, your allele burden can go up to a maximum of 50% (although tests have a bit of error, so even if the results are slightly above 50%, that is most often error), because your other allele of the gene is not mutated.

There is another situation in which you could have two different pathogenic mutations that together cause you the illness. In that case, you have a compound heterozygous genotype. Both alleles of the gene have a pathogenic mutation, only that it is not the same mutation. Your genetic testing report will have this information, including the VAF% for each of the two mutations in this compound heterozygous genotype.

[RoundTheWorld in reply to TTA_]

Thanks for the clear description TTA_.

(My Jak2 report shows only the allele burden percentage - low enough to indicate my case is heterozygous, although I have been diagnosed high risk PV, due to history of blood counts and a previous thrombosis).

[EPguy]

Zygousity is not usually reported in test results. I asked My Dr about it long ago. It's more often checked as part of research. But as TTA_notes in good detail, it can often be inferred. From that it also can be inferred that ET is more likely to be heterozy since VAF tends to be lower. But as always exceptions can be expected.

There is a correlation of having homozy and better response to IFN. This is one post and a sample note from it:

"INF works better for homozygous compared to a heterozygous JAK2V617F" ... "For Jak 2 homozygous type mutation, AB (VAF) reductions occur with low doses and don't improve with more. Heterozygous Jak 2 requires higher doses to get AB reductions"

healthunlocked.com/mpnvoice...

This plot I've posted variously before shows this probable effect, large reductions for PV and proportionately less dramatic for ET. This could reflect their respective VAFs and thus zygousity. So PV with its higher avg VAF shows the larger benefit with presumed higher homozy.

Non-driver mutations can influence these effects.

A separate issue seen in this plot: IFN reductions on avg mildly reverse for PV after 6 years. This was also seen in the Besremi trials. The best VAF responders did not have this reversal I've posted in a different plot. There should be other data on this and we will get better data in ~5 years when both PEG and Bes have been in wide clinical use longer.

PEG 7 year

[RoundTheWorld in reply to EPguy]

Thanks EPGuy.

I don't fit neatly as have PV but allele burden (bloods) is 20%.

What maybe fits better is that I've been on (low and slow approach) Interferon for a while now (5 months); last month's bloods were the first to show a clear improvement in most counts after a move up to 90mcg Peg mid September. I think that fits what you have said re. PV needing a higher dose (shame as I was noticing side effects of more frequent mild dizziness and slight nausea, altho' these may have improved with time).

It's certainly not clear yet - I'd had a venesection a couple of days before the improved blood test and this month several counts have gone back up (maybe partly due to a longer gap between doses due to Peg shortage).

I've moved to Besremi; hopefully will get a more reliable view over the next few months.

Thanks for the info. Hope you are feeling well.

[EPguy in reply to RoundTheWorld]

I'm the same with low VAF with PV. I was 14% at Dx, last read at 5%. But my BMB pointed to ET so I consider my MPN to be vague.

On the dose, it's actually somewhat confusing. Homozy response to lower doses according to the report I cited, and high VAF is likely to be PV with homozy, hence the steep curve. So a PV pt with high VAF fits nicely with this theory.

But we are PV with lower VAF. You may be PV with heterozy and thus need the higher doses as you say. Your IFN response does point that way. Do you have any non-driver mutations? This can have an influence for any zy. I could have held CHR (good blood counts) on 50-70mcg of Bes. (I did an experiment to confirm that) So maybe I am homozy even with Dx of 14%.

Thanks for asking. I had a rare ok month or two, now back to no good. Hence I continue to nag any member on IFN with signs of Sjo risk. I suspect if I'd held the Bes to ~70mcg I might have avoided the outcome in my case.

[RoundTheWorld in reply to EPguy]

I recently had a myeloid panel run; haven’t seen what was included but the Consultant said no mutations were seen other than Jak2.

Sorry you’re back to feeling no good. Hope the next ok period isn’t far away.

[Manouche in reply to EPguy]

Hi EPguy,

You wrote: «  A separate issue seen in this plot: IFN reductions on avg mildly reverse for PV after 6 years. This was also seen in the Besremi trials ».

I suppose you mean VAF and not IFN. In my opinion the slight JAK2 increase after 5 years is due to the gradual lower IFN dosage over the years. I got the same response recently after gradually reducing the dose from weekly 135mcg to 30mcg. I’ve got a very stable complete haematological response for 5 years, but my JAK2 is now up from 2 to 5 % after about 12 months on weekly 30mcg. (Jak2 was 83% at diagnosis in 2019). So we have decided to slightly increase the dose (45mcg) before re-testing the JAK2 VAF in 4 month. Therefore the idea at this stage is not to get an already complete haematological response at the lowest dose, but to get a better molecular response at the lowest dose. As you can see, CHR and CMR are not always connected!

[EPguy in reply to Manouche]

That is a good point, the "maintenance dose" stage may break the CHR- MR correlation. Look fwd to your results, it is a great case study. Do you have approx VAFs thru time and dose at the time? Understand if this is too much hassle.

This plot is a companion to the one above. It shows a fast and complete MR predicted sustained CMR, with non-CMR showing a leveling at years 5-6 and increase after 6. I failed to document where these Figs. come from, likely buried in one of my replies. Also what definition of CMR was used, looks like 1-2%. From this plot, post 6 years was the point of clear divergence.

In this report Bes has a similar leveling at years 5-6, to 8.5% VAF, there is no year 7 data I know of. In another report I will try to relocate the Bes study had a similar divergence relative to the best molecular responders.

nature.com/articles/s41375-...

-

Interesting side note in this report on the point of this thread "allele burden >50%, which is presumed to reflect homozygosity for the JAK2V617F mutation...homozygous JAK2V617F were found in only 11.6% of patients in the ropeginterferon alfa-2b arm in the 6th year of treatment compared with 50.0% of patients receiving hydroxyurea/BAT " So zygousity can change along with VAF reduction.

For Rux users there is no publication to get these sorts of info, (median VAF over long times, zygousity) it would be nice to have.

7 year IFN

[Manouche in reply to EPguy]

Hi EPguy,

You wrote: »Do you have approx VAFs thru time and dose at the time? Understand if this is too much hassle »

My AB test last year (JAK2 5.2%) was done at 115mcg . I was then on 30mcg for about 12 months. I’m now on Pegasys 45mcg/10 days. I’ll re-check the AB in 4 months and I’ll up the Pegasys dose if the JAK2 still goes in the wrong direction! The idea would be to perform an AB test each time the dose is modified.

[EPguy in reply to Manouche]

I found the study this 2nd Figure comes from.

sciencedirect.com/science/a...

"Nine (28%) patients still on study are currently on a dose equal or higher than 90 mcg/week and 15 (47%) are on dose equal or smaller than 45mcg/week. JAK2 status (presume at Dx) or allele burden had no impact on achievement of response (clinical or molecular), time to response or duration of therapy."

CMR was "undetectable". But this study is old (2015) back then undetectable was near 1% I think. We've seen some studies where 2% is a magic number and a recent thread with 10% being that.

It was a small phase 2 study.

[Manouche]

Hi EPguy,

Thanks for sharing this interesting article. Hard to draw any conclusion. This is what ChatGPT has to say about that:

« In long-term studies on polycythemia vera (PV) patients treated with interferon (IFN), median durations of hematologic and molecular response are generally reported between 5 and 10 years, particularly for pegylated interferon-alpha (Peg-IFNα). However, the specific duration varies based on response criteria, IFN type, study cohort, and response definitions. Here’s an overview of current findings:

1. **Hematologic Response**: Studies often report a median hematologic response duration of around 5-10 years. In patients with sustained hematologic control, many maintain complete or partial responses well into the second decade of treatment.

2. **Molecular Response**: Molecular response is generally slower to achieve than hematologic response, with a gradual reduction in the JAK2 V617F allele burden over several years. Median molecular response duration in patients achieving complete response can exceed 5 years, with some studies reporting stability beyond 7-10 years. A subset of patients achieves "deep" molecular responses (e.g., complete molecular remission) but these outcomes are less common and are usually achieved after several years of continuous therapy.

3. **Long-term Studies**: One of the longest follow-up studies (over 7-10 years) demonstrated that pegylated interferon therapy leads to durable responses in a significant proportion of patients, with some maintaining response without therapy after discontinuation.

While more specific median durations vary by cohort, treatment protocol, and IFN type, interferon’s long-term effects in PV remain a benchmark in achieving durable responses, both hematologic and molecular, with ongoing response stability for many patients well beyond 7 years of treatment ».

[Manouche in reply to Manouche]

« In polycythemia vera (PV) patients treated with interferon (IFN) for over five years, a dissociation between **complete hematologic response (CHR)** and **complete molecular response (CMR)** can occur. This means that some patients achieve hematologic control (normalized blood counts) without achieving a deep molecular response (significant reduction or elimination of JAK2 V617F mutation burden). Key predictors and factors associated with this dissociation include:

1. **Initial JAK2 V617F Allele Burden**:

- Patients with a **higher baseline JAK2 V617F allele burden** are less likely to achieve CMR, even if they achieve CHR. High initial mutational loads often require longer treatment duration or higher IFN doses to achieve molecular responses, and some patients may never reach CMR despite long-term treatment.

2. **Duration of Disease Before Starting IFN Therapy**:

- A **longer disease duration prior to IFN initiation** is often associated with a lower likelihood of achieving molecular remission. Patients with longstanding disease may have a more stable clonal population of JAK2-mutated cells, which can be less responsive to IFN at the molecular level.

3. **Age at the Start of IFN Therapy**:

- **Older age** at the start of IFN therapy may reduce the likelihood of CMR. Aging is associated with a higher prevalence of additional genetic mutations, and older patients often show slower or less complete molecular responses.

4. **Presence of Additional Mutations Beyond JAK2 V617F**:

- PV patients who have **additional mutations** (such as in TET2, ASXL1, or DNMT3A) alongside JAK2 V617F tend to have a reduced chance of achieving CMR. These mutations are linked to clonal hematopoiesis and may contribute to molecular persistence despite hematologic control.

5. **IFN Dosage and Treatment Adherence**:

- **Lower cumulative IFN doses** or interruptions in therapy can contribute to the dissociation of CHR and CMR. Patients who receive higher or uninterrupted doses are generally more likely to achieve molecular response, though this must be balanced with tolerability.

6. **Patient's Immune Response Variability**:

- Variations in individual immune response may affect IFN's efficacy in eliminating clonal cells. Some patients have a robust immune response that helps in reducing clonal burden, while others primarily see a normalization of blood counts without significant molecular change.

7. **Bone Marrow Fibrosis**:

- Patients with **early or advancing bone marrow fibrosis** may experience hematologic control through IFN therapy but find it difficult to achieve molecular remission, possibly due to the bone marrow environment supporting persistent clonal hematopoiesis.

Understanding these predictors can help clinicians tailor expectations and therapeutic strategies, monitoring patients for both hematologic and molecular responses and adjusting IFN dosing or considering additional therapies based on individual patient profiles ».

[EPguy in reply to Manouche]

I'm always concerned about hallucinations with AI. When their sources match then I 'm ok with it.

Taking it at its word, CHR and MR "can exceed 5 years" and durations of 5-10 years points to an inflection point after 5 years. A subset gets past this point while the others lose some benefit after 5. This would match the plot above and the apparent trend seen with Bes.

For all our meds studies regularly include a duration of CHR, and thus a loss of it after that for a signif portion of pts, consistent with this AI answer.