A Spreadsheet for Calculating Your Levine Phenotypic Age
An excellent paper by M. E. Levine, et al, entitled "An epigenetic biomarker of aging for lifespan and healthspan" describes a technique for combining nine blood-work values with calendar age to calculate your Mortality Score (probability of death in the next ten years) and your Phenotypic Age, i.e., your apparent biological age as implied by your blood variables. The calculation procedure is rather arcane, involving non-obvious unit conversions, exponentials, and logarithms, so I have produced an Excel spreadsheet (LINK) for performing these calculations.
Levine, et al., also used an elaborate DNA analysis of many blood samples to find what they call the DNAm PhenoAge, a measure of the degree of DNA methylation present, a phenomenon associated with aging. They correlate this measure with the Phenotypic Age, showing that they track very well. My spreadsheet uses a fit to their plots to estimate your DNAm PhenoAge and the modified Mortality Score that it implies.
You may already have blood-work giving the nine blood variables needed to use this spreadsheet, but if not they can be obtained by purchasing the blood-work of LifeExtension's Chemistry Panel & Complete Blood Count (CBC) ($35) and their C-Reactive Protein (CRP), Cardiac ($42). On the spreadsheet at the upper line of blue numbers, you simply enter your values in place of the ones presently there and enter your decimal calendar age in the last column. The calculated results then appear in red on the last line.
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albedo said:
JGC
Along the lines of the answer you got from Dr. Horvath (thank you), Dr. Levine answered my note on the relative roles played by the clinical biomarkers used for the phenotypic age calculation. While recognizing the RDW's big impact on the estimate, she warns the weights listed in the table were not standardized to allow for a direct comparison.JGC DanMcL
Thinking about the weights in Levine et al paper and the discussion here and in the previous thread on their relative importance, I wonder if you have any take on her reply that they are not standardized to allow for a direct comparison.
Happy and healthy new year!
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albedo
I take her reply to mean that the weights came out of an inscrutable digital optimization, with no input from the researchers as to what the importance of the input factors should be. As for the "standardized" comment, I don't know what that means or how it would be done.
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JGC
I understand and I am a bit disappointed this is not addressed in the paper, neither it is in the Phenotypic Age paper yet to be published though.
For "standardized" I understand it as previously mentioned but of course I might be wrong and never went really through the details, I might ask the authors again.
“...In statistics, standardized [regression] coefficients, also called beta coefficients or beta weights, are the estimates resulting from a regression analysis that have been standardized so that the variances of dependent and independent variables are 1.[1] Therefore, standardized coefficients refer to how many standard deviations a dependent variable will change, per standard deviation increase in the predictor variable…. Standardization of the coefficient is usually done to answer the question of which of the independent variables have a greater effect on the dependent variable in a multiple regression analysis, when the variables are measured in different units of measurement (for example, income measured in dollars and family size measured in number of individuals).”
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albedo JGC
Yes that's the correct quote in this context I believe. In simple terms they found the coefficients from a model fit (the model has many inputs and from a large sample set), so in this sense it's only relevant/accurate by plugging all your values into the resultant equation. To 'standardize' the variables would mean that you would be able to look at them in isolation.
I think it gets back to my hack earlier; the most accurate way of learning how to 'optimize' your blood work would be to play with the numbers in the spread sheet and see how they affect the output. But going further and saying one variable is 'more important' than another is going out on a limb.
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DanMcL albedo
You may recall that a month ago I made 5% variations in all the variables and generated a table that is shown above. This indicated the importance of age, RCDW, MCV, and glucose in influencing the resulting value. What it doesn't show is the correlations between the variables (i.e, are they measuring the same thing), which would show up in a more thorough statistical analysis.
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JGC DanMcL
Thank you for your replies. Food for thought ...
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Thank you JGC for making this excellent spreadsheet.
From your calculations RDW, MCV and glucose are the top three markers affecting PhenoAge. It seems all three can be changed with dietary interventions, namely reducing iron, increasing HDL, and altering food choices to reduce insulin. I looked at my bloodwork from twelve years ago and I my PhenoAge has declined 10 years. I am now 57 with a PhenoAge of 45. My wife is 48 with a PhenoAge of 33.
With this new knowledge I will work on reducing iron further and see what the calculator has to say.
It might be useful for people to share their data and the slowest agers habits might then be able to be copied by others.
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Anyone here who tried to compare aging.ai and Levine's Phenotypic Age results?
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Thanks much JGC! Finally, a decent (r=.94 vs. .8 for aging.ai according to Mike Lustgarten, ie. much better correlation).
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Dennis
I guess you refer to this reference right?
https://michaellustgarten.com/2019/09/09/quantifying-biological-age/
(also, what Mike Lustgarten refers to as "PhenoAge" should be referred to as "Phenotypic Age" as in the original Levine's paper, IMHO)
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Dennis
For the record, at 64 I have aging.ai at 40 and Phenotypic Age at 50, over 15 years a quadratic fit shows r=0.73 and r=0.89 respectively.
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albedo Right!
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albedo I corrected this to "Phenotypic Age" in the original post. Thanks!
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michael lustgarten
Thank you. Must absolutely free time to look more at your great blog. We have a very similar approach. I am also on Loncecity and its Biological Age thread in particular. I recollect a particular attention to AI and microbiome which is essential, it is one of my next steps.
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Thanks for the great info JGC! I just got my bloodwork the other day but they gave me a BUN/creatinine ratio vs. just creatinine and I haven't been able to get the spreadsheet to work since I am retired and don't have a spreadsheet program. I have all the other info and would love to know my pheno age after a year on Met and 8 months on Rap. etc. Uping my DHEA, Zn, and HGH secretagogues after the Fahy art. Any suggestions anyone? I imagine if I call and pester them, I could get a creatinine value since they must have it since they have the ratio! I have been using fisetin, quercetin and PL as well as the LEF senolytic tabs, and NMN, etc., so am doing pretty good at 75.
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Dennis
Great. Really wonder why you only have the ratio. I have done a couple of tests in US in the past (LabCorp) and always got BUN and Creatinine separately as in my my EU lab. Here (EU) they usually do not give RDW (but MCV) but I extrapolated my US values. I would ask them.
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Dennis
I haven't actually tried it, but I believe that OpenOffice, which is free, provides an Excel-like alternative that will execute my spreadsheet.
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Dennis Google sheets works with the file. It's free.
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Larry Thanks!
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Dennis said:
Uping my DHEA, Zn, and HGH secretagogues after the Fahy art.What do you take as HGH secretagogues? Also have you ever checked also your IGF-1? Just curious, need to have that in good balance too, not too high, not too low.
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albedo Don't see an IGF-1 listed this last time but I'll check back later since I don't remember it being of concern. I'm trying Arg but even more importantly have upped my workouts since that can up HGH like 350% vs. Arg which you have to take like 12-15g to even get a 100% increase if memory serves me.
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I used Google Sheets which worked great with the Excel file. I'm 58 years old. My AI3.0 age was 38, my Phenotypic age is 45.17 and my DNAage using a urine sample was 63! That last number is terrible and is in the >99 percentile. What the hell is with that? Something really wrong with my kidneys? All my lab work looks normal. 😲
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Again and again (on myself and those daring to share results) I am seeing AI 1.0 higher than AI 3.0 with a trend different than Phenotypic Age and DNAage (not done yet) much closer to CA. Looking at trends there looks to be a sort of break-even intercept with AI (both versions) higher than Phenotypic Age at low CA and vice-versa at higher CA. Phenotypic Age includes CA and increases monotonically with CA. I wonder about statistical and ethnicity biases. I guess large longitudinal population studies would be needed to compare results.
@Larry
I would not panic. Look carefully at your clinical, check you eGFR and other kidney markers, read, fight aging but be happy!
CA=chronological age
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Larry You said you did a DNAage test with URINE? I did one July 2020, it was a blood kit using latest Horvath clock. I am 55 yo, came back 52 (85th percentile).
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