The anatomy of a VAP test report

The vertical auto profile (VAP) test is an enhanced lipid profile test. It has been proposed, chiefly by the company Atherotech (), as a more complete test that relies on direct measurement of previously calculated lipid measures. The VAP test is particularly known for providing direct measurements of LDL cholesterol, instead of calculating them through equations ().

At the time of this writing, a typical VAP test report would provide direct measures of the cholesterol content of LDL, Lp(a), IDL, HDL, and VLDL particles. It would also provide additional measures referred to as secondary risk factors, notably particle density patterns and apolipoprotein concentrations. Finally, it would provide a customized risk summary and some basic recommendations for treatment. Below is the top part of a typical VAP test report (from Atherotech), showing measures of the cholesterol content of various particles. LDL cholesterol is combined for four particle subtypes, the small-dense subtypes 4 and 3, and the large-buoyant subtypes 2 and 1. A breakdown by LDL particle subtype is provided later in the VAP report.

In the table above, HDL cholesterol is categorized in two subtypes, the small-dense subtype 2, and the large-buoyant subtype 3. Interestingly, most of the HDL cholesterol in the table is supposedly of the least protective subtype, which seems to be a common finding in the general population. VLDL cholesterol is categorized in a similar way. IDL stands for intermediate-density lipoprotein; this is essentially a VLDL particle that has given off some of its content, particularly its triglyceride (or fat) cargo, but still remains in circulation.

Lp(a) is a special subtype of the LDL particle that is purported to be associated with markedly atherogenic factors. Mainstream medicine generally considers Lp(a) particles themselves to be atherogenic, which is highly debatable. Among other things, cardiovascular disease (CVD) risk and Lp(a) concentration follow a J-curve pattern, and Lp(a)’s range of variation in humans is very large. A blog post by Peter (Hyperlipid) has a figure right at the top that illustrates the former J-curve assertion (). The latter fact, related to range of variation, generally leads to a rather wide normal distribution of Lp(a) concentrations in most populations; meaning that a large number of individuals tend to fall outside Lp(a)’s optimal range and still have a low risk of developing CVD.

Below is the middle part of a typical VAP report, showing secondary risk factors, such as particle density patterns and apolipoprotein concentrations. LDL particle pattern A is considered to be the most protective, supposedly because large-buoyant LDL particles are less likely to penetrate the endothelial gaps, which are about 25 nm in diameter. Apolipoproteins are proteins that bind to fats for their transport in lipoproteins, to be used by various tissues for energy; free fatty acids also need to bind to proteins, notably albumin, to be transported to tissues for use as energy. Redundant particles and processes are everywhere in the human body!

Below is the bottom part of a typical VAP report, providing a risk summary and some basic recommendations. One of the recommendations is “to lower” the LDL target from 130mg/dL to 100mg/dL due to the presence of the checked emerging risk factors on the right, under “Considerations”. What that usually means in practice is a recommendation to take drugs, especially statins, to reduce LDL cholesterol levels. A recent post here and the discussion under it suggest that this would be a highly questionable recommendation in the vast majority of cases ().

What do I think about VAP tests? I think that they are useful in that they provide a lot more information about one’s lipids than standard lipid profiles, and more information is better than less. On the other hand, I think that people should be very careful about what they do with that information. There are even more direct tests that I would recommend before a decision to take drugs is made (, ), if that decision is ever made at all.

Triglycerides, VLDL, and industrial carbohydrate-rich foods

Below are the coefficients of association calculated by HealthCorrelator for Excel (HCE) for user John Doe. The coefficients of association are calculated as linear correlations in HCE (). The focus here is on the associations between fasting triglycerides and various other variables. Take a look at the coefficient of association at the top, with VLDL cholesterol, indicated with a red arrow. It is a very high 0.999.

Whoa! What is this – 0.999! Is John Doe a unique case? No, this strong association between fasting triglycerides and VLDL cholesterol is a very common pattern among HCE users. The reason is simple. VLDL cholesterol is not normally measured directly, but typically calculated based on fasting triglycerides, by dividing the fasting triglycerides measurement by 5. And there is an underlying reason for that - fasting triglycerides and VLDL cholesterol are actually very highly correlated, based on direct measurements of these two variables.

But if VLDL cholesterol is calculated based on fasting triglycerides (VLDL cholesterol  = fasting triglycerides / 5), how come the correlation is 0.999, and not a perfect 1? The reason is the rounding error in the measurements. Whenever you see a correlation this high (i.e., 0.999), it is reasonable to suspect that the source is an underlying linear relationship disturbed by rounding error.

Fasting triglycerides are probably the most useful measures on standard lipid panels. For example, fasting triglycerides below 70 mg/dl suggest a pattern of LDL particles that is predominantly of large and buoyant particles. This pattern is associated with a low incidence of cardiovascular disease (). Also, chronically high fasting triglycerides are a well known marker of the metabolic syndrome, and a harbinger of type 2 diabetes.

Where do large and buoyant LDL particles come from? They frequently start as "big" (relatively speaking) blobs of fat, which are actually VLDL particles. The photo is from the excellent book by Elliott & Elliott (); it shows, on the same scale: (a) VLDL particles, (b) chylomicrons, (c) LDL particles, and (d) HDL particles. The dark bar at the bottom of each shot is 1000 A in length, or 100 nm (A = angstrom; nm = nanometer; 1 nm = 10 A).

If you consume an excessive amount of carbohydrates, my theory is that your liver will produce an abnormally large number of small VLDL particles (also shown on the photo above), a proportion of which will end up as small and dense LDL particles. The liver will do that relatively quickly, probably as a short-term compensatory mechanism to avoid glucose toxicity. It will essentially turn excess glucose, from excess carbohydrates, into fat. The VLDL particles carrying that fat in the form of triglycerides will be small because the liver will be in a hurry to clear the excess glucose in circulation, and will have no time to produce large particles, which take longer to produce individually.

This will end up leading to excess triglycerides hanging around in circulation, long after they should have been used as sources of energy. High fasting triglycerides will be a reflection of that. The graphs below, also generated by HCE for John Doe, show how fasting triglycerides and VLDL cholesterol vary in relation to refined carbohydrate consumption. Again, the graphs are not identical in shape because of rounding error; the shapes are almost identical.

Small and dense LDL particles, in the presence of other factors such as systemic inflammation, will contribute to the formation of atherosclerotic plaques. Again, the main source of these particles would be an excessive amount of carbohydrates. What is an excessive amount of carbohydrates? Generally speaking, it is an amount beyond your liver’s capacity to convert the resulting digestion byproducts, fructose and glucose, into liver glycogen. This may come from spaced consumption throughout the day, or acute consumption in an unnatural form (a can of regular coke), or both.

Liver glycogen is sugar stored in the liver. This is the main source of sugar for your brain. If your blood sugar levels become too low, your brain will get angry. Eventually it will go from angry to dead, and you will finally find out what awaits you in the afterlife.

Should you be a healthy athlete who severely depletes liver glycogen stores on a regular basis, you will probably have an above average liver glycogen storage and production capacity. That will be a result of long-term compensatory adaptation to glycogen depleting exercise (). As such, you may be able to consume large amounts of carbohydrates, and you will still not have high fasting triglycerides. You will not carry a lot of body fat either, because the carbohydrates will not be converted to fat and sent into circulation in VLDL particles. They will be used to make liver glycogen.

In fact, if you are a healthy athlete who severely depletes liver glycogen stores on a regular basis, excess calories will be just about the only thing that will contribute to body fat gain. Your threshold for “excess” carbohydrates will be so high that you will feel like the whole low carbohydrate community is not only misguided but also part of a conspiracy against people like you. If you are also an aggressive blog writer, you may feel compelled to tell the world something like this: “Here, I can eat 300 g of carbohydrates per day and maintain single-digit body fat levels! Take that you low carbohydrate idiots!”

Let us say you do not consume an excessive amount of carbohydrates; again, what is excessive or not varies, probably dramatically, from individual to individual. In this case your liver will produce a relatively small number of fat VLDL particles, which will end up as large and buoyant LDL particles. The fat in these large VLDL particles will likely not come primarily from conversion of glucose and/or fructose into fat (i.e., de novo lipogenesis), but from dietary sources of fat.

How do you avoid consuming excess carbohydrates? A good way of achieving that is to avoid man-made carbohydrate-rich foods. Another is adopting a low carbohydrate diet. Yet another is to become a healthy athlete who severely depletes liver glycogen stores on a regular basis; then you can eat a lot of bread, pasta, doughnuts and so on, and keep your fingers crossed for the future.

Either way, fasting triglycerides will be strongly correlated with VLDL cholesterol, because VLDL particles contain both triglycerides (“encapsulated” fat, not to be confused with “free” fatty acids) and cholesterol. If a large number of VLDL particles are produced by one’s liver, the person’s fasting triglycerides reading will be high. If a small number of VLDL particles are produced, even if they are fat particles, the fasting triglycerides reading will be relatively low. Neither VLDL cholesterol nor fasting triglycerides will be zero though.

Now, you may be wondering, how come a small number of fat VLDL particles will eventually lead to low fasting triglycerides? After all, they are fat particles, even though they occur in fewer numbers. My hypothesis is that having a large number of small-dense VLDL particles in circulation is an abnormal, unnatural state, and that our body is not well designed to deal with that state. Use of lipoprotein-bound fat as a source of energy in this state becomes somewhat less efficient, leading to high triglycerides in circulation; and also to hunger, as our mitochondria like fat.

This hypothesis, and the theory outlined above, fit well with the numbers I have been seeing for quite some time from HCE users. Note that it is a bit different from the more popular theory, particularly among low carbohydrate writers, that fat is force-stored in adipocytes (fat cells) by insulin and not released for use as energy, also leading to hunger. What I am saying here, which is compatible with this more popular theory, is that lipoproteins, like adipocytes, also end up holding more fat than they should if you consume excess carbohydrates, and for longer.

Want to improve your health? Consider replacing things like bread and cereal with butter and eggs in your diet (). And also go see you doctor (); if he disagrees with this recommendation, ask him to read this post and explain why he disagrees.

The China Study II: Cholesterol seems to protect against cardiovascular disease

First of all, many thanks are due to Dr. Campbell and his collaborators for collecting and compiling the data used in this analysis. This data is from this site, created by those researchers to disseminate the data from a study often referred to as the “China Study II”. It has already been analyzed by other bloggers. Notable analyses have been conducted by Ricardo at Canibais e Reis, Stan at Heretic, and Denise at Raw Food SOS.

The analyses in this post differ from those other analyses in various aspects. One of them is that data for males and females were used separately for each county, instead of the totals per county. Only two data points per county were used (for males and females). This increased the sample size of the dataset without artificially reducing variance (for more details, see “Notes” at the end of the post), which is desirable since the dataset is relatively small. This also allowed for the test of commonsense assumptions (e.g., the protective effects of being female), which is always a good idea in a complex analysis because violation of commonsense assumption may suggest data collection or analysis error. On the other hand, it required the inclusion of a sex variable as a control variable in the analysis, which is no big deal.

The analysis was conducted using WarpPLS. Below is the model with the main results of the analysis. (Click on it to enlarge. Use the "CRTL" and "+" keys to zoom in, and CRTL" and "-" to zoom out.) The arrows explore associations between variables, which are shown within ovals. The meaning of each variable is the following: SexM1F2 = sex, with 1 assigned to males and 2 to females; HDLCHOL = HDL cholesterol; TOTCHOL = total cholesterol; MSCHIST = mortality from schistosomiasis infection; and MVASC = mortality from all cardiovascular diseases.

The variables to the left of MVASC are the main predictors of interest in the model – HDLCHOL and TOTCHOL. The ones to the right are control variables – SexM1F2 and MSCHIST. The path coefficients (indicated as beta coefficients) reflect the strength of the relationships. A negative beta means that the relationship is negative; i.e., an increase in a variable is associated with a decrease in the variable that it points to. The P values indicate the statistical significance of the relationship; a P lower than 0.05 generally means a significant relationship (95 percent or higher likelihood that the relationship is “real”).

In summary, this is what the model above is telling us:

- As HDL cholesterol increases, total cholesterol increases significantly (beta=0.48; P<0.01). This is to be expected, as HDL is a main component of total cholesterol, together with VLDL and LDL cholesterol.

- As total cholesterol increases, mortality from all cardiovascular diseases decreases significantly (beta=-0.25; P<0.01). This is to be expected if we assume that total cholesterol is in part an intervening variable between HDL cholesterol and mortality from all cardiovascular diseases. This assumption can be tested through a separate model (more below). Also, there is more to this story, as noted below.

- The effect of HDL cholesterol on mortality from all cardiovascular diseases is insignificant when we control for the effect of total cholesterol (beta=-0.08; P=0.26). This suggests that HDL’s protective role is subsumed by the variable total cholesterol, and also that it is possible that there is something else associated with total cholesterol that makes it protective. Otherwise the effect of total cholesterol might have been insignificant, and the effect of HDL cholesterol significant (the reverse of what we see here).

- Being female is significantly associated with a reduction in mortality from all cardiovascular diseases (beta=-0.16; P=0.01). This is to be expected. In other words, men are women with a few design flaws. (This situation reverses itself a bit after menopause.)

- Mortality from schistosomiasis infection is significantly and inversely associated with mortality from all cardiovascular diseases (beta=-0.28; P<0.01). This is probably due to those dying from schistosomiasis infection not being entered in the dataset as dying from cardiovascular diseases, and vice-versa.

Two other main components of total cholesterol, in addition to HDL cholesterol, are VLDL and LDL cholesterol. These are carried in particles, known as lipoproteins. VLDL cholesterol is usually represented as a fraction of triglycerides in cholesterol equations (e.g., the Friedewald and Iranian equations). It usually correlates inversely with HDL; that is, as HDL cholesterol increases, usually VLDL cholesterol decreases. Given this and the associations discussed above, it seems that LDL cholesterol is a good candidate for the possible “something else associated with total cholesterol that makes it protective”. But waidaminet! Is it possible that the demon particle, the LDL, serves any purpose other than giving us heart attacks?

The graph below shows the shape of the association between total cholesterol (TOTCHOL) and mortality from all cardiovascular diseases (MVASC). The values are provided in standardized format; e.g., 0 is the average, 1 is one standard deviation above the mean, and so on. The curve is the best-fitting S curve obtained by the software (an S curve is a slightly more complex curve than a U curve).

The graph below shows some of the data in unstandardized format, and organized differently. The data is grouped here in ranges of total cholesterol, which are shown on the horizontal axis. The lowest and highest ranges in the dataset are shown, to highlight the magnitude of the apparently protective effect. Here the two variables used to calculate mortality from all cardiovascular diseases (MVASC; see “Notes” at the end of this post) were added. Clearly the lowest mortality from all cardiovascular diseases is in the highest total cholesterol range, 172.5 to 180; and the highest mortality in the lowest total cholesterol range, 120 to 127.5. The difference is quite large; the mortality in the lowest range is approximately 3.3 times higher than in the highest.

The shape of the S-curve graph above suggests that there are other variables that are confounding the results a bit. Mortality from all cardiovascular diseases does seem to generally go down with increases in total cholesterol, but the smooth inflection point at the middle of the S-curve graph suggests a more complex variation pattern that may be influenced by other variables (e.g., smoking, dietary patterns, or even schistosomiasis infection; see “Notes” at the end of this post).

As mentioned before, total cholesterol is strongly influenced by HDL cholesterol, so below is the model with only HDL cholesterol (HDLCHOL) pointing at mortality from all cardiovascular diseases (MVASC), and the control variable sex (SexM1F2).

The graph above confirms the assumption that HDL’s protective role is subsumed by the variable total cholesterol. When the variable total cholesterol is removed from the model, as it was done above, the protective effect of HDL cholesterol becomes significant (beta=-0.27; P<0.01). The control variable sex (SexM1F2) was retained even in this targeted HDL effect model because of the expected confounding effect of sex; females generally tend to have higher HDL cholesterol and less cardiovascular disease than males.

Below, in the “Notes” section (after the “Reference”) are several notes, some of which are quite technical. Providing them separately hopefully has made the discussion above a bit easier to follow. The notes also point at some limitations of the analysis. This data needs to be analyzed from different angles, using multiple models, so that firmer conclusions can be reached. Still, the overall picture that seems to be emerging is at odds with previous beliefs based on the same dataset.

What could be increasing the apparently protective HDL and total cholesterol in this dataset? High consumption of animal foods, particularly foods rich in saturated fat and cholesterol, are strong candidates. Low consumption of vegetable oils rich in linoleic acid, and of foods rich in refined carbohydrates, are also good candidates. Maybe it is a combination of these.

We need more analyses!

Reference:

Kock, N. (2010). WarpPLS 1.0 User Manual. Laredo, Texas: ScriptWarp Systems.


Notes:

- The path coefficients (indicated as beta coefficients) reflect the strength of the relationships; they are a bit like standard univariate (or Pearson) correlation coefficients, except that they take into consideration multivariate relationships (they control for competing effects on each variable).

- The R-squared values reflect the percentage of explained variance for certain variables; the higher they are, the better the model fit with the data. In complex and multi-factorial phenomena such as health-related phenomena, many would consider an R-squared of 0.20 as acceptable. Still, such an R-squared would mean that 80 percent of the variance for a particularly variable is unexplained by the data.

- The P values have been calculated using a nonparametric technique, a form of resampling called jackknifing, which does not require the assumption that the data is normally distributed to be met. This and other related techniques also tend to yield more reliable results for small samples, and samples with outliers (as long as the outliers are “good” data, and are not the result of measurement error).

- Colinearity is an important consideration in models that analyze the effect of multiple predictors on one single variable. This is particularly true for multiple regression models, where there is a temptation of adding many predictors to the model to see which ones come out as the “winners”. This often backfires, as colinearity can severely distort the results. Some multiple regression techniques, such as automated stepwise regression with backward elimination, are particularly vulnerable to this problem. Colinearity is not the same as correlation, and thus is defined and measured differently. Two predictor variables may be significantly correlated and still have low colinearity. A reasonably reliable measure of colinearity is the variance inflation factor. Colinearity was tested in this model, and was found to be low.

- An effort was made here to avoid multiple data points per county (even though this was available for some variables), because this could artificially reduce the variance for each variable, and potentially bias the results. The reason for this is that multiple answers from a single county would normally be somewhat correlated; a higher degree of intra-county correlation than inter-county correlation. The resulting bias would be difficult to control for, via one or more control variables. With only two data points per county, one for males and the other for females, one can control for intra-country correlation by adding a “dummy” sex variable to the analysis, as a control variable. This was done here.

- Mortality from schistosomiasis infection (MSCHIST) is a variable that tends to affect the results in a way that makes it more difficult to make sense of them. Generally this is true for any infectious diseases that significantly affect a population under study. The problem with infection is that people with otherwise good health or habits may get the infection, and people with bad health and habits may not. Since cholesterol is used by the human body to fight disease, it may go up, giving the impression that it is going up for some other reason. Perhaps instead of controlling for its effect, as done here, it would have been better to remove from the analysis those counties with deaths from schistosomiasis infection. (See also this post, and this one.)

- Different parts of the data were collected at different times. It seems that the mortality data is for the period 1986-88, and the rest of the data is for 1989. This may have biased the results somewhat, even though the time lag is not that long, especially if there were changes in certain health trends from one period to the other. For example, major migrations from one county to another could have significantly affected the results.

- The following measures were used, from this online dataset like the other measures. P002 HDLCHOL, for HDLCHOL; P001 TOTCHOL, for TOTCHOL; and M021 SCHISTOc, for MSCHIST.

- SexM1F2 is a “dummy” variable that was coded with 1 assigned to males and 2 to females. As such, it essentially measures the “degree of femaleness” of the respondents. Being female is generally protective against cardiovascular disease, a situation that reverts itself a bit after menopause.

- MVASC is a composite measure of the two following variables, provided as component measures of mortality from all cardiovascular diseases: M058 ALLVASCb (ages 0-34), and M059 ALLVASCc (ages 35-69). A couple of obvious problems: (a) they does not include data on people older than 69; and (b) they seem to capture a lot of diseases, including some that do not seem like typical cardiovascular diseases. A factor analysis was conducted, and the loadings and cross-loadings suggested good validity. Composite reliability was also good. So essentially MVASC is measured here as a “latent variable” with two “indicators”. Why do this? The reason is that it reduces the biasing effects of incomplete data and measurement error (e.g., exclusion of folks older than 69). By the way, there is always some measurement error in any dataset.

- This note is related to measurement error in connection with the indicators for MVASC. There is something odd about the variables M058 ALLVASCb (ages 0-34), and M059 ALLVASCc (ages 35-69). According to the dataset, mortality from cardiovascular diseases for ages 0-34 is typically higher than for 35-69, for many counties. Given the good validity and reliability for MVASC as a latent variable, it is possible that the values for these two indicator variables were simply swapped by mistake.