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When they warn of rare disorders, these prenatal tests are usually wrong

nytimes.com

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Re: When they warn of rare disorders, these prenatal tests are usually wrong

#151

Post by thaumasiotes »

OJFord wrote: post #149
thaumasiotes wrote: post #104

Earlier quoted context omitted.

> Its lunacy for tests to be regulated beyond requiring rough false positive false negative rates There is a good reason tests are described in terms of sensitivity and specificity ("if the answer in reality is yes, how often will the test say no?") rather than in terms of false positive or false negative rates ("if the test says no, how often is the true answer yes?"). The sensitivity and specificity are facts about…

I'm not sure GP was intending to make that distinction (rates globally for the test vs. the sample population being tested by.. what a given doctor/hospital?) - I haven't come across that before. If the population is the same then your changed-order definitions are just inverses, and they're just different terms for the same thing.

> I'm not sure GP was intending to make that distinction (rates globally for the test vs. the sample population being tested by.. what a given doctor/hospital?) - I haven't come across that before.

> If the population is the same then your changed-order definitions are just inverses

No, you just haven't understood the concept.

Let's assume some condition has a prevalence of 20%, and a test for it will correctly identify presence of the condition 95% of the time, while correctly identifying absence of the condition 90% of the time. We can immediately answer the first question: when the answer is "yes", the test will say "no" 5% of the time.

You have proposed that when the test says "no", the answer is "yes" a share of the time that might be the inverse of 5%, or perhaps 5% itself. I have no idea what you meant -- and I suspect you didn't either -- but the correct rate of false negatives is not 5%, 95%, nor 2,000%.

In a model population of 10,000 people, we will see this:

                  |  condition present  |  absent  |
    test positive |               1900  |     800  |
         negative |                100  |    7200  |
From this table we can see that the false negative rate is 100/7300 or 1.4%. The false negative rate looks much better than the sensitivity and specificity figures because the condition is rare. The corollary to that is a horrific false positive rate of 800/2700 = 30%.

Re: When they warn of rare disorders, these prenatal tests are usually wrong

#152

Post by derbOac »

rscho wrote: post #144
derbOac wrote: post #99

Earlier quoted context omitted.

I've worked clinically and taught this in professional training programs. It's a classical clinical decision making problem. The solution is fairly straightforward I think: require the test companies to report the posterior probability of the illness given the test result. Probably with some kind of uncertainty interval.

The posterior depends on the prior. So not very feasible in practice.

Generally speaking in clinical settings there are rough estimates of base rates of diseases available, either through biological theory (eg, mutation rates) or empirical studies or both. Not always to be sure, but often enough to mitigate against some of the problems discussed.

Re: When they warn of rare disorders, these prenatal tests are usually wrong

#153

Post by OJFord »

thaumasiotes wrote: post #151
OJFord wrote: post #149

Earlier quoted context omitted.

I'm not sure GP was intending to make that distinction (rates globally for the test vs. the sample population being tested by.. what a given doctor/hospital?) - I haven't come across that before. If the population is the same then your changed-order definitions are just inverses, and they're just different terms for the same thing.

> I'm not sure GP was intending to make that distinction (rates globally for the test vs. the sample population being tested by.. what a given doctor/hospital?) - I haven't come across that before. > If the population is the same then your changed-order definitions are just inverses No, you just haven't understood the concept. Let's assume some condition has a prevalence of 20%, and a test for it will correctly ident…

I don't think I have, it sounds like you think I'm saying false negatives are the inverse of false positives? Not at all, that's obviously not true.

I was surprised at 'sensitivity and specificity' (jointly) being considered different from 'false negatives and false positives' (jointly).

The given reasoning was about population differences, which.. fair enough, I understand that makes a difference, I just wasn't aware that was a standard difference in definition (if it is) and suggested the up thread commenter wasn't (or wasn't meaning to use it) either.

> correctly identify presence of the condition 95% of the time, while correctly identifying absence of the condition 90% of the time. We can immediately answer the first question: when the answer is "yes", the test will say "no" 5% of the time. You have proposed that when the test says "no", the answer is "yes" a share of the time that might be the inverse of 5%, or perhaps 5% itself. I have no idea what you meant -- and I suspect you didn't either

10%. 'inverse', as I called it, of 90%, not 95%.

(That's why I think you think I think (..!) that false negatives/positives rates are derivable from one another. Sorry if not and I'm just still not getting it...)

I don't think I am misunderstanding though - Wikipedia calls them 'true pos/neg rate', and gives formulae for false pos/neg rates as 1-true: https://en.m.wikipedia.org/wiki/Sensitivity_and_specificity

Re: When they warn of rare disorders, these prenatal tests are usually wrong

#154

Post by thaumasiotes »

OJFord wrote: post #153
thaumasiotes wrote: post #151

Earlier quoted context omitted.

> I'm not sure GP was intending to make that distinction (rates globally for the test vs. the sample population being tested by.. what a given doctor/hospital?) - I haven't come across that before. > If the population is the same then your changed-order definitions are just inverses No, you just haven't understood the concept. Let's assume some condition has a prevalence of 20%, and a test for it will correctly ident…

I don't think I have, it sounds like you think I'm saying false negatives are the inverse of false positives? Not at all, that's obviously not true. I was surprised at 'sensitivity and specificity' (jointly) being considered different from 'false negatives and false positives' (jointly). The given reasoning was about population differences, which.. fair enough, I understand that makes a difference, I just wasn't awar…

> it sounds like you think I'm saying false negatives are the inverse of false positives? Not at all, that's obviously not true.

No, I think you're saying that the false negative rate as I defined it in my comment is the inverse of sensitivity. You've corrected me to say that you think the rate I defined is the inverse of specificity, which makes even less sense. And you did that despite the fact that I included a full calculation demonstrating that that isn't true.

Wikipedia's definition of the false negative rate differs from mine. Wikipedia indeed defines the false negative rate as (1 - sensitivity), though not, as you seem to believe, (1 - specificity). But you get no credit for this, because I explicitly defined what I meant by the false negative rate, and you echoed that definition in your response to my comment:

>>> your changed-order definitions

So: you think you haven't misunderstood what's happening. I ask you this: in my table above, I believe that prevalence is 20%, sensitivity is 95%, and specificity is 90%. Please verify that.

I have said that the conditional probability P(condition present | test negative) is 1.4%. You responded saying that that probability is actually 10%:

>> You have proposed that when the test says "no", the answer is "yes" a share of the time that might be the inverse of 5%, or perhaps 5% itself.

> 10%

Where are you getting that figure from? Show me in the table.

Re: When they warn of rare disorders, these prenatal tests are usually wrong

#155

Post by rayiner »

lelanthran wrote: post #123
rayiner wrote: post #112

Earlier quoted context omitted.

Why stop there? It can be a challenge to have a kid who is ADHD, or is susceptible to depression or mental illness, or a different sexual orientation, etc. It’s not wrong to abort those children either, right?

> Why stop there? It can be a challenge to have a kid who is ADHD, or is susceptible to depression or mental illness, or a different sexual orientation, etc. It’s not wrong to abort those children either, right? But we don't stop there. The bar is considerably lower than "the kid might have problems". The mother, exclusively, can decide whether or not she wants to proceed with the pregnancy through to birth, and she…

> The mother, exclusively, can decide whether or not she wants to proceed with the pregnancy through to birth, and she doesn't need a reason other than "I don't feel like it".

The morality of that is quite vigorously contested. And even in places that have elective abortion, it’s often only available in the first trimester, while many of these tests are performed after that.

But even if we accept the notion of elective abortions, it doesn’t follow that any reason is morally acceptable. What if the parents don’t want girls, like often is the case in India and China. It’s okay to abort them? What if we had an in vitro test for sexual orientation? Would it be okay to abort fetuses in that basis?

Re: When they warn of rare disorders, these prenatal tests are usually wrong

#156

Post by BoorishBears »

jacobolus wrote: post #143
BoorishBears wrote: post #141

Earlier quoted context omitted.

The passive-aggression will only get you so far... here's the comment you seem to have already forgotten replying to: > Anyone trying to shickle a few dollars from the medical system to provide "pre-natal diagnosis" without sound science - they can come burn in the same hell I live in every day. Where's the ambiguity?! How much more clear could this be? > Anyone trying to shickle a few dollars from the medical system…

You are repeatedly making very strong, incorrect (quite aggressively insulting) claims about my intentions based on your own invented assumptions, despite having been told directly that you were incorrect. You now claim that actually I am lying about what my intentions were. You insist that I was previously intending to be insulting and cruel and that by (a) apologizing for being insensitive and (b) denying that was…

I love this.

I ask a very simple question:

> Anyone trying to shickle a few dollars from the medical system to provide "pre-natal diagnosis" without sound science - they can come burn in the same hell I live in every day.

Where's the ambiguity?

And there is none so you're forced to divert the conversation to... literally anything but that.

"I don't see any way of convincing you that incredibly direct statement was ambiguous" would have been shorter, no?

-

Continuing this conversation was futile the moment you decided to lie instead of admitting there was no ambiguity and you had just asked a stranger if they wish they had aborted their child for no good reason.

And who knows. Maybe despite appearances some basic understanding of why you don't make statements like the ones you did so casually... has permeated into your subconscious after being schooled on the concept for this many words?

I guess the world will never know

Re: When they warn of rare disorders, these prenatal tests are usually wrong

#157

Post by OJFord »

thaumasiotes wrote: post #154
OJFord wrote: post #153

Earlier quoted context omitted.

I don't think I have, it sounds like you think I'm saying false negatives are the inverse of false positives? Not at all, that's obviously not true. I was surprised at 'sensitivity and specificity' (jointly) being considered different from 'false negatives and false positives' (jointly). The given reasoning was about population differences, which.. fair enough, I understand that makes a difference, I just wasn't awar…

> it sounds like you think I'm saying false negatives are the inverse of false positives? Not at all, that's obviously not true. No, I think you're saying that the false negative rate as I defined it in my comment is the inverse of sensitivity. You've corrected me to say that you think the rate I defined is the inverse of specificity, which makes even less sense. And you did that despite the fact that I included a fu…

Ok, fine, 'as you defined it'. It's hard to read your table on mobile. My only suggestion was that your definition might not be what the original commenter meant, because it's not my layman's understanding that they're different, but I don't know, maybe they also use your definition, no point arguing about it.

(Though it does seem a little odd to me to object to the comment on the basis of a definition you introduce yourself that even if some sort of standard is something that varies enough that Wikipedia uses a crucially different one.)

Re: When they warn of rare disorders, these prenatal tests are usually wrong

#158

Post by thaumasiotes »

OJFord wrote: post #157
thaumasiotes wrote: post #154

Earlier quoted context omitted.

> it sounds like you think I'm saying false negatives are the inverse of false positives? Not at all, that's obviously not true. No, I think you're saying that the false negative rate as I defined it in my comment is the inverse of sensitivity. You've corrected me to say that you think the rate I defined is the inverse of specificity, which makes even less sense. And you did that despite the fact that I included a fu…

Ok, fine, 'as you defined it'. It's hard to read your table on mobile. My only suggestion was that your definition might not be what the original commenter meant, because it's not my layman's understanding that they're different, but I don't know, maybe they also use your definition, no point arguing about it. (Though it does seem a little odd to me to object to the comment on the basis of a definition you introduce…

> Though it does seem a little odd to me to object to the comment on the basis of a definition you introduce yourself

Notice that I always talk in terms of the question being asked. And your response to me was phrased in the same terms. You didn't say 10% was "the false negative rate", you said it was "the share of the time for which, when the test says 'no', the answer is 'yes'". You didn't say "the false negative rate is the inverse of the true positive rate"; you said "your changed-order definitions are just inverses [of each other]". Those claims are wildly false regardless of what you think "the false negative rate" means, for the simple reason that they make no reference to a "false negative rate".

> It's hard to read your table on mobile.

The table has four cells, eight if you count the labels. I have every confidence that you can do it.

Re: When they warn of rare disorders, these prenatal tests are usually wrong

#159

Post by honkycat »

rayiner wrote: post #155
lelanthran wrote: post #123

Earlier quoted context omitted.

> Why stop there? It can be a challenge to have a kid who is ADHD, or is susceptible to depression or mental illness, or a different sexual orientation, etc. It’s not wrong to abort those children either, right? But we don't stop there. The bar is considerably lower than "the kid might have problems". The mother, exclusively, can decide whether or not she wants to proceed with the pregnancy through to birth, and she…

> The mother, exclusively, can decide whether or not she wants to proceed with the pregnancy through to birth, and she doesn't need a reason other than "I don't feel like it". The morality of that is quite vigorously contested. And even in places that have elective abortion, it’s often only available in the first trimester, while many of these tests are performed after that. But even if we accept the notion of electi…

Moral and legal are two different classifications.

I think it should be LEGAL to have an abortion no matter your reasoning. The reason for this is we need to preserve the bodily autonomy of people who can become pregnant.

Weather or not it is MORAL is another question.

It is LEGAL to protest outside of a veteran's funeral. However, I would argue it is not a MORAL thing to do.

Re: When they warn of rare disorders, these prenatal tests are usually wrong

#160

Post by watwut »

xyzzyz wrote: post #140
watwut wrote: post #131

Earlier quoted context omitted.

This is not true in every state. Abortion is in the process of being outlawed in United States. Texas outlawed it. Supreme court is hostile to it for religious reasons.

It is being outlawed in some states of the Union, not in the United States as a whole. Even if it repeals Roe/Casey, I don’t think that Supreme Court is at all likely to hold that abortion is in fact unconstitutional. As a result, some states will restrict abortion, but others will not.

Roe effectively does not exists. Protections that have been there are not anymore. And the court has very clear politics on the matter.
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