On BioScience and Life and Such

Flip a coin Diagnostics ? Worse ? Better ?

In Uncategorized on February 25, 2009 at 3:40 pm

post to news.thinkgene.com

A good easy to do , quick test for colorectal cancer is something diagnostic labs have been wanting (and trying to make) for many years. Now, DNA-direct has introduced a new genetic test. The test is based on methylation of the vimentin gene.

As a learning excercise for myself (and my lab), I’m going to run through the numbers to try to assess whether this is a good test or not and consequently whether we should look into something similar (like this commercial test-kit).

The Bayesian method of assessment is very general and can be used for any diagnostic test where the following is known:

  1. Disease incidence – Colorectal cancer in US approx 50 / 100 000 = 0,05 % (numbers from National Cancer Institute).
  2. Test specificity (true negatives) – approx 86 % (from DNA-direct web site).
  3. Test sensitivity (true positives) – approx 75 % (from DNA-direct web site).

Now what we want to do is calculate the Bayesian probability of actually having cancer when you have a positive test result (procedure from here). Summary of calculations as follows: i) 75 % of 50 true cancer patients test positive = 37,5, ii) 100-86 = 14 % of 99950 true healthy patients test positive = 13993. Bayesian probability i/ii = 0,27 %.

The test may be cost-effective as a general population screening test since a positive test means your chances of having colon cancer at the time of testing has increased from 1/2000 to 6/2000. In addition, if you choose the right age group (aged over 50), screening using this test may be a good thing. Decisions on population screening however, are made  by health officials on a national level and not by individual labs.

Representing an individual lab and seeing that the chances of you having cancer when you receive a positive test result using this test is, – believe it or not -, o,3 %, which means that out of a thousand people tested only 3 of them will be diagnosed correctly, – the only possible conclusion must be:

Worse than a coin flip, – Not a test I would use in my laboratory.

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  1. Once again, surprisingly a new genetic test is announced for detecting colon cancer or cancer localized elsewhere. In my opinion, we all, including NCI Members, who did not responde me UNTIL NOW to my question, referred later on, have to think that ignoring or overlooking Oncological Terrain “and” Oncological Terrain-Dependent COLON Inherited Real Risk, we shall not be able to realize who has to be enrolled in the research, aiming to prevent malignancy! Please read the following mail, I have sent to NCI:
    23 October 2007 h 7,24 AM
    cancer.gov_staff@mail.nih.gov
    Dear NCI Cancer USA,
    I’m not surprised reading your (not) answer, at all.
    You are – as usually – evidently “evasive” (See Attachment) in answering me, who suggest also you from years a new way in the war against cancer: at my best knowledge, the ONLY primary prevention of malignancy, i.e., performed exclusively in individuals involved by both ONCOLOGICAL TERRAIN and ONCOLOGICAL REAL RISK! (Ask to Google.com…..)
    What do you think about these new concepts in Medicine?
    In your modest opinion, do ONCOLOGICAL TERRAIN and ONCOLOGICAL REAL RISK really exsists? Please give me a CLEAR answer!
    I fear that you all ignore complitely what newborn-pathological, type I, subtype a) ONCOLOGICAL, INHERITHED Endoarteriolar Blocking Devices do means! (See Bibliography in http://www.semeioticabiofisica.it , for instance, N° 140: The Lancet, …
    Admittedly, oncologists all around the world, including those of my “dear” country, prefer “CURE” (!!!) patients involved by cancer, rather than to prevent it, due to clear reasons.
    Perhaps, you do not apparently understand my thoughts and theories, due to my POOR english.

    Have you fortune in discover a new, wonderfull, efficacious drug against malignancy.

    Best regards.

    Sergio Stagnaro MD
    Riva Trigoso (Genova) EUROPE
    Who’s Who in the World, and in America
    since 1996 to 2007
    Presentation in http://www.semeioticabiofisica.it

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