Reproducibility of results in the genetics of predisposition eng 2014

REPRODUCIBILITY OF RESULTS IN THE GENETICS OF

PREDISPOSITIONS AND THEIR PREDICTIVE VALUES

Nikita N. Khromov-Borisov

First Pavlov State Medical University of St. Petersburg

[email protected]

+7 952-204-89-49; +7 921-449-29-05

http://independent.academia.edu/NikitaKhromovBorisov

1

• Reported at the Seminar of Theodosius Dobzhansky Center for Genome Bioinformatics

• 25 June 2014

• http://dobzhanskycenter.bio.spbu.ru/en/seminar

2

Key words:

• genetics of predisposition,

• genetic polymorphism,

• genetic association,

• evolutionary medical genomics,

• neutral evolution,

• genetic load,

• opposite pleiotropy,

• homeostasis,

• reproducibility,

• predictive values,

• Bayesian graphs,

3

The best way to discuss scientific issues is to discuss them in a foreign language

Max Ludwig Henning Delbrück, FRS (September 4, 1906 – March 9, 1981)

Piotr Slonimski (9 November 1922–25 April 2009)

4

Methodology of restrictions and limitations

• Most fundamental scientific principles are in fact exclusions (“taboos”) and the progress of science is associated with the recognition of the importance of some principal restrictions and/or limitations.

• It is impossible to create perpetuum mobile.

• It is impossible to move with the superluminal speed.

• It is impossible to heat the hot body by the cold one.

• Two identical fermions (e.g. two electrons) cannot occupy the same quantum state simultaneously (Pauli exclusion principle).

• Replication, transcription and/or translation of proteins is impossible (Central dogma of molecular biology). Etc.

5

Science is not omnipotent

• Not always and not all of the results of basic research lead immediately to practical application.

• Some of them only indicate the insurmountable uncertainty and fundamental limitations of our abilities.

• These include attempts to diagnose the predisposition to the multifactorial diseases and syndromes using genetic testing.

6

The essences of science are replication and reproducibility

• The essence of science is replication:

• a scientist should always be concerned about what would happen if he or another scientist were to repeat his experiment. Guttman, 1983.

• Scientists have elaborated method of determining the validity of their results.

• They learned to ask the question: are they reproducible? Scherr, 1983.

• Reproducibility is like the ghost that will always come back to haunt you.

• http://datapede.blogspot.ru/2014/03/part-1z-p-value-surviving-mosquito.html

7

Begley C.G., Ellis L.M. Raise standards for preclinical cancer research // Nature, 2012. – Vol. 483. – P. 531-533.

• Glenn Begley, former vice president of the well-known biotech company Amgen, and his colleague Lee Ellis recently have reported that scientists of the company failed to confirm the results of 47 of the 53 articles that appeared to be very fruitful to run programs for manufactioring new drugs.

• Begley and Ellis state that the poor reproducibility of the results becomes a systemic problem of modern science.

• In one study, which was cited in a short period more than 1900 times, even the authors themselves later were unable to reproduce their own results.

8

From the history of epidemiological studies: Risk factors for cancer (Jenks S., Nancy Volkers N. Razors and Refrigerators and

Reindeer — Oh My! JNCI, 1992)

• Using electric razor: increase the risk of developing leukemia.

• Distal forearm fractures in women: Reduction in overall cancer incidence, breast cancer incidence, and incidence of tumors.

• Fluorescent lighting: melanoma in male but not in females.

• Allergies and cancer: At first the inverse relationship. Later several types of cancer were elevated. However, ovarian cancer risk decreased with increasing numbers of allergies.

• Breeding reindeer (разведение оленей): in Swedish Lapps decreased risks for cancers of the colon, female breast, male genital tract, kidneys, respiratory system, and for lymphomas. However, increased risk for stomach cancer.

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• Waiters in Norway: decreased risk of stomach cancer but excess risks of cancers of the liver, rectum, upper respiratory and digestive tracts, and lung. Higher mortality rate from lung cancer.

• Owning a pet bird: fourfold increase in lung cancer risk among pigeon fanciers (more hazardous than living with a smoker). Owners of budgies, canaries, finches, or parrots were OK.

• Height: lower risks for some cancers in short men, particularly colorectal cancer, and lower risks for this cancer and for breast cancer in short women. But being tall may confer some advantage for certain cancers (esophageal, endometrial and cervical), while tall men have only a slightly elevated risk for prostate, kidney and colon cancers.

• Refrigerators: seems protect everyone from stomach cancer.

10

• An extensive list of curious and questionable medical observations about the various risk factors, was given in the work:

• Buchanan A.V., Weiss K.M., Fullerton S.M.

• Dissecting complex disease: the quest for the Philosopher’s Stone?

• International Journal of Epidemiology 2006. – Vol. 35. – P. 562–571

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Table of irreproducible results?

• Hormone replacement therapy and heart disease

• Hormone replacement therapy and cancer • Stress and stomach ulcers • Annual physical checkups and disease

prevention • Behavioural disorders and their cause • Diagnostic mammography and cancer

prevention • Breast self-exam and cancer prevention • Echinacea and colds • Vitamin C and colds • Baby aspirin and heart disease prevention • Dietary salt and hypertension • Dietary fat and heart disease • Dietary calcium and bone strength • Obesity and disease • Dietary fibre and colon cancer • The food pyramid and nutrient RDAs • Cholesterol and heart disease • Homocysteine and heart disease

• Inflammation and heart disease • Olive oil and breast cancer • Fidgeting and obesity • Sun and cancer • Mercury and autism • Obstetric practice and schizophrenia • Mothering patterns and schizophrenia • Anything else and schizophrenia • Red wine (but not white, and not grape juice)

and heart disease • Syphilis and genes • Mothering patterns and autism • Breast feeding and asthma • Bottle feeding and asthma • Anything and asthma • Power transformers and leukaemia • Nuclear power plants and leukaemia • Cell phones and brain tumours • Vitamin antioxidants and cancer, aging • HMOs and reduced health care cost • HMOs and healthier Americans • Genes and you name it!

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Myths about AB0

• Human blood group system AB0 can serve as an classic example of unacknowledged associations with the different conditions.

• Several incredible phenomenon were reported:

• Persons with A have more severe hangovers;

• Persons with 0 have more healthy teeth;

• Military with 0 are spineless and with B are more impulsive;

• Persons with B are more prone to crime;

• There is strong connection between AB0 and nutrition: for each group its own diet; allele 0 is supposedly more ancient and therefore its carriers were hunters and carnivores, and allele A is younger and therefore its carriers were farmers and vegetarians;

• Persons with A2 have higher IQ;

• Persons with B defecate too often.

• All these connections are not reproduced and virtually forgotten.

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• The only associations between AB0 blood groups and malignant neoplasms, thrombosis, peptic ulcers, bleeding, bacterial and viral infections are still regarded as statistically “proven“.

• Alas, these associations have no clinical (practical) importance due to low values of odds ratio (OR) which do not exceed the value of OR = 1.5.

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Associations between AB0 blood groups and diseases, which are considered to be statistically “proven”

Medical condition A > 0 0 > A B/AB > A/0 OR

Malignancy X 1.2 – 1.3

Thrombosis X

Peptic ulcers X 1.2 – 1.4

Bleeding X 1.5

E. coli / Salmonella X

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Edgren G, Hjalgrim H., Rostgaard K., Norda R, Wikman A, Melbye M., Nyré O. Risk of gastric cancer and peptic ulcers in relation to AB0 blood type: a cohort study

Am. J. Epidemiol., 2010. – Vol. 72. – P. 1280–1285

Blood group

Donors Cases with the gastric cancer

N f with 99% CI Cause N f with 99% CI

A 478633 0.4380.4400.441 Deficit 331 0.410.470.52

AB 57904 0.05260.05320.0539 Excess 45 0.0410.0670.102

B 122819 0.1120.1130.114 Deficit 66 0.070.100.14

0 428978 0.3930.3940.396 Excess 246 0.310.370.43

HWE, Pval 9∙10-83 0.12

Homoge-neity

Pval 0.034

BF01 68.5

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The authors argue that this large Danish-Swedish cohort study confirms the “association” between blood group A and gastric cancer. Actually in control group the deviations from the HWE is observed due to deficiency of allele A. Moreover, the difference between groups is statistically minor and OR = 1.15.

Rubanovich A.V., Khromov-Borisov N.N. Theoretical Analysis of the Predictability Indices of the Binary Genetic Tests. Russian Journal of

Genetics: Applied Research, 2014, Vol. 4, No. 2, pp. 146–158.

• It is customary to interpret OR values ≤ 1.5 as virtually worthless, from 1.5 to 3.5 - very low, from 3.5 to 9.0 - moderate, from 9.0 to 32 - high and > 32 - very high.

• Our theoretical study shows that when OR < 2.2, marker has notoriously low predictive performance in all respects and at all frequencies of occurrence of the disease and the marker.

• The marker can be a good classifier, if OR > 5.4, provided that its population frequency is sufficiently high (pM > 0.3).

• In practice, this means that to these inequalities must satisfy the lower bounds of the confidence interval for the estimated value of OR.

• Earlier, similar values of critical levels for observed effects in the genetics of predispositions were offered for the relative risk (RR < 2 and RR > 5, respectively).

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Zhang B., Beeghly-Fadiel A., Long J., Zheng W., Genetic Variants Associated with Breast Cancer Risk: Comprehensive Field Synopsis, Meta-Analysis, and

Epidemiologic Evidence. Lancet Oncol., 2011; 12(5): 477–488

• More than 1,000 candidate-gene in breast cancer association studies have been published in the last two decades, which have evaluated more than 7,000 genetic variants.

• While some of these variants may represent true associations with breast cancer risk, many more are false-positive associations which fail to replicate among additional study populations.

• 51 variants in 40 genes showed statistically significant associations with breast cancer risk.

• Cumulative epidemiologic evidence for an association with breast cancer risk was graded as strong for 10 variants in six genes (ATM, CASP8, CHEK2, CTLA4, NBN, and TP53),

• moderate for four variants in four genes (ATM, CYP19A1, TERT, and XRCC3), and

• weak for 37 additional variants. • Additionally, in meta-analyses that included a minimum of 10,000 cases and

10,000 controls, convincing evidence of no association with breast cancer risk was identified for 45 variants in 37 genes.

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High- and moderate-penetrance breast cancer susceptibility genes

Gene Variants Relative Risk,

RR

Population Frequency

(%)

BRCA1 Multiple mutations >10 0.1

BRCA2 Multiple mutations >10 0.1

TP53 Multiple mutations >10 <0.1

PTEN Multiple mutations >10 <0.1

ATM Truncating and missense mutations 2–4 <0.5

CHEK2 1100delC 2–5 0.7

BRIP1 Truncating mutations 2–3 0.1

PALB2 Truncating mutations 2–5 <0.1

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Post genomic era

• We bought at the price of a dollar for

• letter huge book without a table of contents.

• Eric Lander

• After sequencing the human genome we found ourselves in a position of the player of Russian TV capital-show “Field of Dreams”, hwo has guessed all the letters, but was unable to read the word.

20

The number of allele combinations (DNA-sequence variations) is rather incalculable

• As of 23 July 2013, dbSNP listed 62,676,337 SNPs in humans.

• As of 2013, the world population on Earth is estimated at 7.171 billion by the United States Census Bureau (USCB).

• It is obvious that each person carries unique combination of such variants.

• For instance, in forensic genetics using 15 loci with about 10 different STR number in each is sufficient to identify any unrelated person.

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• If to ponder, it is the

• Pauli exclusion principle

• that causes a variety of forms

• of matter at all levels,

• from atoms to living beings,

• the genetics variation in particularly.

22

Sample sizes in physics, chemistry, biology and medicine

• Physicists and chemists works with the samples of different substances which contain 6∙1023 of particles (atoms or molecules) in 1 mole of the pure substance.

• Even 1 nanomole of given substance contains about 1014 such particles.

• These particles may be regarded as rather identical.

• However, we need not to forget that even on the atomic level there are several isotopes of a given chemical element.

• And some of them are radioactive.

• In medicine researchers are limited with the size of the world population which is less then 1010.

• And human population are very heterogeneous.

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Principal contradiction

• Almost all people are dissimilar, even monozygotic (“identical”) twins (CNV, immunoglobulins, fingerprints ).

• Surely this fact is one of the main sources of the low reproducibility and predictive ability of the results in biomedicine.

• Thus, the genetic uniqueness of each person comes into contradiction with the statistical methodology, which requires to analyze large amounts (hundreds and thousands) of identical persons to achieve the certain conclusions.

• When the prevalence of given disease is low and association between a genotype and the disease is weak, the required sample sizes must be of several thousands in both the case and control groups.

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Situation when genetic uniqueness is practically useful: Genetic passport

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Sources of uncertainty of genetic chiromancy and

predictions

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P = G + E + (G x E) + (Gj x Gk) + …

• We should remember the fundamental statement:

• Phenotype (P) is the product of the interaction between genotype (G) and environment (E).

• Such interaction can be primitive (linear, additive) or sophisticated (nonlinear, multiplicative, compensatory, neutralizing, opposite, etc.).

• Some of them can be cryptic, which are not exhibited under normal conditions and so it is hard to reveal them.

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Padmanabhan S., Newton-Cheh C., Dominiczak A.F. Genetic basis of blood pressure and hypertension. Trends in Genetics, 2012. – Vol. 28. – No. 8. - P 1–12

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(a) Hypertension is caused by one mutation and occurs in discrete subpopulations. (b) There is no clear distinction between hypertension and normotension. Hypertension is extreme variant of the continuum and has a polygenic nature.

Heritability and the environment

Components of genetic and environmental variability are clearly distinct

Continuity and interpenetration of genetic and environmental variability

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There are no common disorders — just the extremes of quantitative traits

• We predict that research on polygenic liabilities

• will eventually lead to a focus on quantitative

• dimensions rather than qualitative disorders.

• The extremes of the distribution are important medically and socially, but we see no scientific advantage in reifying diagnostic constructs that have evolved historically on the basis of symptoms rather than aetiology.

• A more provocative way to restate our argument is that from the perspective of polygenic liability, there are no common disorders — just the extremes of quantitative traits.

• Plomin R., Haworth C.M.A., Davis O.S.P. Common disorders are quantitative traits. Nature Rev. Genet., 2009. – Vol. 10. – P. 872-878.

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Alexey Matveyevich Olovnikov Алексей Матвеевич Оловников

• Aging as an universal chronic “disease of quantitative traits”: cell aging and RNA-dependent ion-modulated gene expression genes.

• Биомедицинский журнал Medline.ru

• Том 4, СТ. 28 (стр. 31)

• Февраль, 2003 г.

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Aging is an universal genetic “disease of quantitative traits”

• During the aging of humans and animals no expression of principally new macromolecules is observed.

• All that occurs during aging, is not a qualitative but quantitative change of various traits, whose number is enormous.

• If aging is really a disease of quantitative

• traits, it is appropriate to target the

• biogerontological research to those key

• molecular mechanisms that underlie the

• regulation of quantitative traits in eukaryotes.

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Environment – internal and external: «Exposome»

Wild C.P. The exposome: from concept to utility. International Journal of Epidemiology, 2012; 41: 24–32

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Influence of the micribiote on the physiology of the human dody

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Variety of determinants of complex phenotype exemplified by the heart hypertrophy

Marian A.J. Molecular genetic studies of complex phenotypes. Translational Research, 2012; 159: 64–79

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A great variety of genetic polymorphism

• SNP — single nucleotide polymorphism,

• miRNA — RNA interference and micro-RNA,

• piRNA — piwi-interacting RNA,

• lncRNA — long non-coding RNA,

• tmRNA — transfer-messenger RNA,

• eccDNA — extrachromosomal circular DNA,

• microDNA — short eccDNA,

• CNV — copy number variations.

• It seems that the association of the last 7 newly discovered elements with diseases is stronger than for SNP.

• They differ even in monozygotic twins and can vary between individual cells of the same tissue (e.g., in the neurons of the brain).

• Let’s don’t forget also about the individual variation in the immunoglobulin genes.

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• The larger the number of factors, both genetic and environmental, influencing given trait (disease or inclination), the greater the unpredictability of the manifestation of this trait.

• The same disease can be determined by different versions of different genes.

• The same gene may be involved in the development of various diseases and syndromes.

• Some versions of the gene (DNA sequence variants, alleles) may predispose to one disease, and other versions - to another disease.

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• Each gene affects many traits, and each trait is determined by many genes.

• Sources of uncertainty and unpredictability:

• penetrance

• expressiveness,

• pleiotropy

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One disease can be influenced by many genes

G-1 G-2 G-3 . . . G-k

Disease

One gene can affect many diseases

Gene

D-1 D-2 D-3 . . . D-k

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Ubiquitous VDR and ESR - receptors of “vitamin” D and estrogen

• VDR activity extends far beyond the metabolism of calcium and parathyroid hormone (PTH).

• It participates in the transcription of 900 genes, some of which are key to health, such as MTSS1 (metastasis suppressor), as well as key components of innate immunity (cathelicidin antimicrobial peptide, beta-defensins, TLR2 - toll-like receptor, etc. ).

• VDR role in innate immunity is unique to humans. • No other animal model (e.g. mouse) did not develop such an

evolutionary function for this receptor. • Estrogen receptor ESR directly or indirectly is responsible for

the expression of 6,000 genes, i.e. 26% of the entire genome.

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ESR

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Unpredictability of genetic predispositions

• Knowing the genotype we cannot unambiguously predict the phenotype, and vice versa:

• Knowing the phenotype it is not possible to predict unequivocally the genotype.

• The validity of the uncertainty principle in genetics is extremely clear:

• even knowing the genome sequence of the person, we will never be able to predict many of its features, e.g., to predict the circumference of his waist.

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Multidirectional pleiotropy

• One of the main mechanisms for maintaining homeostasis is pleiotropy (i.e., multiple, branched action of a gene on several traits), especially when it is mutually opposite (“compromise” or “compensatory”) and / or antagonistic.

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Example: The multiplicity of physiological functions of ACE

• Angiotensin-converting enzyme (ACE), is not only the blood pressure monitors, but it also participates in the fertilization process, the formation of immune cells, the development of atherosclerosis.

• Its high expression in macrophages, immune cells, prevents the formation of malignant tumors.

• Therefore, the use of ACE inhibitors can cause cancer and Alzheimer's disease.

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Nawaz S.K., Hasnain S. Pleiotropic effects of ACE polymorphism. Biochemia Medica, 2009. – Vol. 19. – No 1. – P. 36–49.

Association present Association absent Controversial

Diabetic nephropathy Type 2 diabetes Hypertension

Atherosclerosis Diabetic retinopathy Coronary heart disease and stroke

Alzheimer disease Allele D is “preventing”

Gastric cancer Colorectal cancer

Parkinson’s disease Systemic lupus erythematosus Longevity

Breast cancer

Oral cancer

Treatment of osteoporosis

Diseases allegedly “associated” with the indel dimorphism in the ACE gene

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Brown highlighted associations that in Russia continue to be considered established.

Sivakumaran S., Agakov F., Theodoratou, E., Prendergast J.G., Lina Zgaga L., Manolio T., Rudan I., McKeigue P., Wilson J.F., Campbe H. Abundant Pleiotropy in Human

Complex Diseases and Traits. Am. J. Hum. Genet., 2911; 89: 607–618

Demonstration of «abundant» pleiotropic action of genes associated with Crohn’s disease

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Conclusion

• Щелкни кобылку в нос – она махнет хвостом

• Козьма Прутков

• Click the filly on the nose - it wag its tail

• Koz’ma Petrovich Prutkov

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Janssens A.C.J.W., van Duijn C.M. An epidemiological perspective on the future of direct-to-consumer personal genome testing.

Investigative Genetics, 2010; 1:10

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Amizing phenomena of genetic predisposition testing

• Fuzzy phenotypes.

• Winner's curse.

• Discordant conclusions.

• Genotyping errors.

• Mania of secrecy.

• Multi- and oppositely directed pleiotropy.

• Inadequate statistical analysis.

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Fuzzy (poorly distinguishable, not alternative) phenotypes – the shadow of Lamarck

• Low efficiency of results in the genetics of predispositions already lies in the uncertainty of the determination (diagnosis) of the studied trait.

• For example, how to distinguish an “athlete” from a “smug”?

• As non-athletes the persons leading a sedentary lifestyle are often sampled.

• But if you think about it, this is pure Lamarckism asserting the influence of "exercise" and “non-exercise“ of an organ on its evolutionary destiny.

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Winner's curse

• Too often, initially promising discoveries that typically cause great excitement, are not reproduced in subsequent studies.

• This phenomenon is called the “winner's curse” (проклятье победителя).

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Discordant conclusions

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Ng P.C., Murray S.S., Levy S., Venter J.C. An agenda for personalized medicine. Nature, 2009; 461: 724-726. About one half of conclusions presented by two companies (23andMe and

Navigenics) contradicts one another.

Imai K., Kricka L.J., Fortina P. Concordance Study of 3 Direct-to-Consumer Genetic-Testing Services. Clin. Chem., 2011; 57(3): 518–521

Relative disease risk assigned by 3 DTC services for a series of diseases evaluated by all 3 services. Values in parentheses indicate the number of SNPs analyzed .

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Kalf R.R.J., Mihaescu R., Kundu S., de Knijff P., Green R.C., Janssens A.C.J.W. Variations in predicted risks in personal genome testing for common complex diseases. Genetics in Medicine, 2014; 16(1): 85-91

• Predicting risks vary significantly between companies due to differences in the sets of SNPs used and the average values of the population risk, as well as the differenses in the formulas used to calculate the risks.

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Comparison of risks for three multifactorial diseases predicted by 23andMe, deCODEme and Navigenics

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Comparison of risks for three multifactorial diseases predicted by 23andMe, deCODEme and Navigenics

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Adams S.D., Evans J.P., Aylsworth A.S. Direct-to-Consumer Genomic Testing Offers Little Clinical Utility but Appears to Cause Minimal

Harm. N. C. Med. J.m, 2013; 74(6): 494-499

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CURRENT ONCOLOGY, 2009; 16(1): 56-58

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Conspiracy mania

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Honesty: article retraction due to genotyping errors

• Sebastiani P., Solovieff P.N., Puca A., Hartley S.W., Melista E., Andersen S., Dworkis D.A., Wilk J.B., Myers R.H., Steinberg M.H., Montano M., Baldwin C.T., Perls T.T. Retraction. Science, 2011; 333: 404

• After online publication of our Report "Genetic Signatures of Exceptional Longevity in Humans“ in Science Express, July 1, 2010, we discovered that technical errors and an inadequate quality control protocol had introduced errors in our results.

• We engaged an outside academic laboratory to independently assess the quality of the data and remove ambiguous data that could lead to false results and then a portion of the remaining data was double checked using a different genotyping platform.

• We then re-performed the same analysis and found that the main scientific conclusions are supported by the corrected results.

• Because some details of the new analysis do change however, we are voluntarily retracting the original manuscript and are pursuing alternative publication of the corrected results.

• We will be happy to discuss our amended findings as soon as they are published.

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Growth of the number of publications on genotyping error

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• Too many sloppy mistakes are creeping into scientific papers.

• Lab heads must look more rigorously at the data — and at themselves.

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Theodosius Dobzhansky, 1973

• Nothing in Biology Makes Sense

Except in the Light of Evolution.

• The American Biology Teacher, 1973. – Vol. 35. – P. 125-129.

• «Ничто в биологии не имеет смысла кроме как в свете эволюции».

• Феодосий Добржанский

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Pierre Teilhard de Chardin

• “Evolution is a light which illuminates all facts, a trajectory which all lines of thought must follow - this is what evolution is”. • «Эволюция есть свет, который освещает все

факты, траектория, которой должны следовать все линии мышления – вот что такое эволюция».

• Pierre Teilhard de Chardin - one of the greatest thinkers of our time.

• Teilhard was a creationist, but such who understood that Creation is realized in this world through evolution.

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Peter Brian Medawar

• “For a biologist, the alternative

to thinking in evolutionary terms

is not to think at all”

• Medawar P., Medawar J.S, The Life Science: Current Ideas in Biology, London: Wildwood House, 1977

• «Для биолога альтернативой мышлению в эволюционных терминах является не думать вообще».

• «Биолог может мыслить только эволюционно — другой альтернативы для него не существует».

• Медавар П., Медавар Дж. Наука о живом.—М.: Мир, 1983.—207 с.

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Ajit Varki, J. Mol. Med., 2012

• “Nothing in medicine makes sense, except in the light of evolution”. • «Ничто в медицине не имеет смысла кроме

как в свете эволюции». • “Understanding human evolution, where we

came from, is very important to understanding who we are and where we’re going.”

• «Понимание эволюции человека, т.е. того, откуда мы пришли, очень важно для понимания, куда мы идем».

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Two fundamental questions

• «Nothing in biology [as well as in medicine] makes sense except in the light of evolution».

• From such point of view, genetics of predispositions has to answer two basic questions:

• 1. Is the natural genetic polymorphism identified with modern genomics proved to be the result of neutral evolution or whether it is an aggravated genetic (mutation) load determining the susceptibility to common diseases, which inexplicably has not been culled by the natural selection well-timed?

• 2. Are effects of different predisposing alleles synergistic or at least additive when combined in a single genotype, or they are mutually neutralized?

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• Evolutionary and population arguments help us to understand that the «genetics of predispositions» studies natural balanced genetic polymorphism, i.e. not newly formed alterations of genes (mutations), but alleles passed natural selection and fixed in human populations; not anomalies, not pathological or pathogenic variants of the genome are investigated, but infinite number of its natural, «normal» variants.

• Thus the answers on the above two questions are:

• 1. Evolutionary medical genomics testifies that the vast majority of polymorphic variants of genes (alleles) that are observed in the genomes of modern human populations are selectively neutral.

• 2. In many cases, the effects of various predisposing alleles are mutually neutralized through the mechanisms of opposite (antagonistic) pleiotropy and homeostasis.

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• Indeed, it appears that the coding, i.e. functionally important regions in the human genome, show a much lower degree of variation than non-coding, i.e. whose function is unknown.

• The absolute number of synonymous variants outnumber nonsynonymous (missense) variants, despite the fact that the number of positions at which non-synonymous variants can occur, is 3 times higher than the position with the possibility of synonymous mutations.

• Proportion of synonymous variants is 4 times greater than non-synonymous (80% and 20% respectively).

• In general, the neutralist evolutionary views lead to the conclusion that historical adaptive evolutionary events are not the source diseases.

• On the contrary, evolution is a source of stability and the reason why human beings so successfully exist in widely varying conditions.

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• Neutrality and balance explain the fact that the predisposing genotypes are found both in patients and in healthy, and the only difference is their frequency in groups of subjects with given disease and without it.

• That is, certainly the presence of predisposing alleles in the genotype of given person is not indicative of the inevitable presence of given disease or other propensity in the present or its occurrence in the future.

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• The second principal question:

• Are effects of different predisposing alleles synergistic or at least additive when combined in a single genotype, or they are mutually neutralized?

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Frequency distributions in two sample of persons with extreme values of blood pressure for 35 alleles predisposing to

hypertension

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The distributions are almost completely overlapping.

Paynter N.P., Chasman D.I., Pare G., Buring J.E., Cook N.R., ScD, Miletich J.P., Ridker P.M. Association between a literature-based genetic risk score and cardiovascular

events in 19,313 women // JAMA, 2010. – Vol. 303. – No. 7. – P. 631–637.

GRS - genetic risk score – do not improve risk prediction for cardiovascular diseases.

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Thromboembolism, 11 markers (Капустин С.И., 2007)

76

0 2 4 6 8 10 12Число предрасполагающих аллелей

0

25

50

75

100

125

Чи

сл

ен

но

сть

593 patients with venous thrombosis, Control group of 225 persons

Pval = 0.046 (Mann-Whitney test); Pval = 0.52 (χ2); BF01 = 105

Bayes’ theorem in action

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DgPDPDgPDP

DgPDPgDPPPV

||

||

11

111

DgPDgPDPDgPDgPDP

DgPDgPDPggDPPPV

||||

||,|

2121

21212,1

Artificial, but rather typical example

• Let the prevalence of the disease with the elements of hereditary predisposition (D) in a population is

• P(D+) = 1%.

• Assume that the proportion of carriers of the genotype (allele or haplotype) g1, predisposing to this disease equals

• P(g1|D+) = 20%,

• and it is two times higher than for individuals without this disease:

• P(g1|D-) = 10%.

• This corresponds to the values RR = 2 and OR = 4,4.

• According to Bayes formula the probability of this disease in patients with the genotype g1 at approximately 2-fold higher than its prevalence:

• PPV1 = P(D+|g1) = 1,98% ≈ 2%.

• Obviously, on the basis of such a small value it is hardly to get convincing predictions about the presence or development of this disease in a particular individual.

78

Predictive values of several predisposing genetic markers

Number of predisposing loci in a genotype

PPV

Proportion of carriers of the predisposing genotype in population

1 0.020 0.1

2 0.039 0.01

3 0.075 0.001

4 0.14 0.0001

5 0.24 10-5

6 0.39 10-6

7 0.71 10-7

8 0.84 10-8

9 0.91 10-9

10 0.95 10-10

79

Odds ratios (OR) for the 2 type diabetes corresponding to the number of the predisposing allele in the genotype

80

Persons at high genetic risk are very rare

• Really, the larger the number of predisposing alleles in the genotype, the higher the risk of disease.

• Theoretically it is possible to identify people with a very high risk of the disease, but in practice they will be extremely rare.

• And it is difficult if impossible to prove that given rare combination of predisposing alleles is responsible for the presence of given disease in given person.

• In vast majority of persons the risk of disease only slightly higher (or lower) than the average risk of disease in the population.

81

• Let us imagine that we will be able to gather in one genome almost all known alleles predisposing to a particular sport pursuits.

• Obviously, due to the non-additivity of interactions of intergenic and environmental factors the athletic performance of a person with such genotype will not be proportional to the number of predisposing alleles.

• It seems to be unlikely that combining 200 predisposing alleles in one genome will result in a 200-fold increase in sports performance of such persons.

• And due to opposite directed pleiotropic action of these alleles will our Superman appear to become a “superidiot”?

82

The predictive ability of clinico-genetic certification

83

The main measures of the quality of diagnostic test with the binary outcomes

• Even if the genetic association is statistically highly significant, it certainly raises the question of how useful is this information for risk assessment and prediction of disease?

• For these purposes it is necessary to measure well-known indicators of the diagnostic test quality, such as the sensitivity (Se), specificity (Sp), positive prediction value (PPV), negative prediction value (NPV), positive likelihood ratio (LR[+]) and negative likelihood ratio (LR[+]).

84

Better to see once

• Results of statistical quality control of diagnostic tests is useful to visualize as predictive graphs.

• Examples are shown in Figs.

• The spreadsheet created by R.G. Newcombe PPVNPV.xls may be used

• http://medicine.cf.ac.uk/media/filer_public/2012/11/01/PPVNPV.xls

86 23.04.2014

Lotufo P.A., Chae C.U., Ajani U.A., Hennekens C.H., Manson J.A.E., Male pattern baldness and coronary heart disease: The Physician's Health Study, Arch. Intern. Med. 2000; 160(2): 165-71.

Simon A., Worthen D. M., Mitas J. A.1979. An evaluation of iridology // JAMA, V. 242, N 1, P. 1385-1389.

Alopecia and CAD Iridology and renal failure

87

127/1224/548/7611 LR[+] = 1.01.41.8; LR[-] = 1.01.061.1

29/59/19/36 LR[+] = 0.71.01.4; LR[-] = 0.71.01.5

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• Since the time of Hippocrates (c. 460 – c. 370 BC) it is known that eunuchs do not go bald when they become eunuchs before the age of 25.

• It’s unlikely that any doctor on the basis of these data will recommend to young people to have children up to 25 years and then became eunuchs not to go bald and thus to reduce the risk of developing coronary heart disease by 2%.

• Nevertheless, it is very similar to the recommendations of medical geneticists, most of which are too often based on clinically insignificant values of the indices of predictive abilities of genetic testing.

• Rarely odds ratios in these studies exceed the value • OR > 2.

88

Druzhevskaya A.M, Ahmetov I.I., Astratenkova I.V., Rogozkin V.A. 2008. Association of the ACTN3 R577X polymorphism with power athlete status in Russians // Eur. J. Appl. Physiol., 2008. – Vol. 103. – P. 631–634.

Кундас Л.А., Жур К.В., Бышнев Н.И. и др. Анализ молекулярно-генетических маркеров, ответственных за устойчивость к физическим нагрузкам, у представителей академической гребли // Молекулярная и

прикладная генетика: сб. науч. тр. Институт генетики и цитологии НАН Беларуси; (гл. ред. А.В. Кильчевский). 2013. - Минск: ГНУ «Институт генетики и цитологии НАН Беларуси», Т. 14. – C. 101-105.

Gene ACTN3 and elite athletes Gene PPARG and elite rowers

89

455/1027/31/170 LR[+] = 1.01.11.1; LR[-] = 1.42.23.7

3/3/21/147 LR[+] = 0.95.840; LR[-] = 1.11.21.6

23.04.2014

Mayeux R., Saunders A.M., Shea S., et al. 1998. Utility of the apolipoprotein E genotype in the diagnosis of Alzheimer’s disease // N. Engl. J. Med., 1998. – Vol. 338. – P. 506-511.

Mäki M., Mustalahti K., Kokkonen J., et al. 2003. Prevalence of celiac disease among children in Finland // N. Engl. J. Med, 2003. – Vol. 348. – P. 2517-2524.

Gene APOE and Alzheimer's disease HLA haplotypes and celiac disease

90

1142/133/622/285

LR[+] = 1.72.02.5; LR[-] = 1.71.92.2

54/1357/2/2214 LR[+] = 2.72.52.7; LR[-] = 4.112103

23.04.2014

Banks E., Reeves G., Beral V. et. al. Influence of personal characteristics of individual women on sensitivity and specificity of mammography in the Million Women Study: cohort study // BMJ, 2004. 329(7464): 477-479. Kevin P. Delaney K.P., Branson B.M., Apurva Uniyal A. et al. Performance of an oral fluid rapid HIV-1/2 test:

experience from four CDC studies // AIDS, 2006. – Vol. 20. – P. 1655–1660.

Mammography and breast cancer Rapid test for HIV OralQuick®

91

629/3885/97/117744 LR[+] = 262729; LR[-] = 5.77.29.3

327/12/1/12010 LR[+] = 4959192141; LR[-] = 451653171

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Temptations which should be disposed of

• (1) Catastrophism (or “trillerism") – hypnotizing ourselves and others that our genome is a dump of hazardous alleles.

• (2) Genetitsism - genetic determinism - the blind, fanatical belief in the omnipotence of genes like the statement: "Genetics - the basis of medicine”.

• (3) Eugenics - an underlying desire to correct human nature and to select for a breed of "good" or "right" people, "elite", such as e.g., athletes.

• (4) The commercialization of basic science, which, God forbid, may fall to criminalization.

• Fundamental science loses its chastity and becomes mercenary (corrupt).

• It is pushing on this slippery slope (“on the street") by the science administrators who require science to be self-supporting.

92

Summary

• Poor reproducibility and low predictive values of the results in the genetics of predispositions (genetic association studies) become a systemic problem.

• Results of the statistical quality control of genetic tests in the study should be supported with not only integral indices such as odds ratios (OR), but with the post-test (posterior) predictive probabilities (PPV and NPV) and likelihood ratios (LR[+] and LR[-]).

• Predictive values of the vast majority of genetic markers differs little from the population prevalence of the disease.

• This means that such tests despite high statistical significance of their results are not able to provide clinically important association between the disease and biomarker.

• Extremely rare the odds ratios in the studies on the genetics of dispositions exceed practically critical OR = 5.

• As a result, in most cases, recommendations of medical geneticists are based on clinically negligible (though statistically significant) recognizablity and predictability of genetic markers.

93

Some practical conclusions

• Genetics is the science of heredity and heredity is the fundamental property organisms to pass their traits and peculiarities to the offspring.

• Therefore, results of the genetic association studies should be confirmed by the studies of genetic predispositions at the level of least two generations of relatives, i.e. it is necessarily to analyze families, pedigrees and twins.

• Before engaging in genomics, the registration of genealogies should be initially introduced into clinical practice.

• It is cheaper and more efficient.

94

Statistical audit and free access to the data

• Greatly needed is statistical expertise of papers submitted for publication in biomedical journals.

• Abroad several editorial boards of scientific journals have invited experts on statistics.

• It is necessary to impute the responsibility of reviewers to check the correctness of the calculations.

• For this we need to open the initial (raw) data, as is done, for example, in the journals Science, International Forensic Sciences: Genetics.

• When the results were published in the press, then the original data are no longer the intellectual property of the authors and should be accessible to specialists.

95

Francis Galton, 1901

• “I have begun to think that no one ought to publish biometric results, without lodging a well-arranged and well-bound copy of his data in some place where it should be accessible, under reasonable restrictions, to those who desire to verify his work.”

• «Я начинаю думать, что никто не должен публиковать биометрические результаты без представления хорошо организованной и хорошо переплетенной копии своих данных в некотором месте, где она будет доступна (при разумных ограничениях) тому, кто пожелает проверить его работу».

• Френсис Гальтон

96

Be honest and responsible

• It is necessary to impose a moratorium on hasty clinical (and other practical) application of the results of the genetics of predispositions and their commercialization.

• It is necessary to suspend the activities of firms and companies who engage in “genetic chiromancy”, guessing on “gene tarot”, casting “genetic horoscopes”, etc.

• We urgently need the “genetic laws” and “genetic ethics code.”

• Medical geneticists and clinicians must bear not only moral but also a legal responsibility for their argueble diagnoses and practical advices to patients.

97

FDA warns and accuses: genetic testing is not scientifically justified

• Food and Drug Administration USA (FDA) has sent a WARNING LETTER to 17 companies (23andMe, Navigenics, deCODEme, EasyDNA and others) who are engaged in genetic testing, an order to cease their activities because of the lack of scientific evidence and the inability to accurately predict the risk of diseases.

• http://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/default.htm

23.04.2014 98

Михаил Ефимович Лобашев (11.11.1907 – 04.01.1971) Mikhail Efimovich Lobashev

• In science you can do anything,

• just don’t forget about the consequences and the responsibility.

99

• One of the most common testimony that leads to the greatest disasters is a testimony to acquit one’s action by the words: “all people act in such manner.” Л.Н.Толстой

• Leo Tolstoy

100 23.04.2014

Thank you for attention! Slides are available for anybody

Nikita N. Khromov-Borisov Department of Physics, Mathematics and Informatics

First Pavlov State Medical University of St Petersburg

[email protected]

8-952-204-89-49 (Теле2); 8-921-449-29-05 (Мегафон)

http://independent.academia.edu/NikitaKhromovBorisov

101 23.04.2014

References http://independent.academia.edu/NikitaKhromovBorisov

• Глотов Н.В., Животовский Л.А., Хованов Н.В., Хромов-Борисов Н.Н. Биометрия, Л.: Изд-во ЛГУ, 1982. – 264 с.

• Хромов-Борисов Н.Н. Биометрические аспекты популяционнной генетики. Новые генетические механизмы и их роль в генетико-популяционных процессах. Список рекомендуемой литературы. / Л.З. Кайданов, Генетика популяций, Высшая школа, М., 1996, с. 251-308.

• Хромов-Борисов Н.Н. Синдром статистической снисходительности или значение и назначение P-значения // 16.02.2011 г.

• http://tele-conf.ru/aktualnyie-problemyi-tehnologicheskih-izyiskaniy/

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http://tele-conf.ru/aktualnyie-problemyi-tehnologicheskih-izyiskaniy/









• Хромов-Борисов Н.Н. Современное общедоступное программное обеспечение статистического анализа в молекулярной медицине и генетике. Мастер-класс // Мультидисциплинарные аспекты молекулярной медицины: сборник материалов I Международного форума «Молекулярная медицина – новая модель здравоохранения XXI века: технологии, экономика, образование». 26-27 июня 2013 года. – СПб.: изд-во СПбГЭУ. 2013. – С. 298-307.

• Рубанович А.В., Хромов-Борисов Н.Н. Воспроизводимость и предсказательная ценность результатов в генетике предрасположенностей // Мультидисциплинарные аспекты молекулярной медицины: сборник материалов I Международного форума «Молекулярная медицина – новая модель здравоохранения XXI века: технологии, экономика, образование». 26-27 июня 2013 года. – СПб.: изд-во СПбГЭУ. 2013. – С. 307-314.

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• Хромов-Борисов Н.Н., Рубанович А.В. Эволюционная медицинская геномика // Мультидисциплинарные аспекты молекулярной медицины: сборник материалов I Международного форума «Молекулярная медицина – новая модель здравоохранения XXI века: технологии, экономика, образование». 26-27 июня 2013 года. – СПб.: изд-во СПбГЭУ, 2013. – С. 315-324.

• Обеснюк В.Ф., Хромов-Борисов Н.Н. Интервальные оценки показателей сравнительного медико-биологического исследования // Актуальные проблемы современной науки, 2013. – Т. 2. – № 1. – С. 154-156.

• Рубанович А.В., Хромов-Борисов Н.Н. Теоретический анализ показателей предсказательной эффективности бинарных генетических тестов. Экол. генетика, 2013. – Т. 11. – С. 77-90.

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• Тишков А.В., Хромов-Борисов Н.Н., Комашня А.В., и др. Статистический анализ таблиц 2х2 в диагностических исследованиях. СПб.: Изд-во СПбГМУ, 2013. – 20 с.

• Хромов-Борисов Н.Н., Рубанович А.В. Статистические аспекты генетики предрасположенностей // Иммунофизиология: Аутоиммунитет в Норме и Патологии, Москва, 1-3 Октября, 2012. – C. 305-314.

• Хромов-Борисов Н.Н., Рубанович А.В. Генетика предрасположенностей – разбитые мечты и утраченные грёзы // Иммунофизиология: Аутоиммунитет в Норме и Патологии, Москва, 1-3 Октября, 2012. – C. 315-323.

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• Сельков С.А., Королева Л.И., Тишков А.В., Аникин В.Б., Хромов-Борисов Н.Н. Применение современных статистических методов для оценки взаимосвязи интерферонового статуса здорового новорожденного и его матери // Инфекция и иммунитет, 2012. – Т. 1. – № 4. – С. 331–340.

• Тишков А.В., Хромов-Борисов Н.Н., Комашня А.В., и др. Статистический анализ таблиц 2х2 в диагностических исследованиях. СПб.: Изд-во СПбГМУ, 2013. - 20 с.

• Рубанович А.В., Хромов-Борисов Н.Н. Воспроизводимость и предсказательная ценность результатов в генетике предрасположенностей // Молекулярная медицина, 2014. - № 2. – С. 8-12.

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• Хромов-Борисов Н.Н., Рубанович А.В. Эволюционная медицинская геномика // Молекулярная медицина, 2014. – № 2, С. 13-17.

• Rubanovich A.V., Khromov-Borisov N.N. Theoretical Analysis of the Predictability Indices of the Binary Genetic Tests // Russian Journal of Genetics: Applied Research, 2014, Vol. 4, No. 2, pp. 146–158.

• Хромов-Борисов Н.Н., Тишков А.В., Комашня А.В., Марченкова Ф.Ю., Семенова Е.М. Статистический анализ клинических исследований: таблица 2х2. Версия 1.0. Свидетельство о государственной регистрации программы для ЭВМ № 2012616821 31 июля 2012 г.

23.04.2014 107

Supplement

108

P-value

• P-value is the most controversial concept in statistics.

• The concept of a P-value lies so far from the intuitive understanding that no ordinary person can hold it in memory.

• This cannot do even by many of the statisticians.

• Thus, by definition, the P-value (Pval) is the conditional probability of obtaining the observed data (dobs) and all the others less likely, or more deviated from the expected (D ≥ dobs|H0 ), when the null hypothesis is true.

109

Р-value, Рval

• Thus, in terms of the statistical hypothesis testing, P-value is:

• The probability to obtain observed value tobs. of the t-test statistic and all others less probable (or the values even more deviating from the expected one)

• under assumption that the null hypothesis H0 is true:

•

• Pval = Pr[|T| ≥ |tobs.| | H0].

• Note that the “less probable values” are not observed.

• We infer them out of all possible values in the frame of the chosen (null) model.

110

Popular delusion

• P-value is not a probability of null hypothesis!

• P-value is calculated

• under the assumption

• that null hypothesis H0 is true:

• Pval = Pr{ T* ≥ tobs|H0},

• Hence, P-value cannot be a probability of null hypothesis:

• P{D|H0} ≠ P{H0|D}

111

Meaning of the P-value

112

Nice metaphor

• “Perhaps p values are like mosquitos.

• They have an evolutionary niche somewhere and no amount of scratching, swatting, or spraying will dislodge them”.

• Campbell J.P. Editorial: Some remarks from the outgoing editor. Journal of Applied Psychology, 1982; 67: 691-700

113

• It has long been known that the P-value tells us nothing about the probability of the null hypothesis, or about the size of the effect.

• For this drawback P-value is subjected to severe criticism since its introduction even by William Gosset (Student).

• This is reflected in the International "Uniform Requirements for Manuscripts Submitted to Biomedical Journals":

• “Avoid relying solely on statistical hypothesis testing, such as P values, which fail to convey important information about effect size.”

114

Repeat!

• Often it is believed that if the “statistically significant” result is obtained, this excludes the need of repeating the experiment.

•

• Testing the significance of statistical hypotheses is a method to detect rare events which deserve further investigation.

• Fisher

115

P-value is the realization of corresponding random variable P

• P-value is an observed value of the corresponding random variable

• P*

• When null hypothesis H0 is true, then Pval has so called (continuous) standard uniform distribution, that is uniform distribution on the interval [0; 1]:

• P* ~ Uni[0; 1].

116

P-value distributions Pike N. spreadsheet: FDR.xls http://www.webcitation.org/5rxSzU7qL

Δ = μ1 – μ2 = 0;

χ2 = 390,6; df = 400; Pval = 0,62

Δ = μ1 – μ2 = 10;

χ2 = 1348,8; df = 400; Pval = 4∙10-101

117

0

20

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120

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0

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0.2

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5

0.5

0

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0

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5

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0

0.7

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0

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5

0.9

0

0.9

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p-value defining upper limit of range

Frequency distribution of p-values

Observed frequency Expected frequency

0

2

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10

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Frequency distribution of p-values

Observed frequency Expected frequency

Reproducibility of P-values and confidence intervals Cumming, G. (2008). Replication and p intervals: p values predict the future only vaguely, but confidence intervals do much better. Perspectives on Psychological Science, 3, 286-300.

Program ESCI PPS p intervals http://www.latrobe.edu.au/psy/esci/

mdiff

.001

.074

.798

.818

.006

.096

.011

.125

.905

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** ? *

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118

Reproducibility and predictive ability of P-values and confidence intervals (n = 32)

The program “ESCI PPS p intervals” http://www.latrobe.edu.au/psy/esci/. Cumming G. Replication and p intervals: p values predict the future only vaguely, but confidence intervals do much better // Persp. Psychol. Sci., 2008. - Vol. 3. – P. 286-300.

119

http://www.latrobe.edu.au/psy/esci/














Reproducibility and predictive ability of P-values and confidence intervals (n = 32)

Использована программа “ESCI PPS p intervals” http://www.latrobe.edu.au/psy/esci/. Cumming G. Replication and p intervals: p values predict the future only vaguely, but confidence intervals do much better // Persp. Psychol. Sci., 2008. - Vol. 3. – P. 286-300.

120















Calibration of P-values

• Sellke T., Bayarri M.J., Berger J.O.

• Calibration of p Values for Testing Precise Null Hypotheses

• The American Statistician, Vol. 55, No. 1. (2001), pp. 62-71.

• При

1

0

11

ppeDHP

ln

ep 1

121

122

The “price” of P-values

P-value

Upper limit of 80% intreval for

Pval

Lower limit for the probability of hull

hypothesis P(H0)

Upper limit for the probabililty of

repeat Рrepr

0.05 0.44 > 29% < 50%

0.01 0.22 > 12% < 73%

0.001 0.07 > 2% < 90%

Sellke T., Bayarri M.J., Berger J.O. Calibration of p values for testing precise null hypotheses. The American Statistician, Vol. 55, No. 1. (2001), pp. 62-71. Goodman S.N. A comment on replication, p-values and evidence // Statistics in Medicine, 1992. – Vol. 11. – P. 875-879. Cumming G. Replication and p intervals: p values predict the future only vaguely, but confidence intervals do much better // Perspectives on Psychological Science, 2008. – Vol. 3. – No. 4. – P. 186-300.

122

• Оhence, it is risky to rich definite conclusion from a single experiment only.

• Any scientific investigation should be repeated manifold.

• And a reproducibility of the results must be studied.

123

Джон Уайлдер Тьюки (John Wilder Tukey, 16.04.1915 — 26.07.2000)

• Any research should be at least two-staged.

• First stage – exploratory (preliminary, pilot, hypotheses generating) study.

• Second stage – confirmatory study.

• The second stage is designed on the basis of the results obtained at the first stage.

124

Statistical significance and the effect size

• Effect (difference, association, correlation, risk, benefit, etc.) can be statistically significant, however, its practical (e.g., clinical) importance can appeared to be worthless.

• “Statistically significant” does not imply “substantial”, “practically important”, “valuable”.

• Effects can be real, nonrandom, but nonetheless, negligibly small.

125

Effect Size, ES

• Question of the clinical (practical) importance of the observed

• Effect Size

• is a key when interpreting results of biomedical investigations (e.g., clinical trials).

• ES can be expressed either in the real measurement units, or

• as standardized (nonmetric) quantity.

126

Standardized Cohen’s effect size, dC

pooleds

MMd 21

C

127

Verbal scale for the interpretation of the standardized Cohen’s effect size (Hopkins)

http://www.sportsci.org/resource/stats/

Standardized Cohen’s effect size, dC

Interpretation

0 – 0,2 Negligibly small (worthless)

0,2 – 0,6 Small (weak)

0,6 – 1,2 Moderate

1,2 – 2,0 Large (strong)

2,0 – 4,0 Very large (very strong)

4,0 - Extremely

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Reproducibility of results in the genetics of predisposition eng 2014

Science

Transcript of Reproducibility of results in the genetics of predisposition eng 2014