Re: Vaccine safety claims do not stand up to scrutiny
Thanks to John Stone for raising the issue of long term MMR vaccine safety.
Almost 50 years after the introduction of the MMR vaccine, I was the first to describe the role of GAD65 containing chick embryo cell culture contamination of the MMR vaccine in causing type 1 diabetes (T1D). [1–3] GAD65 is of course a major autoantigen in T1D. What does that tell us about current vaccine safety systems?
As expected, the tick-borne encephalitis (TBE) vaccine, another GAD65 containing chick embryo cell culture contaminated vaccine, was found to significantly increase risk of T1D. 
This problem is identical to the Pandemrix induced narcolepsy  disaster – a case of molecular mimicry between a non-target protein in the vaccine and a self antigen, resulting in an autoimmune disease.
DeStefano et al. reported T1D odds ratio for MMR vaccine is 1.36, Hib is 1.14, Varicella is 1.16. Patterson et al. reported T1D odds ratio for tetanus vaccine is 1.57 and diphtheria is 1.27. 
Assuming 90% vaccine uptake and calculating the number of cases for the US population of 320 million, we get ~1 million cases of T1D. Estimated total for T1D cases from American Diabetes Association is 1.25 million. So epidemiological studies show that the vast majority of T1D cases in the US were vaccine induced.
Szumilas  points out that, “In practice, the 95% CI is often used as a proxy for the presence of statistical significance if it does not overlap the null value (e.g. OR=1). Nevertheless, it would be inappropriate to interpret an OR with 95% CI that spans the null value as indicating evidence for lack of association between the exposure and outcome.”
As described above, DeStefano et al.  inappropriately dismissed their MMR/T1D OR=1.36 (0.70-2.63) finding, due to this common mistake in interpreting the statistics. The consequences are devastating.
1. Arumugham V. Role of MMR II vaccine contamination with GAD65 containing chick embryo cell culture in the etiology of type 1 diabetes [Internet]. 2017. Available from: https://www.zenodo.org/record/1034771
2. Arumugham V. Cancer immunology, bioinformatics and chemokine evidence link vaccines contaminated with animal proteins to autoimmune disease: a detailed look at Crohn’s disease and Vitiligo [Internet]. 2017. Available from: https://www.zenodo.org/record/1034777
3. Arumugham V. Bioinformatics analysis links type 1 diabetes to vaccines contaminated with animal proteins and autoreactive T cells express skin homing receptors consistent with injected vaccines as causal agent [Internet]. 2017. Available from: https://www.zenodo.org/record/1034775
4. Beyerlein A, Strobl AN, Winkler C, Carpus M, Knopff A, Donnachie E, et al. Vaccinations in early life are not associated with development of islet autoimmunity in type 1 diabetes high-risk children: Results from prospective cohort data. Vaccine. 2017;35(14):1735–41.
5. Ahmed SS, Volkmuth W, Duca J, Corti L, Pallaoro M, Pezzicoli A, et al. Antibodies to influenza nucleoprotein cross-react with human hypocretin receptor 2 (ABSTRACT ONLY). Sci Transl Med. 2015;7(294):294ra105–294ra105.
6. Stratton K, Ford A, Rusch E, Clayton EW. Adverse Effects of Vaccines : Evidence and Causality. Injury. 2011. 0-24 p.
7. Szumilas M. Explaining Odds Ratios. J Can Acad Child Adolesc Psychiatry. Canadian Academy of Child and Adolescent Psychiatry; 2010 Aug;19(3):227–9.
8. DeStefano F, Mullooly JP, Okoro CA, Chen RT, Marcy SM, Ward JI, et al. Childhood vaccinations, vaccination timing, and risk of type 1 diabetes mellitus. Pediatrics. United States; 2001 Dec;108(6):E112.
Competing interests: No competing interests