Science in Society Archive

MMR Controversy Reignites

CDC senior scientist confesses "omitted data" on MMR vaccine safety, while whistleblower virologists accuse vaccine manufacturer of fraud, will the truth out at last? Dr. Mae-Wan Ho

Important developments have come to light in the long-running measles-mumps-rubella (MMR) vaccine controversy, but practically no mainstream media are covering the story; and if they do, they tell a very partial tale.

William Thompson, a senior scientist with the US Center for Disease Control and Prevention (CDC), released a statement via a law firm saying [1]: "I regret that my coauthors and I omitted statistically significant information in our 2004 article published in the journal Pediatrics.  The omitted data suggested that African American males who received the MMR vaccine before age 36 months were at increased risk for autism."

Meantime, pharmaceutical Merck is facing at least two federal court cases over the MMR vaccine, and may well also have to defend itself in US Congress [2]. Representative Bill Posey (a longtime critic of the CDC) and his staff are now reviewing a thousand documents that William Thompson has turned over to Congress.

The controversy was ignited by UK pediatrician Andrew Wakefield in the late 1990s (see [3] The MMR vaccine Controversy*, SiS 13/14). As a result, Wakefield not only lost his job, the paper he coauthored with 12 other researchers reporting a potential link between MMR vaccine, autism, and gastrointestinal inflammation was unilaterally retracted by the Lancet and "discredited", and he was struck off by UK's General Medical Council for serious professional misconduct [4]. Since then, Wakefield has been subject to almost universal vilification by the medical/scientific establishment and the mainstream media. He is still blamed for "measles epidemics", including the current one that appeared to have started in California, but has actually been traced to the Philippines [5]. Wakefield is consistently wrongly accused of being ‘anti-vaccine' [6]. He had only advised against the MMR triple vaccine, recommending instead the single vaccines including the one for measles, which governments have since withdrawn. Merck, the sole manufacturer of MMR vaccine had stopped making the single vaccines since 2008 [7].

Senior scientist went public 10 years after publication

In 2004, William Thompson was one of the five scientists who coauthored a paper entitled, "Age at first measles-mumps-rubella vaccination in children with autism and school-matched control subjects: a population-based study in metropolitan Atlanta" published in the Journal Pediatrics [8].  It reported a case-controlled study in metropolitan Atlanta, Georgia, in which 624 case children (diagnosed with autism and identified from multiple sources) were matched to 1 824 control children on age, gender and school. Vaccination data were abstracted from immunization forms required for school entry. In a separate subgroup, records of children born in Georgia were linked to Georgia birth certificates for "information on maternal and birth factors."

The team used conditional logistic regression to assess the relative risk of autism diagnosis with the age of first MMR vaccination as the independent variable and the incidence of autism the dependent variable. The relative risks were assessed for children receiving the first MMR vaccine before and after 18 months, 24 months and 36 months respectively. The results showed more case than control children were vaccinated before 36 months: 93.4 % vs 90.6 %; the odds ratio (OR) for diagnosis of autism was 1.49, with 95 % confidence interval (CI) 1.04-2.14for the total sample.

This association was explained away by noting that, "vaccination before 36 months was more common among case children than control children, especially among children 3 to 5 years of age, likely reflecting immunization requirements for enrollment in early intervention programs."

The analysis of the birth certificate subsample was ostensibly to adjust for "potential confounding variables", i.e., "maternal and birth characteristics", but "the ORs were not different from unadjusted results for the birth certificate sample." In other words, those potentially confounding variables did not account for the statistically significant increased risk of autism diagnosis.

From Table 3 in the paper summarizing the results in the birth certificate sample, the adjusted analyses (for birth weight, multiple gestation, maternal age and maternal education) gave OR 1.64 (95% confidence interval 0.77 – 3.49) for boys and OR 2.63 (95% confidence interval 0.51 – 13.45 for boys aged 3-5 y.  From Table 5 again for the birth certificate sample, the OR adjusted for black race vaccinated <36 months was 1.68 (CI 0.52-3.47), not too different from the entire subsample.

However, it turns out that the subgroup appears to have been introduced specifically to omit data from hundreds of black boys who did not have birth certificates (see below).

There, the matter might have rested, had William Thompson not gone public over the omitted data.

Re-analysis highlighted increased risk to black boys

Another player enters the fray. Californian biomechanical engineer Brian Hooker had spent 10 years battling the CDC, having submitted over 1 000 Freedom of Inf0rmation Acts to obtain the raw data of the 2004 paper from the CDC. In February 2014, he succeeded with the help of Congressman Bill Posey [9]. Hooker did a re-analysis of the study, restoring the 260 black boys that were omitted because they did not have a Georgia birth certificate [10]. He replicated the earlier results for the total sample, i.e., a statistically significant effect at 36 months (relative risk (RR) 1.49 95% CI 1.04-2.14, p = 0.0289) [11]. However, he also showed that the result appears to be due almost entirely to a stronger risk in boys (RR 1.69, 95% CI 1.11-2.57, p = 0.0138), with girls showing no increase in risk for autism and timing of MMR vaccination at any age group.

Although Hooker used a "more conservative" Pearson's chi-squared method, repeating the analysis with the original conditional logistic regression gave the same results.

When looking specifically at African American children, the results were striking (see Table 2 of the paper). The relationship between the timing of MMR first vaccination and autism becomes more profound, and again it was exclusively in boys. There were statistically significant effects at both age 24 months (RR 1.73 95% CI, 1.09-2.77, p = 0.0200) and 36 months (RR 3.36, 95% CI 1.50-7.51, p = 0.0019). No statistically significant effects were found in girls.

When the African American children were excluded in a third analysis, no significant risks were found for any age group or gender.

Hooker commented (p.3) [11]: "The results show a strong relationship between child age at the administration of the first MMR and autism incidence exclusively for African American boys which could indicate a role of the vaccine in the etiology of autism within this population group. The particular analysis was not completed in the original Destefano et al (CDC) study…the CDC study limited the total African American cohort to include only those individuals who possessed a valid State of Georgia birth certificate which decreased the statistical power of their analysis. Although a statistically significant relationship between the first MMR age and autism incidence was seen in the general (all races) population within the earlier Destefano et al… study, the coauthors interpreted this result as an artifact of "healthcare seeking behavior" citing that autistic children would receive their vaccines earlier in order to enroll in State of Georgia early intervention programs. However, it is highly unlikely that this type of behavior would be seen exclusively in African American males and thus, alternative hypothesis must be explored, including the possibility that the MMR vaccine may be causally linked to autism in African American males."

Hooker cited a previous study [12] that found the prevalence of autism in African Americans nearly 25 % higher than that of the white population, and suggested it might be linked to vitamin D deficiency. Another study Hooker cited [13] reported vitamin D sufficiency among whites between 30 and 50 %, but only 5 to 1o % among African Americans. This is an interesting hypothesis that should be investigated further.

Hooker's study was published online 8 August [10]. On 27 August, the journal removed the article and replaced it with the statement: "This article has been removed from the public domain because of serious concerns about the validity of its conclusions. The journal and publisher believe that its continued availability may not be in the public interest. Definitive editorial action will be pending further investigation."

On 3 October 2014, the journal issued an official retraction:

"The Editor and Publisher regretfully retract the article as there were undeclared competing interests on the part of the author which compromised the peer review process. Furthermore, post-publication peer review raised concerns about the validity of the methods and statistical analysis, therefore the Editors no longer have confidence in the soundness of the findings. We apologise to all affected parties for the inconvenience caused."

But the retracted article was again posted on line (with the "RETRACTED" shadow over all its pages). The grounds for retraction are by no means clear. As far as statistical methods are concerned, Hooker has already stated that both methods gave the same results. As for undeclared "conflict of interest", Hooker has explicitly declared his involvement in "vaccine/biologic litigation"; not surprisingly, as he is father of an autistic son. Counting this as a "conflict of interest" is surely adding insult on misfortune, if not injury.

Wakefield's retracted findings amply replicated worldwide

Meanwhile, the original findings reported in the retracted Lancet paper [14] had been replicated worldwide. A recent follow up paper [15] by Stephen Walker and colleagues at Wake Forest Institute for Regenerative Medicine, North Carolina USA highlighted the fact that prospective , controlled studies now suggest as many as 70 % of autistic children exhibit chronic gastrointestinal (GI)symptoms, and endoscopy examination of ASD (autism spectrum disorder) children with GI symptoms finds high frequency of inflammatory pathology. It appears that the immunologic and inflammatory activity in the bowel may be part of a larger, systemic multi-organ immunopathology.

The team carried out transcriptome profiling of GI muscle biopsy tissue from ASD children and three non-ASD control groups: Crohn's disease, ulcerative colitis and histologically normal. Comparison of differentially expressed transcripts between the groups demonstrated that normal tissue segregated almost completely from inflamed tissue in all cases. Gene expression profiles in intestinal biopsy tissue from patients with Crohn's disease, ulcerative colitis and ASD, while having significant overlap with each other, also showed distinctive features for each group. Taken together, the researchers concluded, the results demonstrate that ASD children with GI inflammation have a gastrointestinal transcriptome that "overlaps significantly with known inflammatory bowel disease, yet has distinctive features that further supports the presence of an ASD-associated IBD variant."

Earlier in 2006, Walker was reported examining 275 children with regressive autism and bowel disease; and of the 82 tested then, 70 proved positive for the measles virus [16]. He was also reported to have said: "What it means is that the study done earlier by Dr Wakefield and published in 1998 is correct. That study didn't draw any conclusions about specifically what it means to find the measles virus in the gut, but the implication is it may be coming from the MMR vaccine. If that's the case, and this live virus is residing in the gastrointestinal tract of some children, and then they have GI inflammation and other problems, it may be related to the MMR."

In June, however, Walker was described reporting his findings at the International Meeting for Autism Research, and saying that an actual link between the MMR vaccine and regressive autism is "tough to prove", and even if a link can be found between the MMR virus and bowel disease, the conclusion will be simply that the measles virus is in the gut of a large number of children who have regressive autism and bowel disease. We haven't done anything to demonstrate that the measles virus is causing autism." This reassured the journalist who reported, wrongly, that there was "no link" [17].

General Medical Council's decision quashed and criticized

Prof. John Walker-Smith, Wakefield's coauthor of the retracted Lancet paper was struck off by the General Medical Council along with Wakefield. But unlike Wakefield, he decided to appeal his case, and won [18]. Justice John Mitting ruled the GMC decision that Walker-Smith was guilty of serious professional misconduct "cannot stand". Calling for changes in the way GMC ‘fitness to practice' panel hearings are conducted, the judge said of the flawed handling of Walker-Smith's case: "it would be a misfortune if this were to happen again." Walker-Smith was supported by parents of some of the children with autism and bowel disease he treated at the Royal Free hospital until his retirement in 2001.

Wakefield is reported to have filed a defamation lawsuit against Brian Deer (the journalist whose accusation of professional misconduct caused him to be struck off by the GMC), the British Medical Journal (BMJ), which featured articles by Brian Deer, and Fiona Godlee, BMJ's editor, for falsely accusing him of "fraud" [19]. The suit is currently underway in Texas, where Wakefield now lives.

Merck faces multiple charges over its MMR vaccine

Merck is meanwhile embroiled at least in two federal court cases [2]. The first court case, United States v. Merck & Co., arises from two former Merck scientists claiming that Merck "fraudulently misled the government and omitted, concealed, and adulterated material information regarding the efficacy of its mumps vaccine in violation of the FCA [False Claims Act]." According to the court documents, Merck  "(i) failed to disclose that its mumps vaccine was not as effective as Merck represented, (ii) used improper testing techniques, (iii) manipulated testing methodology, (iv) abandoned undesirable test results, (v) falsified test data, (vi) failed to adequately investigate and report the diminished efficacy of its mumps vaccine, (vii) falsely verified that each manufacturing lot of mumps vaccine would be as effective as identified in the labeling, (viii) falsely certified the accuracy of applications filed with the FDA, (ix) falsely certified compliance with the terms of the CDC purchase contract, (x) engaged in the fraud and concealment describe herein for the purpose of illegally monopolizing the U.S. market for mumps vaccine, (xi) mislabeled, misbranded, and falsely certified its mumps vaccine, and (xii) engaged in the other acts described herein to conceal the diminished efficacy of the vaccine the government was purchasing." These fraudulent activities, say the whistleblowers, were designed to produce test results that would meet the FDA's requirement that the mumps vaccine was 95 % effective.

The second court case, Chatom Primary Care v. Merck & Co., is a class action suit that relies on the same whistleblower evidence, claiming damages because Merck had fraudulently monopolized the mumps market. Doctors and medical practices in the suit would be able to obtain compensation for having been sold an overpriced monopolized product, and a defective one at that, for the mumps vaccine was not effective. The suit alleges that Merck expected outbreaks to occur, and they did. Mumps epidemics occurred in 2006 in a highly vaccinated population and again in 2009-2010.

Information provided by the Courthouse News Service back in 2012 provides additional information. The complainant Chatom claims that staring in the late 1990s, Merck set out on its sham testing program with the objective of reporting an efficacy of 95% or higher regardless of the vaccine' true efficacy [20]. Chatom says Merck initially called the testing program Protocol 007. Under Protocol 007, Merck did not test the vaccine's ability to protect children against a wild type mumps virus, "the type of real-life virus against which vaccines re generally tested". Instead, Merck tested children's blood using its own attenuated strain of the virus. "This was the same mumps strain with which the children were vaccinated."

Obama has granted immunity to William Thompson, CDC whistleblower who is planning to testify before Congress [21]. The senior scientist is still employed by the Centers for Disease Control and Prevention, and is working closely is Bill Posey's office to tell his story.

Further developments are eagerly awaited.

Article first published 23/02/15


  1. Morgan Verkamp LLC News August 27, 2014 Press Release, "Statement of William W. Thompson Ph.D. Regarding the Article Examining the Possibility of a Relationship Between MMR Vaccine and Autism".
  2. "Merck has some explaining to do over its MMR vaccine claims", Lawrence Solomon, Huffington Post 25 September 2014, updated 27 November 2014,
  3. Ho MW. The MMR vaccine controversy. Another scientist falls victim over findings against MMR vaccine. -sis news13/14 2001.
  4. "Ruling on doctor in MMR scare", NHS Choice, 29 January 2010,
  5. "Measles outbreak –California, December 2014-February 2015, 20 February 2015,
  6. "Anti-vaccine movement causes worst measles epidemic in 20 year", Steven Salzberg, Forbes, 1 February 2015,
  7. "Andrew Wakefield, father of the anti-vaccine movement, responds to the current measles outbreak for the first time", Stav Ziv, Newsweek, 10 February 2015,
  8. DeStefano F, Bahsin TK, Thompson WW, Yeargin-Allsopp M and Boyle C. Age at first measles-mumps-rubella vaccination in children with autism and school-matched control subjects: a population-based study in metropolitan Atlanta. Pediatrics 2004, 113, 259-66.
  9. "Obama grants immunity to CDC whistleblower on measles vaccine link to autism", Health Impact News, 13 February 2015,
  10. "How a now-retracted autism study went viral – again", Sydney Lupkin, abcNews, 9 October 2014,
  11. Hooker BS. Measles-mumps-rubella vaccination timing and autism among young African American boys: a reanalysis of CDC data. Translational Neurodegeneration 2014, 3, 16.
  12. Durkin MS, Maenner MJ, Meaney FJ, Levy SE, DiGuiseppi C, Nicholas JS, Kirby RS, Pinto-Martin JA, Schieve LA: Socioeconomic inequality in the prevalence of autism spectrum disorder: evidence from a U.S. cross-sectional study. PLoS One 2010, 5:e11551.
  13. Ginde AA, Liu MC, Camargo CA Jr: Demographic differences and trends of vitamin D insufficiency in the US population, 1988–2004. Arch Intern Med 2009, 169, 626–32.
  14. Wakefield AJ, Murch SH, Anthony A, Linnell J, Casson DM, Malik M, Berelowitz M, Dhillon AP, Thompson MA, Harvey P. Valentine A, Davies SE and Walker-Smith JA. Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. The Lancet 1998, 351, 637-41.
  15. Walker SJ, Fortunato J, Gonzalez LG and Krigsman A. Identification of unique gene expression profile in children with regressive autism spectrum disorder (ASD) and Ileocolitis. PLOS one 2013, 8, e58058. doi:10.1371/journal.pone.0058058
  16. "Scientists fear MMR link to autism", Sally Beck, Mail on Sunday 28 May 2006,
  17. "Dr. Stephen walker on MMR: no link", Kristina Chew, Blisstree, 2 June 2006,
  18. "MMR row: high court rules doctor should not have been struck off", Press Association, The Guardian 7 March 2012,
  19. "British court throws out conviction of autism/vaccine MD:Wakefield's co-author completely exonerated", Autism Action Network, The Millennium Report 18 February 2015,
  20. "Why is the mainstream media ignoring measles vaccine fraud cases", Brian Shilhavy Health Impact News Editor, accessed 15 February 2015,
  22. "Obama admin grants immunity to CDC scientist that fudged vaccine report… whistle blower plans to testify before congress",  Patrick Howler,  Daily Caller, The Briefing Room, 4 February 2015,,161286.0.html

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There are 9 comments on this article so far. Add your comment above.

mae-wan Comment left 24th February 2015 21:09:17
John Wilson, Research by William Thompson et al did not involve random sampling. It was not possible, as over 90% of children had been vaccinated with MMR. So they did a very good alternative, using cases and matched controls, for age, gender and school, i.e., those that had received diagnosis of ASD and those that had not, and compared the numbers in age groups identified by first vaccination, ie, before 18 months, before 24 months and before 36 months. The only wrong-doing was to omit large numbers of cases with ASD, which limited the analysis to those with a Georgia birth certificate, thereby concealing the highly increased risk for ASD diagnosis for African American boys.

tony villar Comment left 24th February 2015 20:08:25

Walter Carpenter Comment left 24th February 2015 05:05:00
This is real science reporting. thank you for taking the time to explain the whole situation.

Rory Short Comment left 24th February 2015 05:05:57
Sadly when money is involved the truth becomes a fatality.

Karen Adler Comment left 24th February 2015 08:08:27
Thank you for this important article. I thought there must have been more to this story after mainstream media went quiet on it. As Mahatma Gandhi said "First they ignore you, then they laugh at you, then they fight you, then you win." And as the bard said "at length, Truth will out"

John Wilson Comment left 24th February 2015 20:08:55
Re: Andrew Wakefield. His book " Callous Disregard" is well worth reading. It is a very clear response to the many serious accusations laid against him by the medical establishment. Re: Research by William Thompson. A complicated piece of research which I don't fully understand. What about this for a trial. You take a random sample of 1,000 children aged 10 to 12 who have had the MMR jab and count the number who have been diagnosed with autism. You take another random sample of children who have never had the MMR jab and record the incidence of autism in this group. Compare the two. Too simple?

Brian Sandle Comment left 25th February 2015 19:07:28 “the prosecutor must disclose evidence or information that would prove the innocence of the defendant or would enable the defense to more effectively impeach the credibility of government witnesses. Evidence that would serve to reduce the defendant’s sentence must also be disclosed by the prosecution.” That should be considered in the light of drug companies who may be turning arguments like vaccination into facets of their responsibilities to their shareholders. They should not be allowed to selectively disseminate information they are in possession of. Life should not be treated cynically as a pawn for shareholders.

Todd Millions Comment left 1st March 2015 22:10:23
Now that the Merck mmr test details are public ally available(court sealed previously) we also have inside reports that the test plates the FDA allowed MERCK to destroy,where smeared with rabbit sourced antibodies,too make the effectiveness appear higher.Serum from such sources-isn't used in treatment nor vaccines due to shock reactions last I checked.Merck could not have being unaware of this.So why has the court submissions being sealed for 5 years?

Oliver Tickell Comment left 1st March 2016 18:06:12
I came across this article thanks to mark Lynas, whose article in The Guardian ( describes it as 'anti-vaccine misinformation'. But on examination at appears thoroughly cogent, well argued and well referenced. Lynas's disgraceful slur should not pass unchallenged.