Flawed because:
1) Measles vaccine virus is live and attenuated. After inoculation, the vaccine virus probably replicates (or reproduces itself) about 15 to 20 times. Measles vaccine virus is likely to be taken up by specific cells responsible for virus uptake and presentation to the immune system (termed antigen-presenting cells or APCs). Because all APCs are mobile, and can travel throughout the body (including the intestine), it is plausible that a child immunized with MMR would have measles virus detected in intestinal tissues using a very sensitive assay. To determine if MMR is associated with autism, one must determine if the finding is specific for children with autism. Therefore, children with or without autism must be identical in two ways. First, children with or without autism must be matched for immunization status (i.e., receipt of the MMR vaccine). Second, children must be matched for the length of time between receipt of MMR vaccine and collection of biopsy specimens. Although this information was clearly available to the investigators and critical to their hypothesis, it was specifically omitted from the paper.
2) Because natural measles virus is still circulating in England, it would have been important to determine whether the measles virus detected in these samples was natural measles virus or vaccine virus. Although methods are available to distinguish these two types of virus, the authors chose not to use them.
Flawed because: (part 2):
3) The method used to detect measles virus in these studies was very sensitive. Laboratories that work with natural measles virus (such as the lab where these studies were performed) are at high risk of getting results that are incorrectly positive. No mention is made in the paper as to how this problem was avoided.
4) As is true for all laboratory studies, the person who is performing the test should not know whether the sample is obtained from a case with autism or without autism (blinding). No statements were made in the methods section to assure that blinding occurred.