I would think that it is quite possible that a neurological infection, such as Lyme, could interfere with gene expression at a crucial time in a baby's development. I do not know if infection was explored as a possible cause.
The National Institute of Mental Health funded the study, which means it should come out in full text in Pub Med Central within the year. Otherwise, check your local hospital library for a copy, if you don't want to buy the copy online.
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Don't know how this all fits together but the work that Dr. Yasko has done on genetic mutations in the methylation cycle and autism is very useful. Many autistic people are getting help through her nutrigenomic treatments.
Interestingly, I've heard from several doctors that they are finding a high number of their lyme and CFS patients have similar methylation cycle issues.
My tests revealed significant mutations. We'll see how the work around for my particular mutations affect my ability to get rid of lyme and co-infections.