Autism is a complex and still poorly understood disorder. It has genetic and environmental causes, and there is a growing belief that to understand autism well enough to develop innovative and personalized treatments, studies will need to evaluate a large number of affected individuals.

Started in 2006 by MIND Institute Research Director David G. Amaral with the collaboration of numerous MIND Institute faculty and staff, the Autism Phenome Project (abbreviated APP) is intended to gather biological and behavioral information on a large number of families affected by autism in order to define clinically meaningful subtypes of autism spectrum disorder (ASD). There is no doubt that there are multiple causes and multiple types of ASD. The hope is that by identifying markers of these subtypes, more effective diagnosis and treatment will be achieved. Since its inception, more than 300 families have participated in the Autism Phenome Project. It has become the largest and most comprehensive assessment of children with autism in the world. We are very appreciative to all of the families that have participated thus far and have helped us to explore the mysteries of ASD.

What is it?

The Autism Phenome Project is a longitudinal analysis of children diagnosed with autism spectrum disorder and age-matched typically developing children. Families are recruited into the APP soon after diagnosis, when the child is 2 - 3 1/2 years old. Families are invited to come to the MIND Institute where the child's diagnosis is confirmed, and several behavioral tests are carried out. The medical records for the child since birth are requested from family physicians. The parents also provide information through questionnaires. The child has an MRI of their brain at night during sleep, and they also provide a small blood sample for immune and genetic testing. The families are invited to come back one year and two years later to follow-up the development of the child.

What has been discovered?

The APP has generated an unprecedented amount of data on children with autism - much of this is still being analyzed. Some of the results obtained already include:

  1. Girls with autism have different patterns of altered brain development than boys.
  2. About 15% of boys with autism have abnormally enlarged brains starting around 6 months of life. Research is now attempting to determine whether the pattern of autism symptoms that these children have is different from those of boys with typical sized brains.
  3. The immune system of some children with autism and some parents of the children is different. Studies are ongoing to determine whether this may contribute to the cause of autism.
  4. Different subsets of children with autism have distinct patterns of metabolites in their blood that may be related to the cause of their autism and may be a target for treatment.

The Autism Phenome Project Now

The unique contribution to autism research that the Autism Phenome Project provides has been appreciated by scientists and funding organizations alike. Many researchers and organizations are using data from the APP to uncover the mysteries of the disorder. At the MIND Institute, the APP is not only continuing with the families that have already been recruited but is also recruiting new children into the program. In fact, the program has expanded so much that leadership of different components of the project has been distributed among several faculty members. Each of these components is fully explained by in the links below.

Gain Study
The GAIN Study:

families with girls
between 2-3 ½ years old

New APP:

families with boys
between 2-3 ½ years old

APP Middle Childhood
APP Middle Childhood:

APP current participants
between 9-12 years old


The Autism Phenome Project is funded through philanthropy and NIH grants. We welcome private contributions to help fund the APP, expand the project nationally and carry it through to completion.

To donate, please go to UC Davis Healths' On-line Donation Form and designate “APP” in the “Special instructions for this gift”.