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Autism Phenome Project (APP)

Just as the genome represents all of an organism’s genes or inheritable traits, the phenome encompasses all of an organism’s phenotypic traits such as skin color, eye color, hair color, body height, etc. For the purposes of the Autism Phenome Project (APP), the phenotypic traits being studied are behavior, brain structure/function, and immune function.1 The APP will also employ proteomics and metabolomics to search for potential biomarkers that could distinguish the different subtypes of autism.1 The Autism Phenome Project (APP) was launched in 2006 by a multi-disciplinary team of scientists and physicians at the University of California Davis’ M.I.N.D. Institute.2 The longitudinal study is “the nation’s most comprehensive assessment of children with autism to detect the biological and behavioral patterns that define subtypes of the disorder.”3 The study is founded on the principle that autism does not likely have just one biological cause, but instead a number of different biological causes. All people on the autism spectrum share the common mild to severe symptoms of impaired social skills, difficulty with social interaction, and a tendency towards restricted, repetitive moments and behaviors.4 However, there are other related conditions of autism that are only present in select individuals, such as seizures, gastrointestinal problems, epilepsy, and low IQ.5 In fact, there are many individuals with autism that have average or even enhanced IQs. The Autism Phenome Project project hopes to produce precise definitions of possible autism subtypes based on biomedical and behavioral characteristics of individuals with autism to one day produce effective treatments specific to any possible autism subtype.2

The Autism Phenome Project Process
The APP involves 52 scientists across eight fields headed by Dr. David Amaral, former President of the International Society of Autism Research and director of the M.I.N.D. Research Institute at UC Davis.6 The Autism Phenome Project aims to collect data on 1,800 children from ages 2 to 3 ½ years old from several research sites across the country.3 Participants in the study will undergo an initial medical examination from a pediatrician with expertise in developmental disorders, which will collect data on height, weight, and head circumference. Blood samples will also be taken from the participant and family members to inspect for the presence of metals and other environmental toxins, which have been implicated as possible influences that cause of autism spectrum disorder.2 Infant participants of the APP will undergo MRI and electroencephalography (EEG) scans to observe how each child’s brain has developed, if blood is flowing naturally, whether neurons are connecting and firing properly, and whether brain chemicals are present at normal levels.2 All in all, the study will focus on many characteristics of autism including behavior, immune function, brain structure/function, genetic analyses, and environmental exposures.7

Findings of the Autism Phenome Project (APP)
One of the first studies of the Autism Phenome Project, which was published in the Proceeding of the National Academy of Sciences Early Edition, centers on the brain development of children with both regressive and non-regressive types of autism.8 Regressive autism occurs when children who are seemingly undergoing typical development abruptly lose acquired skills, such as language, motor, or other life skills that they have already mastered.9 The study evaluated head circumference and total brain volume of 180 children (114 with autism, 54% of which were diagnosed with the regressive form of autism) aged 2 to 4 with autism, and found that abnormal brain growth was found most common in boys with regressive autism.10 The results of this study are significant in that “there may be distinct neural phenotypes associated with different onsets of autism. For boys with regressive autism, divergence in brain size occurs well before loss of skills is commonly reported. Thus, rapid head growth may be a risk factor for regressive autism.”10 Dr. Amaral and members of the APP have also conducted studies focusing on other regions of the brain to find other autism subtype clues.

In an interview with Amy Lennard Goehner of The New York Times, Dr. Amaral explains how “the amygdala, for example, which controls emotion—particularly negative emotion—undergoes an accelerated growth in about 40 percent of the boys with autism in our study.”11 These results are important as they may lead to being able to develop a specific subtype. The longitudinal aspect of this study is the only way to create accurate subtypes of autism spectrum disorder. Dr. Amaral goes on to explain “many people with autism have anxiety disorder. And the amygdala is a danger detector and involved in the generation of fear…as they get older we’ll be able to determine whether they are showing greater signs of anxiety. So several features would come together that would constitute one type.”11 The research conducted by the Autism Phenome Project not only focuses on how ASD affects the brains of individuals, but also investigates how the effect of ASD on their bodies can help identify potential subtypes.

Since immune dysfunction is reported in only some individuals with autism, it provides the APP with a promising area of examination for the discovery of autism subtypes. Paul Ashwood, Ph.D., and Judy Van de Water, Ph.D., are the head researchers investigating immune function for the Autism Phenome Project.1 Their research has focused on how environmental and genetic factors are influencing immune function in individuals with autism. Their research has focused on the complexities of the immune system. The subject matter of their research includes topics like altered T cell responses, elevated plasma cytokines, and autoantibodies in autism.12 A 2008 study on maternal autoantibodies on the fetal brain led the researchers to believe that “further studies of prenatal immune markers might be a productive area for etiologic (bold for glossary) and biologic marker discovery for autism.”13 Although these antibodies are associated with 13-15% of cases of ASD, this work suggests “that detection of antibodies directed against fetal brain proteins may in the future serve as valuable biomarkers to identify women who have an increased risk of having a child with autism.”14 The exploration of how autism affects the brain as well as the body is important. If researchers are able to develop specific treatments for different subtypes of autism, then it would do little good to prescribe a treatment to improve brain function if the child is suffering from a damaged immune system.15

After several years of research, the Autism Phenome Project confirmed through biological and behavioral analysis that autism can be defined either genetically, by the patterns of brain development, and even by immune abnormalities.11 The APP has accomplished a great deal in an effort to subtype autism, but there is a still a great deal of work to be done. The researchers of the Autism Phenome Project must continue their hard work if they are going to accomplish their ultimate goal of being able to specifically diagnosis children with autism type A, type B, or type C, as oppose to simply just autism.16 Dr. Amaral believes in the end, the types of ASDs found will be in the tens, and once science has identified the different types of ASD, they will search for overlaps. Perhaps the director of the APP summed it up best with this analogy, “[j]ust as many tributaries feed into one main river, it may be that different genetic and neurobiological problems feed into one final common pathway that produces the behavioral characteristics of autism.”11

The Autism Genome Project (AGP) is a similar large-scale, multi-site longitudinal project that focuses on the search for autism susceptibility genes to help improve approaches for diagnosis, prevention, and treatment of autism spectrum disorder.17