This was a project for BMI520. The purpose was to learn to use Collab and use the available tools to analyze a topic. I chose Autism! I will continue to research and expand this area as I learn more - This is a preliminary,learn how to use the tools, to evaluate our hypothesis. The direct quote from Erik Holmlin PHD in the article below highlights that the American Academy of Pediatrics recommends children with ASD receive clinical genetic testing while ONLY 3% actually get tested. In my family we have twins with autism and it was not suggested by their pediatrician. Austism is a personlized disorder that requires personalized treatment. Symptoms currently are treated as they surface and are unique to each indiviual. Rather than treat the symptoms as they surface, genetic testing can detect which genes are the cause of the individuals diagnosis and identify symptoms before they arise that are related to their particular gene set variants. The pathways associated with the gene can also be derived. This can lead to some exciiting opportunities for cures using CRISPR technology, hopefully in the near future. Genetic testing can currently offer this personalized scientific approach while assisting with studies for further understanding of ASD and its causes. I have included my Collab notebook with the analysis and some of the tools in python to play with. Feel free to download the Powerpoint presentation. Hope you enjoy!!!
Only "3% of children with an ASD diagnosis get clinical genetic testing, which is recommended by a number of professional medical organizations including the American College of Medical Genetics and Genomics and the American Academy of Pediatrics!" Erik Holmlin PHD(see article below:
Genome Sequencing Analysis of Individuals with autism can locate genes which indicate comorbidities. This can be used to identify potential health risks, help identify effective personalized treatment plans and help to understand the cause to develop a cure.
Sfari Gene Scoring in relation to autism:
https://gene.sfari.org/database/human-gene/ SfariDisorders.xls SFARIGenes.xls
BMC Genomics Genes and disorder association:
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3667-9#Sec16 all_gene_disease_associations.xls
Panther- Disease Association with Snps Gene List Analysis: http://pantherdb.org/index.jsp MappedGenesToPanther.xlsx
Pathways: https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp c2.cp.kegg.v7.4.symbols.gmt.xls Kegg Pathways - All
Pathways - Data Cleaned for use KeggPaths.xls
Children with ASD should get clinical genetic testing and should be recommended by pediatricians. We have come from, "Fee for Service" to "Patient Centered Care" and are moving to "Personalized Patient Care based on Science" There is still much to learn. Getting genetic testing will help to identify how we can treat our children before symptoms develop and wiill help future generations by better understanding ASD. Each person with ASD has a uniques set of symptoms based on their gene set which are associated with pathways. Further research in this area will offer a better quality of life for our loved ones and hopefully a cure in the near future.