Mosaic mutations in autism

Rates, Distribution, and Implications of Post-zygotic Mosaic Mutations in Autism Spectrum Disorder

This site is a collection of the scripts and data files used for the research.

To evaluate mosaics
Click here for an R script to evaluate the mosaics in Groups B and C. A sample input file can be found here.
The input columns are: (1) num_alternate_reads, (2) num_total_reads, (3) 0, (4) 0, (5 to n columns) Details of variant, e.g. Variant 1

Click here to see a sample output file.
The 3rd column in the output file is the alternate allele fraction (AAF), and we used a threshold of 80% modal allele fraction for defining mosaics in Group B.
The 4th column in the output file is the binomial P-value (and we used a threshold of <=1e-04 for defining mosaics in Group C).

Replication timing
Click here for the list of all de novo mutations found in probands with the replication timing.
Click here for the list of all de novo mutations found in siblings with the replication timing.
Original list courtesy of Amon Koren.

Gene lists
Click here to obtain the gene lists used to evaluate the enrichment with FMRP targets (courtesy of Menachem Fromer).

Any questions? Please contact Elaine at elimtt[[a.t.]]gmail.com