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Protocol publication

[…] The samples in the ARRA Autism Sequencing Consortium study consisted of 869 subjects (‘cases') and 869 non-ASD comparison subjects (‘controls'). ASD cases were previously assessed using the Autism Diagnostic Interview-Revised and the Autism Diagnostic Observation Schedule-Generic|. All cases met criteria for autism on the ADI and either autism or ASD on the Autism Diagnostic Observation Schedule-Generic|. ASD cases belong to various collections within the NIMH Center for Collaborative Genomic Studies of Mental Disorders (NIMH Repository; http://nimhgenetics.org) maintained at the Rutgers University Cell and DNA Repository (RUCDR; http://rucdr.org). Non-ASD control samples consist of subjects pair-matched to cases by Eigen vector analysis of genotype data to be of similar ancestry. All subjects provided informed consent, and the research was approved by each institutional board. Exome capture, sequencing, data processing and variant calling were conducted as described previously.,, A559V variants were validated and inheritance within the respective families determined by Sanger sequencing of proband and parents. Amplifying primers were designed using Primer3 (http://frodo.wi.mit.edu/) and subjected to a BLAST-Like Alignment Tool search to ensure no significant matches existed elsewhere in the genome. Ideal annealing temperature was determined, and polymerase chain reaction carried out containing 7.1 nmol of amplifying primers and 12 ng of DNA in a final volume of 20 μl. Sequence analysis was performed using Sequencher v5.0.1 (Gene Codes, Ann Arbor, MI, USA). […]

Pipeline specifications

Software tools Primer3, BLAT, Sequencher
Application qPCR
Organisms Homo sapiens