Computational protocol: Cerebral organoids model human brain development and microcephaly

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Protocol publication

[…] Genomic DNA was extracted from peripheral blood of Patient 3842 and the patient’s parents by standard methods. Informed consent was obtained from the family and the study approved by the Multi-centre Research Ethics Committee for Scotland (04:MRE00/19). Whole exome capture and sequencing was performed at the Welcome Trust Sanger Institute (WTSI), UK. DNA was sheared to 150bp lengths by sonification (Covaris, Woburn, Massachusetts, USA) prior to whole exome capture and amplification using the SureSelect Human All Exon 50Mb kit (Agilent, Santa Clara, CA). Fragments were sequenced using the Illumina Hiseq platform. 76bp paired end sequence reads were aligned to the UCSC genome browser hg19 reference sequence using BWA. Sequence variants were obtained using GenomeAnalysisTK ( and annotated with transcript and protein consequence, polyphen, condel and SIFT scores. Mutations were confirmed by bi-directional sequencing of PCR products using dye terminator chemistry on an ABI 3730 capillary sequencer (Applied Biosystems). […]

Pipeline specifications

Software tools BWA, GATK, PolyPhen, Condel, SIFT
Databases UCSC Genome Browser
Applications WES analysis, Genome data visualization
Organisms Mus musculus, Homo sapiens
Diseases Brain Diseases, Microcephaly