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Protocol publication

[…] es were greater than 98%., The 8q21.3-24.12 region spans approximately 35.6 Mb and contains numerous genes. To identify variants in other genes under the linkage peak, we performed whole exome sequencing on all available affected and connecting family members. The SureSelect Human All Exon 50 Mb + UTRs kit (Agilent, Santa Clara, CA) was used for in-solution enrichment of coding exons and flanking intronic sequences following the manufacturer’s standard protocol. Adapter sequences for the Illumina HiSeq2000 were ligated and the enriched DNA samples were prepared using the standard methods for the HiSeq2000 instrument (Illumina). Paired-end reads of 99 bases length were produced. The Illumina CASAVA v1.8 pipeline was used to assemble 99 bp sequence reads. BWA (Li and Durbin ) was used to align sequence reads to the human reference genome (hg19) and variants were called using the GATK software package (McKenna et al. ; DePristo et al. ). All variants were submitted to SeattleSeq134 to assess functional consequences., Gene sequence for FZD6 was obtained from NCBI and two oligonucleotide probes were designed to incorporate approximately 10 bp upstream and downstream from rs138557689. Oligonucleotides were synthesized by Integrated DNA Technologies (Coralville, IA), annealed and end-labeled with P32 dCTP (Perkin Elmer, Waltham, MA). Cos-7 cell nuclear extracts were purchased from ActiveMotif (Carlsbad, CA). Electrophoretic mobility shift assy (EMSAs) were performed by incubating 2.5 μg nuclear extract, radiolabeled probe and 1 μL of dG/dC in a 20 μL mixture containing 2 […]

Pipeline specifications

Software tools BCL2FASTQ Conversion Software, BWA, GATK
Organisms Danio rerio
Diseases Abnormalities, Drug-Induced, Mouth Abnormalities, Stomatognathic System Abnormalities, Lip Diseases, Jaw Abnormalities, Musculoskeletal Abnormalities, Mouth Abnormalities, Craniofacial Abnormalities, Stomatognathic System Abnormalities, Maxillofacial Abnormalities, Musculoskeletal Abnormalities, Craniofacial Abnormalities