Computational protocol: COLEC10 is mutated in 3MC patients and regulates early craniofacial development

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Protocol publication

[…] Patients and families samples were screened by whole-exome sequencing, including the proband and both parents when available. In each case, genomic DNA was enriched for exonic regions using the SureSelect All Exon 50Mb Targeted Enrichment kit (targeting 202,124 exons from 20,718 genes) from Agilent Technologies, according to the manufacturer's protocol. Captured libraries were sequenced on an Illumina HiSeq 2000 instrument using Illumina sBot clustering and HiSeq chemistries v1.0, under a paired-end 100-bp read-length protocol, with four samples per flow cell lane to achieve minimum median coverage of 60×. All exomes for COLEC11, COLEC10 and MASP1/3 have a coverage of at least x15. For specific exonic coverage of 3MC family 19 see . The variant annotation and interpretation analyses were generated through the use of Ingenuity Variant Analysis software version 3.1.20140902 from Ingenuity Systems. For the recessive model, homozygous/compound heterozygous variants in the affected individual were retained. Intronic and exonic synonymous variants were filtered out; exonic and splice variants (up to 2 base pairs into intron or predicted pathogenic on MaxEntScan) with a public databases (ExAC, 1000 Genomes and ESP Exomes) frequency <0.01% (3MC phenotype) were retained. All disease causing variants (COLEC10) were validated by Sanger sequencing. Filtering pipelines for variants, ingenuity and a final list of all variants identified are presented in , and . [...] 1000 Genomes, http://www.1000genomes.orgEnsembl Genome Browser, http://www.ensembl.org/index.htmlExAC Browser, http://exac.broadinstitute.org/OMIM, http://www.omim.org/PolyPhen-2, http://genetics.bwh.harvard.edu/pph2/SIFT, http://sift.bii.a-star.edu.sg/ […]

Pipeline specifications

Software tools PolyPhen, SIFT
Databases OMIM
Application Genome data visualization
Organisms Mus musculus, Homo sapiens, Caenorhabditis elegans
Diseases Congenital Abnormalities, Cleft Lip, Craniosynostoses, Genetic Diseases, Inborn