Computational protocol: Mutation spectrum of RB1 mutations in retinoblastoma cases from Singapore with implications for genetic management and counselling

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Protocol publication

[…] The DNA obtained from all 59 tumors and corresponding blood samples was sequenced for 27 exons and promoter region of RB1 gene after PCR amplification using 27 sets of primers as described previously []. Some cases were sent out to an international laboratory (Impact Genetics Inc., Canada) for RB1 gene sequence analysis and Allele-specific PCR (AS-PCR) for eleven recurrent RB1 mutations. Additional information about RB1 gene mutations were confirmed from gene locus specific mutation database (rb1-lsdb) and The Human Gene Mutation Database (HGMD). Predictive analysis tools were used to determine the pathogenicity status of novel variants. Missense mutations were analyzed by SIFT (http://sift.jcvi.org/www/SIFT_BLink_submit.html), CADD (http://cadd.gs.washington.edu/score) and Mutation taster (http://www.mutationtaster.org/), while all frameshift variants were predicted by PROVEAN (http://provean.jcvi.org) and Mutation Taster, respectively. […]

Pipeline specifications

Software tools SIFT BLink, CADD, MutationTaster, PROVEAN
Application WGS analysis
Organisms Homo sapiens