Targeted Sequencing of Melanoma and Mucosal Tumors

An Agilent Haloplex custom target enrichment kit that captured all exons in 89 genes related to melanoma and tumors from mucous membranes [5 (link), 16 (link)–19 (link)] was designed using the Agilent SureDesign software (Agilent Technologies, Santa Clara, CA). The genes on the panel are listed in Additional file 2: Table S2. Target-enriched libraries were constructed from genomic DNA (3 μg), following an instruction from HaloPlex Target Enrichment for Illumina Kit (Agilent Technologies) [13 (link)]. Only library fragments within 175 to 625 bp were considered for the final quantification, normalization, and pooling. The final multiplexed Haloplex custom target library pool was sequenced on the Illumina HiSeq 2500 (Illumina, San Diego, CA) on rapid mode using paired-end 100 bp reads. Overall, the panel showed high coverage rates (median 349x) for all the target regions.

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Iida Y., Salomon M.P., Hata K., Tran K., Ohe S., Griffiths C.F., Hsu S.C., Nelson N, & Hoon D.S. (2018). Predominance of triple wild-type and IGF2R mutations in mucosal melanomas. BMC Cancer, 18, 1054.

Publication 2018

Haloplex custom target enrichment kit Illumina HiSeq 2500

Exons Genes Genomic Library Melanoma Mucous membranes Tumors

Corresponding Organization :

Other organizations : Saint John's Health Center

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Variable analysis

independent variables

Agilent Haloplex custom target enrichment kit that captured all exons in 89 genes related to melanoma and tumors from mucous membranes

dependent variables

Coverage rates for the target regions

control variables

Genomic DNA (3 μg) used for target-enriched library construction
Library fragments within 175 to 625 bp considered for final quantification, normalization, and pooling
Final multiplexed Haloplex custom target library pool sequenced on the Illumina HiSeq 2500 on rapid mode using paired-end 100 bp reads

controls

No positive or negative controls were explicitly mentioned in the provided information.

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