Computational protocol: Accurate Breakpoint Mapping in Apparently Balanced Translocation Families with Discordant Phenotypes Using Whole Genome Mate Pair Sequencing

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Protocol publication

[…] In order to validate selected patient-specific structural variants, qRT-PCR was performed using SsoFast™ Evagreen® Supermix (Bio-Rad Laboratories Inc., Hercules, CA, USA) and Primer3-designed PCR primer pairs (0.5μM) (Metabion) spanning the SVs (qRT-PCR primer sequences are available in ). An internal control primer-pair at 18q12.2 was selected to confirm the efficiency of the reaction and normalize the results. All reactions for each primer pair were run in triplicates on a CFX96 Touch™ Real-Time PCR Detection System machine (Bio-Rad Laboratories, Inc.), and results were analyzed using the Bio-Rad CFX Manager analysis software (comparative Ct method). […]

Pipeline specifications

Software tools Primer3, CFX Manager
Application qPCR
Organisms Ilex paraguariensis, Homo sapiens