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- person_outline Li Ding
Resistance promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient
[…] y manual review to differentiate somatic from germline copy-number events.Putative structural variants were detected using the union of BreakDancer 1.4.5 () filtered by novo-realign and tigra-sv, and squaredancer 0.1 (https://github.com/genome/genome/blob/master/lib/perl/Genome/Model/Tools/Sv/SquareDancer.pl). […]
Integrated genomic and molecular characterization of cervical cancer
[…] irs supporting each event and at least one read covering the breakpoint junction. High-pass WGS data were analyzed to detect somatic structural variations using two runs of BreakDancer and one run of SquareDancer (https://github.com/ding-lab/squaredancer). The gene fusion lists generated by all methods and platforms were integrated (See ). […]
Clonal Architectures and Driver Mutations in Metastatic Melanomas
[…] Structural variants (SVs) in all samples were predicted by BreakDancer and SquareDancer (https://github.com/genome/gms-core/blob/master/lib/perl/Genome/Model/Tools/Sv/SquareDancer.pl). All SV predictions were filtered using TIGRA (Chen et al., in preparation) to identify ass […]
Whole Genome Analysis Informs Breast Cancer Response to Aromatase Inhibition
[…] identified by combining results from a modified version of the Samtools indel caller (http://samtools.sourceforge.net/), GATK, and Pindel. Structural variations were identified using BreakDancer and SquareDancer (unpublished). All putative somatic events found in 46 cases were validated by targeted custom capture arrays (Nimblegen)/Illumina sequencing and all tier 1 mutations for 46 WGS cases als […]
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