Whole Genome Sequencing for SNP Detection

Genomic DNA for WGS was isolated using standard techniques. Genome sequencing and analysis of SNPs were carried out by Life Sequencing S.L. (www.lifesequencing.com) (Illumina HiSeq. 100PE, 50–100x, MAD4650) or Otogenetics corporation (www.otogenetics.com) [Illumina HiSeq. 2500, PE 100–125, 100x, MAD4738(A^R), MAD4747 (E^R), MAD4751 (F^R) and MAD2 (wt)]. To pick candidate SNPs to cause resistance in each strain, we selected all missense, frameshift or 5′UTR mutations that were not present in the genomes of the strains with resistance mutations that were classified to different linkage groups. We visualized WGS data with the Integrative Genomics Viewer^{70 (link),71 (link)}.

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Pantazopoulou A., Galmarini C.M, & Peñalva M.A. (2018). Molecular basis of resistance to the microtubule-depolymerizing antitumor compound plocabulin. Scientific Reports, 8, 8616.

Publication 2018

HiSeq. 2500, PE

5 utr Frameshift Genomes Mutations Snps Strains

Corresponding Organization :

Other organizations : Centro de Investigaciones Biológicas Margarita Salas, PharmaMar (Spain)

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Variable analysis

independent variables

Genome sequencing and analysis of SNPs

dependent variables

Identification of candidate SNPs to cause resistance in each strain

control variables

Genomic DNA for WGS was isolated using standard techniques
Genome sequencing was carried out by Life Sequencing S.L. and Otogenetics corporation
Illumina HiSeq. 100PE, 50–100x, MAD4650 was used for genome sequencing by Life Sequencing S.L.
Illumina HiSeq. 2500, PE 100–125, 100x, MAD4738(A^R), MAD4747 (E^R), MAD4751 (F^R) and MAD2 (wt) were used for genome sequencing by Otogenetics corporation

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