X ten sequencing

We analysed 78 tumours from high-risk familial BC patients to investigate how WGS could impact the management of both risk and therapy for individuals and their families. Cases were carriers of a BRCA1 pathogenic germline variant (n = 26), a BRCA2 pathogenic germline variant (n = 22) or neither (non-BRCA1/2, n = 30) (supplementary Table S1, available at Annals of Oncology online). In order to characterise the somatic landscape of these cases, matched germline/tumour DNA underwent WGS using Illumina X-Ten sequencing to an average fold depth of 34× and 68×, respectively. WGS data were analysed to characterise somatic mutations [single nucleotide variants (SNVs), insertions-deletions, structural variants, copy number], mutational signatures and measures of HR-deficiency (HRDetect, HRD Index) (supplementary Table S2, available at Annals of Oncology online). This approach highlighted important mechanisms of genomic instability that underly familial BC.
Please refer to supplementary Material, available at Annals of Oncology online for details.

Total RNA was isolated from the livers of Gfer^+/− mice or Gfer^+/+ mice fed the CDE diet with TRIzol (Invitrogen, Carlsbad, CA) and then sequenced by Illumina Xten sequencing (San Diego, CA). The analysis of RNA sequence (RNA‐seq) was performed as previously described.⁽¹⁸⁾ The Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway analysis was used for enrichment analysis of different expressed genes. The expressed genes with a corrected P value of less than 0.05 were considered significantly different and being enriched. All data analyses were performed in the R statistical environment (version 3.5.1).