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Over half of these are second primaries in the contralateral breast (Supplementary Table 3).
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With these estimates in mind, it can be approximated that among every 10,000 screened women 4000 have dense breasts (Supplementary Table 5A).
The same was true for somatic SNPs differing from germ line in human breast carcinoma (supplementary fig. S1 B, Supplementary Material online).
These included breast MCF7 (Supplementary Fig. S2), and neuroblastoma SH-SY5Y (Supplementary Fig. S3) and SK-N-SH cells (data not shown).
Using comparison methodology similar to that described above, healthy, NAT, and tumor tissues cleanly segregated as seen in the initial comparisons in the colon, liver, and breast cohorts (Supplementary Fig. 4); a trend towards this pattern of segregation was also observed in the prostate cohort (Supplementary Fig. 5).
Examination of the TCGA dataset revealed that CBX6 is not differentially expressed in different subtypes of breast cancer (Supplementary Fig. S1A).
Moreover, examination of TCGA dataset disclosed a marked increase in BST2 expression in breast cancer (Supplementary Fig. S5) and CBX6 and BST2 were negatively correlated in breast cancer (Spearman r = −0.1804, P < 0.0001) (Fig. 7D).
The pathological relevance of the identified MYC signature was further corroborated by the observation that the expression of these genes correlated with reduced metastatic-free survival in patients affected by high-grade breast cancer (Supplementary Fig. 9i).
No other associations were significantly modified by family history of breast cancer (Supplementary Table 2).
Moreover, metastases displayed higher percentage of MnSOD positivity than primary breast tumors (Supplementary Figure S2).
Eight tumours contained classic amplicons previously reported in ER+ breast tumours (Supplementary Figure 2).
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