Journal
BMC Medical Genomics
Publication Date
2015
Volume
8
Inclusive Pages
54
Document Type
Open Access Publication
DOI
10.1186/s12920-015-0129-6
Rights and Permissions
Wallden et al. BMC Medical Genomics (2015) 8:54 DOI 10.1186/s12920-015-0129-6
Recommended Citation
Snider, Jacqueline; Vickery, Tammi; Davies, Sherri R.; Mardis, Elaine R.; and et al, "Development and verification of the PAM50-based Prosigna breast cancer gene signature assay." BMC Medical Genomics. 8, 54. (2015).
https://digitalcommons.wustl.edu/open_access_pubs/4128
s12920-015-0129-6-s1.docx (12 kB)
Study inclusion and exclusion criteria for tumor subtyping
s12920-015-0129-6-s2.docx (16 kB)
Description of FFPE breast cancer patient samples used for training and verifying the Prosigna Algorithm
s12920-015-0129-6-s3.pdf (231 kB)
Coefficient of variation of each gene, B) interclass correlations for subtype call, and C) replicate ROR-S comparisons. Subtype and ROR-S were generated using the published PAM50 classifier, between NanoString nCounter replicate samples
s12920-015-0129-6-s4.doc (57 kB)
Accuracy estimates (ICC, Slopes, and R-squared) for all genes between nCounter and qRT-PCR
s12920-015-0129-6-s5.pdf (101 kB)
Comparison of ROR-S and proliferation between NanoString nCounter and PCR data. ROR-S and proliferation scores were generated using the published PCR-based PAM50 classifier
s12920-015-0129-6-s6.docx (11 kB)
Number of patient samples from each of the three training cohorts. Numbers represent patient samples used to define each of the four tumor centroids
s12920-015-0129-6-s7.pdf (114 kB)
Principal component analysis performed on the gene expression data from the training cohorts. Data from each sample are colored by subtype classification (A) or cohort (B)
s12920-015-0129-6-s8.pdf (136 kB)
Four tumor subtype centroids of the Prosigna test. Data are Log2 transformed, reference sample and geomean normalized, and gene scaled nCounter data
s12920-015-0129-6-s9.pdf (59 kB)
RFS Kaplan–Meier plot for BC No AST, BC TAM, and NKI cohorts. Cohort colors and numbers of patients are included in the plot along with the results from the Log Rank test
s12920-015-0129-6-s10.doc (28 kB)
Genes used to calculate the Prosigna proliferation score
s12920-015-0129-6-s11.pdf (83 kB)
Distribution of the ROR scores for ABCSG8 and transATAC patient tumor samples.
Study inclusion and exclusion criteria for tumor subtyping
s12920-015-0129-6-s2.docx (16 kB)
Description of FFPE breast cancer patient samples used for training and verifying the Prosigna Algorithm
s12920-015-0129-6-s3.pdf (231 kB)
Coefficient of variation of each gene, B) interclass correlations for subtype call, and C) replicate ROR-S comparisons. Subtype and ROR-S were generated using the published PAM50 classifier, between NanoString nCounter replicate samples
s12920-015-0129-6-s4.doc (57 kB)
Accuracy estimates (ICC, Slopes, and R-squared) for all genes between nCounter and qRT-PCR
s12920-015-0129-6-s5.pdf (101 kB)
Comparison of ROR-S and proliferation between NanoString nCounter and PCR data. ROR-S and proliferation scores were generated using the published PCR-based PAM50 classifier
s12920-015-0129-6-s6.docx (11 kB)
Number of patient samples from each of the three training cohorts. Numbers represent patient samples used to define each of the four tumor centroids
s12920-015-0129-6-s7.pdf (114 kB)
Principal component analysis performed on the gene expression data from the training cohorts. Data from each sample are colored by subtype classification (A) or cohort (B)
s12920-015-0129-6-s8.pdf (136 kB)
Four tumor subtype centroids of the Prosigna test. Data are Log2 transformed, reference sample and geomean normalized, and gene scaled nCounter data
s12920-015-0129-6-s9.pdf (59 kB)
RFS Kaplan–Meier plot for BC No AST, BC TAM, and NKI cohorts. Cohort colors and numbers of patients are included in the plot along with the results from the Log Rank test
s12920-015-0129-6-s10.doc (28 kB)
Genes used to calculate the Prosigna proliferation score
s12920-015-0129-6-s11.pdf (83 kB)
Distribution of the ROR scores for ABCSG8 and transATAC patient tumor samples.
