lcis: Breast cancer data

In Clonality: Clonality testing

Description

Data from the LCIS study, with mutations listed for all pairs of LCIS-invasive tumors in a series of breast cancer cases.

Usage

  data(lcis)

Details

This is exome sequencing data from study of Lobular Carcinoma in Situ (LCIS) and Invaisve lobular carcinomas (ILC) or Invasive Ductal Carcinomas (IDC) in the same patients. Each row represents single mutation in a patient. This structure is similar to MAF (mutation annotation format) files.

The columns are "PatientID, Lesion,Hugo_Symbol, Chromosome, Start_Position, Reference_Allele, Tumor_Seq_Allele2 (Alternative allele), Tumor_Sample_Barcode (sample ID). Lesion contains Lesion type, which takes values DCIS (ductal carcinoma in situ), IDC (invasive ductal carcinoma), IDC2 (second profiled IDC), ILC (invasive lobular carcinoma), LCIS and LCIS1,2, etc.

References

Begg CB, Ostrovnaya I, Carniello JV, Sakr RA, Giri D, Towers R, Schizas M, De Brot M, Andrade VP, Mauguen A, Seshan VE, King TA. "Clonal relationships between lobular carcinoma in situ and other breast malignancies.", Breast Cancer Res. 2016 Jun 23;18(1):66. doi: 10.1186/s13058-016-0727-z.

Clonality documentation built on Nov. 8, 2020, 7:45 p.m.