Targeted capture massively parallel sequencing analysis of LCIS and invasive lobular cancer: Repertoire of somatic genetic alterations and clonal relationships

Mol Oncol. 2016 Feb;10(2):360-70. doi: 10.1016/j.molonc.2015.11.001. Epub 2015 Nov 14.


Purpose: Lobular carcinoma in situ (LCIS) has been proposed as a non-obligate precursor of invasive lobular carcinoma (ILC). Here we sought to define the repertoire of somatic genetic alterations in pure LCIS and in synchronous LCIS and ILC using targeted massively parallel sequencing.

Methods: DNA samples extracted from microdissected LCIS, ILC and matched normal breast tissue or peripheral blood from 30 patients were subjected to massively parallel sequencing targeting all exons of 273 genes, including the genes most frequently mutated in breast cancer and DNA repair-related genes. Single nucleotide variants and insertions and deletions were identified using state-of-the-art bioinformatics approaches.

Results: The constellation of somatic mutations found in LCIS (n = 34) and ILC (n = 21) were similar, with the most frequently mutated genes being CDH1 (56% and 66%, respectively), PIK3CA (41% and 52%, respectively) and CBFB (12% and 19%, respectively). Among 19 LCIS and ILC synchronous pairs, 14 (74%) had at least one identical mutation in common, including identical PIK3CA and CDH1 mutations. Paired analysis of independent foci of LCIS from 3 breasts revealed at least one common mutation in each of the 3 pairs (CDH1, PIK3CA, CBFB and PKHD1L1).

Conclusion: LCIS and ILC have a similar repertoire of somatic mutations, with PIK3CA and CDH1 being the most frequently mutated genes. The presence of identical mutations between LCIS-LCIS and LCIS-ILC pairs demonstrates that LCIS is a clonal neoplastic lesion, and provides additional evidence that at least some LCIS are non-obligate precursors of ILC.

Keywords: Clonality; Invasive lobular carcinoma; Lobular carcinoma in situ; Massively parallel sequencing; Somatic genetic alterations.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigens, CD
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / pathology
  • Cadherins / genetics*
  • Carcinoma in Situ / genetics*
  • Carcinoma in Situ / pathology
  • Carcinoma, Lobular / genetics*
  • Carcinoma, Lobular / pathology
  • Class I Phosphatidylinositol 3-Kinases
  • Cohort Studies
  • Core Binding Factor beta Subunit / genetics
  • Exons / genetics
  • Female
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Mutation
  • Neoplasm Invasiveness
  • Phosphatidylinositol 3-Kinases / genetics*
  • Receptors, Cell Surface / genetics


  • Antigens, CD
  • CBFB protein, human
  • CDH1 protein, human
  • Cadherins
  • Core Binding Factor beta Subunit
  • Receptors, Cell Surface
  • fibrocystin -L, human
  • Phosphatidylinositol 3-Kinases
  • Class I Phosphatidylinositol 3-Kinases
  • PIK3CA protein, human