Distribution of receptor tyrosine kinase (RTK) nsSNPs in breast cancer (BC) patients (pts) using Next-Generation Sequencing (NGS)


Lindsay K Morris, Matthew K Stein, Saradasri Karri, Shristi Sareen, Kruti Patel, Gregory A Vidal, Lee S Schwartzberg, Mike G Martin


  • Receptor tyrosine kinase (RTK) pathways are aberrantly activated in cancer, and gain-of-function mutations and alterations in RTKs serve as attractive drug targets.
  • Comprising 20 families, the 58 known human RTKs each contain an extracellular domain (ECD), single transmembrane helix (TM), and cytoplasmic domain with juxtamembrane (JM) and C-terminal (CT) regulatory regions flanking a tyrosine kinase domain (TKD). 1
  • Tumor profiling with next-generation sequencing (NGS) can reveal novel non-synonymous single nucleotide polymorphisms (nsSNPs) along RTKs’ entire amino acid sequence that need further classification.
  • We sought to classify nsSNPs within RTKs among breast cancers identified by NGS.


  • Institutional review board approval was obtained. A database of breast cancer patients treated at West Cancer Center (Memphis, TN) from 2013-2015 was reviewed.
  • Inclusion Criteria:
    • Known ER, PR, HER2 status
    • Received tumor profiling including NGS with a 592 cancer-related gene panel from Caris Life Sciences2
  • Caris NGS interrogated 29 RTKs. All mutations testdefined as either pathogenic (PATH) or nsSNPs deemed variants of undetermined significance (VUS) were included. All variants had >99% detection confidence based upon allele frequency and amplicon coverage. 2
  • nsSNPs were arranged by amino acid location including the ECD, TM, JM, TKD, or CT
  • In order to classify VUS, nsSNPs underwent in silico analysis using PolyPhen 2 (Harvard)3,4 to predict pathogenicity, denoted pnsSNP.


  • 66% of breast cancer patients carried ≥1 RTK nsSNP, with 35% patients harboring a predicted-damaging lesion (pnsSNP) following in silico analysis with PolyPhen 2.
  • RTK nsSNPs were distributed in various breast cancer phenotypes and included frequent mutations in potentially actionable genes such as ROS1 and ALK.
  • 26% (9/35) of ER+/HER2- patients had pnsSNPs in ROS1 or ALK.
  • nsSNPs in the ECD or TKD were most frequent and also most likely to be damaging

Novel RTK pnsSNPs identified in breast cancer patients warrant further classification and collaboration.

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