Challenges in Next Generation Sequencing Analysis of Somatic Mutations in Transplant Patients

Publication date: Available online 10 May 2018 Source:Cancer Genetics Author(s): Hui Chen, Rajyalakshmi Luthra, Keyur P Patel, Mark Routbort, Asif Rashid, Sinchita Roy-Chowdhuri, Alexander Lazar, Russell Broaddus, Jawad Manekia, Rajesh R Singh, Anna Yemelyanova Analysis of somatic mutations in solid tumors and hematologic malignancies using targeted next generation sequencing (NGS)-based assays has become part of routine oncology practice as well as clinical trials. The use of paired tumor-normal DNA samples increases confidence of somatic calls. NGS assays that utilize unique patient identifiers (SNP IDs) allow further comparison of samples within a run or paired tumor/normal samples. The sources of germline DNA include peripheral blood (PB) and formalin-fixed paraffin-embedded tissue (FFPE). However, the source of normal can be problematic, especially in transplant setting. Herein, we report two cases of NGS-based molecular testing in a patient with mycosis fungoides treated with stem cell transplant [SCT] (Pt1) and a patient with lung adenocarcinoma who previously had acute leukemia cured by SCT. These cases highlight the importance of selecting an appropriate normal sample for excluding germline polymorphisms during somatic mutation testing. Initial analyses that included concurrent PB sample failed to filter known germline polymorphisms. Repeat analyses using pre-transplant PB/bone marrow allowed for the successful subtraction of germline variants. Somatic m...
Source: Cancer Genetics - Category: Cancer & Oncology Source Type: research