title: Low Input Whole-Exome Sequencing to Determine the Representation of the Tumor Exome in Circulating DNA of Non-Small Cell Lung Cancer Patients.
abstract: Circulating cell-free DNA (cfDNA) released from cancerous tissues has been found to harbor tumor-associated alterations and to represent the molecular composition of the tumor. Recent advances in technologies, especially in next-generation sequencing, enable the analysis of low amounts of cfDNA from body fluids. We analyzed the exomes of tumor tissue and matched serum samples to investigate the molecular representation of the tumor exome in cfDNA. To this end, we implemented a workflow for sequencing of cfDNA from low serum volumes (200 μl) and performed whole-exome sequencing (WES) of serum and matched tumor tissue samples from six non-small cell lung cancer (NSCLC) patients and two control sera. Exomes, including untranslated regions (UTRs) of cfDNA were sequenced with an average coverage of 68.5x. Enrichment efficiency, target coverage, and sequencing depth of cfDNA reads were comparable to those from matched tissues. Discovered variants were compared between serum and tissue as well as to the COSMIC database of known mutations. Although not all tissue variants could be confirmed in the matched serum, up to 57% of the tumor variants were reflected in matched cfDNA with mutations in PIK3CA, ALK, and PTEN as well as variants at COSMIC annotated sites in all six patients analyzed. Moreover, cfDNA revealed a mutation in MTOR, which was not detected in the matched tissue, potentially from an untested region of the heterogeneous primary tumor or from a distant metastatic clone. WES of cfDNA may provide additional complementary molecular information about clinically relevant mutations and the clonal heterogeneity of the tumors.
authors.affiliation: Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg, Germany.|Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Dietz
authors.affiliation: Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg, Germany.|Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Schirmer
authors.affiliation: Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg, Germany.|Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.
authors.forename: Clémentine
authors.initials: C
authors.lastname: Mercé
authors.affiliation: Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany.|German Cancer Consortium (DKTK), Heidelberg, Germany.
authors.forename: Nikolas
authors.initials: N
authors.lastname: von Bubnoff
authors.affiliation: Molecular Oncology Group, Institute of Pathology, RWTH Aachen University, Aachen, Germany.
authors.forename: Edgar
authors.initials: E
authors.lastname: Dahl
authors.affiliation: Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.|Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Meister
authors.affiliation: Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.|Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Muley
authors.affiliation: Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.|Department of Oncology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Thomas
authors.affiliation: Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg, Germany.|Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany.|German Cancer Consortium (DKTK), Heidelberg, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Sültmann
mesh_terms: D002289:Carcinoma, Non-Small-Cell Lung / Q000097:blood* / Q000235:genetics* / Q000473:pathology; D059472:Exome / Q000235:genetics*; D005260:Female; D006801:Humans; D008175:Lung Neoplasms / Q000097:blood* / Q000235:genetics* / Q000473:pathology; D008297:Male; D009154:Mutation; D009367:Neoplasm Staging; D017422:Sequence Analysis, DNA