Author of

• 20151

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  OA 18 - Lung Cancer Pathology and Genetics (ID 687)

  • Event: WCLC 2017
  • Type: Oral
  • Track: Biology/Pathology
  • Presentations: 1
  • Moderators:George R. Simon, Yoon-La Choi
  • Coordinates: 10/18/2017, 14:30 - 16:15, Room 316

  • 24449

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    OA 18.04 - Whole Genome Tumor-Normal Sequencing Reveals Potential False Positives Versus Standard CGP Sequencing in Patients with NSCLC (ID 10453)

    15:00 - 15:10  |  Presenting Author(s): C.P. Garner
    • Abstract
    • Presentation
    • Slides

    Background:
    Matched tumor-normal sequencing analyses are essential for precise identification and interpretation of somatic and germline alterations. A 2015 study of 815 paired tumor and normal genomes showed that both genomes are required for precise identification and interpretation of both somatic and germline variation. In this study, we further demonstrate the critical importance of both tumor and germline sequencing using a selected panel of genes that are relevant to cancer prognosis and treatment.
    
    Method:
    Tumor and normal (germline) genomes were sequenced using the Illumina HiSeqX platform. Data was aligned to GRCh37 using methods described previously. Tumor versus matched-normal variant analysis was performed using the NantOmics Contraster analysis pipeline to determine somatic and germline genomic variants. RNA-Seq libraries were prepared from tumor samples using KAPA stranded RNA-Seq with RiboErase kit and sequencing on the Illumina platform. RNA sequencing reads were aligned and variants were identified using methods that have been previously described.
    
    Result:
    44 patients with NSCLC with tumor-normal sequencing were analyzed. 29 patients also had RNA-Seq whole transcriptome data available for analysis. Focusing on somatic SNVs in ALK, BRAF, CDKN2A, CEBPA, DNMT3A, EGFR, ERBB2, EZH2, FLT3, IDH1, IDH2, JAK2, KIT, KRAS, KMT2A (MLL), NPM1, NRAS, MET, NOTCH1, PDGFRA, PDGFRB, PGR, PIK3CA, PTEN, RET; 427 germline plus somatic variants were detected in these 25 genes in 44 patients; 386 out of 427 (90%) variants detected in somatic tissue were also present in germline (true positive germline variant, false positive somatic variant). 5 out of 29 patients (17%) did not have detectable expression in at least one somatic variant. Focusing on germline SNVs in APC, MYH, MLH1, MSH2, MSH6, PMS2, EPCAM, POLE, POLD1, BMPR1A, PTEN, STK11; 350 germline plus somatic variants were detected in these 12 genes in 44 patients, 10 out of 44 patients (23%) had at least one variant detected in their tumor DNA in these 12 genes that was not detected in the patient’s germline DNA (false positive germline variant, true positive somatic variant).
    
    Conclusion:
    Somatic-only sequencing may lead to false positive variant calls which has important clinical implications for highly actionable targets and for the veracity of mutational load algorithms. Calling germline variants from somatic DNA has a false positive risk---called variants may truly be somatic mutations. This is further complicated by the presence of circulating tumor DNA which may also lead to a false positive “germline” result in the absence of a true normal comparator.
    
    

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