Germline Sequencing Improves Tumor-Only Sequencing Interpretation in a Precision Genomic Study of Patients With Pediatric Solid Tumor

Abstract

PURPOSE Molecular tumor profiling is becoming a routine part of clinical cancer care, typically involving tumor-only panel testing without matched germline. We hypothesized that integrated germline sequencing could improve clinical interpretation and enhance the identification of germline variants with significant hereditary risks. MATERIALS AND METHODS Tumors from pediatric patients with high-risk, extracranial solid malignancies were sequenced with a targeted panel of cancer-associated genes. Later, germline DNA was analyzed for a subset of these genes. We performed a post hoc analysis to identify how an integrated analysis of tumor and germline data would improve clinical interpretation. RESULTS One hundred sixty participants with both tumor-only and germline sequencing reports were eligible for this analysis. Germline sequencing identified 38 pathogenic or likely pathogenic variants among 35 (22%) patients. Twenty-five (66%) of these were included in the tumor sequencing report. The remaining germline pathogenic or likely pathogenic variants were single-nucleotide variants filtered out of tumor-only analysis because of population frequency or copy-number variation masked by additional copy-number changes in the tumor. In tumor-only sequencing, 308 of 434 (71%) single-nucleotide variants reported were present in the germline, including 31% with suggested clinical utility. Finally, we provide further evidence that the variant allele fraction from tumor-only sequencing is insufficient to differentiate somatic from germline events. CONCLUSION A paired approach to analyzing tumor and germline sequencing data would be expected to improve the efficiency and accuracy of distinguishing somatic mutations and germline variants, thereby facilitating the process of variant curation and therapeutic interpretation for somatic reports, as well as the identification of variants associated with germline cancer predisposition.

A systematic review of the prevalence of pathogenic or likely pathogenic germline variants in individuals with FOXO1 fusion‐positive rhabdomyosarcoma

“…[15][16][17] Studies reporting on germline P/LP variants in RMS (without clarifying FOXO1 fusion status) are presented in Table 1. 11,13,[15][16][17][18][19][20][21][22] In these studies, P/LP germline variants were most frequently detected in TP53, neurofibromatosis type 1 (NF1), and DICER1, which is consistent with the classic CPSs known to predispose to RMS: NF1, Li-Fraumeni syndrome (LFS), DICER1 syndrome, as well as Beckwith-Wiedemann syndrome (BWS) and Costello syndrome. Young age of RMS onset (≤3 years), as well as specific tumor locations (e.g., cervical/ovary) and presence of anaplasia are indicators that there may be an underlying CPS.…”

Tumor Molecular Profiling in Hispanics: Moving Towards Precision Oncology and Health Equity

“…Additionally, there must be a careful selection when deciding how to discriminate somatic from germline variants. However, tumor-only sequencing has the advantage of being cost-effective, helping inform a diagnostic, predict prognosis for certain tumors, and providing tumor profiling for mutational burden [ 40 , 41 ].…”

The genetic era of childhood cancer: Identification of high‐risk patients and germline sequencing approaches

“…Some authors have described the benefits of matched paired tumor‐normal sequencing tests, which include the reduction of the number of germline variants that often are filtered out in somatic sequencing depending on their population frequency or some computational filters that may also mask germline variants associated with cancer predisposition genes, allowing improvement of the accuracy of variant reporting to refine diagnoses, aid in a treatment decisions, and refer patients and families to genetic counseling when indicated. Schienda and collaborators showed how the integration of germline sequencing with molecular tumor profiling in a subset of children with solid malignancies enrolled in the Genomic Assessment Improves Novel Therapy (GAIN) consortium (Clinical Trials ID: NCT02520713) could improve clinical interpretation and enhance the identification of germline variants with significant hereditary risks (Schienda et al., 2021). They found that 66% of SNVs identified in the tumors were reported as pathogenic, likely‐pathogenic or variants of uncertain significance in germline sequencing and only 29% of them were present solely in the tumor sequencing data, and thus determined to be of somatic origin.…”