Integrative Molecular Analysis of Patients With Advanced and Metastatic Cancer

Abstract

Purpose: We developed a precision medicine program for patients with advanced cancer using integrative whole-exome sequencing and transcriptome analysis.

Patients and methods: Five hundred fifteen patients with locally advanced/metastatic solid tumors were prospectively enrolled, and paired tumor/normal sequencing was performed. Seven hundred fifty-nine tumors from 515 patients were evaluated.

Results: Most frequent tumor types were prostate (19.4%), brain (16.5%), bladder (15.4%), and kidney cancer (9.2%). Most frequently altered genes were TP53 (33%), CDKN2A (11%), APC (10%), KTM2D (8%), PTEN (8%), and BRCA2 (8%). Pathogenic germline alterations were present in 10.7% of patients, most frequently CHEK2 (1.9%), BRCA1 (1.5%), BRCA2 (1.5%), and MSH6 (1.4%). Novel gene fusions were identified, including a RBM47-CDK12 fusion in a metastatic prostate cancer sample. The rate of clinically relevant alterations was 39% by whole-exome sequencing, which was improved by 16% by adding RNA sequencing. In patients with more than one sequenced tumor sample (n = 146), 84.62% of actionable mutations were concordant.

Conclusion: Integrative analysis may uncover informative alterations for an advanced pan-cancer patient population. These alterations are consistent in spatially and temporally heterogeneous samples.

FIG 1.

Selected primary tumor sites of 515 Englander Institute for Precision Medicine patients and patient status at time of enrollment. (A) The majority of patients with non-CNS tumors presented with metastatic disease. (B) Most common biopsy or resection sites and information, whether a sample was procured from a primary, metastatic, or recurrent site. (C) Clinical history of a female patient with breast cancer who participated in the precision medicine trial. An AKT1 mutation was discovered in a liver sample and she was treated with an AKT1 inhibitor, albeit without achieving disease remission. ER, estrogen receptor; HER2, human epidermal growth factor receptor 2; PR, progesterone receptor; WES, whole-exome sequencing.

FIG 2.

Landscape of genomic alterations in the Englander Institute for Precision Medicine cohort. The most common alterations are nonsynonymous TP53 mutations (Category 2). This alteration is found often in advanced prostate cancer, bladder cancer, and brain tumors. Amp, amplification; Del, deletion; Ins, insertion.

FIG 3.

Multiple samples from same patients enrolled in the precision medicine trial at the Englander Institute for Precision Medicine (EIPM) and clinically relevant examples. (A) Venn Diagram showing the relationship of multiple tissue samples from individual patients. Multiple samples from 146 individuals in the EIPM cohort underwent whole-exome sequencing. Paired primary–metastatic tumor samples from 59 patients were the most frequent combination. Spatially and/or temporally heterogeneous metastases and primary tumors from 35 and 29 patients, respectively, also underwent sequencing. Primary tumors were usually sequenced at different timepoints—for example, tumor samples at initial diagnosis and subsequent residual tumor postneoadjuvant treatment. (B) Activating ALK mutation in both primary tumor and bone marrow metastasis; partial remission after crizotinib therapy. (C) Shared and potentially actionable mutation in the ERBB gene in both primary tumor and lymph node metastasis of an individual with micropapillary urothelial carcinoma. (D) Early divergent evolution in both histologically distinct epithelial and mesenchymal components in an individual with uterine carcinosarcoma. (E) Different KRAS mutations in two morphologically similar lung cancer samples from the same patient, thus confirming two separate primary tumors.

FIG 4.

Germline DNA-repair defects (DRDs) in Englander Institute for Precision Medicine (EIPM) cohort. (A) The frequency of germline DRD alterations in our cohort is 10.7%. CHEK2, BRCA1/2, and MSH6 are the most frequently mutated genes. (B) High frequency of germline mutations in breast, prostate, and lung tumors is observed.

FIG 5.

Detection of potential clinically relevant alterations through transcriptome analysis. (A) Novel RBM47-CDK12 gene fusion in a metastatic prostate cancer sample, detected by RNA sequencing and confirmed by polymerase chain reaction. (B) RNA sequencing outlier analysis and investigation of FGFR3 outlier in a bladder cancer cell line. (C) Circos plots of gene fusions identified in select cases (brain, soft tissue, bladder).