The oncogenic impact of somatic driver alterations is shaped by tissue context. Classifying alterations by cancer type and evaluating their context-specific properties requires large cohorts of genomically profiled and clinically annotated tumors. Here, we define cancer type-specific patterns of driver alterations, including 164 newly identified hotspots, in 54,331 tumors from 48,179 patients spanning 448 histological cancer subtypes. One-third of all drivers arose in non-canonical contexts and exhibited distinct features, including increased subclonality, later emergence, and divergent biological properties. Within cancer types, gene fusions and other distinct patterns of co-occurring drivers are indicative of earlier age of disease onset. We also identify ancestry-specific differences in human leukocyte antigen (HLA)-restricted driver neoantigens affecting T cell receptor therapy eligibility, and demonstrate cancer-type-specific patterns of intrinsic resistance via somatic HLA loss. Our findings highlight that functional roles of driver alterations depend on the cancer types and clinical contexts in which they arise.

Figure S1. Mutation signatures and altered canonical pathways in GBC.

Table S2. Oncogenic/Likely-oncogenic structural variants in GBC

Table S1. Sample list (cBioPortal identifiers, ‘DMP_SAMPLE_ID’). Only the primary tumor (if available) or the earliest collected metastasis are included (n=233)

Figure S2. Microbiome analysis in GBC.

Microsatellite instability (MSI) is a critical phenotype of cancer genomes and an FDA-recognized biomarker that can guide treatment with immune checkpoint inhibitors. Previous work has demonstrated that next-generation sequencing data can be used to identify samples with MSI-high phenotype. However, low tumor purity, as frequently observed in routine clinical samples, poses a challenge to the sensitivity of existing algorithms. To overcome this critical issue, we developed MiMSI, an MSI classifier based on deep neural networks and trained using a dataset that included low tumor purity MSI cases in a multiple instance learning framework. On a challenging yet representative set of cases, MiMSI showed higher sensitivity (0.895) and auROC (0.971) than MSISensor (sensitivity: 0.67; auROC: 0.907), an open-source software previously validated for clinical use at our institution using MSK-IMPACT large panel targeted NGS data. In a separate, prospective cohort, MiMSI confirmed that it outperforms MSISensor in low purity cases (P = 8.244e-07). Identifying microsatellite instability (MSI) from routine next generation sequencing assays is an important part of clinical patient care. Here, authors develop a deep-learning based algorithm, highlighting its performance in a large validation cohort.

Tissue availability is often a limiting factor in obtaining comprehensive genomic profiling to identify actionable oncogenic drivers in tumors from patients with cancer. The utility of performing complementary DNA and RNA sequencing to better identify targetable gene fusions was previously reported. Here, we report our experience using RNA recovered from lysate material, following DNA extraction, to perform targeted RNA sequencing and identify gene fusions and oncogenic transcript variants in a large cohort of patients with solid tumors. To validate this approach, RNA-sequencing results of lysate-extracted RNA and direct formalin-fixed, paraffin-embedded (FFPE) extracted RNA from the same tumors were compared. After finding equivalent identification of oncogenic gene fusions and transcript variants, efforts were expanded to a larger cohort across more diverse tumor types. Lysate-extracted RNA performed comparably to freshly FFPE extract RNA, with 97% and 96% success rates, respectively. Within the lysate-extracted group, it was documented that lysate was the only material available for RNA extraction (n = 1862, 42% of all tested samples) and, within this subgroup, 364 (20%) samples were positive for actionable fusions or oncogenic isoforms. Using RNA recovered from lysate can permit sequential or simultaneous comprehensive DNA/RNA sequencing from scant FFPE samples in laboratories where dual sample extraction is not logistically possible, allowing more complete profiling to enhance the identification of actionable oncogenic gene fusions to guide care.

Objective: To explore pre-treatment imaging findings of neurotrophic tyrosine receptor kinase ( NTRK )-rearranged spindle cell neoplasm, an emerging group of molecularly defined soft tissue tumors and summarize the clinical course, including TRK inhibitor therapy response. Materials and methods: This retrospective study included 8 women and 4 men with NTRK -rearranged spindle cell neoplasm (median age, 35.5 years, range, 0 -66). Available pre-treatment MRI, CT, PET, and US imaging were reviewed. Tumor histology and the patients' clinical course were reviewed. Results: Primary tumors were located within the soft tissue, lungs, kidney, and breast with soft tissue being the most prevalent site ( n = 6). Pre-treatment MRI ( n = 4) revealed linear hypointense signal foci and contrast enhancement in all patients with hemorrhage in half of the tumors. A tail sign ( n = 1) and fluid levels (n = 1) were less frequent. Ultrasound showed well -marginated hypoechoic masses with internal flow. Primary tumors were all non -calcified on CT (4/4). Metastases were FDG-avid (4/4). Among the 8 patients who developed metastasis, 7 developed pulmonary metastases. All four patients who received NTRK inhibitor therapy showed an initial decrease in tumor size or FDG uptake. Conclusion: NTRK -rearranged neoplasms may occur as enhancing masses with linear hypointense signal foci on MRI and FDG avid metastases on PET. Pulmonary metastases were frequent in our study. Initial treatment response is observed in most patients.

INTRODUCTION:Microsatellite instability (MSI) and mismatch repair (MMR) deficiency represent a distinct oncogenic process and predict response to immune checkpoint inhibitors (ICIs). The clinicopathologic features of MSI-high (MSI-H) and MMR deficiency (MMR-D) in lung cancers remain poorly characterized. METHODS:MSI status from 5171 patients with NSCLC and 315 patients with SCLC was analyzed from targeted next-generation sequencing data using two validated bioinformatic pipelines. RESULTS:MSI-H and MMR-D were identified in 21 patients with NSCLC (0.41%) and six patients with SCLC (1.9%). Notably, all patients with NSCLC had a positive smoking history, including 11 adenocarcinomas. Compared with microsatellite stable cases, MSI-H was associated with exceptionally high tumor mutational burden (37.4 versus 8.5 muts/Mb, p < 0.0001), MMR mutational signatures (43% versus 0%, p < 0.0001), and somatic biallelic alterations in MLH1 (52% versus 0%, p < 0.0001). Loss of MLH1 and PMS2 expression by immunohistochemistry was found in MLH1 altered and wild-type cases. Similarly, the majority of patients with MSI-H SCLC had evidence of MLH1 inactivation, including two with MLH1 promoter hypermethylation. A single patient with NSCLC with a somatic MSH2 mutation had Lynch syndrome as confirmed by the presence of a germline MSH2 mutation. Among patients with advanced MSI-H lung cancers treated with ICIs, durable clinical benefit was observed in three of eight patients with NSCLC and two of two patients with SCLC. In NSCLC, STK11, KEAP1, and JAK1 were mutated in nonresponders but wild type in responders. CONCLUSIONS:We present a comprehensive clinicogenomic landscape of MSI-H lung cancers and reveal that MSI-H defines a rare subset of lung cancers associated with smoking, high tumor mutational burden, and MLH1 inactivation. Although durable clinical benefit to ICI was observed in some patients, the broad range of responses suggests that clinical activity may be modulated by co-mutational landscapes.

Comprehensive genomic sequencing is becoming a critical component in the assessment of hematologic malignancies, with broad implications for patients' management. In this context, unequivocally discriminating somatic from germline events is challenging but greatly facilitated by matched analysis of tumor:normal pairs of samples. In contrast to solid tumors, in hematologic malignancies conventional sources of normal control material (peripheral blood, buccal swabs, saliva) could be highly involved by the neoplastic process, rendering them unsuitable. In this work we describe our real-world experience using cell-free DNA (cfDNA) isolated from nail clippings as an alternate source of normal control material, through the dedicated review of 2,610 tumor:nail pairs comprehensively sequenced by MSK-IMPACT-heme. Overall, we found that nail cfDNA is a robust germline control for paired genomic studies. In a subset of patients, nail DNA may be contaminated by tumor DNA, reflecting unique attributes of the hematologic disease and transplant history. Contamination is generally low level, but significantly more common among patients with myeloid neoplasms (20.5%; 304/1,482) than among those with lymphoid diseases (5.4%; 61/1,128) and particularly enriched in myeloproliferative neoplasms with marked myelofibrosis. When identified in patients with lymphoid and plasma-cell neoplasms, mutations commonly reflected a myeloid profile and correlated with a concurrent/evolving clonal myeloid neoplasm. Donor DNA was identified in 22% (11/50) of nails collected after allogeneic stem-cell transplantation. In this cohort, an association with a recent history of graft- versus-host disease was identified. These findings should be considered as a potential limitation to the use of nails as a source of normal control DNA but could also provide important diagnostic information regarding the disease process.

Breakdown of MAP2K1, RAF1, ARAF, FGFR3-TACC3 fusion and CDKN2A loss patients

Supplementary Methods Supplementary References Supplementary Figure 1. Effect of acquired resistance mutations on TRK inhibitor activity. Supplementary Figure 2. Further characterization of LOXO-195 inhibitory activity against acquired resistance mutations. Supplementary Figure 3. LOXO-195 is selectively cytotoxic to TRK-fusion cell lines. Supplementary Figure 4. Identification of a clonal NTRK1 (TRKA)-G595R mutation after larotrectinib treatment. Supplementary Table 1. LOXO-195 ADME properties. Supplementary Table 2. Selectivity of LOXO-195 for 228 kinases. Supplementary Table 3. Summary of LOXO-195 PK parameters for each patient during intra-patient dose escalation.

Supplementary Table 3: Prevalence of oncogenic RET fusions in solid tumors analyzed by MSK-IMPACT.

Supplemental Figure 5. Timeline for Patients with Emergent or Lost TRK Fusions.

Abstract Mosaic mutations in normal tissues can occur early in embryogenesis and be associated with hereditary cancer syndromes when affecting cancer susceptibility genes (CSG). Their contribution to apparently sporadic cancers is currently unknown. Analysis of paired tumor/blood sequencing data of 35,310 patients with cancer revealed 36 pathogenic mosaic variants affecting CSGs, most of which were not detected by prior clinical genetic testing. These CSG mosaic variants were consistently detected at varying variant allelic fractions in microdissected normal tissues (n = 48) from distinct embryonic lineages in all individuals tested, indicating their early embryonic origin, likely prior to gastrulation, and likely asymmetrical propagation. Tumor-specific biallelic inactivation of the CSG affected by a mosaic variant was observed in 91.7% (33/36) of cases, and tumors displayed the hallmark pathologic and/or genomic features of inactivation of the respective CSGs, establishing a causal link between CSG mosaic variants arising in early embryogenesis and the development of apparently sporadic cancers. Significance: Here, we demonstrate that mosaic variants in CSGs arising in early embryogenesis contribute to the oncogenesis of seemingly sporadic cancers. These variants can be systematically detected through the analysis of tumor/normal sequencing data, and their detection may affect therapeutic decisions as well as prophylactic measures for patients and their offspring. See related commentary by Liggett and Sankaran, p. 889. This article is highlighted in the In This Issue feature, p. 873

Supplemental Figure 6. Distribution of Surgery, Radiotherapy, Systemic Therapy, and Chemotherapy.

Supplemental Figure 4. Pathologic and preclinical characterization of melanoma with concurrent GON4L-NTRK1 and NRAS Q61R mutations.

PURPOSE:Clonal hematopoiesis (CH), the expansion of clones in the hematopoietic system, has been linked to different internal and external features such as aging, genetic ancestry, smoking, and oncologic treatment. However, the interplay between mutations in known cancer predisposition genes and CH has not been thoroughly examined in patients with solid tumors.METHODS:We used prospective tumor-blood paired sequencing data from 46,906 patients who underwent Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) testing to interrogate the associations between CH and rare pathogenic or likely pathogenic (P/LP) germline variants.RESULTS:We observed an enrichment of CH-positive patients among those carrying P/LP germline mutations and identified a significant association between P/LP germline variants in ATM and CH. Germline and CH comutation patterns in ATM, TP53, and CHEK2 suggested biallelic inactivation as a potential mediator of clonal expansion. Moreover, we observed that CH-PPM1D mutations, similar to somatic tumor-associated PPM1D mutations, were depleted in patients with P/LP germline mutations in the DNA damage response (DDR) genes ATM, CHEK2, and TP53. Patients with solid tumors and harboring P/LP germline mutations, CH mutations, and mosaicism chromosomal alterations might be at an increased risk of developing secondary leukemia while germline variants in TP53 were identified as an independent risk factor (hazard ratio, 36; P < .001) for secondary leukemias.CONCLUSION:Our results suggest a close relationship between inherited variants and CH mutations within the DDR genes in patients with solid tumors. Associations identified in this study might translate into enhanced clinical surveillance for CH and associated comorbidities in patients with cancer harboring these germline mutations.