Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer

Driver mutations in oncogenes encode proteins with gain-of-function properties that enhance fitness. Heterozygous mutations are thus viewed as sufficient for tumorigenesis. We describe widespread oncogenic mutant allele imbalance in 13,448 prospectively characterized cancers. Imbalance was selected for through modest dosage increases of gain-of-fitness mutations. Negative selection targeted haplo-essential effectors of the spliceosome. Loss of the normal allele comprised a distinct class of imbalance driven by competitive fitness, which correlated with enhanced response to targeted therapies. In many cancers, an antecedent oncogenic mutation drove evolutionarily dependent allele-specific imbalance. In other instances, oncogenic mutations co-opted independent copy-number changes via the evolutionary process of exaptation. Oncogenic allele imbalance is a pervasive evolutionary innovation that enhances fitness and modulates sensitivity to targeted therapy.

New developments in liquid-liquid extraction, surface modification and agglomerate-free processing of inorganic particles

This review describes new methods for the particle extraction through liquid-liquid interface (PELLI). The discovery of new surface modification techniques, advanced extractors and new adsorption mechanisms enabled novel applications of PELLI in nanotechnology of metals, quantum dots, oxides and hydroxides. Colloidal and interface chemistry of PELLI is emerging as a new area of technological and scientific interest. The progress achieved in the understanding of particle behavior and interactions at the liquid-liquid interface, phase transfer and interface reactions allowed for the development of new extraction mechanisms. An important breakthrough was the development of surface modification techniques for extraction of functional oxides. Especially important is the possibility of particle transfer from the synthesis medium to the device processing medium, which facilitates agglomerate-free processing of functional nanoparticles. Multifunctional extractor molecules were discovered and used as capping and reducing agents for particle synthesis or dispersing and charging agents for colloidal processing. The progress achieved in the development of extractors and extraction mechanisms has driven the advances in the surface modification and functionalization of materials. New PELLI techniques were used for the development of advanced materials and devices for optical, photovoltaic, energy storage, electronic, biomedical, sensor and other applications.

Validation of Memorial Sloan Kettering Cancer Center nomogram to detect non-sentinel lymph node metastases in a United Kingdom cohort

AIM

Axillary lymph node dissection, although associated with long-term morbidity, has been the standard of treatment for all nodepositive breast cancer patients. We assessed the risk prediction ability (validity) of Memorial Sloan Kettering Cancer Center (MSKCC) nomogram for non-sentinel lymph node metastases and analysed the outcome of patients with sentinel node metastases.

PATIENTS AND METHODS

All operable early breast cancer patients with sentinel node macro metastases (size > 2mm) who underwent axillary dissection from April 2009 to March 2015 were considered eligible. The risk of non-sentinel lymph node metastases was calculated using an online MSKCC calculator, and accuracy was determined based on the area under the receiver-operating characteristic curve (AUC-ROC). Tumour characteristics and overall survival were also analysed as secondary end points.

RESULTS

Of 1745 patients who were diagnosed with operable breast cancer during the study period, 114 patients were considered eligible. The AUC-ROC was 0.66 suggestive of lesser accuracy in prediction and not statistically significant (p value = 0.7303). Seventysix (50.7%) of these patients did not have any non-sentinel node metastases. At a mean follow up of four years, the disease-free survival was 86.4% and overall survival rate was 88.4%.

CONCLUSIONS

The MSKCC nomogram was unable to accurately predict the risk in our cohort of patients with more than half of this cohort of patients not requiring axillary dissection. These findings are consistent with other European studies. This study thus highlights the need for modified prediction model for European cohorts.

Clinical Sequencing Defines the Genomic Landscape of Metastatic Colorectal Cancer

Metastatic colorectal cancers (mCRCs) are clinically heterogeneous, but the genomic basis of this variability remains poorly understood. We performed prospective targeted sequencing of 1,134 CRCs. We identified splice alterations in intronic regions of APC and large in-frame deletions in CTNNB1, increasing oncogenic WNT pathway alterations to 96% of CRCs. Right-sided primary site in microsatellite stable mCRC was associated with shorter survival, older age at diagnosis, increased mutations, and enrichment of oncogenic alterations in KRAS, BRAF, PIK3CA, AKT1, RNF43, and SMAD4 compared with left-sided primaries. Left-sided tumors frequently had no identifiable genetic alteration in mitogenic signaling, but exhibited higher mitogenic ligand expression. Our results suggest different pathways to tumorigenesis in right- and left-sided microsatellite stable CRC that may underlie clinical differences.

Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing

IMPORTANCE

Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention.

OBJECTIVE

To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue ("tumor-normal sequencing") compared with genetic test results based on current guidelines.

DESIGN, SETTING, AND PARTICIPANTS

From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing. Since May 2015, 1040 of these patients with advanced cancer were referred by their oncologists for germline analysis of 76 cancer predisposition genes. Patients with clinically actionable inherited mutations whose genetic test results would not have been predicted by published decision rules were identified. Follow-up for potential clinical implications of mutation detection was through May 2017.

EXPOSURE

Tumor and germline sequencing compared with the predicted yield of targeted germline sequencing based on clinical guidelines.

MAIN OUTCOMES AND MEASURES

Proportion of clinically actionable germline mutations detected by universal tumor-normal sequencing that would not have been detected by guideline-directed testing.

RESULTS

Of 1040 patients, the median age was 58 years (interquartile range, 50.5-66 years), 65.3% were male, and 81.3% had stage IV disease at the time of genomic analysis, with prostate, renal, pancreatic, breast, and colon cancer as the most common diagnoses. Of the 1040 patients, 182 (17.5%; 95% CI, 15.3%-19.9%) had clinically actionable mutations conferring cancer susceptibility, including 149 with moderate- to high-penetrance mutations; 101 patients tested (9.7%; 95% CI, 8.1%-11.7%) would not have had these mutations detected using clinical guidelines, including 65 with moderate- to high-penetrance mutations. Frequency of inherited mutations was related to case mix, stage, and founder mutations. Germline findings led to discussion or initiation of change to targeted therapy in 38 patients tested (3.7%) and predictive testing in the families of 13 individuals (1.3%), including 6 for whom genetic evaluation would not have been initiated by guideline-based testing.

CONCLUSIONS AND RELEVANCE

In this referral population with selected advanced cancers, universal sequencing of a broad panel of cancer-related genes in paired germline and tumor DNA samples was associated with increased detection of individuals with potentially clinically significant heritable mutations over the predicted yield of targeted germline testing based on current clinical guidelines. Knowledge of these additional mutations can help guide therapeutic and preventive interventions, but whether all of these interventions would improve outcomes for patients with cancer or their family members requires further study.

TRIAL REGISTRATION

clinicaltrials.gov Identifier: NCT01775072.

Therapy-Related Clonal Hematopoiesis in Patients with Non-hematologic Cancers Is Common and Associated with Adverse Clinical Outcomes

Clonal hematopoiesis (CH), as evidenced by recurrent somatic mutations in leukemia-associated genes, commonly occurs among aging human hematopoietic stem cells. We analyzed deep-coverage, targeted, next-generation sequencing (NGS) data of paired tumor and blood samples from 8,810 individuals to assess the frequency and clinical relevance of CH in patients with non-hematologic malignancies. We identified CH in 25% of cancer patients, with 4.5% harboring presumptive leukemia driver mutations (CH-PD). CH was associated with increased age, prior radiation therapy, and tobacco use. PPM1D and TP53 mutations were associated with prior exposure to chemotherapy. CH and CH-PD led to an increased incidence of subsequent hematologic cancers, and CH-PD was associated with shorter patient survival. These data suggest that CH occurs in an age-dependent manner and that specific perturbations can enhance fitness of clonal hematopoietic stem cells, which can impact outcome through progression to hematologic malignancies and through cell-non-autonomous effects on solid tumor biology.

Abstract 4380: Integrative genomics analysis of metastatic colorectal cancer

We performed an integrated clinical and bioinformatic analysis of colorectal cancers (CRCs) genotyped at our institution from 4/2014-7/2016 to comprehensively characterize genomic alterations in metastatic CRC (mCRC). We analyzed 1008 samples (474 primaries, 534 metastases) from 985 mCRC patients and 128 early stage CRCs sequenced with MSK-IMPACT, a hybridization capture next generation sequencing assay. Metastatic CRCs were divided into 3 groups by mutation burden and MSIsensor algorithm score: microsatellite stable (MSS) (n=939; 95%), microsatellite-high (MSI-H) (n=41; 4%), and ultra-mutated (n=5; 1%). Early stage CRC were enriched for MSI-H due to clinical selection and were 53% MSS, 44% MSI-H, and 4% ultra-mutated. Ultra-mutated tumors exhibited >100 mutations and harbored hotspot mutations in POLE in 8 cases and a potential novel POLE alteration in 1 case.

We evaluated the frequency of oncogenic alterations in MSI-H and MSS mCRCs. The frequency of the resistance biomarkers KRAS and NRAS did not vary between MSI-H and MSS mCRCs (46% v 41%, p=0.6). Potentially actionable alterations were enriched in MSI-H tumors (78% v 33%, p<0.001). Metastases did not have more actionable alterations than primary tumors. We classified clinically relevant targets using the OncoKB classification as level 2B (FDA-approved target in another disease type), 3A (target with compelling early clinical evidence in CRC), and 3B (target with compelling early clinical evidence in another disease type). Twelve percent (109/939) of MSS mCRCs had a level 2B target: BRAF V600E (5%), ERBB2 amplification (AMP) (4%), MET AMP (1%), BRCA1/BRCA2 alteration (1%), TSC1/TSC2 mutation (1%), EGFR mutation (<1%), RET fusion (<1%); there was significant enrichment of BRAF V600E (24%) and BRCA1/BRCA2 alterations (29%) in MSI-H versus MSS mCRC (p<0.001). NTRK fusions, the main 3A alteration identified, occurred in 7% of MSI-H and <1% MSS CRC (p<0.01). Level 3B alterations at ≥ 1% in MSS CRC included PIK3CA (15%), NRAS (3%), AKT1 (1%), MAP2K1 (1%), and ERBB2 (1%) mutations and FGFR1 AMP (2%). PIK3CA and PTCH1 mutations were both enriched in MSI-H versus MSS mCRC (32% v 15%, p<0.01; 27%,v <1%, p<0.001, respectively).

Analysis of mutation frequencies in 3 MSS CRC disease states - early stage resected primary (The Cancer Genome Atlas, TCGA), primary site of mCRC, and metastatic site - found significant depletion of FBXW7 mutations in metastases. We also found significant and progressive enrichment of TP53 alterations (58% TCGA, 73% primaries of mCRC, 79% metastases) and BRAF mutations (4% TCGA, 9% primaries of mCRC, 10% metastases) in advanced disease, suggesting a role of these genes in aggressive disease. One third of the BRAF mutations in our cohorts were not V600 but known to be oncogenic.

In this large dataset, we identified markers of advanced CRC and found that while MSI-H and MSS CRC have a similar frequency of resistance biomarkers, MSI-H CRC more commonly harbor actionable alterations.

Citation Format: Marla Lipsyc, Walid Chatila, Jaclyn F. Hechtman, Francisco Sanchez-Vega, Sumit Middha, Andrea Cercek, Zsofia Stadler, Ritika Kundra, Aijazuddin Syed, David M. Hyman, Ahmet Zehir, Armin Shahrokni, Anna Varghese, Diane Reidy, Neil H. Segal, Efsevia Vakiani, David B. Solit, Marc Ladanyi, Michael F. Berger, Nancy Kemeny, Leonard Saltz, Nikolaus Schultz, Rona Yaeger. Integrative genomics analysis of metastatic colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4380. doi:10.1158/1538-7445.AM2017-4380

Abstract 971: Genome directed diagnosis informs clinical cancer care

Cancer treatment is primarily guided by the organ of origin, which despite extensive histopathological and clinical evaluation, remains ambiguous in many cases and may be inaccurate in cases of occult primary. We determine the extent to which routine prospective tumour sequencing, combined with conventional histopathology, can be used to infer the tumor type and thereby direct clinical decisions.

Characteristic patterns of somatic mutations, broad and focal copy number alterations, structural rearrangements, mutational signatures, and other facets acquired from prospective tumor sequencing can inform the tissue of origin classification of patient disease. Such prospective sequencing of active cancer patients presents an opportunity to guide diagnosis and therapy beyond the identification of individual biomarkers of treatment response. Probabilistic classification allows for systematic combination of genome-directed diagnosis with conventional histopathology and clinical history in the course of disease management.

Using more than 10,000 tumors collected from advanced cancer patients at our institution and sequenced using a comprehensive cancer panel (MSK-IMPACT) encompassing 341 genes, we have developed a probabilistic classifier that infers the tumor type from nine broad categories of genomic aberrations. Scores from a RandomForest classifier are calibrated to correspond to the probability for each of the 22 interrogated tumor types. In 18% of all cases, a prediction is made with very high confidence (greater than 99%), of which just over 99% agree with the existing diagnosis. The classifier has been used to guide clinical decision making, including re-diagnoses that distinguish between a recurrence and a new primary, spare or encourage surgery, facilitate access to FDA-approved molecularly targeted drugs and prompt germline genetic testing.

We demonstrate that genome-directed diagnosis, based on alterations routinely identified from prospective sequencing, can inform clinical cancer care with the potential to improve patient outcomes.

Citation Format: Alexander Penson, Niedzica Camacho, Anna M. Varghese, Adam Abeshouse, Pedram Razavi, Aijazuddin Syed, Ahmet Zehir, Nikolaus Schultz, David B. Solit, David Hyman, Barry S. Taylor, Michael F. Berger. Genome directed diagnosis informs clinical cancer care [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 971. doi:10.1158/1538-7445.AM2017-971

Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making

PURPOSE

A long natural history and a predominant osseous pattern of metastatic spread are impediments to the adoption of precision medicine in patients with prostate cancer. To establish the feasibility of clinical genomic profiling in the disease, we performed targeted deep sequencing of tumor and normal DNA from patients with locoregional, metastatic non-castrate, and metastatic castration-resistant prostate cancer (CRPC).

METHODS

Patients consented to genomic analysis of their tumor and germline DNA. A hybridization capture-based clinical assay was employed to identify single nucleotide variations, small insertions and deletions, copy number alterations and structural rearrangements in over 300 cancer-related genes in tumors and matched normal blood.

RESULTS

We successfully sequenced 504 tumors from 451 patients with prostate cancer. Potentially actionable alterations were identified in DNA damage repair (DDR), PI3K, and MAP kinase pathways. 27% of patients harbored a germline or a somatic alteration in a DDR gene that may predict for response to PARP inhibition. Profiling of matched tumors from individual patients revealed that somatic TP53 and BRCA2 alterations arose early in tumors from patients who eventually developed metastatic disease. In contrast, comparative analysis across disease states revealed that APC alterations were enriched in metastatic tumors, while ATM alterations were specifically enriched in CRPC.

CONCLUSION

Through genomic profiling of prostate tumors representing the disease clinical spectrum, we identified a high frequency of potentially actionable alterations and possible drivers of disease initiation, metastasis and castration-resistance. Our findings support the routine use of tumor and germline DNA profiling for patients with advanced prostate cancer, for the purpose of guiding enrollment in targeted clinical trials and counseling families at increased risk of malignancy.

The relationship between eosinophilic esophagitis and esophageal cancer

Eosinophilic esophagitis (EoE) is a disorder characterized by long-term chronic eosinophilic inflammation, which may predispose patients for malignant transformation. To determine if EoE is associated with an increased risk for esophageal cancer (EC) over time. This was a cross-sectional population-based study using the Explorys Platform. Data were collected from January 1999 to December 2014 and the search terms 'Eosinophlic esophagitis', gastroesophageal reflux disease, and Barrett's esophagus were used. The latter two served as comparison groups. The term 'malignant tumor of esophagus' was searched in Explorys and was accepted only if it was established after the aforementioned diagnoses. Analysis was performed using social science statistical software. A total of 27,183,310 subjects were included in the study. Of those 5,370 (0.02%) had the diagnosis of EoE, 25,610 (0.09%) BE, and 2,606,640 (9.59%) gastroesophageal reflux (GERD). In general, diagnosis of EC was rare prior to age 40. Therefore, subsequent analysis was done on subjects between 40 to 79 years of age (N = 20,257,480). The prevalence of EC was 0.05% (N = 2420), in BE (N = 19,640) 2.65%, and in GERD (N = 1,696,230) 0.22%. No cases of EC were identified among those with EoE. We found no significant difference or increased risk in the rate of EC in the EoE group (P = 0.575) when compared to the control population. In this largest study, we found no association between esophageal cancer and EoE. Further long-term prospective studies are needed to better characterize the relationship between EoE and esophageal malignancy.

Determining if Positive Predictive Value using Laboratory Risk Indicator for Necrotising Fasciitis is Applicable in Malaysian Patients with Necrotising Fasciitis

Introduction: Necrotising fasciitis (NF) is a rapidly progressive infection of the subcutaneous tissue and fascia which spreads rapidly. The scoring system of Laboratory Risk Indicator for Necrotising Fasciitis (LRINEC) developed by Wong et al has been proposed as a tool for distinguishing NF and other soft tissue infections (STI) in Singapore. We set out to establish whether the LRINEC score is applicable in our Malaysian setting.

Materials and Methods: A cross sectional study of all patients admitted to our hospital diagnosed with NF or To Rule Out NF (TRO NF) between January 1st 2016 to 30th June 2016. The sensitivity, specificity, positive and negative predictive values were then calculated for LRINEC score of ≥ 6 and ≥ 8.

Results: Fourty-four patients were identified with the diagnosis of NF or TRO NF in the study. Twenty-seven patients (61.4%) were deemed post-operatively as having NF and 17 patients (38.6%) not having NF. A sensitivity of 59.3% and specificity of 47.1% when a LRINEC score of ≥ 6 was taken with positive predictive value (PPV) of 64.0% and the negative predictive value (NPV) of 42.1%. When score ≥ 8 was taken, the sensitivity was 48.1% and specificity of 58.8% with PPV of 65% and NPV of 41.7%.

Conclusion: The low sensitivity and low PPV achieved in this study as well as other studies makes the LRINEC score unsuitable to be used solely to distinguish NF with other soft tissue infections.

Variability in genomic alterations between right- and left-sided microsatellite stable (MSS) metastatic colorectal cancer and impact on survival

3534

Background: Metastatic colorectal cancers (mCRCs) with a right-sided primary site are associated with shorter survival and insensitivity to EGFR inhibitors compared to those originating in the left side of the colon or rectum. Methods: We performed targeted gene sequencing of 928 consecutive MSS mCRCs. Primary tumor site was divided into right-sided for cecum to distal transverse colon (n = 242), left-sided for splenic flexure to rectum (n = 673), or unknown colonic location (n = 13). Histologic subtypes were conventional (adenocarcinoma not otherwise specified), conventional with mucinous features ( < 50% mucinous), mucinous, signet ring, and poorly differentiated. To evaluate receptor tyrosine kinase (RTK) signaling, we analyzed ligand mRNA expression in TCGA. Results: Overall survival from time of metastasis was shorter for right-sided than left-sided primary site (survival at 5 years: 45% v 67%, p < 0.001). Right-sided tumors had more mutations (5.60 v 4.62 per MB, p < 0.001) but fewer copy-number changes (0.18 v 0.22 fraction genome altered, p = 0.001) compared to left-sided tumors. Alterations of KRAS, BRAF, PIK3CA, PTEN, AKT1, RNF43, and SMAD4 were significantly enriched in right-sided tumors, and of APC and TP53 in left-sided tumors. In a multivariate model, APC (HR = 0.7, p = 0.03), BRAF (HR = 3.7, p < 0.001), and KRAS (HR = 1.7, p < 0.01) alterations predicted for survival, but primary site did not (HR = 0.74, p = 0.07). Amphiregulin, epiregulin, neuregulin, and HGF expression was significantly higher in left-sided tumors. We found a higher proportion of conventional histology (83% v 63%) and moderate differentiation (82% v 69%) for left versus right-sided cases. Conclusions: We find that within MSS mCRC there are significantly more oncogenic mutations in right-sided tumors, and the difference in survival between right- and left-sided mCRC is primarily driven by differences in mutations. Left-sided tumors more commonly exhibit a “simpler” conventional histology that is lower grade and may rely on native RTK signaling, such as EGFR, for growth, providing a potential mechanism for the differential sensitivity to EGFR inhibitors seen by primary tumor site.

Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing

Background

The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mutation in a cancer predisposition gene is not only diagnostic for a cancer predisposition syndrome, but also has significant clinical implications in the clinical management of patients and their families.

Methods

Here, we evaluated the performance of MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) in detecting genetic alterations in 76 genes implicated in cancer predisposition syndromes. Output from hybridization-based capture was sequenced on an Illumina HiSeq 2500. A custom analysis pipeline was used to detect single nucleotide variants (SNVs), small insertions/deletions (indels) and copy number variants (CNVs).

Results

MSK-IMPACT detected all germline variants in a set of 233 unique patient DNA samples, previously confirmed by previous single gene testing. Reproducibility of variant calls was demonstrated using inter- and intra- run replicates. Moreover, in 16 samples, we identified additional pathogenic mutations other than those previously identified through a traditional gene-by-gene approach, including founder mutations in BRCA1, BRCA2, CHEK2 and APC, and truncating mutations in TP53, TSC2, ATM and VHL.

Conclusions

This study highlights the importance of the NGS-based gene panel testing approach in comprehensively identifying germline variants contributing to cancer predisposition and simultaneous detection of somatic and germline alterations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12920-017-0271-4) contains supplementary material, which is available to authorized users.

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically defined tumor types, coupled with an expanding portfolio of molecularly targeted therapies, demands flexible and comprehensive approaches to profile clinically relevant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which we have compiled tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.

Genetic Determinants of Cisplatin Resistance in Patients With Advanced Germ Cell Tumors

Purpose Owing to its exquisite chemotherapy sensitivity, most patients with metastatic germ cell tumors (GCTs) are cured with cisplatin-based chemotherapy. However, up to 30% of patients with advanced GCT exhibit cisplatin resistance, which requires intensive salvage treatment, and have a 50% risk of cancer-related death. To identify a genetic basis for cisplatin resistance, we performed whole-exome and targeted sequencing of cisplatin-sensitive and cisplatin-resistant GCTs. Methods Men with GCT who received a cisplatin-containing chemotherapy regimen and had available tumor tissue were eligible to participate in this study. Whole-exome sequencing or targeted exon-capture-based sequencing was performed on 180 tumors. Patients were categorized as cisplatin sensitive or cisplatin resistant by using a combination of postchemotherapy parameters, including serum tumor marker levels, radiology, and pathology at surgical resection of residual disease. Results TP53 alterations were present exclusively in cisplatin-resistant tumors and were particularly prevalent among primary mediastinal nonseminomas (72%). TP53 pathway alterations including MDM2 amplifications were more common among patients with adverse clinical features, categorized as poor risk according to the International Germ Cell Cancer Collaborative Group (IGCCCG) model. Despite this association, TP53 and MDM2 alterations predicted adverse prognosis independent of the IGCCCG model. Actionable alterations, including novel RAC1 mutations, were detected in 55% of cisplatin-resistant GCTs. Conclusion In GCT, TP53 and MDM2 alterations were associated with cisplatin resistance and inferior outcomes, independent of the IGCCCG model. The finding of frequent TP53 alterations among mediastinal primary nonseminomas may explain the more frequent chemoresistance observed with this tumor subtype. A substantial portion of cisplatin-resistant GCTs harbor actionable alterations, which might respond to targeted therapies. Genomic profiling of patients with advanced GCT could improve current risk stratification and identify novel therapeutic approaches for patients with cisplatin-resistant disease.