Tumor sequencing of African ancestry reveals differences in clinically relevant alterations across common cancers

Cancer genomes from patients with African (AFR) ancestry have been poorly studied in clinical research. We leverage two large genomic cohorts to investigate the relationship between genomic alterations and AFR ancestry in six common cancers. Cross-cancer type associations, such as an enrichment of MYC amplification with AFR ancestry in lung, breast, and prostate cancers, and depletion of BRAF alterations are observed in colorectal and pancreatic cancers. There are differences in actionable alterations, such as depletion of KRAS G12C and EGFR L858R, and enrichment of ROS1 fusion with AFR ancestry in lung cancers. Interestingly, in lung cancer, KRAS mutations are less common in both smokers and non-smokers with AFR ancestry, whereas the association of TP53 mutations with AFR ancestry is only seen in smokers, suggesting an ancestry-environment interaction that modifies driver rates. Our study highlights the need to increase representation of patients with AFR ancestry in drug development and biomarker discovery.

Germline Pathogenic Variants and Genetic Counseling by Ancestry in Patients With Epithelial Ovarian Cancer

PURPOSE

To evaluate rates of germline pathogenic/likely pathogenic variants (PVs) and genetic counseling by ancestry in patients with epithelial ovarian cancer (EOC).

METHODS

Patients with pathologically confirmed EOC who underwent clinical tumor-normal sequencing from January 1, 2015, to December 31, 2020, inclusive of germline analysis of ≥76 genes were included. Patients with newly identified PVs were referred for Clinical Genetics Service (CGS) counseling. Ancestry groups were defined using self-reported race/ethnicity and Ashkenazi Jewish (AJ) heritage. Genetic ancestry was inferred computationally using validated algorithms. Logistic regression models were built.

RESULTS

Of 1,266 patients, self-reported ancestry (AJ, 17%; Asian, 10%; Black/African American, 5.4%; Hispanic, 6.2%; non-Hispanic White, 57%; other, 0.16%; unknown, 4.0%) correlated with genetic ancestry (AJ ancestry, 18%; admixed, 10%; African, 4%; East Asian [EAS], 6%; European, 56%; Native American, 0.2%; South Asian [SAS], 4%; unknown, 2%). Germline PVs were observed in 313 (25%) patients, including 195 (15%) with PVs in EOC-associated genes. Those with PVs were younger at diagnosis (59 v 62 years; P < .001) and more likely to have high-grade serous ovarian cancer (83% v 72%; P = .009). PV prevalence varied between ancestry groups (P < .001), with highest rates in the AJ (39.9%) and Asian (26.5%) groups and similar rates (>10%) across other ancestry groups. Use of genetic ancestry demonstrated similar findings and further characterized high rates of PV in EAS/SAS groups. Younger age, high-grade serous histology, and self-reported AJ or Asian ancestry were associated with PV in an EOC-associated gene. Rates of CGS counseling for newly identified PVs were high (80%) across ancestry groups.

CONCLUSION

Rates of PV, particularly in EOC-associated genes, were high regardless of ancestry, with similar rates of counseling between groups, emphasizing the importance of universal genetic testing in all patients with EOC.

Ancestry-driven recalibration of tumor mutational burden and disparate clinical outcomes in response to immune checkpoint inhibitors

The immune checkpoint inhibitor (ICI) pembrolizumab is US FDA approved for treatment of solid tumors with high tumor mutational burden (TMB-high; ≥10 variants/Mb). However, the extent to which TMB-high generalizes as an accurate biomarker in diverse patient populations is largely unknown. Using two clinical cohorts, we investigated the interplay between genetic ancestry, TMB, and tumor-only versus tumor-normal paired sequencing in solid tumors. TMB estimates from tumor-only panels substantially overclassified individuals into the clinically important TMB-high group due to germline contamination, and this bias was particularly pronounced in patients with Asian/African ancestry. Among patients with non-small cell lung cancer treated with ICIs, those misclassified as TMB-high from tumor-only panels did not associate with improved outcomes. TMB-high was significantly associated with improved outcomes only in European ancestries and merits validation in non-European ancestry populations. Ancestry-aware tumor-only TMB calibration and ancestry-diverse biomarker studies are critical to ensure that existing disparities are not exacerbated in precision medicine.

Abstract 3628: Comprehensive identification of lineage associated cancer genes in 122 histologies

Although the majority of cancer genes show a high degree of specificity for certain lineages, genomic profiling of cancer patients routinely identify alterations in genes that are atypical to the presented cancer type but are canonical drivers in a different lineage. It is often unclear if these atypical drivers arose early in tumorigenesis or were acquired during progression. A complete understanding of lineage associated genes (LAGs) will enable better interpretation of the molecular etiology of each diagnosed tumor.

Here, we used a cohort of 38,912 patients across 122 cancer histologies (each with 50 or more patients) profiled for somatic alterations (mutations, copy number alterations and gene fusions) using the MSK-IMPACT assay. Tumors with TMB &gt; 15 were already excluded. All alterations were classified as drivers using OncoKB. Allele-specific copy number calls were assessed using FACETS.

Overall, 95% of patients harbored at least one oncogenic alteration, with a median of 4 drivers per tumor. We observed widespread prevalence of drivers across lineages with each gene mutated in a median of 36 different lineages. Conversely, a median of 103 genes were mutated at least once in each lineage. Hypothesizing that cancer genes are influenced by cell of origin, we sought to identify lineages harboring significantly higher rates of drivers in a given gene compared to its pancancer driver rate. We identified 1781 significant (adjusted P &lt; 0.05) gene and lineage associations, and an additional 109 involving genes mutated at &gt;10% in the respective lineages but which did not reach significance were also included. Lineage-agnostic genes such as TP53 and CDKN2A were associated with a broad spectrum of lineages (90 and 55, respectively). However, overall, each gene we profiled was found to be associated with a median of 3 distinct lineages. For example, while BRAF drivers are found in nearly all histologies (n=91), it is enriched for drivers in only 8 lineages: melanoma (acral and cutaneous), thyroid (poorly differentiated, anaplastic and papillary) and bowel (mucinous adenocarc. of colon/rectum, colon adenocarc. and neuroendocrine carc. of colon/rectum). In all, nearly a third of all drivers were observed in non-associated lineages.

We next compared the somatic properties of drivers among genes in associated lineages vs. the same genes in non-associated lineages. We observed that mutations in LAGs were more often clonal (83% vs. 73%, associated vs. non-associated, P = 0) and showed enrichment for mutant allele imbalance in oncogenes (40% vs. 23%, P = 2e-111) and biallelic inactivation in tumor suppressor LAGs (71% vs. 58%, P = 4e-130). Furthermore, 93% of all OncoKB Level 1/2/3A actionable alterations, which are classified based on their histology, were in LAGs. In conclusion, our findings enable classification of drivers that are relevant for lineage-specific malignant transformation and advance our understanding of tumor biology.

Citation Format: Chaitanya Bandlamudi, Walid K. Chatila, Shaleigh A. Smith, Subhiksha Nandakumar, Craig Bielski, Bastien Nguyen, Henry S. Walch, Christoph K. Kreitzer, Kanika S. Arora, Tran Thinh Ngoc, Miika Mehine, Irina Ostrovnaya, Ino de Bruijn, Hyung Jun Woo, Ritika Kundra, Christopher J. Fong, Satshil Rana, Gaofei Zhao, Mingxuan Zhang, Mark R. Zucker, Hongxin Zhang, Ryan Ptashkin, Rose Brannon, Eduard Reznik, JianJiong Gao, Maria E. Arcila, Ryma Benayed, Debyani Chakravarty, David Solit, Mark T. Donoghue, Marc Ladanyi, Nikolaus D. Schultz, Michael F. Berger, Ahmet Zehir. Comprehensive identification of lineage associated cancer genes in 122 histologies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3628.

Diverse alterations associated with resistance to KRAS(G12C) inhibition

Inactive state-selective KRAS(G12C) inhibitors^1-8 demonstrate a 30-40% response rate and result in approximately 6-month median progression-free survival in patients with lung cancer⁹. The genetic basis for resistance to these first-in-class mutant GTPase inhibitors remains under investigation. Here we evaluated matched pre-treatment and post-treatment specimens from 43 patients treated with the KRAS(G12C) inhibitor sotorasib. Multiple treatment-emergent alterations were observed across 27 patients, including alterations in KRAS, NRAS, BRAF, EGFR, FGFR2, MYC and other genes. In preclinical patient-derived xenograft and cell line models, resistance to KRAS(G12C) inhibition was associated with low allele frequency hotspot mutations in KRAS(G12V or G13D), NRAS(Q61K or G13R), MRAS(Q71R) and/or BRAF(G596R), mirroring observations in patients. Single-cell sequencing in an isogenic lineage identified secondary RAS and/or BRAF mutations in the same cells as KRAS(G12C), where they bypassed inhibition without affecting target inactivation. Genetic or pharmacological targeting of ERK signalling intermediates enhanced the antiproliferative effect of G12C inhibitor treatment in models with acquired RAS or BRAF mutations. Our study thus suggests a heterogenous pattern of resistance with multiple subclonal events emerging during G12C inhibitor treatment. A subset of patients in our cohort acquired oncogenic KRAS, NRAS or BRAF mutations, and resistance in this setting may be delayed by co-targeting of ERK signalling intermediates. These findings merit broader evaluation in prospective clinical trials.

Cleidocranial Dysplasia: Presentation of Clinical and Radiological Features of a Rare Syndromic Entity

Cleidocranial dysplasia is a developmental anomaly of the skeleton and the teeth. This condition may be inherited and be transmitted as dominant characteristics in either gender, or may appear spontaneously. It presents with skeletal defects of several bones, such as partial or complete absence of clavicles, late closure of the fontanels, presence of open skull sutures and multiple wormian bones. The dental manifestations are mainly delayed exfoliation of primary teeth and delayed eruption of permanent teeth with multiple impacted supernumerary teeth. This case of a 20 year old girl is noteworthy to the dentist as it deals with clinical and radiological features (a high number of impacted and supernumerary teeth as well as brachycephaly, frontal bossing and hypermobility of shoulders) which may come handy in clinical practice.

Peripheral and Central Nervous System Involvement in Recently Diagnosed Cases of Hypothyroidism: An Electrophysiological Study

Background:

Hypothyroidism, one of the most common endocrine disorders, may induce neurological abnormalities at an early stage of the disease.

Aim:

The study was designed to assess the electrophysiological alterations of some selected variables of nerve conduction, brainstem auditory evoked potentials (BAEPs), and visual evoked potentials (VEPs) in hypothyroid patients.

Subjects and Methods:

Sixty patients of newly diagnosed hypothyroidism and an equal number of age-matched controls were selected for the study. Nerve conduction studies that included parameters as latencies, conduction velocities, and amplitude of motor nerves, i.e., median, ulnar, common peroneal, tibial nerve, and sensory nerves, i.e., median and sural nerves was performed in both hypothyroid patients and controls. Further, BAEPs and VEPs of all the patients were done. The data were compiled and statistically analyzed using Student's unpaired t-test to observe any electrophysiological alterations in hypothyroid patients as compared to healthy controls.

Results:

On comparative evaluation, statistically significant increase in latency of median, ulnar, tibial, and sural nerves; decrease in conduction velocities of all the tested nerves and decrease in amplitude of median, tibial, and sural nerves was observed in hypothyroid patients. Statistically significant increase in latencies, interpeak latencies, and decrease in amplitudes of BAEP waves and statistically significant increase in P100 latency of VEP was seen in hypothyroid patients.

Conclusion:

The results of our study suggest that peripheral and central neuropathy develops in patients of hypothyroidism at an early stage of disease and the electrophysiological investigations of such patients can help in timely detection and treatment of neurological disorders that occur due to thyroid hormone deficiency.