TP53 Variants Research Articles

Genomic profiling of thymoma using a targeted high-throughput approach.

Thymomas and thymic carcinoma (TC) are the most common neoplasms localised in the thymus. These diseases are poorly understood, but progress made in next-generation sequencing (NGS) technology has provided novel data on their molecular pathology. Genomic DNA was isolated from formalin-fixed paraffin-embedded tumour tissue. We investigated somatic variants in 35 thymoma patients using amplicon-based TruSeq Amplicon Cancer Panel (TSACP) that covers 48 cancer related genes. We also analysed three samples from healthy individuals by TSACP platform and 32 healthy controls using exome sequencing. The total number of detected variants was 4447, out of which 2906 were in the coding region (median per patient 83, range: 2-300) and 1541 were in the non-coding area (median per patient 44, range: 0-172). We identified four genes, APC, ATM, ERBB4, and SMAD4, having more than 100 protein-changing variants. Additionally, more than 70% of the analysed cases harboured protein-changing variants in SMAD4, APC, ATM, PTEN, KDR, and TP53. Moreover, this study revealed 168 recurrent variants, out of which 15 were shown to be pathogenic. Comparison to controls revealed that the variants we reported in this study were somatic thymoma-specific variants. Additionally, we found that the presence of variants in SMAD4 gene predicted shorter overall survival in thymoma patients. The most frequently mutated genes in thymoma samples analysed in this study belong to the EGFR, ATM, and TP53 signalling pathways, regulating cell cycle check points, gene expression, and apoptosis. The results of our study complement the knowledge of thymoma molecular pathogenesis.

<p>Sequential Whole Exome Sequencing Reveals Somatic Mutations Associated with Platinum Response in NSCLC</p>

PurposeResistance is one of the main limitations of successful platinum treatment in non-small-cell lung cancer (NSCLC) patients. In this study, we aimed to identify somatic mutations associated with platinum response.Patients and MethodsA total of 57 patients who received platinum-based chemotherapy only and 13 patients who received neoadjuvant chemotherapy (NAC) were enrolled. Somatic mutations were obtained from targeted and whole exome sequencing (WES).ResultsSomatic mutations in a total of 225 genes were observed. Nonsynonymous variants in EGFR, TTN, TP53 and KRAS, and copy number variations (SCNVs) in chromosome 8q24.3 and 22q11.21 were identified to be associated with platinum response. Based on these mutations, the mutational signature associated with the failure of DNA double-strand break and calcium signaling pathways were identified to be associated with platinum response. Besides, we observed a decrease in tumor mutational burden after chemotherapy. We also evaluated the mutation spectrum consistency between cell-free DNA (cfDNA) and tissue DNA. Somatic mutations detected in cfDNA were consistent with that in tDNA, which indicated that plasma might be used for somatic mutation detection.ConclusionThese results support that somatic mutations can affect platinum drug response and provide potential clinical biomarkers for NSCLC treatment.

Next-generation sequencing of residual cytologic fixative preserved DNA from pancreatic lesions: A pilot study.

Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is a sensitive and specific tool in the risk stratification of pancreatic lesions, including cysts. The sensitivity and specificity of EUS-FNA has been shown to improve when cytology is combined with next-generation sequencing (NGS). Ideally, fresh cyst fluid is used for NGS. In this pilot study, we explore the possibility of sequencing DNA derived from residual alcohol-fixed pancreatic aspirates. Residual cytologic fixatives (n=42) from 39 patients who underwent EUS-FNA for pancreatic lesions were collected along with demographics, imaging, and laboratory studies. Samples were designated as nonneoplastic/nonmucinous benign (NB), mucinous cyst (MC), pancreatic ductal adenocarcinoma (PDAC), or well-differentiated neuroendocrine tumor (NET) on the basis of cytopathologic evaluation and sequenced on the Oncomine platform (ThermoFisher Scientific, Waltham, Massachusetts). Ten of 14 (71.4%) MCs exhibited clinically significant variants, including KRAS, GNAS, and TP53. Ten of 15 (66.7%) PDACs had KRAS alterations, and 9 of 15 (60%) showed variants in TP53. No variants were detected in any NETs. Only 1 of 9 (11.1%) NB aspirates showed variants in KRAS and MAP2K. Sequencing of formalin-fixed, paraffin-embedded tissue revealed variants identical to those detected in fixative-derived DNA in 4 of 5 cases (80%). Residual DNA from alcohol-fixed aspirates are an underutilized source for NGS. Sequencing residual fixative-derived DNA has the potential to be integrated into the workup of pancreatic aspirates, possibly impacting management.

Molecular Profiles of Mixed Endometrial Carcinoma.

Mixed endometrial carcinomas are defined as a combination of 2 or more distinct histologic subtypes, one of which must be a type II tumor comprising at least 5% of the tumor volume. The oncogenesis of these tumors remains unclear, particularly in light of the increasingly appreciated morphologic overlap among subtypes, as well as evolving molecular data. We evaluated 8 cases of mixed endometrial carcinoma, including 4 endometrioid (EC)/serous (SC), 1 SC/clear cell (CC), and 3 EC/CC cases, to study the underlying molecular features and oncogenic mechanisms at play. Each component was analyzed by a targeted next-generation sequencing assay. All tumors shared mutations in both components. In 6 cases, one component showed additional mutations. Two EC/SC cases showed shared mutations and mutations unique to each component. When present, unique mutations were typically seen in the SC component, including variants in POLE and TP53, as well as potentially targetable genes DDR2, MAP2K1, and CCNE1. In EC/SC tumors, ERBB2 abnormalities were seen in 2 cases. EC/CC cases showed FGFR2 activating mutations in the EC component only. No fusion drivers were identified. Our data suggest that the majority of these tumors begin as a single clone and diverge along 2 pathways: (1) tumor progression, with one component showing additional mutations, and (2) tumor divergence, in which tumor components have both shared mutations and mutations unique to each component. In addition, the findings suggest a component of morphologic mimicry in these tumors. Our findings are clinically relevant since targetable mutations may be present in only one component of mixed tumors.

XAF1 as a modifier of p53 function and cancer susceptibility

Cancer risk is highly variable in carriers of the common TP53-R337H founder allele, possibly due to the influence of modifier genes. Whole-genome sequencing identified a variant in the tumor suppressor XAF1 (E134*/Glu134Ter/rs146752602) in a subset of R337H carriers. Haplotype-defining variants were verified in 203 patients with cancer, 582 relatives, and 42,438 newborns. The compound mutant haplotype was enriched in patients with cancer, conferring risk for sarcoma (P = 0.003) and subsequent malignancies (P = 0.006). Functional analyses demonstrated that wild-type XAF1 enhances transactivation of wild-type and hypomorphic TP53 variants, whereas XAF1-E134* is markedly attenuated in this activity. We propose that cosegregation of XAF1-E134* and TP53-R337H mutations leads to a more aggressive cancer phenotype than TP53-R337H alone, with implications for genetic counseling and clinical management of hypomorphic TP53 mutant carriers.

UKCGG Consensus Group guidelines for the management of patients with constitutional TP53 pathogenic variants

Constitutional pathogenic variants in TP53 are associated with Li-Fraumeni syndrome or the more recently described heritable TP53-related cancer syndrome and are associated with increased lifetime risks of a wide spectrum...

Optimization of a WGA-Free Molecular Tagging-Based NGS Protocol for CTCs Mutational Profiling

Molecular characterization of Circulating Tumor Cells (CTCs) is still challenging, despite attempts to minimize the drawbacks of Whole Genome Amplification (WGA). In this paper, we propose a Next-Generation Sequencing (NGS) optimized protocol based on molecular tagging technology, in order to detect CTCs mutations while skipping the WGA step. MDA-MB-231 and MCF-7 cell lines, as well as leukocytes, were sorted into pools (2–5 cells) using a DEPArray™ system and were employed to set up the overall NGS procedure. A substantial reduction of reagent volume for the preparation of libraries was performed, in order to fit the limited DNA templates directly derived from cell lysates. Known variants in TP53, KRAS, and PIK3CA genes were detected in almost all the cell line pools (35/37 pools, 94.6%). No additional alterations, other than those which were expected, were found in all tested pools and no mutations were detected in leukocytes. The translational value of the optimized NGS workflow is confirmed by sequencing CTCs pools isolated from eight breast cancer patients and through the successful detection of variants. In conclusion, this study shows that the proposed NGS molecular tagging approach is technically feasible and, compared to traditional NGS approaches, has the advantage of filtering out the artifacts generated during library amplification, allowing for the reliable detection of mutations and, thus, making it highly promising for clinical use.

Cancer surveillance and distress among adult pathogenic TP53 germline variant carriers in Germany: A multicenter feasibility and acceptance survey.

Li-Fraumeni syndrome (LFS) is a high-risk cancer predisposition syndrome caused by pathogenic germline variants of TP53. Cancer surveillance has noted a significant survival advantage in individuals with LFS; however, little is known about the feasibility, acceptance, and psychosocial effects of such a program. Pathogenic TP53 germline variant carriers completed a 7-part questionnaire evaluating sociodemographics, cancer history, surveillance participation, reasons for nonadherence, worries, and distress adapted from the Cancer Worry Scale. Counselees' common concerns and suggestions were assessed in MAXQDA Analytics Pro 12. Forty-nine participants (46 females and 3 males), aged 40.0 ± 12.6years, formed the study population; 43 (88%) had a personal cancer history (including multiple cancers in 10 [20%]). Forty-three individuals participated (88%) in surveillance during the study or formerly. Willingness to undergo surveillance was influenced by satisfaction with genetic testing and counseling (P=.019 [Fisher-Yates test]) but not by sociodemographics, cancer history, or distress level. Almost one-third of the participants reported logistical difficulties in implementing surveillance because of the high frequency of medical visits, scheduling difficulties, and the travel distance to their surveillance providers. Self-reported distress and perceived emotional burden for family members and partners were moderate (median for self-reported distress, 3.3; median for perceived emotional burden, 3.0). For both, the interquartile range was moderate to very high (2.7-3.7 and 3.0-3.7, respectively). Individuals with LFS require efficient counseling as well as an accessible, well-organized, interdisciplinary, standardized surveillance program to increase adherence and psychological coping.

A novel hotspot and rare somatic mutation p.A138V, at TP53 is associated with poor survival of pancreatic ductal and periampullary adenocarcinoma patients

BackgroundPancreatic Ductal Adenocarcinoma (PDAC) is a cancer of the exocrine pancreas and 5-year survival rates remain constant at 7%. Along with PDAC, Periampullary Adenocarcinoma (PAC) accounts for 0.5–2% of all gastrointestinal malignancies. Genomic observations were well concluded for PDAC and PACs in western countries but no reports are available from India till now.MethodsTargeted Next Generation Sequencing were performed in 8 (5 PDAC and 3 PAC) tumour normal pairs, using a panel of 412 cancer related genes. Primary findings were replicated in 85 tumour samples (31 PDAC and 54 PAC) using the Sanger sequencing. Mutations were also validated by ASPCR, RFLP, and Ion Torrent sequencing. IHC along with molecular dynamics and docking studies were performed for the p.A138V mutant of TP53. Key polymorphisms at TP53 and its associated genes were genotyped by PCR-RFLP method and association with somatic mutations were evaluated. All survival analysis was done using the Kaplan-Meier survival method which revealed that the survival rates varied significantly depending on the somatic mutations the patients harboured.ResultsAmong the total 114 detected somatic mutations, TP53 was the most frequently mutated (41%) gene, followed by KRAS, SMAD4, CTNNB1, and ERBB3. We identified a novel hotspot TP53 mutation (p.A138V, in 17% of all patients). Low frequency of KRAS mutation (33%) was detected in these samples compared to patients from Western counties. Molecular Dynamics (MD) simulation and DNA-protein docking analysis predicted p.A138V to have oncogenic characteristics. Patients with p.A138V mutation showed poorer overall survival (p = 0.01). So, our finding highlights elevated prevalence of the p53p.A138V somatic mutation in PDAC and pancreatobiliary PAC patients.ConclusionDetection of p.A138V somatic variant in TP53 might serve as a prognostic marker to classify patients. It might also have a role in determining treatment regimes. In addition, low frequency of KRAS hotspot mutation mostly in Indian PDAC patient cohort indicates presence of other early drivers in malignant transformation.

Landscape of Germline Genetic Variants in AGT, MGMT, and TP53 in Mexican Adult Patients with Astrocytoma.

Astrocytoma is the most common type of primary brain tumor. The risk factors for astrocytoma are poorly understood; however, germline genetic variants account for 25% of the risk of developing gliomas. In this study, we assessed the risk of astrocytoma associated with variants in AGT, known by its role in angiogenesis, TP53, a well-known tumor suppressor and the DNA repair gene MGMT in a Mexican population. A case-control study was performed in 49 adult Mexican patients with grade II-IV astrocytoma. Sequencing of exons and untranslated regions of AGT, MGMT, and TP53 from was carried in an Ion Torrent platform. Individuals with Mexican Ancestry from the 1000 Genomes Project were used as controls. Variants found in our cohort were then assessed in a The Cancer Genome Atlas astrocytoma pan-ethnic validation cohort. Variants rs1926723 located in AGT (OR 2.74, 1.40-5.36 95% CI), rs7896488 in MGMT (OR 3.43, 1.17-10.10 95% CI), and rs4968187 in TP53 (OR 2.48, 1.26-4.88 95% CI) were significantly associated with the risk of astrocytoma after multiple-testing correction. This is the first study where the AGT rs1926723 variant, TP53 rs4968187, and MGMT rs7896488 were found to be associated with the risk of developing an astrocytoma.

Performance of the pattern-based interpretation of p53 immunohistochemistry as a surrogate for TP53 mutations in vulvar squamous cell carcinoma.

AimsThe most commonly mutated gene in vulvar squamous cell carcinoma (VSCC) is TP53 and its prognostic value, particularly in HPV‐independent VSCC, is uncertain. In other tumours, p53 immunohistochemistry (IHC) is an excellent surrogate marker for TP53 mutations. In order to study this in VSCC, we assigned six p53 IHC patterns into two final classes: ‘wild‐type’ or ‘mutant’. We determined the performance and interobserver variability of this pattern‐based p53 IHC approach.Methods and resultsTwo experienced gynaecological pathologists scored the predefined p53 IHC patterns of 59 VSCC, independently and blinded for molecular data. Agreement was calculated by Cohen's kappa. All disagreements regarding p53 IHC patterns were resolved by a consensus meeting. After DNA isolation, the presence of pathogenic TP53 variants was determined by next‐generation sequencing (NGS). Sensitivity, specificity and accuracy of p53 IHC as a surrogate marker for TP53 mutation status were calculated. Initial p53 IHC pattern interpretation showed substantial agreement between both observers (k = 0.71, P < 0.001). After consensus, 18 cases (30.5%) were assigned a final p53 IHC class as TP53 wild‐type and 41 cases (69.5%) as mutant. The accuracy between the p53 IHC class and TP53 mutation status, after the consensus meeting, was 96.6%. Moreover, the sensitivity and specificity were high 95.3% [95% confidence interval (CI) = 82.9–99.1% and 100% (95% CI = 75.9–100%)].ConclusionsPattern‐based p53 IHC classification is highly reproducible among experienced gynaecological pathologists and accurately reflects TP53 mutations in VSCC. This approach to p53 IHC interpretation offers guidance and provides necessary clarity for resolving the proposed prognostic relevance of final p53 IHC class within HPV‐independent VSCC.

Malignant teratoid tumor of the thyroid gland: an aggressive primitive multiphenotypic malignancy showing organotypical elements and frequent DICER1 alterations\u2014is the term \u201cthyroblastoma\u201d more appropriate?

Primary thyroid teratomas are exceedingly rare. Mature and immature variants recapitulate their gonadal counterparts (predilection for infants/children, triphasic germ layer differentiation, and favorable outcome). On the other hand, the so-called malignant teratomas affect predominantly adults and elderly, are highly aggressive, and, according to a few published cases, harbor DICER1 mutations. We describe three highly aggressive sporadic malignant teratoid thyroid tumors in 2 females (17 and 45 years) and one male (17 years). Histology showed triphasic neoplasms composed of solid nests of small primitive monomorphic cells embedded in a cellular stroma with primitive immature rhabdomyosarcoma-like (2) or pleomorphic sarcoma-like (1) phenotype. The third component was represented by TTF1+/PAX8+ primitive teratoid epithelial tubules reminiscent of primitive thyroid follicles and/or Wilms tumor, admixed with scattered respiratory- or enteric-type tubules, neuroepithelial rosettes, and fetal-type squamoid nests. Foci of cartilage were seen in two cases, but none contained mature organoid adult-type tissue or skin adnexa. SALL4 was expressed in the small cell (2) and stromal (1) component. Other germ cell markers were negative. Molecular testing revealed a known “hotspot” pathogenic DICER1 mutation in two cases. In addition, case 1 had a missense TP53 variant. This type of thyroid malignancy is distinct from genuine teratomas. The immunoprofile suggests primitive thyroid- or branchial cleft-like differentiation. Given that “blastoma” is a well-accepted terminology in the spectrum of DICER1-associated malignancies, the term “thyroblastoma” might be more convenient for these malignant teratoid tumors of the thyroid gland. Relationship of thyroblastoma to the DICER1 syndrome remains to be addressed.

Targeted germline sequencing of patients with three or more primary melanomas reveals high rate of pathogenic variants.

Individuals with multiple primary melanomas have rates of germline CDKN2A pathogenic variants of 3%-18%, and are also frequent carriers of variants in the melanocortin-1 receptor. Few patients with numerous (≥3) primary melanomas have been studied with respect to these or other potential germline pathogenic variants. We investigated 46 patients with ≥3 primary melanomas (3, n = 17; 4, n = 14; 5-14, n = 15) to determine if higher rates of germline pathogenic variants of CDKN2A, MC1R, or other cancer genes could explain their extreme melanoma phenotype. Most (43/46, 93%) patients had variants in MC1R and 11/46 (24%) had CDKN2A pathogenic variants, but only male sex and having two variants in MC1R correlated with increasing number of melanomas. Panel screening of 56 other cancer predisposition genes did not reveal other germline pathogenic variants associated with melanoma (CDK4, BAP1, POT1), although pathogenic variants in TP53, CHEK2, and BRCA2 were present in three separate patients and some patients had variants of uncertain significance. In summary, targeted germline sequencing of patients with ≥3 primary melanomas revealed a high rate of pathogenic variants in CDKN2A and other known cancer genes. Although further investigation of these pathogenic variants and variants of uncertain significance is needed, these results support cancer gene panel testing in individuals diagnosed with ≥3 melanomas.

Guidelines for the Li\u2013Fraumeni and heritable TP53-related cancer syndromes

Fifty years after the recognition of the Li–Fraumeni syndrome (LFS), our perception of cancers related to germline alterations of TP53 has drastically changed: (i) germline TP53 alterations are often identified among children with cancers, in particular soft-tissue sarcomas, adrenocortical carcinomas, central nervous system tumours, or among adult females with early breast cancers, without familial history. This justifies the expansion of the LFS concept to a wider cancer predisposition syndrome designated heritable TP53-related cancer (hTP53rc) syndrome; (ii) the interpretation of germline TP53 variants remains challenging and should integrate epidemiological, phenotypical, bioinformatics prediction, and functional data; (iii) the penetrance of germline disease-causing TP53 variants is variable, depending both on the type of variant (dominant-negative variants being associated with a higher cancer risk) and on modifying factors; (iv) whole-body MRI (WBMRI) allows early detection of tumours in variant carriers and (v) in cancer patients with germline disease-causing TP53 variants, radiotherapy, and conventional genotoxic chemotherapy contribute to the development of subsequent primary tumours. It is critical to perform TP53 testing before the initiation of treatment in order to avoid in carriers, if possible, radiotherapy and genotoxic chemotherapies. In children, the recommendations are to perform clinical examination and abdominal ultrasound every 6 months, annual WBMRI and brain MRI from the first year of life, if the TP53 variant is known to be associated with childhood cancers. In adults, the surveillance should include every year clinical examination, WBMRI, breast MRI in females from 20 until 65 years and brain MRI until 50 years.

TP53 Arg72Pro polymorphism and neuroblastoma susceptibility in eastern Chinese children: a three-center case-control study.

TP53 is a tumor suppressor gene that regulates cell growth, apoptosis and DNA repair. Previous studies have reported the contribution of TP53 Arg72Pro (rs1042522 C>G) polymorphism to pathogenesis of multiple tumors. Hence, we evaluated the association between this polymorphism and neuroblastoma susceptibility in eastern Chinese children. The Taqman genotyping assay was performed in 373 patients and 762 controls. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the strength of the association. No significant association was found between the TP53 gene rs1042522 C>G polymorphism and neuroblastoma susceptibility in the overall analysis (CG vs. CC: adjusted OR = 0.92, 95% CI = 0.70–1.22, P=0.567; GG vs. CC: adjusted OR = 0.99, 95% CI = 0.69–1.42, P=0.947; CG/GG vs. CC: adjusted OR = 0.94, 95% CI = 0.72–1.23, P=0.639; or GG vs. CC/CG: adjusted OR = 1.04, 95% CI = 0.75–1.43, P=0.814) and stratified analysis by age, gender, sites of origin, and clinical stages. The TP53 gene rs1042522 C>G polymorphism may not be a risk factor for neuroblastoma in eastern Chinese children. Future studies are needed to confirm this negative result and to reveal additional functional TP53 variants predisposing to neuroblastoma.

Clinical utility of comprehensive genomic pathway and integrated network analyses in personalized oncology.

e14051 Background: Adoption of next-generation sequencing (NGS) technology in routine clinical practice has enabled the detection of genetic aberrations such as single nucleotide variants, copy number alterations, and gene fusions. Pathway and network analyses (PNA) are key components for evaluation of NGS data in a clinical setting to explain findings involving thousands of altered genes and proteins with a smaller and more interpretable set of altered processes. Though PNA have been applied to identify driver genes and pathways in cohort-based analyses, its application in precision oncology remains unexplored. We investigate the potential utility of the Watson for Genomics (WfG) pathway analyses tool in interpreting complex and multiple genomic alterations in individual cancers. Methods: DNA and RNA isolated from 70 patient tumors across 30 different cancer types were processed with Illumina’s TST170 NGS platform. WfG’s feature of pathway analyses was used to identify gene variants, signaling pathways, networks, and the drugs targeting these alterations based on evidence in the clinical literature and FDA drug databases. Results: Analyses defined 5 different pathway/network models: 1) downstream therapeutic targets, 2) synthetic lethality, 3) combinatorial downstream targets + synthetic lethality, 4) two or more pathways converging to downstream targets, and 5) complex profile analyses. The five PNA models are illustrated by the following unique cases. 1) A thyroid cancer case with HRAS variant and activated RAF1 downstream pathway showed MAPK1/3 were suggestive of relevant targets. 2) An acute myeloid leukemia case with BRCA1, BRCA2 and PTEN variants, targeting a common synthetic lethal partner PARP1 was ideal for therapy. 3) A penile carcinoma case with BRAF, CDKN2A and TP53 variants, targeting the BRAF downstream pathway in combination with either CDKN2A or TP53 were the likely choice for therapy. 4) A glioma case with activated PI3K and MEK downstream pathway, targeting a common downstream marker would block both pathways. 5) A breast carcinoma case with a complex pathogenic variant profile provided relevant clinical information and levels of evidence for multiple drug targets. Conclusions: We discovered that the integrated WfG pathway analyses tool is ideal for visualization of the variants with levels of evidence from clinical literature and FDA drug databases that can help inform treatment options and provides a holistic understanding of a specific tumor profile allowing the treating clinician to select personalized targeted therapy.

Clinical conundrums: Developing a strategy for discerning TP53-associated chip and coherent clinical care.

1514 Background: Germline TP53 mutations are associated with Li-Fraumeni syndrome (LFS). However, approximately 20% of commercial laboratory multigene panel test (MGPT)-detected pathogenic TP53 variants represent aberrant clonal expansion (ACE), rather than a germline finding, and are often detected in individuals that lack classic features of LFS. Clonal hematopoiesis (CH) is a form of ACE, and in the absence of an abnormal hemogram is termed Clonal hematopoiesis of indeterminate potential (CHIP). CHIP is often associated with a pathogenic variant (PV) in hematopoietic pathway gene(s) at a variant allele frequency (VAF) less than expected for a heterozygous germline finding. The prevalence increases with age and exposure to chemotherapy. The presence of a skewed VAF is usually noted in a comment on a genetic test result, however, clinicians without genetic training often lack understanding of the comment and need strategies to discern the difference between germline findings, CHIP, and post-zygotic mosaicism. Our studies illuminate possible strategies for discernment for clinicians. Methods: Among 113 cases with MGPT-detected TP53 PVs, enrolled in the Clinical Cancer Genomics Community Research Network registry, we obtained additional tissues, family history and complete blood count (CBC) reports on 42 cases. DNA extracted from formalin fixed paraffin embedded (FFPE) tumor/normal tissues, blood, saliva, eyebrow plucks, was analyzed using a previously validated custom myeloid and CH gene (n = 79) amplicon-based QIAseq panel. PVs with VAF &gt; 2% were included in analyses. Results: Germline status was confirmed for 6 cases (one with a CH PV), post-zygotic mosaicism was supported for 5 cases and 2 were indeterminant. 12 had results supporting ACE/CH, with additional CH-associated PV(s) identified in 5/12 (41%); n = 2 of each TET2, ATM, TP53; and increasing VAF over time for the driver TP53 PV was noted in 2. Of these 2 one was identified to have a hematopoietic malignancy identified through analysis of the CBCs and bone marrow biopsy in parallel with the increasing VAF. Additional results are pending for 7 cases. Conclusions: With the use of our multi-tissue NGS strategy, serial sampling of suspected ACE/CH cases, family history and CBC analyses we were able to discern the status of most TP53 genetic findings. This work has direct translational impact, refining risk estimation and improving the clinical care of patients with TP53 PVs, while avoiding unnecessary LFS-related care and enabling appropriate care for those with ACE.

Genotype and phenotype correlation of common cancer predisposition syndromes in sarcoma cases.

1524 Background: Sarcomas are rare heterogenous cancers affecting a predominantly younger population. The most recognised autosomal dominant contributor being pathogenic TP53 variants associated with Li Fraumeni Syndrome (LFS). When referred, patient eligibility for germline TP53 testing is assessed using classic or Chompret LFS criteria. Other heritable cancer syndromes which can be associated with sarcoma (breast/ovarian, colorectal) are more commonly considered in clinical practice. In some centres germline testing is offered to only those who meet established clinical criteria. Heritable cancer predisposition has several implications including therapy and clinical risk management. Here we report the concordance between clinical criteria and genotypes in sarcoma families. Methods: We included 1,664 sarcoma probands from the International Sarcoma Kindred Study. Eligibility for genetic testing was assessed using internationally accepted clinical criteria for recognised cancer syndromes. Whole genome sequencing was performed on peripheral blood DNA and variants in the ACMG cancer gene list were classified as pathogenic or likely pathogenic using established bioinformatics pipelines. Results: The median age of sarcoma diagnosis in 1664 probands (798 males, 866 Females) was 48 years (range 1-93). The median age of first cancer diagnosis was 46.5 years (0-93) with 291 probands having multiple primary cancers. Of 1504 informative pedigrees, 243 (16%) met criteria for testing; 207 (14%) TP53; 19 (1%) BRCA1/2; 2 (&lt;1%) colorectal cancer (CRC) genes and 15 (1%) familial melanoma. Of 12 TP53 PVs identified, 9 met TP53 testing criteria. Of 13 PVs identified in HR genes (7 BRCA2, 4 PALB2 and 2 BRCA1) only 1 ( PALB2) met BRCA1/2 testing criteria and 2 met Chompret criteria. Both BRCA1 cases were male with a 1st degree relative with ovarian cancer. In CRC genes (1 APC, 2 MSH2, 4 MSH6, 1 PMS2), none met CRC testing criteria but 4 met Chompret criteria. No CDKN2A PVs were identified in melanoma families. Conclusions: In probands with sarcoma, clinical criteria for eligibility for testing for common non-LFS heritable syndromes perform poorly. This should be considered when making decisions regarding germline testing.

Contribution of DNA damage repair gene mutations and concomitant TP53 variations to the efficacy of platinum-based chemotherapy as initial therapeutic option in Chinese NSCLC patients.

e21002 Background: Though targeted, immune-, even combinational therapies have been applied widely, platinum-based chemotherapy still plays irreplaceable role as initial management for patient with either resected or advanced NSCLC without actionable target. Platinum is sought to increase DNA damage burden inducing cell death, especially in cells with intrinsic DNA damage repair (DDR) dysfunction. This study aims to explore impact of DDR genes as well as co-occurrence of TP53 mutations on prognosis of NSCLC patients. Methods: 110 NSCLC patients were consecutively recruited from 2016-2018. 508 cancer related genes were sequenced by BGI-seq 500. COX regression was used to evaluate risk of disease progression as well as cancer-related death among patients with various DDR/TP53 status. Results: 61 NSCLC patients with stage II-IV (median age of onset: 55 years) were recruited who received platinum-based therapy as adjuvant or 1st line systemic therapy. Till 15th.Oct.2019, median follow-up time was 24 months. 21 patients (34.4% of 61) carried DDR mutations. TP53 mutations were detected in 36 patients (59% of 61). 11 patients (18% of 61) displayed TP53/DDR co-mutations. COX regression analysis indicated NSCLC patients with DDR mutation would have lower risk of disease progression (HR:0.37, P = 0.19) as well as superior overall survival time (HR:0.35, P = 0.035). Patients with DDR co-mutations had no superior survival benefit. Patients with HRR mutations presented similar result. Patients with TP53 mutations had similar risk as ones with other mutations. While those with DDR concomitant mutations showed significantly improved clinical benefit (HR for PFS:0.28, P = 0.05; HR for OS:0.22, P = 0.023). Conclusions: DNA damage repair genes in Chinese NSCLC patients may play vital roles in predicting efficacy of platinum-based chemotherapy even in the context of TP53 co-mutation. Further, combination of BRCA2 and PALB2 may be better associated with patients’ prognosis. Large cohort should be set up to validate this finding in near future. [Table: see text]

MON-LB88 Positive Predictive Value of TP53 Variants in Bethesda III/IV Thyroid Fine-Needle Aspirates

Introduction: Somatic DNA variants in the tumor suppressor gene TP53 have been reported in papillary thyroid carcinoma (PTC), Hürthle cell carcinoma (HCC), poorly differentiated thyroid cancer (PDTC), and anaplastic thyroid carcinoma. However, TP53 variants are uncommon among cytologically indeterminate thyroid nodules, so their positive predictive value (PPV) for malignancy, when identified, is unknown. The original Afirma Xpression Atlas reported genomic variants from the mRNA of 511 genes, including TP53. Here we report the PPV of TP53 alterations among Afirma Genomic Sequencing Classifier (GSC) Suspicious Bethesda III/IV nodules in real-world clinical practice. Methods: A consecutive cohort of Afirma GSC Suspicious Bethesda III/IV nodules submitted to Veracyte for molecular analysis and positive for only TP53 alterations by the Xpression Atlas was identified. Local surgical pathology diagnoses were sought with IRB approval. One nodule per patient was included. Results: Thirty-eight TP53 variants were present among >13,000 Bethesda III/IV Afirma GSC Suspicious samples. Among the 22 with only a TP53 alteration, the first 16 consecutive nodules were included (7 nodules were Bethesda III and 9 nodules were Bethesda IV). Local surgical pathology diagnoses were available for 11 of these nodules. Seven nodules (64%) were malignant on surgical pathology: 3 cases of HCC, 1 PDTC, 1 follicular thyroid carcinoma (FTC), 1 follicular variant PTC, and 1 classical PTC. The mean size of malignant nodules was 3.6 cm (range 1-7.7 cm). The remaining four nodules (36%) were benign on surgical pathology, with a mean size of 2.6 cm (range 1.5-4.2 cm). Benign cases included 2 follicular adenomas (FA), 1 Hürthle cell adenoma (HCA), and 1 adenomatoid nodule (AN). Seven different TP53 variants were identified, and only one was observed at least 3 times (TP53: p.R248Q in 2 cases of HCC and 1 adenomatoid nodule). Given the small numbers, meaningful estimates of the variants’ individual PPVs could not be calculated. Conclusions: TP53 variants among Afirma GSC Suspicious Bethesda III/IV nodules are very rare and associated with malignancy in 64% of nodules based on local pathology review. A broad range of both benign and malignant neoplasms, including HCC, PDTC, FTC, PTC, FA, HCA, and AN, were reported among nodules with TP53 alterations. The prognostic value of finding an isolated TP53 variant in Afirma Suspicious nodules remains unknown.