Median Allele Frequency Research Articles

Association of BRAF V600E allele frequency with clinicopathologic outcomes in papillary thyroid cancer.

BRAF V600E mutation is the most common genetic driver of papillary thyroid cancer (PTC), where it is found with various allele frequency (AF), reflecting the proportion of cells carrying the mutant and wild-type gene alleles. To determine whether BRAF V600E AF can improve prognostication and inform initial surgical management of PTC. Retrospective cohort study (2016-2019). UCLA health. Consecutive patients with Bethesda V/VI nodules and isolated BRAF V600E mutation who underwent surgery with histopathology showing PTC. Blinded ThyroSeq v3 molecular analysis after completion of initial management and follow-up. Aggressive histopathology and cancer persistence/recurrence. Of 73 patients, the median BRAF V600E AF was 25.5% (IQR, 16.7-34.3%). Higher median AF was seen in patients classified as American Thyroid Association (ATA) high-risk (37%) vs. intermediate-risk (25.3%, p<0.01) and low-risk (24.7%, p<0.01), largely attributed to higher AF in patients with gross extrathyroidal extension (ETE) (40.1% vs. 25.2% without gross ETE, p=0.02). No differences in AF were observed on the basis of lymph node positivity or presence of aggressive variants of PTC. A higher BRAF V600E AF was also found in patients with tumors ≥2cm vs. <2cm (median 32.0% vs. 24.4%, p<0.01). Over 4.1 years of follow-up, disease persistence/recurrence was found in 7 patients (9.4%) and was associated with higher median AF than those without recurrence (35.3% vs. 25.2%, p=0.02). Higher AF was associated with poorer recurrence-free survival (AF≥35%, HR 7.40, CI 1.4-38.1). Higher AF was associated with gross ETE and increased recurrence risk. This may inform initial management in patients with PTC harboring an isolated BRAF V600E mutation.

Identification of primary mediastinal B-cell lymphomas with higher clonal dominance and poorer outcome using 5′RACE

AbstractThere is a scarcity of data on the tumor B-cell receptor (BCR) repertoire and lymphoid microenvironment in primary mediastinal B-cell lymphoma (PMBL). We applied 5ʹ rapid amplification of complimentary DNA ends (5′RACE) to tumor RNA samples from 137 patients with PMBL with available gene expression profiling and next-generation sequencing data. We obtained 5′RACE results for 75 of the 137 (54.7%) patients with the following clinical characteristics: median age (range), 33 years (18-64); female, 53.3%; performance status score 0 to 1, 86.7%; stage I to II, 57.3%; first-line treatment with anti-CD20 plus doxorubicin-based chemotherapy, 100%. Among the 60 biopsies that expressed a productive BCR, we highlighted a strong somatic hypermutation profile, defined as <98% identity to the germ line sequence, with 58 (96.7%) patients carrying mutated IgVH. We then identified a subgroup of 12 of the 75 patients (16%) with a worse prognosis (progression-free survival [PFS]: hazard ratio [HR], 17; overall survival [OS]: HR, 21) that was associated with the highest clonal dominance (HCD) status, defined as the dominant clonotype representing >81.1% and >78.6% of all complementarity-determining region 3 sequences for IgVH and IgVL, respectively. When compared with other patients, this subgroup had similar clinical characteristics but a greater median allele frequency for all somatic variants, a decreased BCR diversity, and greater expression of PDL1/PDL2 and MS4A1 genes, suggesting greater tumoral infiltration. We confirmed this poorer prognosis in a multivariate model and in an independent validation cohort in which 6 of 37 (16%) PMBL patients exhibited HCD (PFS: HR, 12; OS: HR, 17).

Mutations in Histone Lysine Methyltransferase Genes Are Associated with Autoimmune Cytopenias

Introduction Epigenetic mechanisms are important in regulation of gene expression by modifying chromatin structure to facilitate DNA accessibility (Lau et al Nat Immunol. 2018). DNA methylation and histone modifications are critical for the pathogenesis of hematologic malignancies and autoimmune diseases (Surace et al Front Immunol. 2019) Alterations in enzymes involved in histone modification are associated with immunodeficiencies, including Kabuki syndrome (KS), a rare genetic disorder associated with autoimmune cytopenias, such as immune thrombocytopenia (ITP) and autoimmune hemolytic anemia (AIHA) (Margot et al J Am Coll Med Genet 2020) caused by loss-of-function KMT2D and KDM6A mutations. Somatic mutations in the KMT2D gene have also been observed in patients with Cold Agglutinin Disease. (Małecka et al Br J Haematol. 2018). Aims: The aims of this study are: 1) to identify the frequency of mutations in histone methyltransferase genes (MT) KMT2D, KMT2A, KMT2C and KDM6A in patients with autoimmune cytopenias, and 2) to compare clinical, laboratory and immunological characteristics, and response to therapy in patients with or without mutation in MT and autoimmune cytopenias (AIC). Methods Data mining software from the electronic medical record was used to identify patients ≥ 18 years with a diagnosis of AIC, including ITP, warm and cold AIHA, autoimmune neutropenia, and Evans Syndrome (ES), who had Next Generation Sequencing (NGS) performed. Cytopenias due to malignancy, nutritional deficiency, medications, pregnancy, or infection were excluded. Patients were categorized into two groups based on the presence or absence of mutation in the MT genes (MT+, MT-) with variant allelic frequency (VAF) &amp;gt; 2%. Demographic, laboratory, and clinical characteristics, treatment outcomes, and NGS sequencing data were collected and compared between groups. Next, KMT2 mutations seen in patients with AIC were cross-referenced against the 1000 Genome Project (1000GP) population database to evaluate the frequency of polymorphisms in the general population (Auton et al Nature 2015). CADD in silico prediction algorithm was used to score the potential deleterious effect of MT mutations (Kirchner Nat Genet. 2014). Chi-Square test was used for categorical variables. Statistical analysis was completed in R software. Results Among 495 patients who underwent NGS, 79 (16%) had a mutation in MT genes. These mutations were present in 36% of patients with AIC as compared to 13% in those without AIC (p=0.0005). Among 55 patients with AIC, mutations in the MT genes were present in 20 patients (MT+), 35 patients did not have these mutations (MT-). KMT2C mutations were seen in 10 (50%) patients, KMT2D mutations in 9 patients (45%, one patient had two KMT2D mutations), 1 patient (5%) had both KMT2C &amp; KMT2D variants (Figure 1). The median VAF was 39.5% (IQR, 15.45 - 49.80). The MT+ group had a significantly higher proportion of Hispanic (60% vs 31%) and non-Hispanic White patients (25% vs 14%), p=0.038, Table 1. The median age at diagnosis for the MT+ cohort was younger compared to MT- (45.5 vs 58 years old, respectively), though not statistically significant. AIC diagnoses in both groups were ITP (44%) wAIHA (22%) cAIHA (9%) Autoimmune Neutropenia (2%), and ES (24%). Compared to the MT- group, the MT+ group had lower IgG levels (p=0.0041) and absolute lymphocyte count (p=0.041). MT+ patients with AIHA were more likely to have positive Direct Coombs and complement involvement. No significant differences were found in median nadir hemoglobin and platelet counts, need for therapy, or median number of lines of therapy. Best overall response to therapy was similar in the two groups (93%), with more complete responses in MT- group (55% vs 33%) though not statistically significant. Next, we assessed KMT2 polymorphisms in the general population. Most of the polymorphisms were not present in the 1000GP database and none had a frequency &amp;gt; 0.001. The average Phred score was 19.8; 12/20 patients had Phred score &amp;gt; 20, suggesting that most mutations are in the top 1% of the deleterious variants. Conclusion We report for the first time that patients with autoimmune cytopenias have a high frequency of variants in MT genes. Median allelic frequency close to 50% suggests potential germline predisposition to immune dysregulation and autoimmunity however further studies are needed to better understand the impact of these observations.

TSC2 inactivation, low mutation burden and high macrophage infiltration characterise hepatic angiomyolipomas.

Although TSC1 or TSC2 inactivating mutations that lead to mTORC1 hyperactivation have been reported in hepatic angiomyolipomas (hAML), the role of other somatic genetic events that may contribute to hAML development is unknown. There are also limited data regarding the tumour microenvironment (TME) of hAML. The aim of the present study was to identify other somatic events in genomic level and changes in TME that contribute to tumorigenesis in hAML. In this study, we performed exome sequencing in nine sporadic hAML tumours and deep-coverage targeted sequencing for TSC2 in three additional hAML. Immunohistochemistry and multiplex immunofluorescence were carried out for15 proteins to characterise the tumour microenvironment and assess immune cell infiltration. Inactivating somatic variants in TSC2 were identified in 10 of 12 (83%) cases, with a median allele frequency of 13.6%. Five to 18 somatic variants (median number: nine, median allele frequency 21%) not in TSC1 or TSC2 were also identified, mostly of uncertain clinical significance. Copy number changes were rare, but detection wasimpaired by low tumour purity. Immunohistochemistry demonstrated numerous CD68+ macrophages of distinct appearance from Küpffer cells. Multiplex immunofluorescence revealed low numbers of exhausted PD-1+/PD-L1+, FOXP3+ and CD8+ T cells. hAML tumours have consistent inactivating mutations in TSC2 and have a low somatic mutation rate, similar to other TSC-associated tumours. Careful histological review, standard IHC and multiplex immunofluorescence demonstrated marked infiltration by non-neoplastic inflammatory cells, mostly macrophages.

Circulating Tumor DNA as a Prognostic Factor in Patients With Resectable Hepatic Metastases of Uveal Melanoma.

We report here the results of a prospective study of circulating tumor DNA (ctDNA) detection in patients undergoing uveal melanoma (UM) liver metastases resection (NCT02849145). In UM patients, the liver is the most common and often only site of metastases. Local treatments of liver metastases, such as surgical resection, have a likely benefit in selected patients. Upon enrollment, metastatic UM patients eligible for curative liver surgery had plasma samples collected before and after surgery. GNAQ / GNA11 mutations were identified in archived tumor tissue and used to quantify ctDNA by droplet digital polymerase chain reaction which was then associated with the patient's surgical outcomes. Forty-seven patients were included. Liver surgery was associated with a major increase of cell-free circulating DNA levels, with a peak 2 days after surgery (∼20-fold). Among 40 evaluable patients, 14 (35%) had detectable ctDNA before surgery, with a median allelic frequency of 1.1%. These patients experienced statistically shorter relapse-free survival (RFS) versus patients with no detectable ctDNA before surgery (median RFS: 5.5 vs 12.2 months; hazard ratio=2.23, 95% CI: 1.06-4.69, P =0.04), and had a numerically shorter overall survival (OS) (median OS: 27.0 vs 42.3 months). ctDNA positivity at postsurgery time points was also associated with RFS and OS. This study is the first to report ctDNA detection rate and prognostic impact in UM patients eligible for surgical resection of their liver metastases. If confirmed by further studies in this setting, this noninvasive biomarker could inform treatment decisions in UM patients with liver metastases.

Disease Characterization and Response Prediction in Myeloma Patients Undergoing Conventional and Cellular Therapies from Circulating Tumor DNA

Background: Multiple myeloma (MM) is characterized by dramatic biological and clinical heterogeneity. Prognostic biomarkers including genomic alterations and bone marrow (BM) minimal residual disease can resolve some of this heterogeneity; however, these rely on invasive tumor sampling which limits their utility. Here we develop and apply plasma cell-free DNA liquid biopsies via Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) to characterize tumors and quantify treatment response in patients with MM and explore its utility during anti-BCMA CAR T-cell therapy. Methods: We developed a 480 kb MM-specific CAPP-Seq panel, which covers 86 recurrently mutated coding genes as well as other recurrently mutated regions, for disease detection and quantification from circulating tumor DNA (ctDNA). Using this hybrid-capture panel, we profiled 214 plasma, germline and tumor DNA samples from 35 patients including 15 patients undergoing idecabtagene vicleucel (ide-cel) therapy. Samples were sequenced to ultra-high unique molecular depth as previously described (Newman et al, Nat Biotechnol 2016) to quantify ctDNA. Copy number variants (CNVs) were identified using our recently developed method, CANARy (Chabon et al, Nature 2020). Tumor variants and ctDNA levels were identified prior to and following therapy to assess ctDNA dynamics, and were correlated with clinical indices and patient outcomes. Results: We applied CAPP-Seq to samples from 35 patients with newly diagnosed (ND, n=10) or relapsed/refractory (RR, n=25) plasma cell disorders. A median of 87 single-nucleotide variants (SNVs, range 2-283) were detected per case. Among these, a median of 5 mutations/patient were in coding genes such as KRAS (25% of patients), TP53 (25%) and NRAS (19%). Most other SNVs occurred in genomic regions targeted by activation induced deaminase (AID), such as IGH, IGK and IGL. To validate tumor genotyping from plasma, we compared SNVs observed in plasma to paired BM samples in 18 cases. Here, we observed 84% (594/703) of all mutations identified in BM were also present in plasma, including 90% (26/29) of all coding alterations. Interestingly, we detected an additional 259 SNVs in the plasma that were not present in the BM, including KRAS, NRAS, and FAM46C mutations, suggesting ctDNA may better capture spatial tumor heterogeneity. We next utilized CAPP-Seq to quantify disease burden prior to treatment. We detected ctDNA in 97% (31/32) of pretreatment plasma with a median allele frequency of 0.91% (range 0.006 to 36%) and 3.82 log haploid genome equivalents per mL of plasma (hGE/mL). Levels of ctDNA were higher in RRMM compared to NDMM patients (4.26 vs 3.08 log hGE/mL, p=0.02) and correlated with clinical risk factors including R-ISS (stage 1: 2.83 vs stage 2/3: 4.18 log hGE/mL, p=0.01) as well as disease burden measurements including M-spike (rho=0.53, p=0.02) and free light chain ratio (rho=0.40, p=0.03). The fold change in ctDNA level at a median of 36 days from treatment initiation correlated with clinical response (median 0.060 for non-progressors vs 7.0 for progressors, p=0.04). Further, we applied CAPP-Seq to serial samples from 15 patients with RRMM receiving ide-cel. Notably, patients with longer response (>90 days) had significantly lower ctDNA levels at day 28 compared to those with early (<90 days) progression (0.6 vs 4.1 log hGE/mL; p=0.009, Fig 1). Lower ctDNA levels at day 28 predicted longer time to progression (proportional hazard model, p=0.02, HR=1.6). Finally, we assessed clonal evolution upon relapse after ide-cel. In multiple patients we observed emergence of new CNVs in ctDNA, including a case with an emergent loss of chr16, where TNFRSF17 (BCMA) resides (Fig 2). This copy number loss was observed 36 days prior to clinical relapse, was validated through WGS of the relapsed tumor, and resulted in loss of BCMA by immunohistochemistry. Conclusions: Assessment of ctDNA has significant potential utility in MM, as it allows for mutational genotyping, quantification of disease burden, and identification of tumor clonal evolution. Lower levels of ctDNA during treatment and its clearance are associated with improved outcomes, while detection of emergent alterations after targeted therapies may inform subsequent treatment strategies. Use of ctDNA may improve response and relapse prediction and reveal mechanisms of therapy resistance. *SS and DMK are co-senior authors Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

A High Percentage of NSCLC With Germline CHEK2 Mutation Harbors Actionable Driver Alterations: Survey of a Cancer Genomic Database and Review of Literature

IntroductionGermline CHEK2 mutations are rare and have not been associated with increased risk of NSCLC. MethodsWe identified two sequential primary NSCLCs harboring distinct actionable driver alterations (EGFR E746 _S752 delinsV and CD74-ROS1) in a patient with NSCLC with a novel germline CHEK2 mutation S5fs∗54 (c.14_20delCGGATGT). We queried a genomic database of NSCLC samples profiled by plasma next-generation sequencing (Foundation Medicine Inc.) and performed a literature search of germline CHEK2 mutations in NSCLC. ResultsOf 6101 patients with unique NSCLC profiled by plasma next-generation sequencing, 53 cases (0.87%) of germline CHEK2 mutation were identified (male-to-female ratio, 49%:51%; median age = 75 y). The median allele frequency of CHEK2 was 49% (interquartile range: 49%–51%). Ten unique CHEK2 germline mutations were identified. Literature review identified 15 additional cases of germline CHEK2 mutations in NSCLC. Overall, a total of 70 CHEK2 germline mutations (21 unique CHEK2 alterations) were identified. Among these 70 CHEK2 germline mutations, 54.3% were amino acid substitutions (point mutation), 40.0% were frameshift mutations, and 5.7% were splice site mutations. Of these 70 total cases assessed, 29 (41.4%) potentially actionable driver alterations were identified with KRAS G12C mutation (27.6%) being the most common and KRAS G12A/C/D/R/S/V mutations together constituting 51.7% of these driver mutations. ConclusionsGermline CHEK2 mutations are rare in NSCLC. A large proportion of these cases harbor actionable driver alterations. The relationship between germline CHEK2 mutations and actionable driver alterations in NSCLC may be worth further investigation.

P1256: A NOVEL DROP-OFF DIGITAL PCR ASSAY FOR CXCR4 MUTATION SCREENING IN IGM GAMMOPATHIES: FIRST DATA FROM THE FONDAZIONE ITALIANA LINFOMI BIO-WM STUDY

Background: In IgM gammopathies: Waldenström’s Macroglobulinemia (WM) and IgM gammopathy of uncertain significance (IgM-MGUS), MYD88L265P and CXCR4S338X are the most frequent mutations, and both have clinical implications in WM. Recent studies demonstrated that, in unselected bone marrow (BM) samples, allele specific polymerase chain reaction (AS-qPCR) was superior in detecting CXCR4S338X compared to next generation sequencing, and digital PCR (dPCR) was more sensitive than AS-qPCR for MYD88L265P detection, highlighting the lack of a gold standard molecular method in WM diagnostics. Aims: The aim of the present study was to evaluate a new sensitive approach based on a drop-off dPCR assay for CXCR4S338X mutation detection in BM and peripheral blood (PB) samples from WM and IgM-MGUS patients, enrolled between 2018 and 2020 in the multicenter observational trial from the fondazione italiana linfomi (“BIO-WM”, NCT03521516), and to correlate the mutational status with clinical features. Methods: Genomic DNA from 240 patients (184 WM, 56 IgM-MGUS) was analyzed by dPCR: 51 BM-CD19 selected cells (CD19+), 189 BM and 239 PB unselected white blood cells (WBC). Allele frequency (AF) of CXCR4 mutations at p.S388 locus (CXCR4MUT) was detected by a drop-off dPCR assay, with a sensitivity of 0,001%. For all patients, MYD88L265P mutation data were also available. Results: Forty-one out of 184 WM patients (22%) showed CXCR4MUT in BM (median AF 1.6%, range: 0.14%-23.1%) while only 8 were positive also in PB (20% of the BM mutated cases, median AF: 0.6%, range: 0.23%-35.2%). Moreover, 39/41 (95%) were MYD88L265P, too. Conversely, only 5 out of 56 IgM-MGUS patients (9%) scored CXCR4MUT in BM (median AF 0.65%, range: 1.1%-0.2%) and none in PB: all patients were MYD88L265P, too. Interestingly, 38 BM WBC samples (36 WM, 2 IgM-MGUS) mutated for both CXCR4MUT and MYD88L265P showed correlation in mutational levels between the two mutations (R2=0.8). On the contrary, no correlation was observed between the two mutations in CD19+ cells (R2=0.06). Overall, clinical features of CXCR4MUT vs CXCR4WT patients did not differ significantly, except for lower hemoglobin levels (median 11.6 g/dl vs 12.8 g/dl, p=0.002) and higher serum IgM monoclonal component (median 1.76 g/dl vs 1 g/dl, p=0.016). Only 15/41 WM CXCR4MUT patients (37%) received immediate treatment at the time of trial enrollment (7 DRC, 3 R-Benda, 5 others: 2 single agent and 3 R-chemo based therapy). These cases showed higher disease and mutational burden compared to the 26 CXCR4MUT patients still in watch and wait (WW) at the time of the present analysis. Indeed, median histologic BM infiltration was 80% vs 30% (p<0.001), median IgM monoclonal component was 3.6 g/dl vs 1.6 g/dl (p=0.003) and median CXCR4MUT AF was 9.5% vs 0.8% (p<0.001), respectively. Finally, at the present the median follow-up (FU) of the trial is relatively short (34 months) and no statistically significant differences in outcome parameters were recorded between CXCR4MUT and CXCR4WT cases. Summary/Conclusion: We here describe a sensitive, easily applicable and standardizable approach for detection of the most common CXCR4 mutations on BM WBC, with no need for CD19+ selection. A lower mutational AF was observed in IgM-MGUS compared to WM and, similarly to what was previously reported for MYD88L265P, PB resulted suboptimal for CXCR4MUT detection. A statistically significant difference in CXCR4MUT level was observed between patients treated at the time of enrollment and those still in WW. However, a longer FU is needed to better clarify the clinical implications of CXCR4 mutations in our series.

Abstract 3960: BCL-2 G101V mutations develop in one-third of patients on continuous venetoclax

Abstract The development of targeted therapies has revolutionized the treatment of chronic lymphocytic leukemia (CLL). To date, these therapies are generally given continuously, indefinitely, leading to the development of resistance, which is often on target. Venetoclax is the first-in-class BCL-2 inhibitor which was initially approved for continuous therapy in relapsed high-risk CLL. In that context the BCL-2 G101V mutation (mut) was identified in post-progression samples and shown to reduce venetoclax binding to BCL-2, limiting its efficacy. The mut can be identified at low variant allele frequency (VAF) prior to clinical progression. We were therefore interested to identify the frequency of this mut in our cohort of relapsed refractory CLL patients (pts) on continuous venetoclax, and to assess the sensitivity of measurements in blood vs bone marrow. To this end we utilized a ddPCR assay which has LNA probes that specifically bind to either the BCL2 G101wt or G101V sequences, to screen for G101V muts in DNA extracted from patient samples. We also started to investigate additional co-occurring BCL2 muts in G101V positive samples by Sanger sequencing. Our patient cohort included 28 pts, of whom 20 had serial samples collected during venetoclax therapy. The median age of the pts was 66, and they had a median of 3 prior therapies before venetoclax, including chemoimmunotherapy in 67.9% and a BTK inhibitor in 60.7%. Deletion of 17p was present in 43%, with five additional pts having isolated TP53 mut (total with known TP53 aberrancy, 61%). 75% (21/28) of those evaluated had an unmutated IGHV. The median duration of venetoclax treatment was 43.5 months (mos). The timing of the first sample tested was a median of 23.3 mos after venetoclax initiation. We detected the G101V allele in peripheral blood mononuclear cells (PBMCs) in 9 out of 28 pts, at a median allele frequency (AF) of 1.38% (range 0.04%-22.31%), at a median of 44.6 mos on venetoclax. Out of the three pts who had G101V detected at multiple timepoints, two had AF increased with time (7.8 fold increase over 6 mos and 7.7 fold increase over 5 mos, respectively), one had similar AF with time (4.68% at 18.9 mos, 3.43% at 23.8 mos on treatment). Six of these pts also had bone marrow evaluated and all were also positive (at a median AF of 0.21%; range 0.2%-18.66%); one additional patient without a PBMC sample at that timepoint was positive in bone marrow. In order to screen for any co-occurring acquired resistance muts in BCL2 G101V positive samples, we performed Sanger sequencing across the BCL2 open-reading frame. We have identified a duplication mut (R107-R110dup) in one of the samples. In conclusion, this study shows that approximately one-third of pts on continuous venetoclax for 2+ years develop evidence of low-level BCL-2 G101V mut. Further work is underway to identify additional co-existing muts in BCL2 or other genes, and to characterize the additional genetic events at the time of clear clinical progression. Citation Format: Yanan Kuang, Stacey M. Fernandes, Rayan Fardoun, Kevin Vasquez, Abhishek Mogili, Cloud P. Paweletz, Jennifer R. Brown. BCL-2 G101V mutations develop in one-third of patients on continuous venetoclax [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 3960.

The Profiling of Circulating Tumor DNA in Pediatric Mature B-Cell Non-Hodgkin Lymphoma（B-NHL）: A Multicenter and Prospective Clinical Study

BackgroundNext-generation sequencing (NGS) based on liquid biopsy has been an emerging technology to identify tumor-specific genetic aberrations in adult lymphoma. However, there were few studies on the genomic profiling of plasma circulating tumor-derived DNA (ctDNA) in pediatric mature B-NHL.MethodsParaffin-embedded tissue (FFPE) and plasma samples from the newly diagnosed patients were collected and sequenced by 475 genes panel before, during and post of treatment. Clinical stage system, risk stratification and treatment of pediatric mature B-NHL followed a the modified BFM-95 protocol.ResultsA total of 53 pediatric mature B-NHLs were enrolled，including 35 Burkitt lymphoma, 18 diffused large B cell lymphoma/high-grade B cell lymphoma (DLBCL/HGBCL). We collected 38 tissue and 124 plasma samples for somatic mutation testing. The number of somatic mutations and the TOP 5 genes detected in the 38 tissues and 31 baseline plasma samples, were 416 vs 496, and MYC(71%), DDX3X(45%)，ID3 (42%), TP53(40%), SMARCA4(29%) (Fig1. A)vs MYC(52%), DDX3X(45%)，ID3(42%), TP53(36%), GNA13(23%) (Fig1. B), respectively. The median allele frequency of mutations in plasma was 3%(ranged from 0.2% to 96.6%) and MYC, DDX3X, ID3, TP53, SMARCA4,ARID1A shows higher max somatic allele frequency (MSAF), indicated that was the early events in tumor genesis.The sensitivity of plasma ctDNA to detecting tissue mutations was 63.4% in the 19 matched samples (11 samples from BL and 8 samples from DLBCL/HGBCL) and the sensitivity in BL and DLBCL/HGBCL were 64.1% and 62%, respectively. All genomic alteration types, including single nucleotide variants (SNVs), indels, and gene fusions were detected in similar proportions in each sample type and the gene mutation rate of every gene detected in paired tissue and ctDNA samples.Among the 37 mature B-NHL patients, 6 patients were collected plasma samples after resection of tumor, of which 4 patients was not detected the somatic gene mutations in plasma (Fig. 2). The abundance of ctDNA in patients with stage IV (N=10) was significantly higher than that of stage I-II (N=6) (P=0.0002) and stage III patients(N=15)(P<0.0001)(Fig3. A). Similarly the abundance of ctDNA mutations in high risk patients(N =11)was significantly higher than that of low risk patients (N=8)(P<0.0001) and Medium risk patients (N=12) (P<0.0001) (Fig3. B). MSAF of ctDNA mutations was significantly correlated with LDH and the abundance of ctDNA mutations (P<0.0001) (Fig3. C,D).With a median follow-up of 182 Days, 33 patients have completed anti-tumor treatment, 27 patients completed post-treatment PET-CT, and 20 patients have done ctDNA testing synchronously. PET-CT showed tumor residue in 4 patients, of which 2 patients showed no tumor residue in pathology and ctDNA, 1 patient showed tumor residue in pathology but not in ctDNA and with tumor progression 6 months after treatment, 1 patient unable to take biopsy showed no tumor residue in ctDNA and was no tumor reccourence with regular follow-up. At the last follow-up, 1 patient was disease progression, and all of the 53 patients survived.ConclusionPlasma ctDNA testing by NGS was practicable in pediatric mature B-NHL. The abundance of ctDNA is significantly related to tumor burden. CtDNA testing may be more sensitive than PET-CT for residual disease assessment. Nevertheless, sample size expansion is required to verify such conclusions. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

JAK3 Variants in Adults with Myeloid Malignancies and Potential for Response to JAK3 Inhibition

Background: Janus kinases (JAK) family members (JAK1, JAK2, JAK3, TYK2) play an important role in tumorigenesis. JAK3 is involved in the signaling of a number of interleukins (IL) (including IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21), as well as the phosphorylation of the signal transducers and activators of transcriptions (STAT) and PI3K/AKT. JAK3 activating variants, including V722I, demonstrably induce cellular transformation in vitro. The prevalence of JAK3 variants/mutations in myeloid neoplasms, particularly in acute myeloid leukemia (AML), and their role in leukemogenesis, remains unclear.Methods: We reviewed data for myeloid leukemia (AML, MDS and MPN) patients (pts) treated at MD Anderson Cancer Center between 2012 and 2017, whose marrow samples were tested for JAK3 variants/mutations by next generation sequencing. We evaluated the type of variants, the demographics, laboratory, treatment, and clinical information for pts with JAK3 variants. We performed an in vitro drug sensitivity assay using patient-derived xenograft leukemia cells from one patient with a JAK3 variant and using primary AML samples, to test for sensitivity to the JAK3 inhibitor tofacitinib.Results: A total of 35 leukemia pts with JAK3 variants were identified, and included: non-megakaryoblastic AML (n=31), MDS/MPN (n=2) and MDS (n=2). Four AML cases arose from prior MDS or MDS/MPN. All 4 non-AML pts had V722I variant, located in the pseudokinase domain. Of the 31 AML pts with JAK3 variants, 21 (68%) had V722I. Three (10%) other AML pts had P151R (FERM domain), 3 (10%) V718L (pseudokinase), 2 (6%) R925L (kinase), and 1 (3%) 940V (kinase); none of these variants has been previously described. A pt with T815M (between pseudokinase-kinase domains) was identified from outside genetic testing. The median allelic frequency for variants (where available) in AML pts was 53% (range, 41-88) and median marrow blasts was 45% (range 21-97). Overall, cytogenetics were complex in 19 (55%) pts and diploid in 11 (31%); 5 (14%) pts had miscellaneous clones. Concomitant somatic mutations most commonly occurred in IDH1/2 (n=12), TP53 (11), F LT3 (9), NPM1 (6), ASXL1 (5), RUNX1 (4), SRSF2 (4), and DNMT3A (3). Leukemia cells derived from a relapsed/refractory pt with JAK3 T815M variant had significant sensitivity to JAK3 inhibitor tofacitinib, with nearly 50% reduction in viability with 0.1uM drug concentration (Figure 1). Primary AML samples from 3 other pts showed no sensitivity to the drug.Conclusions: We report the largest survey of JAK3 variants among adult myeloid leukemia pts, including novel variants. Given allelic frequencies, some JAK3 variants may represent germline polymorphisms. The activating V722I variant may have increased prevalence among AML pts. The sensitivity of JAK3 T815M AML cells treated with the FDA-approved JAK3 inhibitor tofacitinib, as well as the prevalence and location of JAK3 variants in myeloid malignancies, provide a basis for further investigation. [Display omitted] DisclosuresDiNardo:Novartis: Honoraria, Research Funding; Agios: Honoraria, Research Funding; AbbVie: Honoraria, Research Funding; Celgene: Honoraria, Research Funding; Daiichi-Sankyo: Honoraria, Research Funding. Kantarjian:Bristol-Meyers Squibb: Research Funding; Novartis: Research Funding; Amgen: Research Funding; Pfizer: Research Funding; ARIAD: Research Funding; Delta-Fly Pharma: Research Funding. Verstovsek:Genentech: Research Funding; NS Pharma: Research Funding; Lilly Oncology: Research Funding; Galena BioPharma: Research Funding; Gilead: Research Funding; Promedior: Research Funding; Promedior: Research Funding; Gilead: Research Funding; CTI BioPharma Corp: Research Funding; Astrazeneca: Research Funding; Galena BioPharma: Research Funding; Genentech: Research Funding; Roche: Research Funding; Celgene: Research Funding; CTI BioPharma Corp: Research Funding; Blueprint Medicines Corp: Research Funding; Pfizer: Research Funding; Pfizer: Research Funding; NS Pharma: Research Funding; Blueprint Medicines Corp: Research Funding; Bristol Myers Squibb: Research Funding; Incyte: Research Funding; Seattle Genetics: Research Funding; Incyte: Research Funding; Seattle Genetics: Research Funding; Roche: Research Funding; Lilly Oncology: Research Funding; Astrazeneca: Research Funding; Bristol Myers Squibb: Research Funding; Celgene: Research Funding.

Molecular profiling by NGS upon progression disease in advanced stage NSCLC patients.

e21196 Background: Non-small cells lung cancer (NSCLC) patients treated with Tyrosine Kinase Inhibitors (TKI) at first-line ultimately develop disease progression after 10 to 14 months. Mechanisms underlying TKI-resistance are not complete understood. Tumor re-biopsy is often unfeasible for NSCLC patients and liquid biopsy is a suitable alternative in identify mechanism by which tumors progress. Methods: 113 plasma samples were collected from advanced stage EGFR positive NSCLC patients upon disease progression according to RECIST V1.1. cfDNA NGS profiling was carried out using the Oncomine™ Pan-Cancer Cell-Free Assay and sequenced on an Ion GeneStudio S5 Plus System. Variant calling and annotation were performed with Torrent Suite and Ion Reporter (v5.16) software, respectively. In addition, we developed a bioinformatic pipeline, using RStudio for variant filtering. Results: Overall, 344 somatic variants were detected with an average number of variants per patient of 2.32 and a median Mutant Allele Frequency (MAF) of 0.83%. Most mutated genes were EGFR (63.72%), TP53 (60.18%), APC (16.81%), MAP2K1 (11.50%), PIK3CA (10.62%), FGFR3 (7.08%), KRAS (7.08%) and BRAF (6.19%). As expected, SNPs were the most frequent mutation type (72.67%), following by INDELs (24.41%) and CNVs (2.91%). We found high co-occurrence between MYC-GNA11, MYC-CCND2, HRAS-AR and EGFR-TP53 genes using Jaccard’s score (0.5, 0.5, 0.5 and 0.46, respectively). Within EGFR-mutated patients, 40% had T790M resistance mutation. Finally, we found KRAS mutations and missense PIK3CA mutations were mutually exclusive. Conclusions: Molecular profiling of liquid biopsies collected upon disease progression using NGS help to identify molecular mechanisms underlying treatment failure.

High concordance of actionable genomic alterations identified between circulating tumor DNA-based and tissue-based next-generation sequencing testing in advanced non-small cell lung cancer: The Korean Lung Liquid Versus Invasive Biopsy Program.

Because of the growing number of actionable biomarkers in non-small cell lung cancer (NSCLC), sufficient tissue availability for testing is becoming a greater challenge. Liquid biopsy offers a potential solution by complementing standard tissue-based methods. In this study, the authors analyzed the concordance of actionable genomic alterations sequenced from circulating tumor DNA (ctDNA; Guardant360) and tissue (Oncomine Focus Assay). From September 2015 to May 2018, 421 paired plasma and tissue samples from patients with advanced NSCLC who had previously undergone tissue testing by standard methods were collected. Both types of samples were available for 287 patients (262 in cohort 1 [treatment-naive] and 25 in cohort 2 [treatment failure]), and only 1 sample type was available for 134 patients (50 in cohort 3 [plasma only] and 84 in cohort 4 [tissue only]). In cohort 1, 198 samples (77.6%) showed concordance between tissue and plasma next-generation sequencing (NGS). Among the discordant cases, plasma testing detected additional genomic alterations in 11 patients (4.2%). In 50 patients without tissue-based NGS results (cohort 3), the ctDNA-based test detected genomic alterations in 20 samples (40.0%). The median allele frequency (AF) of mutations identified with ctDNA-based NGS (0.74%) was lower than that identified with the tissue-based NGS test (13.90%). Clinical responses to matched targeted therapy occurred, regardless of the ctDNA AF. Upfront ctDNA-based testing identified 60.4% of patients with genomic alterations. In addition, ctDNA-based testing uncovered 12.0% more actionable alterations when it was performed after tissue-based NGS testing. The results indicate that a ctDNA-based test identifies additional patients with actionable genomic alterations and could, therefore, be used to complement traditional tissue-based testing for NSCLC. Circulating tumor DNA (ctDNA)-based next-generation sequencing (NGS) testing is becoming essential as the number of actionable genomic biomarker increases for the treatment selection of non-small cell lung cancer. This study demonstrates the additive value of ctDNA-based testing in addition to tissue-based NGS and standard of care-based biomarker testing for detecting additional patients with actionable genomic alterations. Clinical responses have also been observed in patients with a low allele frequency detected by ctDNA-based NGS testing.

Contribution of Mitochondrial DNA Heteroplasmy to the Congenital Cardiac and Palatal Phenotypic Variability in Maternally Transmitted 22q11.2 Deletion Syndrome.

Congenital heart disease (CHD) and palatal anomalies (PA), are among the most common characteristics of 22q11.2 deletion syndrome (22q11.2DS), but they show incomplete penetrance, suggesting the presence of additional factors. The 22q11.2 deleted region contains nuclear encoded mitochondrial genes, and since mitochondrial function is critical during development, we hypothesized that changes in the mitochondrial DNA (mtDNA) could be involved in the intrafamilial variability of CHD and PA in cases of maternally inherited 22q11.2DS. To investigate this, we studied the transmission of heteroplasmic mtDNA alleles in seventeen phenotypically concordant and discordant mother-offspring 22q11.2DS pairs. We sequenced their mtDNA and identified 26 heteroplasmic variants at >1% frequency, representing 18 transmissions. The median allele frequency change between a mother and her child was twice as much, with a wider distribution range, in PA discordant pairs, p-value = 0.039 (permutation test, 11 concordant vs. 7 discordant variants), but not in CHD discordant pairs, p-value = 0.441 (9 vs. 9). Only the variant m.9507T>C was considered to be pathogenic, but it was unrelated to the structural phenotypes. Our study is novel, yet our results are not consistent with mtDNA variation contributing to PA or CHD in 22q11.2DS. Larger cohorts and additional factors should be considered moving forward.

Abstract 3390: Predictive and prognostic value of circulating tumor DNA (ctDNA) compared to circulating tumor cells (CTC) in a prospective cohort of metastatic breast cancer patients: The UCBG COMET trial

Abstract Background: In metastatic breast cancer (MBC), monitoring circulating tumor DNA (ctDNA) can detect mutation associated with resistance to treatment and its variations reflect changes in tumor burden. We prospectively monitored CTC and ctDNA during first line chemotherapy for MBC. Methods: The French cohort COMET is a prospective study including first line HER2- negative pts receiving weekly paclitaxel and bevacizumab. Blood samples were obtained at baseline (BL) and before the second cycle of chemotherapy (C2). ctDNA was analyzed by targeted resequencing (custom panel 220kb) SNV (28 genes + 8 promoters and CNA (18 genes). Results: For ctDNA, out of 196 pts analyzed, 147 had at least one somatic mutation (SNV) detected in plasma (75%). Despite no complete overlap, 24 pts (12%) had no CTC nor ctDNA detected at baseline. Including Copy Number Variation analysis (CNV), the number of patients without detectable ctDNA at baseline could be reduced to 18 (9%). The average number of mutations per pt was 2.4 (range 1 to 9). Median Allelic Frequency (MAF) was 9.1%. Most commonly mutated genes were TP53 and GATA3 with 14% and 7% of all mutations, respectively. TP53 mutations were detected in 31 % of patients and were associated with a shorter progression-free and overall survival. PI3KCA mutations were detected in 23.2% of the pts, were correlated with presence of bone metastasis and had no prognostic value. ESR1 was mutated in 10.6% of the pts, restricted to the ER+ subgroup and had no impact on overall survival. At baseline, CTC and ctDNA levels were correlated (r = 0.40, p &amp;lt; 0.0001). CTC detection was correlated with TP53 mutations detection but not with mutations PI3KCA or ESR1. Only 68 pts (36%) had detectable ctDNA at C2 with a MAF of 2% (0.3%-40%). 52.8% of patients positive for ctDNA at D1C1 became negative at D1C2 and only one negative at baseline became positive at C2. Correlation rate with CTC was the same after one cycle of chemotherapy (r = 0.40). Median follow-up was 53 months and median OS was 32 months. At multivariate analysis, triple negative status, detectable ctDNA at C2, CTC ≥5 at C2 and grade 3 on primary tumor were independent prognostic for OS. Conclusion: Early decrease of CTC and/or ctDNA after one cycle of chemotherapy are independent predictive markers of favorable outcome. Compared to CTC, ctDNA allows monitoring of tumor burden during chemotherapy and specific detection of targetable mutations as PI3KCA, HER2 or BRCA. Citation Format: Jean-Yves Pierga, Amanda Silveira, Elodie Girard, Veronique Lorgis, Marie-Laure Tanguy, Benoit Albaud, Olivier Tredan, Coraline Dubot, Caroline Hego, William Jacot, Anthony Goncalves, Marc Debled, Christelle Levy, Jean-Marc Ferrero, Christelle Jouannaud, Marie-Ange Mouret-Reynier, Florence Dalenc, Sylvain Baulande, Jerome Lemonnier, Frederique Berger, Francois-Clement Bidard, Charlotte Proudhon. Predictive and prognostic value of circulating tumor DNA (ctDNA) compared to circulating tumor cells (CTC) in a prospective cohort of metastatic breast cancer patients: The UCBG COMET trial [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3390.

Abstract B21: Oncogenic BRAF and KRAS mutations in endosalpingiosis

Abstract Endosalpingiosis, or ectopic fallopian tube epithelium, frequently involves the peritoneum and lymph nodes in patients with ovarian low-grade serous borderline tumor or carcinoma, but the pathogenic significance of these microscopic lesions remains unclear. Using laser-capture microdissection and digital droplet PCR, we investigated whether endosalpingiosis harbors the driver mutations in BRAF and KRAS, commonly seen in low-grade serous tumors. Of 21 women with endosalpingiosis associated with a synchronous or metachronous ovarian low-grade serous tumor, mutations were identified in 11 (52%) cases and the identical mutation was shared between the tumor and endosalpingiosis in 10/11 cases. In contrast, of 12 cases of endosalpingiosis not associated with an ovarian tumor, only 1 harbored a KRAS mutation. Across mutation-positive cases, the median mutant allelic frequency was 37% (range: 12 – 67%). Ki-67 immunohistochemical staining revealed significantly decreased proliferative index in endosalpingiosis relative to low-grade serous tumors, but no difference with eutopic tubal epithelium. BRAF or KRAS-mutated endosalpingiosis had significantly lower Ki-67 index compared to lesions lacking mutations in both genes. Functional studies using fallopian tube epithelial cell cultures demonstrate that enforced expression of KRAS-G12V causes phosphorylation of downstream ERK, with associated growth impairment and induction of p21, suggesting oncogene-induced senescence. We demonstrate that endosalpingiosis represents a striking example of cancer driver mutations in deceptively normal-appearing cells, signifying this innocuous-appearing lesion as a monoclonal proliferation with neoplastic potential. Citation Format: M. Herman Chui, Ie-Ming Shih. Oncogenic BRAF and KRAS mutations in endosalpingiosis [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B21.

KRAS mutations testing in non-small cell lung cancer: the role of Liquid biopsy in the basal setting.

In advanced stage non-small cell lung cancer (NSCLC) patients, Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) testing may soon acquire a predictive significance to select patients for AMG510 treatment. Since tissue samples are not always available, liquid biopsy may represent a viable option for KRAS testing. Here, we review the last three years clinical practice performed on 194 plasma based liquid biopsies by next generation sequencing (NGS) SiRe® panel. In particular, 36 (18.6%) KRAS mutated cases were identified, with an overall median allelic frequency of 5.0% (ranging between 0.2% and 46.8%). No concomitant mutations were observed in the other NSCLC clinical relevant genes included in the SiRe® panel, such as epidermal growth factor receptor (EGFR) and v-Raf murine sarcoma viral oncogene homolog B (BRAF). Exon 2 p.G12C was the most common detected mutation (13/36, 36.1%). In conclusion, our data update and confirm that SiRe® NGS panel represents a robust analytical tool to assess KRAS mutational status on circulating tumor DNA. Further investigation is required to design more cost-effective diagnostic algorithms to harmonize clinical relevant biomarker testing on tissue and blood in advanced stage NSCLC clinical practice.

Abstract PR08: Validation and clinical implementation of MSK-ACCESS, an ultra-deep sequencing assay for noninvasive somatic mutation profiling

Abstract Introduction: Circulating cell-free DNA (cfDNA) is a source of tumor-derived DNA to interrogate somatic alterations when tissue is not available or of insufficient quantity for analysis. At MSKCC, we have developed and validated MSK-ACCESS (Analysis of Circulating cfDNA to Evaluate Somatic Status), a targeted next-generation sequencing assay that can detect ultra-low frequency somatic variants in select exons and introns of 129 genes. MSK-ACCESS can identify mutations, copy number alterations, gene fusions, and MSI status in plasma and was recently approved by the NYS-DOH for clinical testing. Here, we present the results of the validation study and our clinical experience with MSK-ACCESS since June 2019. Methods: Target regions from 129 genes were selected to maximize coverage of actionable, oncogenic, and hotspot mutations based on the first 25,000 tumors sequenced using MSK-IMPACT, our institutional clinical sequencing assay. Plasma cfDNA and buffy-coat DNA were extracted from whole blood collected in cell-stabilizing tubes (STRECK BCT cell-free DNA tube). Unique molecular indexes were introduced during DNA library construction, allowing for error suppression from consensus reads collapsed by Marianas, an in-house-developed algorithm. These consensus reads enable variant calling at low allelic frequency (AF) based on a 10−6 background error rate. Results: Analytical validation of MSK-ACCESS demonstrated 93% accuracy (n=100 variants), 99% precision (n=153 variants), and 100% sensitivity based on an assay limit of detection of 0.5% AF (n=19 variants). Variants were detected down to 0.1% AF. To date, 240 clinical cfDNA and matched normal DNA pairs have been sequenced, analyzed for somatic alterations, and clinically reported to guide patient management. Most clinical cases were from lung (55%) or prostate (13%) cancers and submitted for diagnostic purposes (71%). Median raw coverage was 18,367X, and median consensus coverage was 1411X. Mutations were detected in 180 (75%) samples with a median variant AF of 1.8% (0.02% - 95%). Comparison of concurrent commercial plasma testing results to MSK-ACCESS revealed multiple variants that were of clonal hematopoiesis or germline origin incorrectly reported as somatic variants. In the lung cohort, 48 patients had tissue testing with MSK-IMPACT; among 32 patients with a driver alteration detected by MSK-ACCESS, 91% had the identical driver alteration reported by MSK-IMPACT. Additionally, MSK-ACCESS identified a MET exon 14 alteration in one lung cancer patient that led to protocol enrollment and partial response. Conclusions: Liquid biopsy testing using MSK-ACCESS reliably detected clinically actionable mutations, reducing the need for multiple biopsies. These results also illustrate the importance of analyzing a matched normal sample when interpreting cfDNA results and highlight the potential of using cfDNA analysis to guide treatment selection, assess for treatment response, and identify mechanisms of treatment resistance. This abstract is also being presented as Poster A20. Citation Format: A. Rose Brannon, Gowtham Jayakumaran, Monica Diosdado, Yu Hu, Anna Razumova, Fanli Meng, Emily Lebow, Juber Patel, Ian Johnson, Preethi Srinivasan, Maysun Hasan, Jenna-marie Dix, Aijazuddin Syed, Brian Houck-Loomis, Bob T. Li, Charles Rudin, David Solit, Marc Ladanyi, Maria Arcila, Dana Tsui, Ahmet Zehir, Michael Berger, Ryma Benayed. Validation and clinical implementation of MSK-ACCESS, an ultra-deep sequencing assay for noninvasive somatic mutation profiling [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr PR08.

A frequent nonsense mutation in exon 1 across certain HLA-A and -B alleles in leukocytes of patients with acquired aplastic anemia.

Leukocytes that lack expression of HLA alleles are frequently detected in patients with acquired aplastic anemia (AA) who respond to immunosuppressive therapy, although the exact mechanisms underlying the HLA loss and HLA allele repertoire likely to acquire loss-of-function mutations are unknown. We identified a common nonsense mutation at codon 19 (c.19C>T, p.R7X) in exon 1 (Exon1mut) of different HLA-A and -B alleles in HLA-lacking granulocytes from AA patients. A droplet digital polymerase chain reaction assay capable of detecting as few as 0.07% Exon1mut HLA alleles in total DNA revealed that the mutation was present in 29% (101/353) of AA patients, with a median allele frequency of 0.42% (range, 0.071% to 21.3%). Exon1mut occurred in only 12 different HLA-A (n=4) and HLA-B (n=8) alleles, including B*40:02 (n=31) and A*02:06 (n=15), which correspond to four HLA class I supertypes (A02, A03, B07, and B44). The percentages of patients who possessed at least one of these 12 HLA alleles were significantly higher in the 353 AA patients (92%, P<0.001) and in 83 AA patients with copy number neutral loss of heterozygosity in chromosome 6p (100%, P<0.001) than the percentage (81%) in 18,604 Japanese healthy individuals. Eighty-two percent (37/45) of AA patients with Exon1mut responded to immunosuppressive therapy. Small populations of leukocytes that lack particular HLA-A or B alleles due to Exon1mut are common in AA patients. The detection of Exon1mut using a droplet digital polymerase chain reaction assay without the need for HLA typing may serve as a powerful tool for diagnosing the immune pathophysiology of patients with bone marrow failure.

CtDNA from ascites as an alternative to tumor sampling for HRD (homologous recombination deficiency) testing in ovarian cancer (OC).

6066 Background: Knowledge regarding HRD status is becoming crucial to guide maintenance strategies for patients with newly diagnosed OC. Unfortunately, for patients (pts) treated with neoadjuvant chemotherapy (NACT), HRD testing on small biopsies from diagnostic laparoscopies (Dx Lap) or interval debulking has a high failure rate. At relapse, biopsies may not be feasible. Aim: Evaluate the feasibility and usefulness of HRD testing on cfDNA from ascites Methods: Pts enrolled in a prospective biological study (OvBIOMark) consented to analysis of biological samples obtained as part of routine diagnosis. cfDNA was extracted from 1-2ml of double-centrifuged fresh ascites and subjected to 1) targeted NGS including the most common somatic mutations in high grade ovarian cancer ( TP53) to confirm presence of tumor cfDNA and 2) SNParray for copy number (CN) analyses to calculate a genomic instability score (GIS) for HRD. Results: Thirty four ascites samples were collected from 25 pts with suspected or confirmed OC. For 15/25 pts samples were obtained at Dx Lap, and for 10 pts samples were obtained at relapse. Seven pts underwent repeat ascitic drains during treatment or at relapse. 97% (33/34) of ascitic samples had detectable cfDNA (median = 980ng, range:80-5730ng) even when obtained during chemotherapy. A deleterious mutation was identified in 87% (29/33) of samples with high allelic frequencies (median allelic frequency, AF = 60%; 3.3-87%), confirming that most of detected cfDNA was tumoral. The most common mutation was a TP53m (86%; 25/29). We have performed CN analysis on cfDNA from ascites on 17 of these patients to evaluate their HRD status. Ten pts had a high GIS (HRD+), and 7 pts a low GIS (HRD-). The 4 pts with confirmed BRCAm included in this study had a high GIS on ascites. When available from the same patient, the CN profiles derived from ascites cfDNA and tumor sampling were superimposable. Conclusions: Ascites yields large amounts of cfDNA, which can be confirmed as tumoral based on TP53 mutation detection. CN analysis on ascitic cfDNA is feasible and can be used to detect the same HRD scar as tumor testing. Ascites is frequent at diagnosis, especially in pts with inoperable disease planned for NACT and could provide a useful alternative to tumor for HRD and BRCA testing.