Targeted Sequencing Panel Research Articles

Abstract B025: Exceptional response to the ataxia telangiectasia and Rad3-related inhibitor (ATRi), camonsertib, in a patient with alternative lengthening of telomeres (ALT)-positive metastatic melanoma

Abstract One hallmark of cancer tumorigenesis is the maintenance of telomere length which canonically occurs through the reactivation of telomerase. Alternative lengthening of telomeres (ALT) is a minor telomere maintenance mechanism that uses homologous recombination (HR) to maintain telomere length and is associated with replication stress and defects in genome maintenance. In preclinical models, ALT positivity (ALT+) has been shown to sensitize tumor cells to ataxia telangiectasia and Rad3-related inhibitors (ATRi). Here we describe a confirmed clinical and molecular response to the ATRi, camonsertib, in a patient with ALT+ metastatic melanoma. To our knowledge, this is the first report of clinical experience with ATRi in ALT+ tumors. A 63-year-old male was diagnosed in July 2019 with stage IV (cTX, cNX, pM1c[1]) metastatic melanoma and treated with nivolumab (nivo) + ipilumumab (ipi) with initial partial response (PR) documented after 3 months which was confirmed on subsequent nivo maintenance. Ipi was resumed following suspected pseudoprogression in March 2020, and continued until confirmed progression in June 2020. Genomic profiling of a liver biopsy collected at the time of progression identified somatic alterations in TP53 (p.S127F, p.R65fs), NF1 (p.K1263*), BRCA2 (p.R2482C) and ATRX (p.R418*), a germline CHEK2 mutation (p.T376fs), and high tumor mutational burden. The patient received additional targeted regimens with olaparib (ola): nivo ± ola and later ola ± trametinib; no response was documented, and progression was noted in April 2021. In June 2021, the patient received camonsertib monotherapy at an initial dose of 120 mg QD 3 days on/4 days off in the phase I TRESR trial (NCT04497116). The patient tolerated treatment well and continued at the same dose until dose was reduced via a change in schedule (to 2 weeks on/1 week off) at 9 months due to anemia. The patient had an initial RECIST PR (-36%) at 3 months with circulating tumor DNA (ctDNA) clearance. The target lesions continued to decrease with a best decline of -74% after about 1 year of treatment. The cancer progressed at 19 months (+105% from nadir, -47% from baseline) though due to ongoing clinical benefit treatment was continued for a total duration of 22 months. Interrogation of ctDNA tumor fraction in longitudinal plasma samples is ongoing and will be reported. To understand the long and deep response to camonsertib treatment in this patient, we further characterized the screening biopsy by a custom targeted sequencing panel, SyNthetic lethal Interactions for Precision Diagnostics (SNiPDx), and whole genome sequencing (WGS). Both the BRCA2 and gCHEK2 mutations were monoallelic and genomic signature analysis defined the tumor as HR-proficient, consistent with the lack of benefit from ola. WGS confirmed a biallelic loss of ATRX with a genomic signature consistent with an ALT+ phenotype. The clinical experience of ATRi therapy in patients with ALT+ tumors is limited but further investigation of ATRi such as camonsertib is warranted in this patient population. Citation Format: Timothy A. Yap, Ian M. Silverman, Adrienne Johnson, Chenfeng Meng, Joseph D. Schonhoft, Michal Zimmermann, Danielle Ulanet, Victoria Rimkunas, Maria Koehler. Exceptional response to the ataxia telangiectasia and Rad3-related inhibitor (ATRi), camonsertib, in a patient with alternative lengthening of telomeres (ALT)-positive metastatic melanoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr B025.

Neurooncology: 2024 update.

As in previous years, including 2023, a major focus in the neurooncological area of neuropathology was put on more precise and constantly faster diagnostic procedures, even reaching the level of ultra-fast intraoperative diagnostics based on methylation profiling. Neuropathological diagnostic precision and clinical follow-up treatment has been further increased by combining DNA methylation profiling with targeted panel sequencing. A few new, molecularly defined tumor subtypes have been proposed, among others, a glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (in its abbreviated form named GTAKA) and the de novo replication repair deficient glioblastoma, IDH-wildtype both having either distinct prognostic or therapeutic implications. Regarding the understanding of brain tumor development and progression, several novel mechanisms have been presented which might also be considered as treatment targets in the future, such as a) autonomous rhythmical Ca2+ oscillations in interconnected glioma cell networks driving tumor growth; b) transfer of mitochondria from normal astrocytes to glioma cells enhancing proliferation and self-renewal; c) brain endothelial cell remodeling upon matrix-metalloprotease 9 secretion by tumor cells metastasizing into the CNS and d) anti-tumor activity of microglia in CNS metastasis of breast cancer. Finally, in contrast to previous years, several very promising neurooncological treatment studies have been conducted, focusing on specific targets such as H3K27M or IDH1/2 mutations for which a proper neuropathological assessment is key. The continuous translation of potential new treatment targets using faster and precise diagnostic procedures will further pave the way for better individualized clinical care of neurooncological patients.

Identifying infrequent genetic changes in monozygotic twins afflicted with hypospadias via targeted panel sequencing.

We aimed to identify the genetic causes of hypospadias in children using targeted gene panel sequencing for disorders of sex development (DSD). This study included 18 twin boys with hypospadias: seven and two pairs were monozygotic and dizygotic twins, respectively, and six were discordant and three were concordant twins. Targeted gene panel sequencing for 67 known DSD genes was performed. Sequence variants were classified into five different categories, pathogenic, likely pathogenic, variants of uncertain significance, likely benign, and benign, following the American College of Medical Genetics and Genomics Standards and Guidelines. The mean gestational age and birth weight were 35.3±2.0 weeks and 1.96±0.61 kg, respectively, with seven patients being small for gestational age. Hypospadias was present in 12 patients, with posterior type in 33.3% and anterior type in 66.7%. In three families with twins, both siblings had hypospadias. In addition, cryptorchidism was observed in one subject. Surgical correction of hypospadias was performed at a mean age of 22.1 months. Molecular analysis identified 12 different genetic variants, including two pathogenic mutations in the AMH (p.E389*) and SRD5A2 (p.R246Q) genes, found in subjects with hypospadias, respectively. However, only heterozygous mutations were detected. This study did not identify a definitive genetic component contributing to the development of hypospadias; however, the findings suggest that intrauterine growth retardation may play a significant role.

Neurooncology: 2024 update.

As in previous years, including 2023, a major focus in the neurooncological area of neuropathology was put on more precise and constantly faster diagnostic procedures, even reaching the level of ultra-fast intraoperative diagnostics based on methylation profiling. Neuropathological diagnostic precision and clinical follow-up treatment has been further increased by combining DNA methylation profiling with targeted panel sequencing. A few new, molecularly defined tumor subtypes have been proposed, among others, a glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (in its abbreviated form named GTAKA) and the de novo replication repair deficient glioblastoma, IDH-wildtype both having either distinct prognostic or therapeutic implications. Regarding the understanding of brain tumor development and progression, several novel mechanisms have been presented which might also be considered as treatment targets in the future, such as a) autonomous rhythmical Ca2+ oscillations in interconnected glioma cell networks driving tumor growth; b) transfer of mitochondria from normal astrocytes to glioma cells enhancing proliferation and self-renewal; c) brain endothelial cell remodeling upon matrix-metalloprotease 9 secretion by tumor cells metastasizing into the CNS and d) anti-tumor activity of microglia in CNS metastasis of breast cancer. Finally, in contrast to previous years, several very promising neurooncological treatment studies have been conducted, focusing on specific targets such as H3K27M or IDH1/2 mutations for which a proper neuropathological assessment is key. The continuous translation of potential new treatment targets using faster and precise diagnostic procedures will further pave the way for better individualized clinical care of neurooncological patients.

Ovarian carcinosarcomas: p53 status defines two distinct patterns of oncogenesis and outcomes.

Ovarian carcinosarcoma (OCS) is a rare and lethal type of ovarian cancer. Despite its incredibly poor prognosis, it has received little research attention. In this study, we aim to evaluate the molecular features of OCS and elucidate their clinical significance. We examined 30 OCS by immunohistochemistry (IHC) and targeted panel sequencing collected from a single institution (2003-2013) as the initial molecularly characterized cohort (Cohort A). From November 2016 to April 2023, we collected an additional 67 OCS cases from three institutions across British Columbia and Alberta as the contemporary cohort (Cohort B) for clinical correlation. The Kaplan-Meier method was used to estimate overall and progression-free survival, and differences in survival rates were compared using the log-rank test. All tests were two-sided. A p-value of less than 0.05 was considered statistically significant. The majority of OCS (82%) in the initial Cohort A were p53-mutated, and the carcinomatous component displayed the histological and molecular features of a high-grade tubo-ovarian serous carcinoma (HGSC-like). In a minority of OCS, the epithelial components were characteristics of endometrioid or clear cell carcinomas, and IHC staining was wild type for p53. In the contemporary Cohort B, we observed the same histological findings related to the p53 IHC staining pattern. The median overall survival of the p53-mutated HGSC-like OCS (47 patients) was significantly higher (43.5 months) compared with that of the p53 wild-type OCS (10 patients, 8.8 months; P < 0.01). Pathogenic BRCA1/2 germline/somatic mutations were observed in 7 patients (17.5%) of HGSC-like OCS, and all these patients were alive at 3 years from diagnosis compared to a 51% 3-year survival among the patients with BRCA1/2 wild-type HGSC-like OCS (33 patients) (p = 0.022). Majority of patients (6/7) with BRCA1/2-mutated OCS received poly (ADP-ribose) polymerase inhibitor as maintenance therapy in this cohort. Most OCSs have a morphologic and molecular profile resembling HGSC; however, some OCSs display a molecular profile that suggests origin through non-serous oncogenic pathways. This molecular distinction has both prognostic and treatment (predictive) implications. These findings underscore the importance of routine p53 IHC testing on all OCS and BRCA1/2 testing on p53-mutated OCS.

Exploring the Heterogeneity of Non-Syndromic Hearing Loss: A Comprehensive Review of Implicated Genes and the Role of Whole Exome Sequencing

Background: Hereditary hearing loss (HHL) accounts for approximately 50-60% of all hearing loss (HL) cases, highlighting the significant role genetics play in this condition. HHL can be mostly classified into two main forms: syndromic and non-syndromic. Of these, non-syndromic hearing loss (NSHL) is the most prevalent, contributing to over 70% of HHL cases. The hearing process involves a complex interplay of various components inside the ear, working together to convert sound waves into comprehensible signals for the brain. Non-syndromic hearing loss (NSHL) is known for its extraordinary diversity and complexity, influenced by a vast array of genes, with more than 120 identified thus far. These genes can be categorized into distinct functional groups, encompassing cochlear ion homeostasis, hair bundle development and cell adhesion, synaptic transmission, transcriptional regulation, and mitochondrial function. The advent of next-generation sequencing (NGS) technologies has been instrumental in unraveling the genetic underpinnings of NSHL. Among NGS techniques, whole exome sequencing (WES) appeared as a revolutionary advancement, outperforming other approaches like targeted panel sequencing and whole-genome sequencing in terms of cost-effectiveness and efficiency. WES not only aids in deciphering the genetic basis of hearing loss but also offers the potential to revolutionize patient care and diagnosis. It paves the way for a new era for precision medicine in the realm of hearing loss, promising more accurate and tailored treatments for affected individuals. This transformative approach is poised to bring about substantial advancements in our understanding of hereditary hearing loss and its clinical management.

Assessments of tumor mutational burden estimation by targeted panel sequencing: A comprehensive simulation analysis.

Tumor mutational burden (TMB), when at a high level, is an emerging indicative factor of sensitivity to immune checkpoint inhibitors. Previous studies have shown that the more affordable and accurate targeted panels can be used to measure TMB as a substitute for whole exome sequencing (WES). However, additional processes, such as hotspot mutations exclusion and TMB adjustment, are usually required to deal with the effect of the limited panel sizes. A comprehensive investigation of the effective factors is needed for accurate TMB estimation by targeted panels. In this study, we quantitatively evaluated the variances of TMB values calculated by WES and targeted panels using 10,000 simulated targeted panels with panel sizes ranging from 0.2 to 3.1 million bases. With The Cancer Genome Atlas (TCGA) cancer samples and mutation profiles, we fixed regressions on WES-TMBs and panel-TMBs to assess the performance of a given targeted panel. Panel size was found as one of the major effective factors of TMB estimation. Meanwhile, by investigating the well-performing small panels that reported TMB values similar to those of WES, we demonstrated the evidence of the cancer type-specific impacts of genes on TMB estimation and identified high-impact gene sets for different cancer types based on the TCGA data. This study revealed the quantitative correlations between TMB variance and panel size, and the potential impacts of individual genes on TMB estimation. Our results suggested that for cancer patients diagnosed using targeted panels, it would be highly beneficial to have the capability to directly measure TMB from the targeted sequencing data. This would greatly assist in making decisions regarding the use of immunotherapies.

The TiHoCL panel for canine lymphoma: a feasibility study integrating functional genomics and network biology approaches for comparative oncology targeted NGS panel design.

Targeted next-generation sequencing (NGS) enables the identification of genomic variants in cancer patients with high sensitivity at relatively low costs, and has thus opened the era to personalized human oncology. Veterinary medicine tends to adopt new technologies at a slower pace compared to human medicine due to lower funding, nonetheless it embraces technological advancements over time. Hence, it is reasonable to assume that targeted NGS will be incorporated into routine veterinary practice in the foreseeable future. Many animal diseases have well-researched human counterparts and hence, insights gained from the latter might, in principle, be harnessed to elucidate the former. Here, we present the TiHoCL targeted NGS panel as a proof of concept, exemplifying how functional genomics and network approaches can be effectively used to leverage the wealth of information available for human diseases in the development of targeted sequencing panels for veterinary medicine. Specifically, the TiHoCL targeted NGS panel is a molecular tool for characterizing and stratifying canine lymphoma (CL) patients designed based on human non-Hodgkin lymphoma (NHL) research outputs. While various single nucleotide polymorphisms (SNPs) have been associated with high risk of developing NHL, poor prognosis and resistance to treatment in NHL patients, little is known about the genetics of CL. Thus, the ~100 SNPs featured in the TiHoCL targeted NGS panel were selected using functional genomics and network approaches following a literature and database search that shielded ~500 SNPs associated with, in nearly all cases, human hematologic malignancies. The TiHoCL targeted NGS panel underwent technical validation and preliminary functional assessment by sequencing DNA samples isolated from blood of 29 lymphoma dogs using an Ion Torrent™ PGM System achieving good sequencing run metrics. Our design framework holds new possibilities for the design of similar molecular tools applied to other diseases for which limited knowledge is available and will improve drug target discovery and patient care.

Genetic variants identified in novel candidate genes for anorexia nervosa and analysis of molecular pathways for diagnostic applications.

Anorexia nervosa (AN) is a severe psychiatric disorder characterized by an intense fear of gaining weight, a relentless pursuit of thinness, and a distorted body image. Recent research highlights the substantial contribution of genetics to AN's etiology, with genes like BDNF, SLC6A4, and DRD2 implicated. However, a comprehensive genetic test for AN diagnosis is lacking. This study aims to elucidate the biological foundations of AN, examining variants in genes associated with syndromic forms, rare variants in AN patients, and candidate genes from GWAS studies, murine models, or established molecular pathways. The study involved 135 AN patients from Italy, diagnosed based on DSM-V criteria. A specialized Next-Generation Sequencing panel targeting 163 genes was designed. Sequencing was performed on an Illumina MiSeq System, and variants were analyzed using bioinformatics tools. Data on clinical parameters, exercise habits, and AN types were collected. The AN cohort, predominantly female, exhibited diverse clinical characteristics. Our analysis identified gene variants associated with syndromic forms of AN, such as STRA6, NF1, MAT1A, and ABCC6. Variants were also found in known AN-related genes (CD36, DRD4, GCKR, GHRL, GRIN3B, GPR55, LEPR) and in other 16 candidate genes (A2M, AEBP1, ABHD4, ACBD7, CNTNAP, GFRAL, GRIN2D, LIPE, LMNA, NMU, PDE3B, POMC, RYR1, TNXB, TYK2, VPS13B), highlighting the complexity of AN's genetic landscape. The endocannabinoid and dopamine pathways play crucial roles. Skeletal muscle-related genes and appetite-regulating hormones also revealed potential connections. Adipogenesis-related genes suggest AN's association with subcutaneous adipose tissue deficiency. This study provides comprehensive insights into the genetic underpinnings of AN, emphasizing the importance of multiple pathways. The identified variants contribute.

Low prevalence of germline TP53 and PALB2 mutations in unselected cohort of breast cancer patients from Brunei Darussalam

Background: Breast cancer is the most frequent malignancy affecting women worldwide. The majority of breast cancer occurs sporadically, with only 5-10% being caused by inheritance of susceptibility genes. In Brunei Darussalam, breast cancer is the leading cause of cancer in women. The prevalence and clinical relevance of breast cancer susceptibility genes in Brunei breast cancer patients is unknown. We investigated the prevalence and clinical relevance of germline TP53 and PALB2 genes, recognised to confer a high and moderate risk respectively, in the development of breast cancer in an unselected cohort of Brunei breast cancer patients. Methods: Genomic DNA was extracted from peripheral blood samples of 54 unselected Brunei breast cancer patients. The DNA samples were sequenced for germline BRCA1, BRCA2, TP53, and PALB2 variants using targeted panel sequencing on a Hi-Plex NGS platform. Identified variants were analysed for their pathogenicity classification based on clinical/population/mutation databases, in-silico data, and available functional data analysis. Chi-square test was used to determine the association between TP53 codon 72 and response to chemotherapy in Brunei breast cancer patients. Results: We identified two TP53 and five PALB2 missense variants in our study population. Five of the identified variants were classified as variants of uncertain significance (one in TP53 and four in PALB2) giving a prevalence of TP53 and PALB2 variant of uncertain significance carriers at 1.9% and 9.3%, respectively. No pathogenic TP53 and PALB2 mutation was identified in this study suggesting the rarity of these genes in breast cancer.TP53 codon 72 had no association with Brunei breast cancer patients’ response to chemotherapy supporting the benign characteristic of the variant P72R. Conclusions: Our current findings suggest that the contribution of germline TP53 and PALB2 genes in unselected Brunei breast cancer patients is rare, and a larger number of participants will be required to confirm this finding.

Automated Machine Learning-Based Diagnosis and Molecular Characterization of Acute Leukemias using Flow Cytometry Data

Abstract Current flow cytometric analysis of blood and bone marrow samples for the diagnosis of acute leukemias relies heavily on manual intervention in both the processing and analysis steps, introducing significant subjectivity into the resulting diagnosis and increasing diagnostic turn-around time. Additionally, concurrent molecular characterization of these samples via cytogenetics and targeted sequencing panels can take multiple days, thereby delaying patient diagnosis and treatment. Attention-based multi-instance learning models are machine learning models that can make accurate predictions and generate interpretable insights regarding the classification of a sample from multiple events/cells; while these models have been developed for anatomic pathology applications, they have yet to be applied to flow cytometry data. By utilizing 1,820 flow cytometry samples from 2019-2022 at Brigham and Women’s Hospital, we developed attention-based multi-instance machine learning models for automated diagnosis of acute leukemia, including differentiation of acute myeloid leukemia (AML) from B-lymphoblastic leukemia/lymphoma (B-ALL). Additionally, using concurrent cytogenetic and targeted sequencing data from 674 acute leukemia samples, machine learning models for prediction of molecular aberrancies from flow cytometry data were developed. Machine learning models were created using the TabNet deep learning architecture and VIME self-supervised training algorithm, which are state-of-the-art approaches towards machine learning from tabular data including flow cytometry data. Attention-based multi-instance models demonstrated strong performance for the automated diagnosis of acute leukemia versus non-leukemia samples (AUROC 0.869), as well as the separation of AML from B-ALL samples (AUROC 0.971). These models also accurately predicted cytogenetic aberrancies among AML samples, including t(15;17);PML::RARA (AUROC 1.00), as well as mutations including NPM1 (AUROC 0.725). These models do not require any manual intervention including compensation or gating, and additionally provide quantitative scores for the relative importance of different flow cytometry events and markers for the diagnosis of a particular sample. These importance scores can be integrated into flow cytometry analysis software for visualization and interpretation by hematopathologists. In this study, we have demonstrated the capability of machine learning models to provide automated diagnoses of acute leukemia, as well as accurately predict cytogenetic and molecular aberrancies in blood and bone marrow samples using flow cytometry data. This automated workflow can significantly decrease diagnostic turn-around time and ultimately improve patient outcomes.

Clonal Hematopoiesis Associated with Rheumatoid Arthritis

Introduction: Clonal hematopoiesis (CH) becomes common with age and can play a role in the pathophysiology of inflammatory diseases by modifying immune cell function. CH is characterized by the presence of somatic mutations in genes such as DNMT3A and TET2 (CH of indeterminate potential, CHIP), and as mosaic chromosomal alterations (mCAs). While CHIP, particularly in the context of TET2 mutations, can promote inflammation in cardiovascular diseases, the association between clonal hematopoiesis and autoimmunity has not been comprehensively studied to date. Rheumatoid arthritis (RA) is one of the most common autoimmune diseases primarily affecting joints. Seropositive RA is defined by the presence of anti-cyclic citrullinated peptide antibodies (ACPA) and/or rheumatoid factor (RF), whereas seronegative RA is a more heterogeneous inflammatory disease entity involving patients with clinical RA manifestations in the absence of ACPA and RF. Understanding of the association between CH and inflammatory processes may yield novel insights into prevention and management of autoimmune diseases. Methods: To comprehensively evaluate the association between CH and autoimmune diseases, we identified CHIP variants in whole exome sequencing (WES) data from the FINRISK study (N=10 129). We also detected mCAs and CHIP in the nationwide FinnGen study (N=340 173), where we manually identified CHIP carriers as outliers in SNP intensity plots at known CHIP loci in DNA microarray data. Only known CHIP loci with variant prevalence comparable to UK Biobank WES data and significant positive associations with age and hematological malignancies were included for downstream analyses. To further characterize the link between CHIP and RA phenotypes, we performed targeted panel sequencing of 69 myeloid driver genes in 675 RA patient blood samples (91% collected at diagnosis) and 60 healthy controls. We studied the association between CH and RA in multivariable models excluding participants with prevalent hematologic malignancies and adjusting for sex, age, smoking, and principal components of ancestry. We performed uni- and multivariable analyses to evaluate the link between CHIP and RA patient phenotypes. Results: We identified CHIP in 381 (3.8%) FINRISK participants. As expected, the prevalence of CHIP increased with age, and CHIP variants were associated with prevalent and incident hematologic malignancies. C-reactive protein values were higher in participants with CHIP (P&amp;lt;0.001). In multivariable models, CHIP status (OR 1.98, 1.13-3.45, P=0.017) was more common in participants with questionnaire-based history of RA (N=151) (Fig 1A). In the FinnGen study, CHIP carrier status was associated with prevalent autoimmune diseases (OR 1.26, 1.05-1.53, P=0.015). We validated the association between prevalent RA (N=10 990) and CHIP carrier status (N=2 393) in the FinnGen study (OR 1.58, 1.18-2.13, P=0.002) (Fig 1A). In particular, CHIP (OR 2.17, 1.40-3.36, P&amp;lt;0.001), and GNB1 variants (OR 4.71, 1.87-11.82, P=0.001) were associated with the seronegative RA, whereas DNMT3A was associated with seropositive RA (OR 1.83, 1.08-3.09, P=0.024). We observed no association between autosomal mCAs and RA. Using targeted panel sequencing, we found CHIP in 22% (146/675) of RA patients. RA patients with CHIP variants were older than those without a CHIP variant (median, 69 vs 63 years, P&amp;lt;0.001). Erythrocyte sedimentation rate (ESR) was higher in those with CHIP (median, 42.5 vs 26.0 mm/h, P=0.043). RA patients with TET2 variants were more likely to have seronegative disease compared with TET2 wild-type patients (proportion of seronegative patients, 56% vs 33%, OR 2.62; P=0.008) (Fig 1B). The association remained significant (OR 2.38, 1.14-4.96, P=0.02) when adjusting for age, sex, and smoking. Evaluation of longitudinal disease outcomes by CHIP status are currently ongoing. Conclusion: CHIP variants were more common in participants with prevalent RA in two population-level cohorts, and the association was specific to seronegative RA in the large FinnGen cohort. In newly diagnosed RA patients, TET2 mutations were more common in seronegative than in seropositive RA. While the causality and the functional basis of these observations remain to be explored in future studies, our results provide additional evidence for the association between CHIP and inflammation in various disease contexts, including autoimmune diseases.

Transcriptomic without Clinical Response to Menin Inhibition As a Mechanism of Upfront Resistance in Samples from Mutliply Relapsed Patients with KMT2A-Rearranged Leukemia

Inhibitors of the Menin-KMT2A interaction are emerging as promising agents for the treatment of KMT2A-rearranged ( KMT2A-r) acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). Menin is required for the recruitment of the KMT2A-fusion to a subset of its target genes. Early phase clinical trials have shown highly encouraging results in patients with relapsed and refractory leukemias with KMT2A rearrangements and NPM1 mutations. In a recently reported early phase clinical trial evaluating the Menin inhibitor revumenib, about 50% of patients failed to show a clinical response despite robust downregulation of known Menin:KMT2A target genes, suggesting on target activity of the drug. This was the most common pattern of upfront resistance. We sought to understand upfront resistance (in contrast to the reported induced resistance via MEN1 mutations) in patient derived xenograft models. To this end, we evaluated the efficacy of Menin-inhibition in KMT2A-r leukemias with high-risk features: high-risk KMT2A fusion partners in AML ( MLLT10, MLLT4), infant ALL, and serial samples from patients with multiply relapsed ALL. We found that AML samples with high-risk fusion partners banked at initial diagnosis were sensitive to Menin-inhibition in xenografts. In contrast, three highly pretreated samples from patients with KMT2A-AFF1 ALL showed only a slight, or no decrease in latentcy in the Menin-inhibitor arm. Interestingly, Menin inhibition showed excellent in vivo efficacy against leukemia samples obtained from the same three patients earlier in their disease course. Therefore, prior chemotherapy (+/- immunotherapy) selects for Menin-inhibitor resistant cells without prior exposure to Menin inhibitor. Transcriptomic analysis (RNA-Seq) documents sustained on-target efficacy of the Menin inhibitor on a transcriptional level in resistant cells. None of the samples contained a MEN1 mutation at any time point. Targeted panel sequencing at initial diagnosis and relapse documented clonal evolution and the emergence of multiple co-mutations (particularly RAS pathway mutations and TP53 mutations), however, all co-mutations tested failed to induce resistance as a single alteration. It is possible that the cooperation of multiple emerging mutations (rather than a single mutation) is sufficient to drive AML in a KMT2A-fusion independent manner, thus mediating Menin resistance. A transcriptomic response (i.e. downregulation of KMT2A-fusion target genes) without a clinical response was the most common pattern of upfront resistance in the recently reported phase I/II clinical trial of the Menin inhibitor revumenib. We conclude that it will be critical to use Menin-inhibitors upfront or in early lines of therapy before substantial clonal evolution has occurred.

The Complex Structural Variant Chromothripsis Can be Defined on Targeted Sequencing Panels, Allowing Direct Clinical Translation in Order to Improve Multiple Myeloma Prognostication

Introduction: the complex structural variant (SV) chromothripsis is an independent predictor of progression-free (PFS) and overall survival (OS) in newly diagnosed multiple myeloma (NDMM); predictive in multivariate analysis when considering ISS, IgH translocations and TP53 status (Rustad BCD 2020). Chromothripsis is not included in current prognostic scores, despite a prevalence of 24% in NDMM. While gold-standard definition requires whole genome sequencing (WGS), we've previously shown that copy-number (CN) signatures are also able to accurately define chromothripsis in whole exome sequencing (WES, Maclachlan Nat Com 2021). As neither WGS nor WES are currently used in clinical medicine, we applied CN signatures to targeted sequencing, aiming for direct clinical translation of this key biological feature into clinical practice. Memorial Sloan Kettering (MSK) now offers the MSK-Heme-IMPACT targeted sequencing panel to all MM patients having a bone marrow biopsy (BMBx), as well as offering retrospective analysis for current patients having leftover DNA from prior BMBx. Methods: We analyzed 420 samples having either myTYPE or MSK-Heme-IMPACT targeted sequencing at MSK prior to July 2023. We excluded those with whole genome duplication, applied CN signatures, then for samples from NDMM performed multivariate analysis for PFS prediction by backwards stepwise regression. In samples with CN signatures predictive for chromothripsis and with DNA available from the same BMBx, we performed parallel WGS in order to check for chromothripsis. WGS sequencing was at 60-80x for tumor, 30-40x for normal, with analysis including Battenberg for CN analysis, with SvABA, BRASS and GRIDSS for SV calling. Additional parallel WGS is in progress for 45 samples with NDMM prior to DVRd or DKRd, in order to examine chromothripsis prediction and PFS impact in the context of highly effective induction. Results: From 420 samples, 48 were collected at the precursor stage, 205 with NDMM, and 167 with relapsed disease. 39 patients had 2 assays performed, while the remainder were unique patient samples. Within NDMM, the range of induction regimens received included lenalidomide and dexamethasone with bortezomib (VRd), carfilzomib (KRd) or daratumumab (DRd), along with quadruplet therapy (DVRd or DKRd). Targeted sequencing data detected all 6 key CN features observed in WGS and WES analysis. Similar to WES, there was a lower contribution from very high breakpoint counts per 10mB and longer lengths of oscillating CN segments, due to the lower resolution of targeted sequencing data. De novo extraction of CN signatures defined 1 signature containing multiple features consistent with chromothripsis; high breakpoint count per 10mB, more jumps between adjacent CN segments, longer lengths of oscillating CN segments and a predominance of small CN segments. When examining samples from NDMM, contribution from this signature was predictive of PFS in multivariate analysis when considering age, ISS, t(4;14), TP53 status and gain1q21 (hazard ratio &amp;gt; 4, p=0.003). 33 samples had a predictive probability for chromothripsis &amp;gt; 0.6 (the cut-off in WGS / WES having the highest sensitivity and specificity for prediction), with also having further DNA available. 30/33 (91%) were confirmed to harbor chromothripsis on manual inspection of WGS data. 19/30 (63%) with chromothripsis were BMBx from NDMM, while 11/30 (37%) were from relapsed disease. Discussion: the complex SV chromothripsis is a key genomic risk factor predicting for poor PFS and OS in MM, which is currently not being captured in routine practice or in clinical trials. Here, we demonstrate that chromothripsis can be predicted from targeted sequencing data, confirmed by gold-standard WGS analysis. Ongoing studies are expanding our cohort of NDMM with concurrent targeting sequencing and WGS, to define the sensitivity and specificity of targeted-sequencing-based CN signature prediction of chromothripsis. The additional cohort largely comprises patients treated with daratumumab-quadruplet induction therapy, aiming to confirm that chromothripsis and CN signatures retain prognostic significance in the context of this therapy. With this data is in hand, we will develop a CN signature fitting tool, similar to mmsig for mutational signatures (Rustad Comm Biol 2021), to allow easily accessible incorporation of chromothripsis assessment into clinical practice.

Clinical and Molecular Characterization of Triple-Negative Essential Thrombocythemia: Data from the Prospective Spanish Registry of Essential Thrombocythemia

Introduction Triple-negative Essential Thrombocythemia (TN-ET) accounts for up to 10-20% of patients with a histological diagnosis of ET. Despite being considered an indolent disease, it remains a diagnostic and therapeutic challenge as it can be confused with non-clonal thrombocytosis and its prognostic factors and management are not standardized. Objectives The aim of this study was to evaluate the utility of a Next Generation Sequencing (NGS) panel targeting recurrently mutated genes in myeloid pathology for detecting genetic variants in patients diagnosed with TN-ET and to assess the significance of these variants in the risk of thrombosis and hemorrhage, progression to Acute Leukemia (AL) or Myelofibrosis (MF), and overall survival. Materials and Methods Data from 151 TN-ET patients with confirmed biopsy and NGS sequencing from the Spanish Registry of Essential Thrombocythemia of the Spanish Group of Philadelphia-Negative Myeloproliferative Neoplasms was obtained. This registry includes information on diagnosis, molecular biology, clinical characteristics, and molecular biology. In addition, 39 patients whose molecular diagnosis was performed at the Molecular Biology Laboratory of the Hematology Department at Hospital Universitario 12 de Octubre, Madrid, Spain were included. This last panel included the genes: ANKRD26, ASXL1, ATG2B, BCOR, BCORL1, CALR, CBL, CEBPA, CSF3R, CUX1, DDX41, DNMT3A, EGLN1, EPAS1, EPOR, ETNK1, ETV6, EZH2, FLT3, GATA2, GNAS, GNB1, GSKIP, IDH1, IDH2, JAK2, KDM6A, KIT, KMT2A, KRAS, MBD4, MPL, NF1, NFE2, NPM1, NRAS, PHF6, PPM1D, PRPF8, PTPN11, RAD21, RIT1, RRAS, RUNX1, SAMD9, SAMD9L, SETBP1, SF3A1, SF3B1, SH2B3, SMC1A, SMC3, SRSF2, STAG2, TERC, TERT, TET2, THPO, TP53, U2AF1, VHL, WT1, ZRSR2. Statistical analyses were performed using SPSS v.29.0. Results A canonical mutation was detected in 20 out of the 190 studied patients, ( JAK2 V617F n=13, CALR n=3 and MPL n=4) being discarded from subsequent studies. Among the other 170 samples, 206 genetic variants were detected in a total of 86 patients (median 2, range 1-9). A total of 39 pathogenic (P) or probably pathogenic (PP) variants were found in 28 patients, whereas 59 uncertain significance (US) and 108 benign (B) variants were found in 44 and 54 patients, respectively. The distribution of genes in which P/PP/US variants were detected is shown in Figure 1. Patients with P /PP mutations had a statistically higher age compared to the remaining (50 vs. 64.8 years; p&amp;lt;0.001). The prevalence of males was higher in the group where P/PP mutations were detected (57.14% vs. 28.87%; p=0.004). No differences were found regarding cardiovascular comorbidity or symptomatology at diagnosis, but the P/PP group presented a higher frequency of thrombosis prior to diagnosis (28.57% vs. 5.64%; p=0.001). There were no differences in hemoglobin, leukocyte, or platelet counts at diagnosis according to the presence of P/PP variants. The presence of P/PP mutations was associated with a higher risk of progression to AL and a lower overall survival. A higher risk of thrombosis or progression to MF was not found (Figure 2). No differences were found in the risk of thrombosis, transformation, or overall survival between patients with or without the presence of US, PB or B variants. Conclusions The use of NGS technology is useful for the diagnosis and prognostication of TN-ET. The detection of P/PP mutations in patients diagnosed with TN-ET is associated with a higher risk of transformation to AL and lower overall survival, but not with higher risk of thrombosis or progression to MF. It is necessary to evaluate the individual risk of each of these mutations and the potential prognostic role of variants of US.

Performance of a Liquid Biopsy Diagnostic Prediction Model for EBV-Positive Burkitt Lymphoma in Sub-Saharan Africa

Burkitt Lymphoma (BL) is classified into EBV-positive BL (EBL) and EBV-negative BL (sporadic BL), the former being more prevalent in SSA (Al-Khreisat et al 2023). Conventional diagnosis of BL depends on the morphological assessment of invasive tissue biopsy followed by immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) to reveal the pathognomonic t(8;14), or t(8;22) translocations. This is associated with significant diagnostic delay in regions with limited pathology services (Mawalla et al 2023), often necessitating initiation of treatment based on clinical or histopathological findings without immunohistochemistry (Ogwang et al 2011), with ensuing mismanagement contributing to poor survival outcomes observed in SSA compared to High-Income Countries (HIC) (Sung et al 2021). Here, we sought to explore whether liquid biopsy could be used as an initial diagnostic aid for EBL in settings without easy access to pathology using different EBV DNA parameters and the MYC-Immunoglobulin ( MYC-Ig) gene rearrangement. This prospective study collected whole blood samples prospectively from 221 participants (90 BL and 131 non-BL) enrolled in the Aggressive Infection-Related East Africa Lymphoma (AI-REAL) project (Legason et al 2022) across 5 sites in Tanzania and Uganda. The revised BL diagnostic algorithm (Naresh et al 2021) was used as a gold-standard diagnosis. CfDNA was extracted using the QIAamp Circulating Nucleic Acid Kit (Qiagen, USA), according to the manufacturer's instructions. DNA libraries were prepared with the Thru PLEX Tag-Seq HV kit (Takara Bio Inc. Japan), and hybridization capture was performed using a custom, next-generation sequencing (NGS) panel targeting genes commonly mutated in BL and three EBV genes: EBER1, EBER2, and EBNA2. All sequencing was performed in-country (MiSeq, Illumina, CA, USA) and analyzed in a custom pipeline. Using custom scripts, EBV DNA copies per cell and EBV DNA fragment size ratio were calculated as the proportion of EBV fragments of length 180 - 200 base pairs (bp) divided by the proportion of autosomal fragments within the same size window. The diversity in the fragment size distribution of the EBV and autosomal DNA was calculated and presented as EBV entropy and autosomal entropy. Translocations were called using IgCaller (Nadeu et al 2020) and Genomic Rearrangement Identification Software Suite (GRIDSS) (Cameron et al 2017). Univariate analysis was performed to assess the association between predictor variables (clinical parameters, EBV parameters, and MYC translocation) and a diagnosis of EBL. Ten-fold cross-validation was performed on a liquid biopsy model consisting of all the liquid biopsy variables with the clinical variables included in the model as covariates. Performance metrics for the liquid biopsy model as a diagnostic aid were calculated, and variable importance was determined to assess each variable's relative influence on the model. In our cohort, EBL diagnosis was negatively associated with tumor site (neck) and not significantly associated with tumor site (jaw). A shorter duration of symptoms was associated with a diagnosis of EBL. Presence of MYC translocation t(8;14), higher EBV fragment size ratio, proportion, entropy, and copies per cell for EBER1, EBER2, and EBNA2 were all associated with a diagnosis of EBL.The combined liquid biopsy diagnostic prediction model had an estimated AUC of 90%, with sensitivity between 85%-90%, specificity between 75% - 80%, and positive and negative predictive values of 85% (Figure 1). MYC translocation t(8;14) was the most important diagnostic variable, followed by EBV entropy (Figure 2). This study demonstrates the feasibility of liquid biopsy as a non-invasive diagnostic aid for EBL in settings without easy access to pathology. To strengthen the application of this technology into clinical practice, further analysis is being conducted for weighting and assigning of scores for each predictor variable. This would assist clinicians in making a precise diagnosis, complementing existing diagnostic modalities for EBL, and reducing the rate of misdiagnosis arising from diagnosis based on clinical suspicion and tissue morphology without immunohistochemistry.

Lymphoma Cell Sorting to Enrich Low Degree Infiltration Clonal B-Cells for Diagnostic Delineation of Molecular Genetic Background By NGS

Introduction: According to WHO 2022 classificationthe vast majority of B-cell lymphoma entities continue to be defined histologically and by their immunophenotype. However, genetics help to define these entities and provide prognostic information. NGS targeted panel sequencing with short turn-around time has emerged as powerful diagnostic tool to uncover relevant genes frequently mutated in B-cell lymphoma. Yet its sensitivity limits its application to lymphoma cases with clone sizes &amp;gt;5%. In case of clinical symptoms and need for therapy small B-cell clones (&amp;lt;5%) can be diagnostically challenging if tissue for histopathology is difficult to obtain and immunophenotype is not characteristic for a specific lymphoma entitiy such as splenic B-cell lymphoma. Aim: To enrich small B-cell clones (&amp;lt;5%) by cell sorting to &amp;gt;15% to enable lymphoma NGS panel sequencing for potential genetic characterization and risk stratification. Methods: Peripheral blood or bone marrow samples (n=43) that containedsmall B-cells clones (&amp;lt;5%) as identified by flow cytometric routine diagnostics were stained for cell sorting by a combination of monoclonal antibodies against 9 B-cell antigens, including CD5, CD19 and CD45. The gating strategy excludes debris and doublets and defines B- and T-cells out of CD45-positive events. By application of cell sorting (SRT Cytoflex, Beckman Coulter) we aimed at &amp;gt;500,000 cells consisting of B- and T-cells, containing &amp;gt;15% clonal B-cells to ensure sufficient NGS sensitivity but minimize sort time. DNA was extracted from sorted samples and lymphoma NGS panel sequencing (66 genes ~ 1,500x coverage, min. 400x) was performed (NovaSeq 6000, Illumina). For technical and biological validation, native sample material was sequenced in parallel for a subset of patient samples (n=30). Results: In total43samples with &amp;lt;5% clonal B-cells were applied for cell sorting and clonal B-cells were enriched to a median of 17% (range, 3-97%) in a median of 800,000 cells (range, 127,400-3,780,000). In a pilot study to optimize the sorting procedure 8 of 13 sorted samples (62%) revealed quantitatively sufficient and good quality DNA and could be successfully analyzed by NGS. In 4 of these 8 samples (50%) mutations were identified. Optimized processing regarding cell sorting and DNA extraction was applied to further 30 samples all of which could be successfully sequenced. Overall, in 50% of all samples with NGS analysis after cell sorting (19/38) one or more mutations (total number of mutations: n=30) associated with B-cell lymphoma were detected. Mutations comprised genes frequently affected in B-cell lymphoma: MYD88 (30% of detected mutations, 9/30), CXCR4 (20%, 6/30), NOTCH1 (7%, 2/30), NOTCH2 (3%, 1/30), KMT2D (7%, 2/30), TP53 (13%, 4/30), BRAF (7%, 2/30), KLF2 (10%, 3/30) and DNMT3A (3%, 1/30). All of the cases negative for NGS after sorting (n=15) were negative also by NGS on matched native sample material without prior enrichment of clonal B-cells. Out of the 15 cases with positive NGS results after sorting NGS on native sample material revealed mutations in only 4 (27%) cases (only 1 case with detection of all mutations) while in 11 (73%) cases no mutations were detected. In the 15 cases positive after sorting median variant allele frequency (VAF) was 8.8% (range 3.4-38.3%). As anticipated, in the 4 cases with mutations detected also without sorting VAF was lower in native sample material (median 3.1%, range 1.98-4.9%) as compared to sorted sample material (median 8.9%, range 6.8-23.2%, p=0.0412). Conclusion: Cell sorting can overcome the diagnostic challenge of low degree infiltration B-cell lymphoma that require molecular genetics for further classification and risk prediction prior to therapy. Analysis of 30 samples and comparison with matched native material revealed that enrichment targeting 15% of clonal B-cells in a total of &amp;gt;500.000 cells are desirable for successful and sensitive NGS panel sequencing. In 50% of such cases mutations are detectable after sorting. Cell sorting to enrich clonal B-cells thus is a powerful tool to enable NGS panel sequencing for low percentage mature B-cell lymphoma and should be considered for routine diagnostics of B-cell lymphoma.

Nanopore Cas9-Targeted Long-Read Sequencing - a Fast and Flexible Diagnostic Tool for the Identification of B-Cell Acute Lymphoblastic Leukemia Associated Gene Rearrangements

B-cell acute lymphoblastic leukemia (B-ALL) is characterized by a multitude of recurrent genetic alterations, which drive malignant transformation. Besides their essential role in leukemia biology these aberrations also serve as predictors of treatment response and survival, making their reliable detection a prerequisite for risk stratification in state-of-the-art clinical trials. Currently, the genetic characterization of B-ALL in most diagnostic laboratories still relies on an integrative approach combining conventional cytogenetics, reverse transcription polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH) assays as well as single nucleotide polymorphism (SNP) array analysis. However, these conventional diagnostic tools fail to identify a considerable number of genetic alterations, particularly cryptic rearrangements such as IGH::DUX4, IGH::EPOR or MEF2D involving fusions. Although next generation DNA- and RNA-based sequencing (NGS) assays have significantly improved the reliable detection of fusion genes, the need for large sample numbers to achieve acceptable turnaround times and cost effectiveness impairs their application in small- to medium-sized diagnostic laboratories. To address these issues, we developed a targeted sequencing assay, based on the commercially available combination of Cas9-mediated target enrichment and Nanopore long-read sequencing, which facilitates the identification of B-ALL associated gene rearrangements on the DNA level in a single sample format. The targeted panel design included an initial review of the literature to define the breakpoint-spanning regions involved in fusion gene formation followed by the design of specific guide RNAs (gRNA) to facilitate Cas9-mediated enrichment of these regions of interest (ROIs). We first conducted ROI enrichment and sequencing with a limited number of gRNAs targeting only ETV6, KMT2A and DUX4 fusions. Then we progressively extended the pool of gRNAs with each sequencing run until it comprised 91 gRNAs covering most B-ALL-associated rearrangements. This stepwise approach allowed us to identify negative effects of increasing panel size on overall enrichment efficacy and simplified the identification and replacement of poor performing gRNAs. Our initial cohort consisted of 12 well-characterized samples harboring 13 gene rearrangements, including ETV6::RUNX1, KMT2A::AFF1, MEF2D::BCL9, ZMIZ1::ABL1, SSBP2::CSF1R, PDGFRB::EBF1, IGH::EPOR, IGH::DUX4, IGH::CRLF2, IGH::CEBPE, IGH::MYC, and IGH::BCL2. To ensure easy implementation in diagnostic workflows, we used genomic DNA, isolated according to standard protocols. Cas9-based target enrichment and long-read sequencing on MinION flow cells (v9.4.1) were performed according to protocols provided by Oxford Nanopore and each sample was sequenced for 72 hours. On average, each run yielded 3.72±1.21 Gb, a mean read length of 7.40±1.00 kb with an N50 value of 12.87±1.71 kb and an average read quality (Q) score of 14.72±0.52. For data processing and analysis, we adapted the existing nextflow nf-core bioinformatics pipeline, nanoseq, to include publicly available structural variation callers and quality control tools. Our approach correctly identified 92.3% (12/13) of the rearrangements with a mean of 42 (range 2-97) breakpoint-supporting reads (BSR) per alteration. Only the IGH::MYC translocation was missed as the breakpoint was located outside of our predefined ROIs for MYC. To corroborate these results, we sequenced an additional cohort of 14 B-ALL samples, including ZNF384::DUX4, KMT2A::MLLT10, KMT2A::USP2, PAX5::SOX5, EP300::ZNF384, P2RY8::CRLF2, and IGH::DUX4 positive cases and were able to correctly identify 100% (14/14) of the fusion genes with an average of 83 (range 7-367) BSR. In conclusion, our newly developed targeted sequencing panel correctly identified 96.3% (26/27) analyzed gene rearrangements in B-ALL, including alterations evading standard diagnostic methodologies such as IGH::DUX4 or IGH::EPOR. Importantly, the assay allows individual analysis in a single sample format, thereby representing a valuable tool for B-ALL diagnostics in small to medium-sized laboratories.

Is Allogeneic Hematopoietic Stem Cell Transplant (HCT) in First Remission Beneficial to Acute Myeloid Leukemia (AML) Patients with Isocitrate Dehydrogenase(IDH) Mutations?

Introduction Somatic mutations in the isocitrate dehydrogenase 1 and 2 genes (IDH1 and IDH2) are relatively frequent in acute myeloid leukemia (AML) but with heterogeneous prognoses. The prognostic impact of this AML subtype with IDH mutations may be influenced by the comutational status with other somatic mutation, the specific types of IDH1/2 mutation (ie, IDH1 R132, IDH2 R140, and IDH2 R172). Allogeneic stem cell transplant allogeneic HCT represents a curative option for subgroups of AML patients (pts), but not for all subtypes. Transplant referral is made based on the ELN risk group classified into favorable, intermediate, and adverse risk. Although many AML pts with IDH1/2 mutations are referred to allogeneic hematopoietic stem cell transplantation (HCT) and transplanted, however it is not fully elucidated whether allogeneic HCT brings definite survival benefit to this group of the pts. Statistical attention is to be paid to the time to HCT from CR1 achievement. Before HCT, the case should be counted as a case of no HCT, while after HCT this case can be accounted as the case received HCT using the Mantel-Byar test (MBT). To handle immortal time bias, the Mantel-Byar method was used to depict outcomes during the follow-up period. Kaplan-Meier curves were avoided as they can introduce immortal bias, considering the period of time before treatment as part of the treatment arm. Instead, the MBT and landmark methods were employed to address this issue. Allogeneic HCT was treated as a time-dependent variable to prevent immortal bias. The aim of the present study is to identify if AML pts with IDH mutations obtain survival benefit from allogeneic HCT in CR1 using HCT as a time-dependent covariate with using Mantel-Byar test. Patients &amp; Method We conducted a retrospective study that included 1,228 adult pts who were diagnosed with AML and achieved CR1 in 5 centers (Toronto, Vancouver, and Montreal, Canada; Hwasun and Seoul, South Korea) from January 1997 to January 2020. Next-generation sequencing was performed in each institution according to their own standard targeted sequencing panel. We considered allogeneic HCT in CR1 as a time-dependent covariate and used a Mantel-Byar test to avoid immortal bias. Relapse-free survival (RFS) was selected for the primary endpoint, defined as the time from CR1 to relapse or death from any cause. EZR software version 1.41 was used throughout the study for statistical analysis. Results Out of 1228, a total of 238 pts (19.4%) was found to have IDH1/2 mutation, among whom 92 pts (38.6%) had isolated IDH1 mutations, 140 pts (58.8%), isolated IDH2 mutations, and 6 pts (2.5%) having coexistence of IDH1 and IDH2 mutations. With a median follow-up duration of 20.8 months (mo) (1-194.3 mo) among survivors after achieving CR1, 91 pts died while 115 pts experienced relapse. One hundred twenty-one pts received HCT in CR1, and 44 pts relapsed after HCT. The 2-year overall survival of those 238 pts was 58.9% (51.3-65.6), and 2-yr RFS was48.9% (41.6-55.8) Between the HCT (n=121) vs non-HCT group (n=117), there were no differences in sex, cytogenetic risk or other somatic mutation except NPM1 mutation which was more frequently detected in the non-HCT group (p =0.002). As expected, the HCT group was younger (55 years (15-74 yrs)) than non-HCT group (62 years (27-82 yrs), p&amp;lt;0.001). First, the RFS and OS was compared between HCT vs non-HCT groups considering HCT as non-time dependent covariate. The 2-year RFS rate was higher in the HCT group (61.0%) compared to the non-HCT group (37.0%, p= 0.0002). However, it was not translated into superior OS in the HCT group: 2-year OS rate, 64.4% in the HCT group vs 53.7% in the non-HCT group, p=0.1). We have conducted time-dependent analysis taking taken HCT in CR1 into account as a time-dependent (td) covariate using MBT. The trend of superior RFS in HCT group was reproduced in MBT: HCT in CR1 was found to improve RFS (Hazard ratio [(HR) of 0.62, (95% C.I. [0.42-0.92]; p=0.02)] as shown in Fig.1B utilizing Simon-Makuch plot. However, Multivariate analysis (MVA) for RFS did not confirm HCT in CR1 as an independent prognostic factor for RFS, while Following factors were found to be associated with RFS adversely: age &amp;gt; 60 years, presence of DNMT3A mutation, and presence of IDH1 mutation. Conclusion Allogeneic HCT in CR1 could bring some survival benefit on RFS in AML pts with IDH1/2 mutation, but not confirmed in MVA. Further study is warranted to reach a clearer conclusion with larger number of

Recent Patterns of Radiotherapy Use in Multiple Myeloma: Clinical Outcomes and Possible Radiologic, Biochemical, and Genomic Correlates of Response

Background/Objectives: Systemic therapies for multiple myeloma (MM) have advanced considerably, changing the landscape of MM treatment paradigms. Yet, the use of radiotherapy (RT) has remained heterogeneous, and even controversial, due to minimal data on outcomes. With the ultimate goal of guiding the design of prospective trials incorporating RT, we initiated a study of our institutional experience treating MM with RT since 1/1/2000. Here we report a preliminary feasibility analysis of an initial sample cohort, identifying patterns of RT use, outcomes, and the impact of RT on radiographic and biochemical markers, with genomic characterization for more recently treated patients. Materials/Methods: 506 pathologically confirmed MM patients who received RT to 1190 sites between 1/1/2000 and 6/1/2022 were identified. Patient, disease, and treatment characteristics were analyzed for 50 consecutive patients treated in 2019 (recent sampling but with reasonable follow for analysis) and tested for association with cumulative incidence of local and distant failure (LF, DF) using univariable and multivariable analysis. Genomic data was obtained via next generation sequencing using an institutional targeted sequencing panel (Memorial Sloan Kettering IMPACT). Results: Among the 50 patients analyzed (median 63 years), 90 lesions were treated with RT, 33% with concurrent systemic therapy, to a median dose of 20 Gy (8-46 Gy) over a median of 5 fractions (1-25). RT Indications were pain (56%), critical structure involvement (25%), peri-operative (9%), salvage/consolidation (8%), and bridging therapy (2%). Median size of RT-treated lesions was 4.2 cm (1.4-7.9) and included non-vertebral bones (62%), spine (24%), and extramedullary sites (14%). The median number of lines of pre-RT therapy was 7 (1-14) and 51% had &amp;gt;9 lesions on imaging, 47% involving both medullary and extramedullary sites. Pre-RT PET imaging was performed in a majority of patients (62%). With a median follow-up of 12.4 months (0.5-46), LF occurred in 5% of treated sites and 89% had DF, most commonly in both medullary + extramedullary (51.4%) sites. Of the patients with DF, 93% had sustained local control of the irradiated site. Absolute decreases 1-week to 1-month post-RT were observed in marrow plasma cell percentage, (median 4.0%), M spike (0.30 g/dL), total protein (0.3 g/dL), K:L ratio (0.01), lesion size (1.5cm), and lesion SUV (3.1) but in this limited sample, none were significantly associated with disease control. A cohort of 62 RT-treated MM patients from 2016-2022 had genomic data available; most common tumor mutations were in TP53 (35%), HIST1 (34%), NRAS (34%), and KRAS (23%). Conclusion: In this pilot analysis of a sampling cohort of RT-treated MM, we report on patterns of utilization, outcomes, and biochemical and radiographic correlates. Ultimately, we aim to characterize the role of RT in the modern era of systemic therapy to guide the design of future prospective trials and to inform novel approaches for incorporating RT into the treatment paradigm. At the meeting, we will present data from a larger cohort of MM patients, with further sub-analyses on the relevance of baseline imaging to subsequent irradiated lesions, as well as toxicity and outcomes data with the use of radiotherapy in conjunction with newer systemic agents (bi-specific antibodies and chimeric antigen receptor T-cell therapy).