Targeted Sequencing Panel Research Articles

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 & 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<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 > 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 >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).

Morphologic and Genetic Features of Unclassifiable Chronic Myeloid Neoplasms: Five-Year Experience of a Canadian Provincial Referral Center

Introduction: The challenge of diagnosing and definitively classifying myeloproliferative neoplasms (MPNs) and myelodysplastic/myeloproliferative neoplasms (MDS/MPNs) remains a conundrum in the field of hematology. While the World Health Organization has outlined diagnostic criteria for various categories, there remain cases that elude specific classification, falling under the umbrella of MPN, unclassifiable (MPN-U) and MDS/MPN, unclassifiable (MDS/MPN-U). In this study, we aimed to compare the morphological and genetic profiles of cases classified as MPN-U or MDS/MPN-U against more definitively classified cases (including chronic myelomonocytic leukemia (CMML), essential thrombocythemia (ET), MDS/MPN with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T), and primary myelofibrosis (PMF), including prefibrotic PMF (pre-PMF)). Methods: Morphologically unclassifiable myeloid neoplasm cases referred for pathologist review to our laboratory in the largest tertiary care center in British Columbia, Canada were identified through pathology database query over a five-year period. Bone marrow materials were reviewed and reanalyzed with standardized collection of qualitative and semiquantitative data by two hematopathologists. Morphological parameters studied included the myeloid to erythroid ratio, bone marrow cellularity, lineage dysplasia, megakaryocyte histotopography, bone marrow blast frequency, fibrotic changes, and bone marrow vascularity, among others. Clinical data, cytogenetic findings, and results of a targeted sequencing panel assessing a set of approximately 50 genes recurrently mutated in myeloid malignancies were collected by electronic medical record review. A cohort of contemporarily collected myeloid neoplasms with definitive pathologic diagnoses was reviewed for comparison. Statistical analyses were performed using python3. Results: The cohort comprised 29 cases classified as MPN-U, 12 cases of MDS/MPN-U, and 5 cases each of ET, PMF, pre-PMF, CMML, and MDS/MPN-RS-T. MPN-U cases were further subcategorized based on the apparent reason for difficulty in classification, including: overlapping features with another MPN; late stage/overt fibrosis; early stage without fully-developed morphologic features; and coexisting atypical morphologic findings. MPN-U with overlapping features had highly variable reticulin fibrosis, while, as expected, late stage entities had a high degree of reticulin fibrosis and early stage entities showed less overt fibrosis (Figure, Left, demonstrating select morphologic features of evaluated chronic myeloid neoplasms). MPN-U as a whole appeared to show less prominent fibrosis-associated findings than MDS/MPN-U and to, in general, show a greater degree of neovascularization, similar to changes observed in cases with PMF. Splicing factor and epigenetic modifier mutations appeared to be overrepresented in MDS/MPN-U relative to MPN-U, notably excluding MPN-U with atypical morphologic features (Figure, Right, demonstrating the distribution of pathogenic variants identified in evaluated myeloid neoplasms; results are indicated as presence (1) or absence (0) of a variant for each gene). Notably, no CALR mutations were identified in the MDS/MPN-U category or early stage / atypical morphology MPN-U, though they were enriched in overtly fibrotic MPN-U entities. Discussion/Conclusion: In this cohort we observed, as expected, significant overlap in cases classified as MPN-U and MDS/MPN-U with better delineated entities, though patterns of morphologic change and mutational spectra suggest potential directions for further investigation of additional criteria that may guide accurate classification of these neoplasms. These findings reflect the heterogeneity of MPNs described in the literature and the complexity of their genetic underpinnings, particularly in the context of concurrent dyshematopoiesis; suggest enhanced bone marrow vascularization may be an informative differential diagnostic criterion in evaluation of these neoplasms, though further study is required; and emphasize the need for broader genetic testing and perhaps further subtyping of MPN-U cases for a more nuanced analytical approaches for these disorders.

BIOM-58. ZERO-WASTE MOLECULAR DIAGNOSTICS FROM BIOPSY NEEDLE WASHES

Abstract BACKGROUND Brain tumor classification has increasingly integrated molecular diagnostics into official criteria. However, biopsy tissue is limited due to the small quantity acquired in eloquent areas of the brain and is, therefore, usually earmarked for histology. We have identified that the fluid used to wash biopsy needles contains excess tumor material that can be diagnostically useful. Characterization of this non-zero-sum waste material provides an opportunity for improvement in the diagnosis and treatment for brain tumor patients. METHODS For suspected or established high grade brain tumor biopsies (n = 37 across a multi-institutional cohort at submission), neurosurgeons were instructed to save fluid used to wash biopsy needles. Samples were processed and characterized in a variety of methods to establish diagnostic utility including (1) cell-free DNA isolation and targeted panel sequencing (n = 13), (2) isothermal amplification of cell-free DNA from raw wash water for rapid diagnostics (n = 2), (3) cell-line generation (n = 24) and, (4) cell-free mutant protein capture and quantification (n = 9). RESULTS (1) 13 wash samples were considered for cf-tDNA extraction and Illumina TruSight Oncology 500 panel sequencing (with extracted DNA ranging from 20ng-40ug). In 2 returned cases (11 pending), concordance was 100% with clinical targeted panel sequencing where panels overlapped. (2) One case suspected of harboring H3K27M was subjected to targeted, loop-mediated isothermal amplification and Oxford Nanopore real-time sequencing, confirming an H3.3K27M diagnosis (11.8% allele fraction) within 1hr35min of receipt of sample from the operating room. (3) 5 cases resulted in primary cell culture generation (4) A novel single-molecule mutant protein quantification technique was performed on 9 cases. RESULTS from all analyses and concordance with outstanding sequencing will be presented. CONCLUSION We demonstrate that biopsy byproducts contain enough high-quality tumor-derived material to perform a variety of useful diagnostics with the potential to have immediate translational impact on standard of care.

Can Whole Genome and Whole Transcriptome Sequencing Replace Standard Procedures in CLL Diagnostics?

Background: The advantages of genome-wide sequencing approaches over conventional methods in CLL diagnostics are a matter of debate and exact guidelines for the application of next-generation sequencing in a diagnostic context are currently missing. Aim: Compare the accuracy of whole genome sequencing (WGS) and whole transcriptome sequencing (WTS) in determining the presence of point mutations, IGHV mutational status (IGHVms), and chromosomal aberrations to conventional procedures in a clinical setting. Patients and Methods: The cohort comprised 317 CLL patients. Diagnosis was established following WHO guidelines. WGS (100x, 2x151bp) and WTS (5x10 7 reads, 2x101bp) data were generated on NovaSeq instruments. For routine diagnostics, sequencing was carried out by Sanger or targeted panel sequencing (1500x, 2x101bp). Chromosome banding analysis (CBA) and FISH were available for 231 patients. WGS data were analyzed for chromosomal aberrations and copy number alterations using Manta and GATK. IGHVms was determined by Sanger sequencing and/or fragment analysis for 248 patients. Analysis of IGHVms was carried out using IgCaller (WGS) and MiXCR (WTS). Results: Comparing copy number variants (CNV) and balanced structural variants (SV) between CBA and WGS revealed a high concordance. In detail, 297 CNV were detected by both techniques while 32 and 52 were detected only by CBA (small subclones) or by WGS, respectively. 33 balanced SV were detected by both while 8 and 3 were detected only by CBA and WGS, respectively. A complex karyotype (≥ 3 abnormalities) was observed by both techniques in 55 cases, while 5 and 10 cases were categorized as complex by CBA only or WGS only, respectively. Survival analysis of cases with 3 to 5 chromosomal aberrations predicted by routine or WGS revealed similar hazard ratios that were positively correlated with the number of aberrations. For comparing SNV calls from routine and WGS, we investigated genes with validated mutations in at least ten patients in routine diagnostics. This criterion was met by ATM, MYD88, NOTCH1, SF3B1, and TP53. We observed high concordance between routine and WGS data ( ATM 99.4%, MYD88 100%, NOTCH1 97.8%, SF3B1 100%, TP53 99.1%). Five mutations were detected in routine only and three in WGS only (routine only/WGS only: ATM 1/0, MYD88 0/0, NOTCH1 2/2, SF3B1 0/0, TP53 2/1) and found to be caused by low variant allele frequency (5 miscalls, VAF < 5%) and/or filtering out of low quality variants (5 cases). IGHV rearrangements analyzed by Sanger (248 patients), WGS (242/248 patients), and WTS (236/248 patients) data were compared for matches in the rearranged IGHV. IGHVms calling employed 98% of sequence identity as cutoff. Calling the rearranged IGHV was concordant in 93%, 95%, and 92% when comparing Sanger/MiXCR, Sanger/IgCaller, and MiXCR/IgCaller calls, respectively. For IGHVms, the corresponding percentages of concordance were 91%, 86%, and 83%. Mismatches in calling the IGHVms were found in borderline cases. Detection of stereotyped IGHV was fully concordant. In addition to reliably replicating routine results, we find that WGS/WTS data can also outperform routine procedures. In our hands, the highest hazard ratio (4.94) in survival analysis distinguishing mutated CLL (mCLL) from unmutated CLL (uCLL) is observed using WTS for IGHVms determination and 97% sequence identity as cutoff (208 patients, up to 30 years follow up). Survival for borderline cases (97.00-97.99% sequence identity) was statistically indistinguishable from uCLL in routine diagnostics as well as WGS/WTS. Furthermore, using WGS, CN-LOH regions and deletions below the detection limit of CBA (10 MB) can be detected. We observed such regions in samples with mutated TP53 (5 CN-LOH), ATM (2 CN-LOH, 4 deletions < 10MB), and deletions of minimally overlapping region chr8:21,700,000-23,600,000, whose loss was associated with poor survival (3/29 deletions < 3.1 MB). Conclusions: WGS/WTS data reliably replicate results obtained by standard procedures in a diagnostic setting. Sequencing offers advantages such as a unified workflow, better sensitivity for small deletions, CN-LOH detection, genome-wide analyses of coding and non-coding mutations, among others. Challenges of short read based sequencing regard the detection limit for point mutations and specificity/sensitivity in detecting chromosomal aberrations.

Acute Myeloid Leukemia (AML) Patients with Myelodysplasia (MDS) Related-Gene Mutations in First Complete Remission (CR1) Found to Have Benefit from Allogeneic Hematopoietic Stem Cell Transplant (HCT)

Introduction: Acute myeloid leukemia (AML) with myelodysplasia-related gene mutations is a new disease entity introduced in the International Consensus Classification of Myeloid Neoplasms 2022 (ICC 2022). Myelodysplasia-related gene mutations include ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1, or ZRSR2 . Allogeneic hematopoietic stem cell transplant (HCT) represents a curative option for subgroups of AML patients, but not for all. In a prior study (Song et al.) reported the survival benefit of allogeneic HCT in 59 patients with AML with secondary type mutations (STM) including SRSF2, SF3B1, U2AF1, ZRSR2, ASXL1, EZH2, BCOR, and STAG2. Allogeneic HCT could abrogate adverse prognosis in AML with STMs, and reduce its mortality risk by 58% (Song et al. BMT 2022). In the present study, we aim to evaluate the frequency of this new disease entity of AML with MDS-related mutations and evaluate the prognostic impact of allogeneic HCT in patients with MDS-related mutations achieving CR1. For comparison of the benefit from HCT, the mantel-Byar test was applied to take into account time-dependent covariate of HCT in CR1 to avoid immortal bias. Patients and Methods: We conducted a retrospective study that included 1,228 adult patients who were diagnosed with AML from January 1997 to January 2020and achieved CR1 in 5 centers (Toronto, Vancouver, and Montreal, Canada; Hwasun and Seoul, South Korea). Next-generation sequencing was performed as their standard clinical practice using targeted sequencing panel in each institution. As defined in ICC 2022, AML with myelodysplasia-related gene mutations was defined as the case of AML with ASXL1, BCOR, EZH2, RUNX1, SF3B1, SRSF2, STAG2, U2AF1, or ZRSR2 mutation(s). We considered allogeneic HCT in CR1 as a time-dependent covariate and used a Mantel-Byar test to avoid immortal bias. We identified 278 pts (22.6%) who had at least one MDS-related gene mutation at diagnosis. Relapse-free survival (RFS) at 2 years 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: The median follow-up duration among survivors after achieving CR1 was 16.5 months (mo) (Range: 1.3-217.9 mo). Between the HCT vs non-HCT group, there were no differences in sex, cytogenetic risk or other somatic mutation except NPM1 mutation which was more frequently detected in non-HCT group (p <0.001). As expected, younger pts were more frequently noted in HCT group, p=0.001). First, considering HCT as non-time dependent covariate, we have compared RFS and OS between HCT vs non-HCT groups. The 1 year RFS rate was superior in the HCT group (77.7%) to that in non-HCT group (49.9%, p<0.0001; Fig.1A). A similar trend was noted for the 1-year OS rate presenting higher OS rate in the HCT group (83.8%) than in the non-HCT group (72.7%, p=0.0003). Next, when HCT in CR1 was taken into account as a time-dependent (td) covariate, Mantel-Byar analysis showed a consistent finding of superior RFS in HCT group to non-HCT group: time dependent covariate of HCT in CR1 was found to be favorable (Hazard ratio [(HR) of 0.45, (95% C.I. [0.31-0.65]; p=0.00003)] as shown in Fig.1B which is a Simon-Makuch plot. In multivariate analysis (MVA) for RFS, time-dependent covariate of HCT in CR1 retained its statistical significance, thus concluding that HCT in CR1 is an independent prognostic factor for RFS (HR: 0.44, 95% CI [0.29-0.68], p =0.0002) together with other variables found to be adverse on RFS including monosomal karyotype (p=0.03), IDH1 mutation (p=0.01), and age > 60 years (p=0.002); while CEBPA (p=0.02) and NPM1 (p=0.049) mutations were found to be favorable on RFS in MVA. Conclusion: In our cohort of 1228 AML patients, we have identified 278 AML patients with myelodysplasia-related gene mutations (22.6%). We have confirmed that allogeneic HCT in CR1 is strongly recommended in a subgroup of AML with myelodysplasia-related gene mutations based on the favorable impact of HCT in CR1 on RFS from the present study. This result supports the urgent referral of this patient group for allogeneic HCT in CR1.

Parallel Genomic Analysis from Paired Bone Marrow and Peripheral Blood Samples of 200 Cytopenic Patients

Background: Analysis of bone marrow is the gold standard in patients with unexplainable cytopenia for diagnosing (or excluding) myelodysplastic neoplasm (MDS). Besides morphology also molecular genetics and cytogenetics are currently assessed from BM as both are required for diagnosis and risk stratification. Substitution of BM analysis with peripheral blood (PB) analysis would be a substantial progress especially in the elderly to allow for a less invasive strategy. Aims: Validate, whether PB reliably reflects molecular and cytogenetic aberrations of BM by evaluating somatic mutations and copy number variations (CNVs) in concurrent PB and BM samples. Methods: We analyzed paired BM and PB samples (time difference of sampling: <15 days) of 200 cytopenic patients. All samples were subjected to targeted panel sequencing analyzing mutations (assessed as positive at variant allelic frequencies/VAFs >1%) in 40 genes associated with myeloid neoplasms (coverage: 1500x). If available, BM chromosome analysis (CA) and BM FISH analysis were compared to NGS CNV analysis from PB using a human CNV backbone hybridization panel (coverage: 50x). Results: In 69 patients (35%) no mutations (MUTs) were detected in either BM or PB (Figure 1A). For the remaining 131 patients at least one MUT was found in BM (median MUTs/patient: 2; range 1-10). In 130/131 patients MUTs were detected in both BM and PB (same number of MUTs: n=121; higher number of MUTs in BM than in PB: n=9) while in only one patient harboring a DNMT3A MUT as the sole MUT in BM (VAF: 9%) no MUT was detected in PB. This resulted in a negative predictive value of 98.6% (69/70). Overall, we detected 364 MUTs in 29 of the analyzed genes (BM MUTs: n=362; PB MUTs: n=349) and a concordance between BM and PB of 95% (347/364; Figure 1A). The median VAF was lower in PB compared to BM across all MUTs (median VAF: 20% vs. 12%; p<0.001). All MUTs detected in BM at VAF ≥13% (n=229) were also detected in corresponding PB. Next, we compared CNVs detected by PB NGS to BM karyotype (KT). For 119/200 patients PB NGS including a CNV-backbone panel was available. BM CA revealed a normal KT in 71 and an aberrant KT in 48 patients. In total, 126 aberrations were detected in BM CA including 7 balanced aberrations that can technically not be detected using the CNV backbone panel. CNV analysis from PB revealed 68 aberrations (of 119 detectable BM CNVs; 54%) with 64 being concordant with BM CA. In total, in 88/119 patients (74%) concordant results were found in BM and PB (70/71 with normal and 18/48 with aberrant BM KT). In 3 patients (2.5%) different CNVs were detected (1/3: no CNV in BM CA), while in 28 (23.5%) either fewer CNVs (n=8; all complex KTs) or no CNVs (n=20) were detected in PB compared to BM. The majority (76%) of BM CNVs not detected by PB NGS with available BM FISH data were small BM clones (clone size ≤30%) and therefore not reliably captured by NGS PB with a technical sensitivity of 30%. Interestingly, 4 of the discordant patients with aberrant BM KT did not harbor any somatic MUT in BM and PB. Regarding the IPSS-R cytogenetic risk group, 95 (80%) patients fell into the same category, while 22 (18%; all with aberrant BM KT) were assigned to a better risk category by NGS PB than based on BM CA data and 2 patients (2%) to a worse risk category by NGS PB (Figure 1B). Conclusion: In cytopenic patients mutations can be reliably detected from PB showing a concordance with BM of individual mutations of 95% and a consistency regarding overall mutation detection between PB and BM in 99.5% of patients. Cytogenetic risk group assignment based on NGS CNV analysis from PB compared to chromosome analysis from BM resulted in the same risk group in 80% of patients. However, to further decrease the number of discrepant cases, the technical limitations (sensitivity, inability to detect balanced CNVs) of the CNV backbone method might be overcome by increasing the sequencing depth and/or using CD34-enriched PB samples and adding probe sets. Alternatively, FISH on PB smears could be used for CNV detection. Overall, our data indicate a high degree of overlap between PB and BM regarding mutational and cytogenetic analysis in patients with unexplained cytopenia and suggest PB as reliable surrogate especially in patients without any genetic aberrations.

The Presence of Somatic Mutations on Specific Pathways Such As Chromatin Modifier, Spliceosome, and Myeloid Transcription Factor at Diagnosis Was Found to Have Benefit from Allogeneic Hematopoietic Stem Cell Transplantation (HCT) in 1,228 Patients with Acute Myeloid Leukemia in First Complete Remission (CR1)

Introduction Allogeneic stem cell transplant (HCT) brings survival benefit to certain subgroups of acute myeloid leukemia (AML) patients, although it may not be suitable for all cases. Decision for HCT referral is based on the ELN risk grouping, which classifies pts into favorable, intermediate, and adverse risk categories. While HCT is recommended for pts in the intermediate and adverse risk, those in the favorable risk are deferred to receive HCT. However, currently, there is a lack of data directly demonstrating benefits of HCT in specific mutation groups. Patients and Method In this retrospective study, out of 1477 newly diagnosed AML pts 1,228 pts achieved CR1 and had undergone baseline next-generation sequencing (NGS) at diagnosis from January 1997 to January 2020. The data were collected from five different centers located in Toronto, Vancouver, and Montreal, Canada, as well as Hwasun and Seoul, South Korea. NGS was performed in each institution with each institution's standard targeted sequencing panel. To assess the effectiveness of HCT, particular attention will be given to the time from achieving complete remission 1 (CR1) to HCT. 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. Gene mutations were grouped into 6 biologic pathways, including DNA methylation, chromatin modifiers, cohesion complex, activated signaling, tumor suppressor, spliceosome, and myeloid transcription factor (TF) mutations. In the multivariate (MVA) analysis, any mutations with a frequency of >5% were included as well as TP53 which has very grave prognosis. The primary objective of this study is to identify specific groups of AML pts who can derive significant benefits from receiving HCT in CR1, treating HCT as a time-dependent (td) covariate in the analysis. Statistical analyses were conducted using EZR version 1.41. Results The median duration of follow-up among survivors after achieving CR1 was 22.6 months (range: 1-217.9 months). Among the 593 pts, who underwent allogeneic HCT in CR1, the HCT group was composed of younger pts, with a median age of 50 years compared to 56 years in the non-HCT group (p < 0.001). Also, there were fewer pts with NPM1 mutation in the HCT group, accounting for 20.7% compared to 32.4% in the non-HCT group (p < 0.001). Apart from these characteristics, the two groups were similar in other parameters. The 2-year overall survival (OS) was higher in the HCT group, at 66.4%, compared to 54.6% in the non-HCT group (p < 0.0001). Similarly, the 2-year RFS was higher in the HCT group, with a rate of 64.8%, compared to 52.1% in the non-HCT group (p =1.82e-15). Furthermore, HCT as a time-dependent covariate was found to be favorable (Hazard ratio [HR] 0.76, 95% C.I. [0.63-0.91]; p=0.003), as demonstrated in the Simon-Makuch plot (p = 0.003). In the MVA, HCT as a time-dependent covariate retained its favorable impact on RFS (HR 0.67, [0.56-0.82]; p<0.0001). The MVA showed several prognostic factors besides HCT such as NPM1 and CEBPA mutations as favorable factors for RFS, being classified under the European Leukemia Network (ELN) favorable risk group. Conversely, FLT3-ITD, DNMT3A, IDH1, KIT, and TP53 mutations, monosomal karyotype, age > 60 years, and white blood count (WBC) at diagnosis > 55,600/mm^3 were associated with worse RFS. In terms of RFS, the greatest benefit of HCT was observed in the pts having mutations in ASXL1 (HR 0.34 [0.15-0.78]), BCOR (HR 0.29 [0.14-0.61]), IDH1/2 (HR 0.62 [0.42-0.92]), and RUNX1 (HR 0.17 [0.08-0.40]) but no significant benefit in those with KRAS (HR 1.59), NRAS (HR 1.21), PTPN11 (HR 1.23), and WT1 (HR 1.30). According to the biological pathway of somatic mutations, the greatest benefit of HCT in terms of RFS was observed in pts with mutations in the chromatin modifier (HR 0.37 [0.22-0.62]), spliceosome (HR 0.32 [0.16-0.65]), and myeloid TF pathway (HR 0.52 [0.34-0.79]). Conclusion Allogeneic HCT exerts a greater benefit on RFS in AML pts with mutations in the chromatin modifier, spliceosome, and myeloid TF pathways. Further study is warranted to replicate this finding.

NKX101, an Allogeneic Off-the-Shelf CAR NK Therapy Targeting NKG2D-Ls, Has Potent In Vitro Cytotoxicity Against Patient-Derived AML Leukemic Stem Cell (LSC) and Non-Leukemic Stem Cell (Non-LSC) Blasts

Introduction Acute myeloid leukemia (AML) is a malignancy of immature myeloid cells characterized by rapid proliferation of abnormal myeloblasts. Treatment options for patients with AML are limited, especially for relapsed/refractory (r/r) disease. Leukemic cells with stem cell features, known as leukemic stem cells (LSCs), have been implicated as the origin of relapse in minimal residual disease positive (MRD +) AML (Khaldoyanidi et al. 2022, Kamel et al. 2022). Additionally, absence of NKG2D-ligand (NKG2D-L) expression has been reported to be associated with stemness and the LSC population in AML (Paczulla et. al, 2019). NKX101 is an allogeneic, off-the-shelf, healthy donor-derived chimeric antigen receptor (CAR) NK cell therapy candidate engineered to express an NKG2D-L targeting CAR as well membrane bound IL-15. In a clinical trial, NKX101 has shown promise for the treatment of r/r AML, including generating complete responses (CR) with MRD negativity (MRD -). In this study, we utilize a flow cytometry-based approach to (i) evaluate NKG2D-L cell surface expression on normal hematopoietic cells vs. primary AML blasts, (ii) assess the expression pattern of NKG2D-Ls on AML blast subsets, and (iii) determine the potency of NKX101 cytotoxic killing of both LSC and non-LSC AML blasts. Methods NKX101 cells were generated from peripheral blood leukopaks from healthy donors. Cryopreserved bone marrow mononuclear cells (BMMCs) were obtained from AML patients in accordance with approved IRB protocols (n=20). BMMCs from healthy donors were used as controls (n=10). AML somatic mutation status was determined using an Illumina TruSight® Myeloid targeted sequencing panel. NKX101 cytotoxicity against patient derived AML blasts was assessed using a flow cytometry-based assay that simultaneously measured specific cytotoxicity AML blast/LSC markers. NKG2D-L protein expression on LSC and non-LSC subsets was determined using flow cytometry with fluorescently labeled monoclonal antibodies specific to MICA, MICB, and ULBP1-6. Results Utilizing patient-derived primary samples, we demonstrate that NKG2D-Ls are expressed on AML blast cells and expressed at higher levels on AML blast cells compared to healthy normal hematopoietic cells (p = 0.002). Furthermore, we show that NKG2D-Ls are expressed at similar levels on both LSC and non-LSC AML blast populations. Target cell specific flow cytometry-based cytotoxicity assays revealed that NKX101 cells potently kill patient-derived AML blasts in a dose-dependent manner. Moreover, NKX101 cells had similar cytotoxic potency on both LSC and non-LSC AML blasts subsets. Conclusions In summary, we show that NKG2D-Ls are expressed on the surface of AML blasts at levels above those observed in normal hematopoietic cells. NKG2D-Ls are expressed on both non-LSC AML blasts and on the LSC population implicated as the origin of relapse in AML. Additionally, the ability of NKX101 to potently kill AML LSC blasts suggests that NKG2D-L targeting may be a viable mechanism for eliminating LSC in the blood and bone marrow of patients with r/r AML. Taken together, these data support NKG2D-Ls as promising therapeutic targets for AML and support further investigation of NKX101 CAR NK cell therapy for the treatment of r/r AML.

The Genomic and Transcriptomic Landscape of Myeloid Sarcoma and Associated Acute Myeloid Leukemia

Background: Myeloid sarcoma (MS) is a distinct form of acute myeloid leukemia (AML) found in ~10% of patients, in which mass-forming myeloid blasts proliferate in extramedullary sites. MS may present as an isolated lesion as the primary manifestation of disease, co-occur with AML, or, more commonly, arise in the setting of AML relapse. It is associated with poor outcomes, and treatment options are sparse. While increased knowledge of AML and its biology have improved the care and survival of AML patients, those with MS continue to have limited successful treatment options, as MS has typically not been included in AML genetic and genomic profiling efforts, and patients are excluded from clinical trials. Leukemia cutis (LC) is a form of extramedullary AML characterized by cutaneous involvement, often with an infiltrative and non-mass forming pattern of growth. Still, historically the literature has not made a clear distinction between MS and LC. Although recent small pilot studies have suggested differences in AML-associated mutations between medullary AML and MS, knowledge of the complete molecular and cellular composition of MS and comprehensive comparison with AML is lacking. While molecular characterization of the extramedullary disease site is encouraged in the updated clinical recommendations, no definitive guidance exists for changes in the management and care of AML patients with MS, given the substantial gap in our current knowledge and understanding of extramedullary AML. Methods: Here, we performed RNA-Seq (n=96), single-cell (sc) RNA-Seq (n=33), and mutation profiling using either whole exome sequencing (WES, n=6) or a 409-gene targeted sequencing panel (n=48) of MS or LC patient samples and bone marrow (BM) aspirates from AML patients with and without extramedullary disease to present the first comprehensive characterization of MS and LC. Results: Our WES data showed thatMS and LC evolve independently in the extramedullary site from concurrent medullary disease with distinct dominant clones, characterized by higher median tumor mutation burden (1.66 vs. 064 mutations per megabase, respectively; p=0.0059) and increased copy number aberrations, which both validated in an MS Tet2 HR mouse model. Notably, we observed location-specific molecular evolution in patients with multiple concurrent MS sites (Figure 1A) and patients with recurring MS in WES and targeted panel data. While targetable mutations (i.e., IDH1/2 mutations and FLT3-ITD/TKD) occur, the inter-site variability of molecular aberrations may explain the short-lived responses of AML patients with MS to IDH/FLT3 inhibitors. Transcriptional profile differences between MS and associated medullary disease included up-regulation of extracellular matrix organization and cell-substrate adhesion and down-regulation of inflammatory response pathways in both bulk and scRNA-seq data (Figure 1B). Further, involved BM malignant cells of MS patients compared to patients without MS up-regulated specific pathways, including interferon-gamma response observed in both bulk and scRNA-seq, as well as chromatin organization and splicing. We further revealed that MS patients without overt BM involvement show remodeling of the BM immune microenvironment, with increased fractions of hematopoietic stem and progenitor cells that down-regulate HLA class II genes. Comparing LC and MS in the skin revealed distinct differences in their expression profiles, including high expression of genes involved in cell migration and immune response in LC, suggesting LC and MS represent distinct disease entities. Lastly, we demonstrated high expression of BCL2 in extramedullary disease (p=0.0074) and presented initial evidence that treatment with BH3-mimetics may be beneficial for the treatment of isolated MS. Conclusions: Myeloid sarcoma shows distinct molecular evolution and microenvironmental composition compared to medullary disease, including location-specific evolution necessitating personalized management consideration. Leukemia cutis is distinct from MS tumorous lesions and should be considered a separate entity. High BCL2 expression in extramedullary disease might represent a promising targetable vulnerability in patients with isolated MS.

Targeted NGS Panel Guides Risk-Adapted Treatment Intention in Newly Diagnosed Myeloma Patients

Introduction While overall survival has improved, patients with high-risk multiple myeloma (MM) have poor outcomes. Fluorescent in situ hybridisation (FISH) is widely used to identify high-risk genomic features at diagnosis, but a significant minority of patients classified with standard-risk disease progress rapidly and in retrospect may have warranted more intense frontline therapy. Recently, we implemented the Myeloma Genome Project Panel (MGPP) into clinical workflows - a myeloma-specific targeted sequencing panel capturing 228 genes, 6 translocation regions and 56 copy number abnormalities (CNAs) in a single assay [PMID: 35522533]. Given that MGPP captures many prognostic regions beyond the limited number assessed by FISH, there is potential to better identify high-risk patients. However, the utility of MGPP in supporting clinical risk designation and therapy choice when compared with FISH in newly diagnosed MM is unknown. Methods A prospective cohort study was conducted to compare the impact of MGPP vs. FISH on baseline risk stratification and treatment intention, in 55 unselected newly diagnosed MM patients. For MGPP, libraries were generated from 100ng DNA from bone marrow (BM) derived CD138 + MM cells and matched germline peripheral blood (Roche KAPA HyperCap Target Enrichment/Hyperplus kit). Reads were aligned to hg38, and somatic mutations, CNAs and translocations called with a custom pipeline. ISO-accredited FISH analysis was performed in NHS laboratories. In a multicentre multidisciplinary team (MDT) meeting, four blinded haematologists independently reviewed each clinical case presented twice with either FISH or MGPP, in a random order. Clinicians designated risk status and treatment intentions using a structured proforma. Therapeutically actionable variants could be selected as per the MyDRUG trial [ClinicalTrials.gov: NCT03732703]. A consensus MDT outcome for high-risk or more intensive therapy required at least 3 out of 4 concordant decisions. Results Data is presented here for 23 of 55 patients. The mean age was 68.9 years, 57% were transplant eligible, with R-ISS-1 (35%), R-ISS-2 (26%) and R-ISS-3 (39%). Firstly, MGPP had greater technical success than FISH, reporting successfully in 100% vs. 83% cases from the same diagnostic BM samples respectively (n=4 assay failures with FISH). Secondly, MGPP reported more genomic features than FISH, detecting 231 vs. 18 somatic variants at 127 vs. 7 regions, respectively. Thirdly, MGPP captured equivalent loci at greater resolution, detecting subclonal CNAs missed by FISH (Figure 1). In a head-to-head comparison with FISH, these additional genomic insights from MGPP influenced clinical treatment decisions. A clinician-led MDT reclassified 9 (39%) patients designated as standard-risk by FISH to high-risk status when presented with MGPP (Table 1). Reclassified patients were enriched for prognostically significant MYC translocations (17%) and subclonal 17p loss (22%), 1p loss (17%) and 1q gain (13%) CNAs that were missed by FISH. Altered risk designation influenced frontline treatment intention; clinicians opted for intensification of induction therapy in 13% (FISH) vs. 48% (MGPP) high-risk patients, and considered tandem autologous transplant as an option in 0% (FISH) vs. 23% (MGPP) transplant-eligible patients. FISH identified a therapeutically actionable variant in 3 (13%) patients [venetoclax, n=3]. MGPP identified 13 (57%) additional patients with opportunity for targeted therapy [MEK inhibitor, n=11; BRAF V600E inhibitor, n=2], which the MDT considered as a treatment option in all cases if available in trial. The full dataset and analysis will be presented at time of the conference. Conclusions We demonstrate that MGPP impacts clinical risk designation and treatment intention in newly diagnosed MM. MGPP had greater technical assay success than FISH and captured a greater range and depth of somatic variants. Importantly, these additional insights led a clinical MDT to reclassify 39% patients as high-risk, consider intensification regimen in 39% cases and potential for actionable targeted therapy in 57% patients. Our results support MGPP as a robust alternative to FISH in supporting risk-adapted treatment decisions. We will implement MGPP in additional large prospective cohorts over the next year, to better understand its prognostic utility and feasibility in routine clinical workflows.

Residual circulating tumor DNA after adjuvant chemotherapy effectively predicts recurrence of stage II-III gastric cancer.

Circulating tumor DNA (ctDNA) is a promising biomarker for predicting relapse in multiple solid cancers. However, the predictive value of ctDNA for disease recurrence remains indefinite in locoregional gastric cancer (GC). Here, we aimed to evaluate the predictive value of ctDNA in this context. From 2016 to 2019, 100 patients with stage II/III resectable GC were recruited in this prospective cohort study (NCT02887612). Primary tumors were collected during surgical resection, and plasma samples were collected perioperatively and within 3 months after adjuvant chemotherapy (ACT). Somatic variants were captured via a targeted sequencing panel of 425 cancer-related genes. The plasma was defined as ctDNA-positive only if one or more variants detected in the plasma were presented in at least 2% of the primary tumors. Compared with ctDNA-negative patients, patients with positive postoperative ctDNA had moderately higher risk of recurrence [hazard ratio (HR) = 2.74, 95% confidence interval (CI) = 1.37-5.48; P = 0.003], while patients with positive post-ACT ctDNA showed remarkably higher risk (HR = 14.99, 95% CI = 3.08-72.96; P < 0.001). Multivariate analyses indicated that both postoperative and post-ACT ctDNA positivity were independent predictors of recurrence-free survival (RFS). Moreover, post-ACT ctDNA achieved better predictive performance (sensitivity, 77.8%; specificity, 90.6%) than both postoperative ctDNA and serial cancer antigen. A comprehensive model incorporating ctDNA for recurrence risk prediction showed a higher C-index (0.78; 95% CI = 0.71-0.84) than the model without ctDNA (0.71; 95% CI = 0.64-0.79; P = 0.009). Residual ctDNA after ACT effectively predicts high recurrence risk in stage II/III GC, and the combination of tissue-based and circulating tumor features could achieve better risk prediction.

STS and PUDP Deletion Identified by Targeted Panel Sequencing with CNV Analysis in X-Linked Ichthyosis: A Case Report and Literature Review.

X-linked recessive ichthyosis (XLI) is clinically characterized by dark brown, widespread dryness with polygonal scales. We describe the identification of STS and PUDP deletions using targeted panel sequencing combined with copy-number variation (CNV) analysis in XLI. A 9-month-old infant was admitted for genetic counseling. Since the second day after birth, the infant's skin tended to be dry and polygonal scales had accumulated over the abdomen and upper extremities. The infant's maternal uncle and brother (who had also exhibited similar skin symptoms from birth) presented with polygonal scales on their trunks. CNV analysis revealed a hemizygous deletion spanning 719.3 Kb on chromosome Xp22 (chrX:7,108,996-7,828,312), which included a segment of the STS gene and exhibited a Z ratio of -2 in the proband. Multiplex ligation-dependent probe amplification (MLPA) confirmed this interstitial Xp22.31 deletion. Our report underscores the importance of implementing CNV screening techniques, including sequencing data analysis and gene dosage assays such as MLPA, to detect substantial deletions that encompass the STS gene region of Xq22 in individuals suspected of having XLI.

Circulating tumor DNA-based copy-number profiles enable monitoring treatment effects during therapy in high-grade serous carcinoma

Circulating tumor DNA (ctDNA) analysis has emerged as a promising tool for detecting and profiling longitudinal genomics changes in cancer. While copy-number alterations (CNAs) play a major role in cancers, treatment effect monitoring using copy-number profiles has received limited attention as compared to mutations. A major reason for this is the insensitivity of CNA analysis for the real-life tumor-fraction ctDNA samples. We performed copy-number analysis on 152 plasma samples obtained from 29 patients with high-grade serous ovarian cancer (HGSC) using a sequencing panel targeting over 500 genes. Twenty-one patients had temporally matched tissue and plasma sample pairs, which enabled assessing concordance with tissues sequenced with the same panel or whole-genome sequencing and to evaluate sensitivity. Our approach could detect concordant CNA profiles in most plasma samples with as low as 5% tumor content and highly amplified regions in samples with ∼1% of tumor content. Longitudinal profiles showed changes in the CNA profiles in seven out of 11 patients with high tumor-content plasma samples at relapse. These changes included focal acquired or lost copy-numbers, even though most of the genome remained stable. Two patients displayed major copy-number profile changes during therapy. Our analysis revealed ctDNA-detectable subclonal selection resulting from both surgical operations and chemotherapy. Overall, longitudinal ctDNA data showed acquired and diminished CNAs at relapse when compared to pre-treatment samples. These results highlight the importance of genomic profiling during treatment as well as underline the usability of ctDNA.

THU191 Update On The Etiological Diagnosis Of Central Precocious Puberty In Both Sexes

Abstract Disclosure: A.P. Canton: None. A. Latronico: None. L.R. Montenegro: None. C.E. Seraphim: None. F.R. Tinano: None. A.G. de Faria: None. B.B. Mendonca: None. V.N. Brito: None. Background: The etiological investigation of central precocious puberty (CPP) has improved with more precise clinical approach, neuroimaging, and genetic studies. CPP can be caused by congenital or acquired conditions, with or without central nervous system (CNS) lesions. More recently, genetic and epigenetic disorders have been identified in children with CPP, previously classified as idiopathic. Objective: To update the etiological diagnosis of a large cohort of children with CPP. Methods: We evaluated retrospectively the distinct etiologies of 292 patients (264 girls) followed in a single university hospital from 2000 to 2022. Among them, 182 patients with CPP without CNS lesions were investigated with genetic/epigenetic studies. We performed Sanger DNA sequencing (n=155), target panel sequencing (n=64), exome sequencing (n=64), genome sequencing (n=5), specific DNA methylation analysis (n=111), and genomic microarray (n=30). Results: Pathological CNS lesions were identified in 51of 292 (17.5%) patients with CPP (17 boys and 34 girls), indicating a prevalence of CNS lesions of 60.7% in boys and 12.9% in girls. These pathological CNS lesions were classified as congenital (n=34) or acquired (n=17). The most common congenital causes were hypothalamic hamartoma (n=20, 11 girls), myelomeningocele (n=4), and neurofibromatosis type 1 (n=2), while the most common acquired causes were hydrocephalus (n=8) and cerebral palsy (n=3). The remaining 241 (82.5%) CPP patients presented without CNS lesions, being classified as apparently idiopathic. In the subset of patients submitted to genetic/epigenetic investigation (n=182; 173 girls, 9 boys), the overall frequency of genetic/epigenetic causes was 12.1% (20 girls, 2 boys); and it was higher in boys (22.2%) than in girls (11.5%). The genetic/epigenetic defects were MKRN3 inactivating mutations (n=8, from 7 families), DLK1 inactivating mutations (n=6, from 2 families), KISS1R activating mutation (n=1), KISS1 activating mutation (n=1), MECP2 mutations (n=2), DDX3X mutation (n=1), and Temple syndrome (n=3). Univariate logistic regression analysis identified positive family history (OR 3.43; 95%CI 1.35-8.69; p=0.009) and associated neurodevelopmental abnormalities (OR 3.53; 95%CI 0.99-12.48; p=0.05) as possible clinical predictors of congenital CPP in patients without CNS lesions. Conclusion: The prevalence of pathological CNS lesions was 17.5%, confirming previous data. Genetic or epigenetic defects were identified in 12.1% of patients with CPP without CNS lesions, and family history and neurodevelopmental abnormalities were predictors of these congenital causes. Our findings evidenced the growing role of congenital causes among children with CPP without CNS lesions. Presentation: Thursday, June 15, 2023

Radiation in a New Era of Multiple Myeloma Management: Patterns of Utilization, Clinical, Radiologic, and Biochemical Outcomes, and Possible Genomic Correlates of Response

Systemic therapies for multiple myeloma (MM) have advanced considerably, improving patient outcomes. 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 utilization, outcomes, and impact of RT on radiographic and biochemical markers, with genomic characterization for more recently treated patients. Five hundred six pathologically confirmed MM patients who received RT to 1190 sites between January 1, 2000, and June 1, 2022, were identified. Patient, disease, and treatment characteristics were analyzed for 50 consecutive patients treated in 2019 and tested for association with 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. Amongthe 50 patients analyzed (median 63 years), 90 lesions were treated with RT, 33% with concurrent systemic therapy, to 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 >9 lesions on imaging, 47% involving both medullary and extramedullary sites. With 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. Absolute decreases 1-week to 1-month post-RT were observed in % of marrow plasma cell (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%). In this pilot analysis of a sampling cohort of RT-treated MM, we report on patterns of utilization, outcomes, and biochemical and radiographic correlates. At the meeting, we will present the full analysis of the >500 MM patients and further analyze emerging genomic data. 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.

B-149 Next-generation Sequencing Via Targeted Metagenomics for Broad Antimicrobial Resistance Surveillance

Abstract Background Antimicrobial-resistant infections secondary to the overuse of antibiotics are a major public health threat. The standard of care for identifying resistance is antimicrobial susceptibility testing, the phenotypic characterization of minimum inhibitory concentrations (mic) for antibiotics in the presence of bacterial growth, but these methods are labor intensive, have long turnaround times, and face challenges with non-cultivable bacteria. Molecular methods for antimicrobial resistance (AMR) ascertainment are high-throughput, robust, and sensitive and have gained interest as a genotypic complement to traditional phenotypic methods. Since the COVID-19 pandemic, next-generation sequencing has emerged as the leading technology for tracking and surveillance of infectious diseases and antimicrobial resistance, emphasizing the need for flexible sequencing panels that are easily interchangeable and capable of detecting pathogens and AMR genes. Methods In a collaboration between Illumina, a national retail pharmacy, and Aegis Sciences Corporation, residual, self-collected nasal swab samples (n = 4390) submitted for COVID-19 testing from patients across the U.S. were sequenced using the Respiratory Pathogen ID/AMR Panel (RPIP, Illumina – For Research Use Only), a target capture-based next-generation sequencing panel targeting 282 respiratory pathogens and 2097 relevant AMR markers. Sequencing data was analyzed using the Explify RPIP Analysis app (BaseSpace, Illumina) and paired with self-reported patient data submitted via an online questionnaire. Data including pathogens and anti-microbial resistance (AMR) genes detected, age, race, gender, residing state of the patient, collection month, self-reported symptoms, and health risks were collated, imported into Microsoft PowerBI software, and used to create interactive visuals for a surveillance dashboard. Results In this cohort of sequenced specimens, 85.1% (n = 3576) had one or more viral, bacterial, or fungal pathogens present, 41% (n = 1816) had one or more AMR genes present, and 38.4% (n = 1685) had one or more pathogens and AMR genes co-detected. Twenty-six different AMR genes were identified with the most prevalent being Erm 23S ribosomal RNA methyltransferase (65.5%; n = 1115). Erm was identified in samples from all 50 US states and was co-detected with staphylococcus aureus (18.2%; n = 216) and streptococcus pneumoniae (4.9%; n = 57), among others. Following Erm in prevalence, this cohort of samples harbored genes for trimethoprim resistant dihydrofolate reductase (dfr = 27.9%), tetracycline-resistant ribosomal protection protein (tet = 21.0%), and macrolide phosphotransferase (MPH = 14.2%). The data also revealed AMR gene-pathogen co-detections listed as CDC serious threats, such as the mecA gene responsible for methicillin resistance in staphylococcal species. The mecA gene was co-detected in 5.3% (n = 28) of staphylococcus aureus positive samples in this cohort. Finally, although not classified as a serious threat, neuraminidase inhibitor resistance, associated with less susceptibility to anti-virals, was found in 12% (n = 15) of all influenza A (H3N2) infected samples (n = 112). Conclusions Completion of these studies demonstrated that next-generation sequencing using targeted metagenomics with RPIP is a cost effective, high-throughput option for large-scale surveillance of AMR genes in potential respiratory infections.

Identification of genomic alterations with clinical impact in canine splenic hemangiosarcoma.

Canine hemangiosarcoma (HSA) is an aggressive cancer of endothelial cells with short survival times. Understanding the genomic landscape of HSA may aid in developing therapeutic strategies for dogs and may also inform therapies for the rare and aggressive human cancer angiosarcoma. The objectives of this study were to build a framework for leveraging real-world genomic and clinical data that could provide the foundation for precision medicine in veterinary oncology,andto determine the relationships between genomic and clinical features in canine splenic HSA. One hundred and nine dogs with primary splenic HSA treated by splenectomy that had tumour sequencing via the FidoCure® Precision Medicine Platform targeted sequencing panel were enrolled. Patient signalment, weight, metastasis at diagnosis and overall survival time were retrospectively evaluated. The incidence of genomic alterations in individual genes and their relationship to patient variables including outcome were assessed. Somatic mutations in TP53 (n = 44), NRAS (n = 20) and PIK3CA (n = 19) were most common. Survival was associated with presence of metastases at diagnosis and germline variants in SETD2 and NOTCH1. Age at diagnosis was associated with somatic NRAS mutations and breed. TP53 and PIK3CA somatic mutations were found in larger dogs, while germline SETD2 variants were found in smaller dogs. We identified both somatic mutations and germline variants associated with clinical variables including age, breed and overall survival. These genetic changes may be useful prognostic factors and provide insight into the genomic landscape of hemangiosarcoma.

Firalink: A bioinformatics pipeline for long non-coding RNA data analysis

SummaryThe Firalink bioinformatics pipeline has been developed to analyse long non-coding RNA (lncRNA) data generated by targeted sequencing. This pipeline has been first implemented for use with the FIMICS panel containing 2906 lncRNAs useful for investigations in cardiovascular disease. It has been subsequently tested and validated using a panel of lncRNAs targeting brain disease. The pipeline can be adapted to other targeted sequencing panels or other transcriptomics data (e.g. whole transcriptome) through a change of the reference genome/panel. Therefore, Firalink can be applied to different lncRNA panels and transcriptomics data targeting multiple diseases. Availability and implementationThe Firalink pipeline works on Linux and is freely available to non-commercial users at https://gitlab.lcsb.uni.lu/covirna/covirna-ext/covirna-firalink-pipeline. Access will be granted after contacting bioinformatics@firalis.com. The pipeline is implemented with the Nextflow workflow manager using Python and R scripts. It will remain available for at least two years following publication and will be regularly updated and upgraded. Supplementary informationFor an example of the application of the Firalink pipeline using the FIMICS panel, see www.covirna.eu.

Novel pathogenic PDX1 gene variant in a Korean family with maturity-onset diabetes of the young.

The diagnosis of maturity-onset diabetes of the young (MODY), a monogenic form of diabetes mellitus caused by a mutation in a single gene, is often uncertain until genetic testing is performed. We report a 13-yr-old Korean boy who was initially diagnosed with type 2 diabetes (T2DM). MODY was suspected because of his nonobese body habitus and family history of multiple affected members. Targeted panel sequencing of all MODY-related genes was performed using the NextSeq 550Dx platform (Illumina). Sanger sequencing was performed using blood samples from the parents, siblings, and other relatives. A frameshift variant in the 3' region of the last exon of PDX1 was detected in the patient and his family members with diabetes. PP1_Moderate criterion was applied and this variant was confirmed to be the genetic cause of diabetes in the family and classified as likely pathogenic. The study highlights the importance of genetic testing for nonobese, early-onset diabetic patients with multiple affected family members. Increased awareness and aggressive genetic testing for MODY are needed.