Cytogenetic Information Research Articles

Accurate identification of locally aneuploid cells by incorporating cytogenetic information in single cell data analysis

Single-cell RNA sequencing is a powerful tool to investigate the cellular makeup of tumor samples. However, due to the sparse data and the complex tumor microenvironment, it can be challenging to identify neoplastic cells that play important roles in tumor growth and disease progression. This is especially relevant for blood cancers, where neoplastic cells may be highly similar to normal cells. To address this challenge, we have developed partCNV and partCNVH, two methods for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. PartCNV uses an expectation-maximization (EM) algorithm with mixtures of Poisson distributions and incorporates cytogenetic information to guide the classification. PartCNVH further improves partCNV by integrating a hidden Markov model for feature selection. We have thoroughly evaluated the performance of partCNV and partCNVH through simulation studies and real data analysis using three scRNA-seq datasets from blood cancer patients. Our results show that partCNV and partCNVH have favorable accuracy and provide more interpretable results compared to existing methods. In the real data analysis, we have identified multiple biological processes involved in the oncogenesis of myelodysplastic syndromes and acute myeloid leukemia.

Comparative Analysis of Two NGS-Based Platforms for Product-of-Conception Karyotyping.

Cytogenetic information about the product of conception (POC) is important to determine the presence of recurrent chromosomal abnormalities that are an indication for preimplantation genetic testing for aneuploidy or structural rearrangements. Although microscopic examination by G-staining has long been used for such an evaluation, detection failures are relatively common with this method, due to cell-culture-related issues. The utility of low-coverage whole-genome sequencing (lcWGS) using short-read next-generation sequencing (NGS) has been highlighted recently as an alternative cytogenomic approach for POC analysis. We, here, performed comparative analysis of two NGS-based protocols for this purpose based on different short-read sequencers (the Illumina VeriSeq system using a MiSeq sequencer and the Thermo Fisher ReproSeq system using an Ion S5 sequencer). The cytogenomic diagnosis obtained with each NGS method was equivalent in each of 20 POC samples analyzed. Notably, X chromosome sequence reads were reduced in some female samples with both systems. The possibility of low-level mosaicism for monosomy X as an explanation for this was excluded by FISH analysis. Additional data from samples with various degrees of X chromosome aneuploidy suggested that it was a technical artifact related to X chromosome inactivation. Indeed, subsequent nanopore sequencing indicated that the DNA in the samples showing the artifact was predominantly unmethylated. Our current findings indicate that although X chromosome data must be interpreted with caution, both the systems we tested for NGS-based lcWGS are useful alternatives for the karyotyping of POC samples.

Chromosome-specific painting reveals the Y genome origin and chromosome rearrangements of the St genome in Triticeae.

Karyotypes provide key cytogenetic information on phylogenetic relationships and evolutionary origins in related plant species. The St genome of Pseudoroegneria contributes to eight alloploid genera, representing over half of the species that are highly valuable for wheat (Triticum aestivum) breeding and for understanding Triticeae species evolution. However, St chromosome characterization is challenging due to limited cytogenetic markers and DNA information. We developed a complete set of St genome-specific chromosome painting probes for identification of the individual chromosomes 1St to 7St based on the genome sequences of Pse. libanotica and wheat. We revealed the conservation of St chromosomes in St-containing species by chromosome painting, including Pseudoroegneria, Roegneria, Elymus, and Campeiostachys. Notably, the Y genome showed hybridization signals, albeit weaker than those of the St genome. The awnless species harboring the Y genome exhibited more intense hybridization signals compare to the awned species in Roegneria and Campeiostachys, yet weaker than the hybridization signals of the St genome in autotetraploid Pse. strigosa. Although awnless species were morphologically more similar to each other, phenotypic divergence progressively increased from awnless to awned species. Our results indicate that the Y genome originated from the St genome and shed light on the possible origin of the Roegneria and Campeiostachys species, enhancing our understanding of St-genome-containing species evolution.

Preliminary cytogenetic study of <em style="mso-bidi-font-style: normal;">Ctenopoma kingsleyae</em> from Esa-Odo water reservoir, Osun State, Nigeria

Ctenopoma kingsleyae belongs to the family Anabantidae covers a wide geographic region. It has been morphologically described by a number of authors, yet it is lacking in adequate cytogenetic information, which is a setback to understanding its karyotypic evolution. This study, therefore, describes the karyotype of C. kingsleyae (n = 10) from Esa-Odo, Reservoir, Osun State, Nigeria. Metaphase chromosome spread was obtained from the gills of fish after intraperitoneal injection with 0.05% colchicines. Slides prepared were stained with Giemsa stain, images of metaphase spread were taken digitally and a karyogram was prepared. The study revealed a karyotypic formula of 2n = 48t with uniarmed chromosomes. This study has provided needful information on C. kingsleyae karyotype and will serve as the basis for further study on its evolution, genetic resource management and production.

First Karyotypic Insights into Potamotrygon schroederi Fernández-Yépez, 1958: Association of Different Classes of Repetitive DNA

Introduction: Currently, there are 38 valid species of freshwater stingrays, and these belong to the subfamily Potamotrygoninae. However, cytogenetic information about this group is limited, with studies mainly using classical techniques, Giemsa, and C-banding. Methods: In this study, we used classical and molecular cytogenetic techniques – mapping of 18S and 5S rDNA and simple sequence repeats (SSRs) – in order to investigate the karyotypic composition of Potamotrygon schroederi and reveal the karyoevolutionary trends of this group. Results: The species presented 2n = 66 chromosomes with 18m + 12sm + 16st + 20a, heterochromatic blocks distributed in the centromeric regions of all the chromosomes, and terminal blocks in the q arm of pairs 2 and 3. Mapping of 18S rDNA regions revealed multiple clusters on pairs 2 and 7 and a homolog of pair 24. The 5S rDNA region was found in the pericentromeric portion of the subtelocentric pair 16. Furthermore, dinucleotide SSRs sequences were found in the centromeric and terminal regions of different chromosomal pairs, with preferential accumulation in pair 17. In addition, we identified conspicuous blocks of (GATA)n and (GACA)n sequences colocalized with the 5S rDNA (pair 16). Conclusion: In general, this study corroborates the general trend of a reduction in 2n in the species of Potamotrygoninae subfamily. Moreover, we found that the location of rDNA regions is very similar among Potamotrygon species, and the SSRs accumulation in the second subtelocentric pair (17) seems to be a common trait in this genus.

Comparative cytogenetics of the families Pteromalidae and Spalangiidae – a review

AbstractAlthough chromosomes of only 20 members of Pteromalidae sensu lato (s.l.), which belong to the families Pteromalidae sensu stricto (hence Pteromalidae) and Spalangiidae, are studied up to now, the accumulated cytogenetic information has important implications for taxonomic and evolutionary studies of these parasitoids. Within the former family, which includes the overwhelming majority of karyotypically studied species of Pteromalidae s.l., the known haploid chromosome number (n) can vary from 4 to 7 in Pachycrepoideus vindemmiae (Rondani) and Anisopteromalus calandrae (Howard), respectively, with a clear mode at n = 5. Among these parasitoids, Nasonia vitripennis (Walker) is the most thoroughly studied species in terms of modern cytogenetic techniques. On the contrary, chromosomes of only two members of Spalangiidae are known, both belonging to the Spalangia endius Walker complex, with n = 4 and 6. A few cosmopolitan cryptic species of the family Pteromalidae were studied using cytogenetic approaches. Specifically, Anisopteromalus quinarius Gokhman et Baur, a newly described parasitoid of stored‐product pests with n = 5, was initially separated from A. calandrae based on its different chromosome number. Another pteromalid with a similar biology, Lariophagus distinguendus (Förster), was also found to harbor two cryptic species with n = 5 and 6. Moreover, a morphometric study of these karyotypes suggested that the largest chromosome in the set with n = 5 has resulted from a fusion of two particular chromosomes in the karyotype with n = 6, and this hypothesis was confirmed using microdissection and whole‐chromosome painting. Recent cytogenetic and bioinformatic research also showed that N. vitripennis, Nasonia longicornis Darling, Nasonia giraulti Darling, Nasonia oneida Raychouhury et Desjardins, Muscidifurax uniraptor Kogan et Legner, and Trichomalopsis sarcophagae (Gahan) (all Pteromalidae) share the TTATTGGG telomeric motif with most other Chalcidoidea. Perspectives of the chromosome study of Pteromalidae s.l. are briefly discussed.

Abstract B110: Race/ethnicity, socioeconomic status, and early death among children enrolled in clinical trials for acute lymphoblastic leukemia

Abstract Introduction: Prior work indicates that Hispanic and Black children diagnosed with leukemia may experience a higher risk of death in the period shortly after diagnosis, but no work has examined these disparities taking into account leukemia subtypes and the role socioeconomic status (SES) may play. We investigated reported race/ethnicity (RRE), health insurance status, neighborhood SES, and early death among pediatric acute lymphoblastic leukemia (ALL) patients enrolled on clinical trials. Methods: Using data from the Childhood Cancer Research Network as well as Children’s Oncology Group therapeutic trials, we estimated the associations between RRE (Non-Hispanic [NH] White, NH Black, NH Asian/Pacific Islander [PI], or Hispanic/Native American), health insurance status, neighborhood SES using the Yost Index, and death within 60 days of diagnosis using multivariable logistic regression. All analyses were adjusted for age at diagnosis, sex, and ALL subtype (Standard Risk B-Cell, High Risk B-Cell, Infant ALL, T-Cell). We also estimated associations among non-infant patients diagnosed with B-Cell ALL, additionally adjusting for standard or high-risk disease. All associations were estimated as odds ratios (OR) with 95% confidence intervals (CI). Results: Overall, we analyzed data from 8,634 pediatric ALL cases (7,559 B-Cell; 122 Infant ALL; 953 T-Cell) enrolled across 7 clinical trials (AALL0232, AALL0331, AALL0434, AALL0631, AALL0932, AALL1131, AALL1231). In total, there were 29 deaths within 60 days of diagnosis, including 22 among B-Cell, 4 among infant ALL, and 3 among T-Cell patients. In the full analysis, infant ALL subtype was very strongly associated with early death compared to Standard Risk B-Cell patients (OR: 37.8 [95% CI: 9.22, 137]). We also observed a suggestive association between NH Asian/PI RRE and higher odds of early death compared to NH Whites (OR: 3.10 [95% CI: 0.71, 9.63]), which remained after limiting the analysis to B-Cell patients (OR: 5.63 [95% CI: 1.24, 18.7]). No association was apparent between NH Black or Hispanic/Native American RRE and odds of early death. Neighborhood SES was not significantly associated with early death, though point estimates suggested a potential protective effect of increasing SES. Lack of health insurance was also suggestively associated with greater odds of early death (OR: 2.78 [95% CI: 0.60, 9.47]). Conclusion: Unlike prior work, we observed increased odds of death soon after diagnosis for NH Asian/PI children. Future work incorporating more detailed treatment and cytogenetic subtype information is needed to identify the factors contributing to this disparity. Citation Format: Sarah Lucht, Jeannette M. Sample, Logan Spector, Jenny N. Poynter, Lucie Turcotte, Erin L. Marcotte. Race/ethnicity, socioeconomic status, and early death among children enrolled in clinical trials for acute lymphoblastic leukemia [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr B110.

BRAF-Mutated Acute Myeloid Leukemia (AML) Represents a Distinct, Prognostically Poor Subgroup Enriched in Myelodysplasia-Related (MR-)AML

Background RAS signaling pathway mutations, mainly NRAS, KRAS, and/or PTPN11 variants, are common somatic events in de novo and MR-AML. BRAF mutations occur with lower frequency in AML and are reported to be associated with poor treatment outcome. However, no comprehensive analysis exists that firmly delineates clinical and molecular characteristics of BRAF-mutated AML, including insights into clonal architecture and co-occurring mutations. Methods We identified 42 patients (pts) with BRAF-mutated AML among pts with molecularly profiled disease in the setting of large comprehensive cancer centers [enriched for relapsed/refractory (R/R) and secondary AML] and cooperative group frontline trials (Cancer and Leukemia Group B/Alliance for Clinical Trials in Oncology, enriched for de novo AML). All pts had NGS-based targeted sequencing data, cytogenetic information, and detailed clinical annotations available. To fully evaluate the molecular landscape, 6 pts underwent integrated genomic profiling including paired tumor/normal whole exome sequencing and total transcriptome sequencing. We also analyzed pt samples using simultaneous single-cell molecular profiling and cell surface protein expression (DNA+Protein) sequencing to assess cell states and clonal make-up at single-cell resolution in a subset of pts (n=8). Results The 42 pts with BRAF-mutated AML had a median age of 67 years (range, 19-84); 57% were male. BRAF mutations were most common in cases of MR-AML (as defined by WHO 5th edition), accounting for 32 (76%) pts. BRAF mutations were found in newly diagnosed (n=19, 45%), R/R (n=8, 19%) and secondary AML (n=15, 36%) pts. As detected by bulk NGS sequencing, BRAF mutations were found both as dominant clonal and subclonal events, present at variant allele fractions (VAF) of 1-83% ( Figure 1, BRAF VAF indicated via color scale). Most (n=30, 71%) pts had non-V600 BRAF mutations (including G469, n=12; D594, n=7 and other, n=12). The most frequent co-occurring mutations were in the TET2 (36%), ASXL1 (33%), NRAS (29%), KRAS (26%), RUNX1 (19%), DNMT3A, FLT3-ITD/TKD, NPM1 and SRSF2 (all 17%) genes. By whole exome sequencing, BRAF-mutated AML samples carried a median mutational burden of 15 non-synonymous coding variants (range, 9-30), including 6 RAS-pathway and 3 MR-AML mutations. In 2 pts with paired relapse material available, the BRAF mutation was either stable at relapse or lost and the pt instead acquired a IQGAP3 mutation, supporting the RAS-pathway “addiction” of this leukemia. Single-cell multi-omic sequencing studies uncovering unique genotype-immunophenotype relationships and confirming clonal hierarchies are ongoing and will be presented at the meeting. Clinically, the BRAF-mutated pts had extremely poor survival, regardless of therapy. Pts were treated with low intensity [LI, n=10 (29%); LI+venetoclax (VEN, n=10 (29%)], high-intensity [HI, n=12 (34%) or HI+VEN, n=3 (9%)] regimens. The overall composite remission (CR+CRi) rate was 39%. Median overall survival (OS) for the entire cohort was 7 months, with 31 (89%) of pts deceased at the time of last follow-up. There were no significant differences in OS based on treatment regimens ( Figure 2). Importantly, there was no impact of BRAF variant allele burden on OS, with pts wiith dominant clonal and those with subclonal mutations having similar outcomes. Given the enrichment of BRAF mutations in MR-AML, we assessed whether RAS pathway mutations generally represented poor outcome prognosticators in this subgroup. A comparison of a control cohort of MR-AML pts with (n=129) and without (n=403) RAS pathway mutations treated on cytarabine/daunorubicin-based frontline protocols, revealed no survival difference between RAS-mutated and wild-type pts, suggesting a negative survival impact specific to BRAF-carrying leukemic clones. Conclusions BRAF mutations are rare, but recurrent molecular alterations in AML that are enriched in MR-AML. They associate with distinctly poor prognosis regardless of their clonal burden, without significant therapeutic advantage of currently available treatment regimens. This suggests the need to assess the utility of BRAF inhibitors and/or RAS pathway-targeting regimens such as MEK inhibitors in pts with AML carrying BRAF mutations. Support: U10CA180821, U10CA180882, U24CA196171; Clinicaltrials.gov: NCT00048958 (CALGB 8461), NCT00899223 (CALGB 9665), NCT00900224 (CALGB 20202)

Multi-Hit TP53 Mutations in Myeloid Neoplasms: Prognostic Impact of Morphologic Subtype Designation and Variant Allele Frequency

Background: Biallelic TP53 alterations result from either sequence variations or deletions involving TP53 and are not necessarily synonymous with “multi-hit TP53”. According to the 2022 international consensus classification (ICC) for myeloid neoplasms (MN), multi-hit TP53 signifies i) the presence of two or more distinct TP53 mutations, each with variant allele frequency (VAF) ≥10%, ii) a single TP53 mutation with VAF ≥50%, or iii) a single TP53 mutation with VAF ≥10% accompanied by a cytogenetically-apparent del(17p13.1), copy-neutral loss of heterozygosity (LOH) at the 17p TP53 locus, or, in the absence of LOH information, complex karyotype ( Arber et al. Blood 2022;140: 1200). The current study is focused on MN with multi-hit TP53 and examines the additional prognostic impact of morphologic subtype designation, bone marrow (BM) or peripheral blood (PB) blast percentage, TP53 VAF, and MN with diagnostic qualifiers (i.e., therapy-related, or secondary progressing from myelodysplastic/myeloproliferative/overlap syndromes/neoplasms). Methods : The current study was conducted under an institutional review board approved minimum risk protocol that allowed retrospective collection and analysis of data from Mayo Clinic patient records. Multi-hit TP53 was defined as per ICC criteria as outlined above ( Arber et al. Blood 2022;140: 1200). Morphologic subtype designations of MN were according to ICC criteria and assigned at the time of TP53 detection. NGS and cytogenetic information was available in all study patients. Survival analyses were calculated from time of TP53 mutation detection. Conventional statistical methods were applied using JMP Pro 16.0.0 software (SAS Institute, Cary, NC, USA). Results : Initial screening flagged 143 patients with biallelic TP53 abnormalities derived from formal laboratory reports of NGS data and cytogenetic studies; of these, 130 met ICC criteria for multi-hit TP53: pure erythroid leukemia (PEL; N=24), acute myeloid leukemia (AML)-not PEL (N=54), myelodysplastic syndromes (MDS; N=36), MDS/AML (N=11), and other MN (N=5). Of these 130 informative cases, 128 (98%) harbored complex/monosomal karyotype (CK/MK). Further analysis excluded patients with “other” MN (N=5) and those without CK/MK (N=2), the latter to mitigate the confounding effect of CK/MK on survival and the former because of small sample size and disease heterogeneity. Clinical and laboratory characteristics of the 124 study patients are outlined in table 1. Survival analysis stratified by ICC-defined MN subtypes revealed the prognostic relevance of morphological distinction between PEL vs “AML-not PEL” (p<0.01; HR 2.4) and PEL vs “ TP53-muated MDS/AML” (p=0.02; HR 2.3) while survival was similar between “AML-not PEL” and “ TP53-mutated MDS/AML” (p=0.9; Figure 1a). Survival in “ TP53-mutated MDS” was significantly longer, compared to PEL (p<0.01; HR 0.2), “ TP53-mutated AML-not PEL” (p=0.01; HR 0.5), and “ TP53-mutated MDS/AML” (p=0.07; HR 0.5), the latter with borderline significance (Figure 1a). Multivariable analysis confirmed the independent prognostic relevance of ICC subtype designation (p<0.01) and also revealed additional negative prognostic contribution from advanced age (p=0.02), male gender (p=0.02), MN, secondary (p<0.01), MN, therapy-related (p=0.03), and DNMT3A mutation (p=0.02). Significance was retained in all instances, with the exception of MN, therapy-related (p=0.15), when analysis was repeated after excluding PEL cases (Figure 1b). Conclusions : The current study confirms the prognostic validity of the ICC morphologic subtype designation and TP53 VAF classification threshold, in the context of multi-hit TP53. The study also highlights the prognostic distinction between PEL and “ TP53-mutated AML-not PEL” and the prognostic alignment between the latter and “ TP53-muated MDS/AML”, both of which displayed inferior survival, compared to “ TP53-mutated MDS”. The study also suggests additional prognostic contribution from secondary and therapy-related qualification while the observation regarding DNMT3A mutation requires validation with higher number of informative cases.

Relapsed and Refractory Multiple Myeloma with Pleural Involvement: A Case Series

Introduction. Development of novel treatments and immunotherapeutics continue to improve outcomes in patients with multiple myeloma (MM), especially in those patients with standard and intermediate risk disease; patients with high-risk disease continue to have dismal outcomes. Secondary extramedullary disease (sEMD) is a high-risk disease feature associated with an expected survival less than one year (Zanwar, AJH, 2023). Detailed description of patients presenting with sEMD involving the pleural has not been previously published. In the present project, we aimed to identify and characterize this patient population. Methods. This study was approved by the University of Utah (UU) IRB (#00156207). Inclusion was determined by search of the UU Department of Radiology database for all imaging including PET, CT, and MRI; search terms included pleura, pleural, lung, extramedullary, plasmacytoma, and multiple myeloma. Descriptive analysis was completed and included patient demographics, treatment, and outcomes. Survival was described with Kaplan-Meier analysis. Results. Fourteen patients treated at the UU between 2004 and 2023 were identified as having sEMD and pleural involvement. Demographics are highlighted in Table 1. The median age was 59 (range 34-79), 50% of patients were male, 86% were Caucasian, and 8% were Hispanic. Patients were treated with a median of 2.5 (range 1-9) lines of therapy prior to sEMD development and 6 (range 2-13) in total. 50% of the patients were penta-class refractory. The median follow-up after MM diagnosis was 34.5 months (range 13.0-162.0), median follow-up after pleural EMD diagnosis was 9.0 months (range 0.4-92.0), and the median time to development of pleural EMD following diagnosis was 18.2 months (range 3.8-142.8). At initial diagnosis, half of the patients had > 50% bone marrow clonal plasma cells, 29% had R-ISS stage 3 disease and 36% had R2-ISS stage III/IV. Of the 11 patients with available cytogenetic information at the time of sEMD diagnosis, 73% had high-risk cytogenetics (defined as presence of del(17p), t(4;14), t(14;16) and/or +1q). The most common cytogenetic abnormalities were +1q in 73%, including 36% with 3 copies and 36% with > 4 copies, amp(1q), and del(17p) in 36% . Of these patients, 18% had double hit and 18% had triple hit disease. The most frequent concomitant cytogenetic abnormalities were +1q and del(17p) seen in 36% of the patients. On imaging, 79% had additional sites of EMD other than the pleura. The most frequent other sites of sEMD were skin/soft tissue, intrabdominal extrahepatic, and hepatic. Pleural effusion was present in only one patient. Following diagnosis of sEMD with pleural involvement, the overall response rate (ORR) was 93% and the ORR was 88% in patients with 1q21 abnormalities. In this population, the median OS from diagnosis was 2.5 years (range 1.1-14) and mOS from diagnosis of pleural EMD was 0.64 years (range 0.03-7.7). Conclusion. To the best of our knowledge, this is the largest case series focused on the characterization of patients with sEMD and pleural involvement. The survival results align with those recently presented by Zanwar et al., suggesting that pleural involvement does not portend worse prognosis than EMD in general. We highlight that the majority of patients have 1q21 abnormalities and additional sites of EMD. Ultimately, patients with sEMD and pleural involvement have extremely high-risk disease, are responsive to treatments but have a drastically shortened survival.

Clinical Outcomes and Mutational Profile Associated with Dysmyelopoiesis in Chronic Myelomonocytic Leukemia

Chronic myelomonocytic leukemia (CMML) is defined by absolute (≥ 0.5 x10 9/L) and relative (≥ 10%) monocytosis in peripheral blood. Presence of significant dysplasia in any of the three myeloid series, in particular dysgranulopoiesis, is an almost constant finding in CMML. In the absence of a clonal marker, a scenario very unlikely with the advent of next-generation sequencing (NGS), significant myeloid dysplasia becomes a crucial criterion for establishing the diagnosis. Although bone marrow dysplasia has demonstrated independent prognostic value in MDS, its significance in relation to CMML has never been assessed. The main interest of our work was to evaluate the genomic determinants of dysplasia and to assess its prognostic impact. We analyzed a series of 240 patients with CMML with clinical, morphological, immunophenotypic, cytogenetic and molecular information. Patients were diagnosed following WHO and ICC 2022 recommendations. As a novelty with respect to previous WHO classifications, the new definition of CMML includes those patients previously categorized as oligomonocytic CMML (OM-CMML). That is, myelodysplastic neoplasms (MDS) or unclassifiable myelodysplastic/myeloproliferative neoplasms with relative monocytosis and a monocyte count of 0.5 × 10 9/L to <1 × 10 9/L. A total of 167 (71%) patients were diagnosed with CMML-1 and 67 (29%) with CMML-2. Likewise, 193 (80%) patients were diagnosed with dysplastic CMML, 55 of whom would meet criteria for OM-CMML, and 47 (20%) were diagnosed with proliferative CMML. We assessed associations between dysmyelopoiesis and gene mutations by Spearman's rank correlation coefficient. Dysgranulopoiesis showed a significant positive correlation with NRAS, TET2 and ZRSR2 mutations; while a significant negative correlation with SETBP1 was observed. Dysmegakaryopoiesis showed a significant positive correlation with ASXL1 and TP53. Dyserythropoiesis showed a significant positive correlation with DNMT3A and SF3B1. The heatmap and matrix showing these correlations, as well as the differences in the degree of dysmyelopoiesis among these specific mutations are depicted in Figure 1-A & 1-B. Later, we wanted to assess the prognostic impact of dysgranulopoiesis, dyserythropoiesis and dysmegakaryopoiesis in terms of overall survival (OS) and leukemia-free survival (LFS) in our series. By applying the MaxStat package in R, it allowed us to detect the best cut-off points for dysgranulopoiesis (>75%) and dysmegakaryopoiesis (>20%) to separate our series into two groups with significantly different outcomes (Figure 1-C). We were unable to detect a significant cut-off point for dyserythropoiesis and the presence of multilineage dysplasia also showed no prognostic impact. CMML patients with dysgranulopoiesis above 75% showed a significant shorter median OS (34.4 vs 67.8 months; Hazard Ratio (HR): 1,99 [1.24-3.19]; P=0.0036) and LFS (33.4 vs 66.6 months; HR: 1,87 [1.17-3]; P=0.008). Likewise, patients with dysmegakaryopoiesis above 20% also showed a significant shorter median OS (30.2 vs 67.1 months; HR: 2.52 [1.63-3.88]; P<0.0001) and LFS (30.4 vs 66.6 months; HR: 2.76 [1.78-4.28]; P<0.0001). Remarkably, dysmegakaryopoiesis above 20% and dysgranulopoiesis above 75% were identified as independent prognostic factors for both OS and LFS after adjustment by multivariable Cox regression analyses by CMML-specific prognostic scoring system (CPSS) and Mayo Prognostic Model. Furthermore, the addition of dysmegakaryopoiesis above 20% and dysgranulopoiesis above 75% to these prognostic indices improved their prognostic accuracy in terms of OS as assessed by a C-index for right-censored data (Figure 1-C). In conclusion, our study has allowed us to detect mutations in genes related to dysmyelopoiesis. In addition, both dysgranulopoiesis and dysmegakaryopoiesis have demonstrated a negative prognostic impact on the survival of patients in our series that was not captured by the CPSS and Mayo prognostic model. Their worse prognosis could be partially justified by their association with poor prognostic mutations (e.g. NRAS, ASXL1, TP53), which allows us to visualize them as a good surrogate of poor prognostic molecular profiles.

The Significance of Variant Allele Frequency in SF3B1 Mutated Myelodysplastic Neoplasms/Syndromes

Introduction: Recent iterations of the World Health Organization (WHO) and international consensus classification (ICC) guidelines for myelodysplastic neoplasms (MDS) refined disease defining characteristics through incorporation of morphologic and genetic criteria. Despite these welcome updates, discrepancies between the WHO and ICC remain, particularly with respect to variant allele frequency (VAF) threshold in disease defining mutations such as SF3B1 and TP53. We evaluated patients with SF3B1-mutated MDS, a specific molecular class of MDS in both classification schemes , providing additional biologic and survival information to inform both diagnosis and prognosis. Methods: We queried the International Working Group for Prognosis in MDS (IWG-PM) cohort of adult (age ≥ 18 years) patients (pts) with MDS (N= 3,323; Bernard et al. NEJM Evidence 2022) for baseline clinical demographic, cytogenetic and molecular information, and clinical outcomes. SF3B1 VAF was assessed using targeted next generation sequencing. Demographics were analyzed using descriptive statistics. Between group differences were assessed using the Wilcoxon rank-sum test or Fisher's exact test as appropriate. Time to event endpoints were analyzed using the log-rank method. Multivariate analysis utilized cox proportional hazards regression. Results: We identified 447 (14%) pts met WHO 5th criteria for MDS with low blasts and SF3B1 mutation. Among these, 30 (7%) of pts had a SF3B1 VAF < 10% ( SF3B1low;currently classified as MDS, not otherwise specified by ICC) while 93% (N=417/447) had SF3B1 VAF of ≥ 10% ( SF3B1high). Median VAF in pts with SF3B1low vs. SF3B1high was 6% (range: 2.2-9.9%) vs. 37% (range: 10.9-54.1%). Pts with SF3B1low vs. SF3B1high were older (median age 79 vs. 74, p=0.010), and had lower median platelet (185 x10 9/L vs. 264 x10 9/L, p < 0.001) and white blood cell levels (3.94 x10 9/L vs. 5.46 x10 9/L , p < 0.001). The median number of mutations other than SF3B1 in SF3B1low and SF3B1high was 2 (range: 0-5 vs. 0-8, p=0.42), and SF3B1 was the sole genetic alteration in 10% vs. 20%, respectively (OR=2.2, p=0.24). Common SF3B1 variants in SF3B1low vs. SF3B1 high included p.K666 (27% vs. 10%, OR: 0.31, p=0.01) and p.K700 (50% vs. 59%, OR: 1.42, p=0.44). In pts with SF3B1low, single-hit mutations in TP53 (13% vs. 3%, OR: 0.21, p=0.021), SRSF2 (10% vs. 3%, OR: 0.25, p=0.06), and RUNX1 (7% vs. 4%, OR: 0.60, p=0.37) were more frequent (Fig. A). Other co-mutations had similar frequencies in SF3B1low vs. SF3B1high MDS: TET2 (33% vs. 42%, OR: 1.45, p=0.44), DNMT3A (23% vs. 27%, OR 1.22, p=0.83), ASXL1 (17% vs. 13%, OR: 0.71, p=0.57).The distribution of SF3B1 VAF, and observed patterns of co-mutations did not differ by sample type (peripheral blood or bone marrow). More pts with SF3B1low vs. SF3B1high (76% vs. 46%, p: 0.0011) had a subclonal SF3B1 mutation compared with other co-occurring mutations. In the 213 (48%) pts with subclonal SF3B1, the most frequent dominant mutations included TET2 (35%, N=75), DNMT3A (21%, N=45), and ASXL1 (4%, N=8). Among the top co-mutations in SF3B1low vs. SF3B1high, SF3B1low was more frequently subclonal to TP53 (50% vs. 0%, p=0.04), SRSF2 (33% vs. 0%, p=0.2), and RUNX1 (50% vs. 0%, p=0.1). As anticipated, SF3B1high cases were enriched for very-low/low risk IPSS-M subtypes (78% vs. 43%, OR: 2.9, p=0.011) compared to SF3B1low cases which had an increased frequency of moderate IPSS-M subtypes (30% vs. 14%, OR: 0.39, p=0.03; Fig.B). Median leukemia free survival (LFS; 5 vs. 6 years, p=0.10) was not significantly different between pts with SF3B1low vs. SF3B1high MDS. Median overall survival (OS; 5 vs. 6.2 years, p=0.04) was significantly shorter in pts with SF3B1low, however after adjusting for SF3B1 VAF, age, and IPSS-M score, only age (HR: 1.05 95% CI: 1.03-1.07, p < 0.0001), and increasing IPSS-M score (HR: 2.60 95% CI: 2.10-3.20, p< 0.0001) significantly associated with OS. Conclusion: Patients with MDS with SF3B1-mutation VAF < 10% are older and have an increased frequency of other clonally dominant co-mutations in adverse risk genes (i.e., TP53, SRSF2, RUNX1). Despite more adverse disease biology, LFS and OS were similar between pts with SF3B1low vs. SF3B1high with respect to SF3B1 VAF after accounting for age and IPSS-M score. Future diagnostic and prognostic schema could account for differences in SF3B1lowdisease biology through use of comprehensive prognostic tools such as the IPSS-M score.

Clinical Application of the IPSS-M Prognostic Score in Myelodysplastic Syndrome

Objectives: Patients with myelodysplastic syndrome (MDS) currently get therapy in accordance with their prognosis scores. The newest MDS risk-stratified score, the IPSS-M, isn't still being extensively used in clinical practice and is based on clinical and molecular data. Comparing the IPSS-M score to the current IPSS-R score will enable us to assess the clinical relevance of the IPSS-M score, especially for low-risk MDS patients. Methods: In order to determine the IPSS-R and IPSS-M scores, we gathered clinical, cytogenetic, and molecular information from 210 MDS patients who were diagnosed between 2016 and 2023 and followed up until April 2023. Harrell's c index and Kaplan-Meier survival analysis were used to examine the impact of the two scores on overall survival (OS).The lower-risk group included patients with IPSS-R≤3.5 and IPSS-M≤0, whereas the higher-risk group included the remaining patients. Analysis was done on the differences in gene mutations between the two risk groups based on the two scoring standards, as well as the impact of IPSS-M reclassification on the choice of therapeutic treatments. Results: At least one genetic mutation was identified in 77.1% of patients. The genes ASXL1 (21.4%), TET2 (19.0%), TP53 (14.8%), and DNMT3A (13.3%) have the highest frequency of mutations. According to IPSS-R score, the higher-risk group's TP53 gene mutation rate was significantly higher than that of the lower-risk group; According to IPSS-M score, the higher-risk group had more instances of TP53 and ASXL1 gene mutations than the lower-risk group did, while the lower-risk group had a relatively higher incidence of SF3B1 gene mutations than the higher-risk group did. The difference in survival between IPSS-M groups was more prominent than that between IPSS-R groups under Kaplan-Meier survival analysis, which was used to assess the prognostic prediction power of IPSS-R and IPSS-M. When t 50 months, the Harrell's c index of OS predicted by IPSS-M exceeded that of IPSS-R (IPSS-R vs IPSS-M c-index: 0.710vs0.747, 0.692vs0.707, 0.705vs0.726, 0.752vs0.759, 0.743vs0.773, t=10, 20, 30, 40, 50 months), demonstrating that IPSS-M enhanced the outcome prediction.87 patients (41.4%) were re-stratified by IPSS-M, with 65 (30.9%) being upgraded and 22 (10.5%) being degraded. 64 patients (30.5%) who had changes in their IPSS-M scores qualified for reduced therapy, whereas 48 (22.9%) qualified for intensive treatment, including 32 patients who were reclassified as being in the lower risk category based on their IPSS-R scores. Conclusions: The research shows that IPSS-M offers a more thorough prognostic evaluation than IPSS-R. Certain patients' treatment modalities may need to be changed as a result of modifying IPSS-M in clinical settings, especially those who were previously classified as low-risk.

Real-World Outcomes with CPX-351 Induction in Adults with Newly Diagnosed Acute Myeloid Leukemia

Introduction: CPX-351 is a dual-drug liposomal encapsulation of daunorubicin and cytarabine with a fixed molar ratio of 1:5. CPX-351 is approved for the treatment of newly diagnosed, therapy-related acute myeloid leukemia (t-AML) or AML with myelodysplasia related changes (AML-MRC) in the U.S. and Europe for adult patients (pts) eligible for intensive chemotherapy. In a randomized phase 3 study of older pts ages 60-75, CPX-351 induction showed improved CR rates and OS compared to conventional 7+3 induction, with the greatest benefit seen in pts with t-AML and those without prior hypomethylating agent (HMA) use. There is limited data on the use of CPX-351 in younger pts, although the U.S. FDA approval was not age-restricted. This study examined real-world CPX-351 usage, including patient selection, clinical outcomes, and complications during induction hospitalizations. Methods: We identified previously untreated AML pts who received CPX-351 induction chemotherapy at the University of Kansas Medical Center via retrospective chart review from August 2017 - May 2023. Determination of t-AML and AML-MRC was made by patient history, bone marrow morphology, and available cytogenetic and molecular information at the time of therapy selection. We excluded pts who received CPX-351 as part of a clinical trial. Data was collected for baseline demographics, disease characteristics, outcomes, and safety profile. The composite complete remission rate (CRc) was defined as CR+CRi+CRh at recovery marrow after induction. Primary refractory disease included pts who failed to achieve CR, CRi, or CRh after 2 courses of intensive induction and excluded those who died in aplasia or due to an indeterminate cause. Results: 74 pts with previously untreated AML who received CPX-351 were identified. Median age was 64 years (21-78): 29% of pts were <60 years old, 50% were males, 84% were Non-Hispanic White, 32% had t-AML, 68% had AML-MRC, 20% had prior HMA treatment, and 22% had prior anthracycline exposure. ELN 2022 risk categories were 13% favorable, 20% intermediate, and 68% adverse. 21 pts had complex karyotype (28%), and 16% were TP53 mutant (Table 1). Indications for induction with CPX-351 versus 7+3 included history of prior chemotherapy (n=24), prior MDS (n=32), or MDS-related changes in bone marrow morphology (n=50). The CRc for the total study population was 61% (45/74). Of these, 29% (13/45) achieved MRD negativity by multiparameter flow cytometry <10 -4. CRc in the ELN adverse risk group was 54% (27/50), 73% (11/15) in the intermediate-risk group, and 78% (7/9) in the favorable risk group. Among TP53 mutant pts, CRc was 42% (5/12). CRc in the t-AML group was 71% (17/24), 56% (28/50) in the AML-MRC group, and 53% (8/15) in the prior HMA treatment group. The CRc in pts ≥60 was 63%, 15% were primary refractory, and 37% underwent alloSCT in CR1. In pts <60, the CRc was 54%, 32% were primary refractory, and 27% underwent an alloSCT in CR1 (Table 2). A second course of induction therapy was given for persistent disease at day 14 or similar time point in 36% (n=27) of pts. Among those, 55% (15/27) had primary refractory disease, 20% of the cohort. At a median follow-up of 11 mos, the mOS was 10.8 mos (0.4-54). The mOS for t-AML was 13 mos, whereas the mOS for the group with prior HMA treatment was 10.4 mos. For pts that achieved CR, mOS was 13.6 mos; for pts that achieved MRD negativity, mOS was 13.8 mos. The mOS for pts <60 was 16 mos, and for pts ≥60 was 10 mos (p=0.39). The mOS for pts that achieved CRc in the group <60 was 20.3mos, and for ≥60 was 11.2 mos (p=0.27). Pts that underwent alloSCT in CR1 <60 had mOS of 25 mos; for ≥60, it was 14.2 mos (p=0.37). During induction hospitalization, febrile neutropenia was the most common adverse event in 84% (n=62). ICU treatment was required in 14% (N=5). There were 2 deaths during induction: one due to respiratory failure and one attributed to sepsis. Conclusion: The use of CPX-351 demonstrated efficacy across subgroups, especially in t-AML and pts without prior HMA exposure, as shown in larger studies. In pts <60 years, even though CRc rates were lower, CPX-351 led to longer mOS in those who achieved CRc and in those who underwent alloSCT compared to pts ≥60 years, although it didn't reach statistical significance in this small cohort. Induction therapy outcomes and treatment-related complications in our study corroborate the data for prior CPX-351 studies.

Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era.

Chromosome studies provide the foundation for comprehending inheritance, variation, systematics, and evolution. Penaeid shrimps are a group of crustaceans with great economic importance. Basic cytogenetic information obtained from these shrimps can be used to study their genome structure, chromosome relationships, chromosome variation, polyploidy manipulation, and breeding. The study of shrimp chromosomes experienced significant growth in the 1990s and has been closely linked to the progress of genome research since the application of next-generation sequencing technology. To date, the genome sequences of five penaeid shrimp species have been published. The availability of these genomes has ushered the study of shrimp chromosomes into the post-genomic era. Currently, research on shrimp cytogenetics not only involves chromosome counting and karyotyping, but also extends to investigating submicroscopic changes; exploring genome structure and regulation during various cell divisions; and contributing to the understanding of mechanisms related to growth, sexual control, stress resistance, and genome evolution. In this article, we provide an overview of the progress made in chromosome research on penaeid shrimp. We emphasize the mutual promotion between studies on chromosome structure and genome research and highlight the impact of chromosome-level assembly on studies of genome structure and function. Additionally, we summarize the emerging trends in post-genomic-era shrimp chromosome research.

An Integral R-Banded Karyotype Analysis System of Bone Marrow Metaphases Based on Deep Learning.

Conventional karyotype analysis, which provides comprehensive cytogenetic information, plays a significant role in the diagnosis and risk stratification of hematologic neoplasms. The main limitations of this approach include long turnaround time and laboriousness. Therefore, we developed an integral R-banded karyotype analysis system for bone marrow metaphases, based on deep learning. To evaluate the performance of the internal models and the entire karyotype analysis system for R-banded bone marrow metaphase. A total of 4442 sets of R-banded normal bone marrow metaphases and karyograms were collected. Accordingly, 4 deep learning-based models for different analytic stages of karyotyping, including denoising, segmentation, classification, and polarity recognition, were developed and integrated as an R-banded bone marrow karyotype analysis system. Five-fold cross validation was performed on each model. The whole system was implemented by 2 strategies of automatic and semiautomatic workflows. A test set of 885 metaphases was used to assess the entire system. The denoising model achieved an intersection-over-union (IoU) of 99.20% and a Dice similarity coefficient (DSC) of 99.58% for metaphase acquisition. The segmentation model achieved an IoU of 91.95% and a DSC of 95.79% for chromosome segmentation. The accuracies of the segmentation, classification, and polarity recognition models were 96.77%, 98.77%, and 99.93%, respectively. The whole system achieved an accuracy of 93.33% with the automatic strategy and an accuracy of 99.06% with the semiautomatic strategy. The performance of both the internal models and the entire system is desirable. This deep learning-based karyotype analysis system has potential in a clinical application.

Divergent karyotypes in five genera of the African endemic fish family Distichodontidae (Cithariniformes, Osteichthyes)

The African family Distichodontidae comprises 109 species in 16 genera. Up-to-date cytogenetic information was available for the only distichodontid species Distichodus affinis Günther, 1873. Here we report chromosome number and morphology in: Distichodus engycephalus Günther, 1864 (2n = 52, FN = 104), Ichthyborus besse (Joannis, 1835) (2n = 46, FN = 92), Nannocharax niloticus (Joannis, 1835) (2n = 54, FN = 106) and three taxa, Nannaethiops bleheri Géry et Zarske, 2003, Nannaethiops sp., and Neolebias unifasciatus Steindachner, 1894, that exhibit the same karyotypes (2n = 50, FN = 98). To confirm the Nannaethiops Günther, 1872 and Neolebias Steindachner, 1894 species identification, mt-DNA sequences of the two markers (COI and 16S rRNA) were obtained from karyotyped specimens and compared with the relevant sequences accessible from GenBank. The great prevalence of biarmed chromosomes (the karyotypes of most species contain exclusively biarmed chromosomes) is a distinctive characteristic of Distichodontidae and Cithariniformes as a whole.

Chromosomal analysis of Sander lucioperca (L., 1758) (Perciformes: Percidae) from Turkey

Sander lucioperca (pikeperch) is a percid fish species of high commercial value and potential for being aquaculture in Turkey. However, karyological studies are deficient for population of Turkey. So, the aim of this study is to carry out diploid chromosome number, karyotype formula, fundamental arm number and chromosomal banding properties (with C-banding and Ag-NOR staining) of S. lucioperca. Specimens of S. lucioperca were captured from Konya, Turkey and alive specimens carried to the laboratory. Chromosome obtaining was provided by using air-drying technique from the head kidney. Chromosome slides were prepared and banding procedures were applied. Result of the analysis, diploid chromosome number was found as 48 and karyotype of the pikeperch consist of 32 biarmed and 16 uniarmed chromosomes. Constitutive heterochromatin regions were observed on the pericentromeres of some of the chromosomes. Ag-NORs were determined on one pair of submetacentric chromosome. This report is the first that determines chromosomal properties of S. lucioperca from Turkey. This study may contribute the cytogenetic information of this species.

Optical genome mapping for cytogenomic analysis of hematological neoplasms.

e19016 Background: Optical genome mapping (OGM) provides a genome-wide analysis for structural variants and copy number changes in one-assay. Compared with conventional G-banded karyotyping (GBK), OGM provides significantly higher resolution and does not require metaphase cells. In this study, we assessed the added value of OGM for cytogenomic analysis of hematological neoplasms. Methods: OGM was performed on blood or bone marrow using Saphyr from Bionano Genomics on 63 patients diagnosed with various types of hematological malignancy (see Table). Variant calling was made by the Rare Variant Analysis pipeline on Bionano Access after applying recommended filters. Each patient had karyotype and/or fluorescence in situ hybridization (FISH) results available for comparison and confirmation. Only Tier 1 (pathogenic) and Tier 2 (likely pathologic) abnormalities were included for comparison purposes in this study. Results: The results were completely concordant between GBK/FISH and OGM in 30 (47.6%) patients, including 10 patients who showed no cytogenetic abnormality (normal). Fully discordant results were found in 8 (12.7%) patients: 2 had an abnormal karyotype but normal OGM, the discrepancy was mainly due to the clonal size (<20%) below the limitation of detection of OGM; 6 had a normal karyotype but cytogenetic abnormalities were detected by OGM, the discrepancy was mainly due to failure of tumor cells growth (n=5) or subtle cytogenetic abnormality undetectable by GBK (n=1). Partially concordant results between karyotype/FISH and OGM were observed in 25 (40%) patients, some abnormalities were detected by both, some were detected by GBK alone (n=4) or by OGM alone (n=25), the latter group included 10 cases with chromothripsis which only be detected by OGM. Overall, OGM provided clinically significant information in 14 (22%) patients regarding diagnosis, risk stratification, and/or identifying therapeutic targets. The added value was more common in lymphoid neoplasms (9 of 27 patients, 33%). Conclusions: OGM provides additional clinically relevant cytogenetic information in the workup of hematological neoplasms. This added value is more apparent in lymphoid neoplasms. These improvements are largely contributable to the higher resolution provided by OGM and analysis independent of metaphase cells. A major limitation of OGM usage is the need for a clonal size of at least 20%. [Table: see text]

Ganglioneuroblastoma intermixed: Clinicopathological implications of diagnosis at presentation and genomic correlations.

Ganglioneuroblastoma intermixed (GNBI) is classified as "favorable" histology by International Neuroblastoma Pathology Classification system. However, the International Neuroblastoma Risk Group (INRG) stratifies patients using wider clinicopathological and cytogenetic/molecular parameters. While the diagnosis of GNBI is typically made on resected tumor, it may sometimes be rendered on initial biopsy. We studied GNBI noted at diagnosis to evaluate its correlation with INRG staging and other clinicopathological and molecular features. In this retrospective study, clinical, radiological, pathological, cytogenetic, and molecular information from patients with GNBI at diagnosis seen between 1995 and 2021 was analyzed. INRG staging was performed. Of the 15,827 neuroblastoma specimens, GNBI was noted in 237 patients. Of these, 53 had the initial pathological diagnosis of GNBI; median follow-up 3.5 (range: 0.2-14) years. Disease was locoregional in 41 (77%, 16 stage L1 and 25 L2); none relapsed. Twelve (23%) had metastatic disease at presentation; six (50%) relapsed, and two died of disease. MYCN was amplified in two metastatic tumors. Six of 31 (19%) tumors tested had recurrent cytogenetic abnormalities and nonrecurrent somatic gene mutations in 10/23 (43%). The presence of any adverse molecular/cytogenetic findings was associated with metastatic disease (p<.05). For patients with localized GNBI undergoing both biopsy and resection, GNBI was diagnosed in both in 17/19 (90%). Localized GNBI at diagnosis has excellent long-term clinical outcome even without cytotoxic therapy. For localized GNBI, a biopsy sample is adequate to make the diagnosis. When associated with metastasis at diagnosis, prognosis is poorer, possibly due to associated adverse biological features.