Cytogenetic Reports Research Articles

Cytogenetics of Diphysa americana (Mill.) M.Sousa (Leguminosae-Papilionoideae-dalbergioid clade), a rare species from the coast of Oaxaca, Mexico

Diphysa Jacq. is an essentially Mexican and Central American genus that includes 21 species and only one cytogenetic report. In this work, a surface spread and air-drying method was used to obtain the karyotype of Diphysa americana (Mill) M.Sousa, a rare native tree that grows in a coastal town in the State of Oaxaca, Mexico. Metaphase cells showed a 2n = 20, consistent with the predominant diploid number in the dalbergioid clade. This number contrasts with a previously reported 2n = 16. The karyotypic formula 5m + 5sm, first proposed for a species of the genus, denotes a slightly asymmetric karyotype. The presence of secondary constrictions associated with satellites on the short arms of a pair of sm chromosomes and other cytogenetic parameters require studies in other species of the genus to verify their taxonomic utility. In addition, cells in prometaphase exhibited a circular fragment of unknown origin like that observed in a species of the genus Aeschynomene, also dalbergioid. This fragment could be related to extrachromosomal circular DNA (eccDNA) observed in other plants. Diphysa is a small, cytogenetically favorable genus, and further studies will exhibit the karyotypic diversity that underlies its diversification.

Automated Cytogenetic Classifier (ACC) to Support Accurate Clinical Decision Making in Acute Myeloid Leukaemia

Introduction Cytogenetic analysis is a recommended test in newly diagnosed AML but requires accurate interpretation of the International System for Human Cytogenomic Nomenclature (ISCN). Keeping up to date across recent published classifications - WHO, the European Leukaemia Net (ELN) and International Consensus Classification (ICC) - is critical for accurate prognostic assessment, but can be challenging for clinicians and laboratory scientists. Furthermore, eligibility to access state-funded treatments in the UK is dictated by certain cytogenetic results. We previously developed a webapp that integrates cytogenetic, molecular and clinical features to aid accurate classification, prognostication and provide treatment recommendations in AML (Coats et al, BJH 2021). To further improve the webapp we have developed a cytogenetic classifier to automatically interpret reports written in ISCN format. In this study we aimed to validate the automated cytogenetic classifier (ACC) in identifying abnormalities that feature in the new WHO, ELN and ICC classifications. Methodology Software for the ACC was written in Python to: 1. count the number and type of karyotypic abnormalities (subdivided into number of monosomies, complete chromosome gains and structural changes) 2. identify presence of clinically relevant, named, abnormalities that feature in international classifications (categorised as an individual abnormalityg. t(9;11)(p21.3;q23.3), or a generic abnormality e.g. any translocation involving 11q23.3). Cytogenetic reports of 50 consecutive AML cases with abnormal karyotypes analysed by Bristol Haematological Oncology Diagnostic Service (BHODS) were selected (training cohort). Each report was uploaded to the ACC and its output independently checked for accuracy. Following review of the software's performance, adjustments to the ACC were made. The updated ACC (Figure 1) analysed 98 additional reports from two other laboratories, UCLH and OUH (validation cohort). Results The ACC analysed 49/50 cytogenetic reports from the BHODS laboratory. One report could not be read by the ACC. The correct quantity of abnormalities was identified in 49/49 cases analysed. Where relevant named abnormalities occurred, these were detected in 79/80 instances. One case of acute promyelocytic leukaemia containing an idic(17p) was not identified as containing an abnormal 17p. Additionally, in one report with a complex karyotype, a monosomy 13 was erroneously detected by the ACC. Adjustments were made to the ACC such that it could analyse all 50 cases with 100% accuracy. The updated ACC then analysed 98 cases from the validation cohort. The correct quantity of abnormalities was detected in 97/ 98 cases. In one case with a highly complex karyotype containing a tetraploid clone, the ACC incorrectly counted 48, as opposed to 45, abnormalities. Clinically relevant, named, abnormalities were correctly identified in 178/179 instances. In one case, containing a 4-way translocation, the ACC did not identify the t(9;11) abnormality. Discussion Here, we show that the updated ACC is accurate in identifying the number and type of karyotypic abnormalities relevant to AML from different laboratories. Reduced accuracy in counting the number of abnormalities in highly complex karyotypes (i.e. >40 abnormalities) is not likely to impact clinical interpretation. Further validation work is needed to analyse 3 and 4-way translocations. User warnings have been added to the ACC for karyotypes containing multiple-translocations and tetraploid/triploid clones to improve clinical safety. The ACC can support clinical decision-making by streamlining cytogenetic interpretation from across multiple clinical classifications. It can be used as a stand-alone programme or integrated into more sophisticated decision support tools. The ACC has the potential to be updated to interpret cytogenetic reports from other classifications or haematological malignancies. The ACC is available as a webapp (Streamlit (ts482-cytogenetics-calculator-extractorstreamlit-w7dq9p.streamlit.app). Figure 1. Flowchart of the methodology of the updated automated cytogenetic classifier (ACC).

Precision Medicine Landscape of Genomic Testing for Patients With Cancer in the National Institutes of Health All of Us Database Using Informatics Approaches.

The rapid growth of biomedical data ecosystems has catalyzed research for oncology and precision medicine. We leverage federal cloud-based precision medicine databases and tools to better understand the current landscape of precision medicine and genomic testing for patients with cancer. Retrospective observational study of genomic testing for patients with cancer in the National Institutes of Health All of Us Research Program, with the cancer cohort defined as having at least two documented or reported cancer diagnoses. There were 5,678 (1.8%) All of Us participants in the cancer cohort, with a significant difference between cancer status by age category, sex, race, and ethnicity (P < .001 for all). There were 295 (5.2%) patients with cancer who received genomic testing compared with 6,734 (2.2%) of noncancer patients, with 752 genomic tests commonly focused on gene mutations (primarily pharmacogenomics), molecular pathology, or clinical cytogenetic reports. Although not yet ubiquitous, diverse clinical genomic analyses in oncology can set the stage to grow the practice of precision medicine by integrating research patient data repositories, cancer data ecosystems, and biomedical informatics.

Impact of p53 Disruption on AML & HR-MDS Treatment out-Come. a Single Centre Experience

Introduction: Acute myeloid leukaemia (AML) is a heterogeneous disorder that arises from clonal expansion of malignant hematopoietic precursor cells. Somatic mutations of the p53 gene have been reported in 5-10% of AML, with a higher incidence therapy-related disease and elderly patients. Alteration or loss of p53 is one of the most powerful independent indicators of poor outcome.Methods: This is a retrospective analysis of AML & high risk-Myelodysplastic syndrome (HR-MDS) patients treated over the study period (2006-2020). Informed consent was obtained. Initial presentation, treatment response, and survival were analysed. Percentage of p53 expression (a surrogate marker for TP53 mutations) by immunohistochemistry (IHC) (>30% cut-off) on BM trephines was analysed and its impact on treatment outcome was evaluated.Results: We identified 114 patients (AML=104 & HR-MDS=10), the median age was 70 years (Range 36-85) with male predominance (M=73 vs. F=41). The AML group included, 57 patients (50%) with Denovo AML and 47 patients (41%) with Secondary AML (MDS=27, MPN=12 / JAKII mutation =7, t-AML=8). The median age was 70 years (Range 36-85) and the median blast count was 70% (Range 25-95%). Cytogenetic analysis reports were available on 78 patients (75%)(Poor risk=40 vs. Intermediate risk=38). NPM1 (22 patients) and FLT3 mutations analysis (33 patients )were available and reported as positive in 4(18%) and 5(15%) patients respectively.The HR-MDS is defined by patients who fall into higher-risk group categories in the original or revised IPSS (N=10), the median age was 74 years (Range 63-83) with male predominance (M=7 vs. F=3). The median blast count was 15% (Range 11-18%). Cytogenetic risk prognostic subgroup results were available on 6 patients (60%), 2 patients (2%) had intermediate-risk and 4 patients (4%) had poor-risk.Ninety-nine patients (87%) were eligible for treatment, 48 patients (42%) were treated with intensive induction chemotherapy, and 51 patients (45%) received less intensive therapy (HMA / LD-Ara C). Five patients (4%) consolidated with allogeneic stem cell transplant (Allo-SCT) post-induction therapy. The remaining (15 patients) were on supportive care. Forty-one AML patients (36%) relapsed post CR1, 3 patients had Allo-SCT in CR2. Table 1At the time of study analysis (31/01/2021), 25 patients (22%) are still alive including 23 patients (20%) with AML (Denovo AML=18 & Sec AML=5) and 2 patients (4%) with HR-MDS. The median age of the survival group was 69 years (Range 51-83). The whole study cohort median OS was 12 months. (Figure. 1) The median OS & PFS for AML patients were 15 & 13 months respectively. According to AML sub-type, t-AML associated with shortest median OS of 2.5 months (P.value 0.0190). (Figure. 2) The median OS was more favourable for intermediate-risk than the high-risk cytogenetic AML, 24 and 10 months respectively (P<00016).(Figure. 3) The HR-MDS group median OS was 22 months.One hundred and four patient's BM trephines (91%) were available and screened for p53 IHC expression (AML= 96 & HR-MDS =8). Eight samples (8%) showed p53 over-expression, all these samples with underlying AML diagnosis. The remaining 96 samples (92%) were negative for high p53 expression. The majority of p53 over-expressed AML harboured complex cytogenetics, 4 patients with Sec AML, 3 patients with Denovo AML, and 1 patient with t-AML. Most of the patients (5 patients) in this sub-set had a refractory disease to induction therapy, of whom 2 patients (25%) had Allo-SCT consolidation in CR2. Only one patient (12%) is still alive in this sub-group.The median OS & PFS in p53 wild-type AML cohort was 16 & 13 months respectively, which compared favourably to 12 & 8 months in those with p53 disruptions. The P. values were 0.134 & 0.193, respectively. The impact of the p53 alterations was more pronounced on the AML sub-group treated with intensive chemotherapy (42%), the median OS & PFS in wild-type p53 AML were 24 & 20 months, while in p53 disrupted cohort were 12 & 10 months respectively (P= 0.030)(95%CI of ratio 0.1755 to 1.425) & (P=0.049)( 95%CI of ratio 0.7015 to 5.702).(Figure.4)Conclusion: In this study we demonstrated the potential role for p53 expression by IHC, which is readily available in routine practice, in assessing AML prognosis. Our real-life data confirms the dismal prognosis of p53 alterations in this disease. Participation in clinical trials based on genetic risk stratification is warranted. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Impact of Specific Adverse Cytogenetic Features on Outcomes after Allogeneic Hematopoietic Cell Transplantation in Myelodysplastic Syndrome with Very Poor Risk Cytogenetics: A Study from the Chronic Malignancies Working Party of EBMT

INTRODUCTIONMyelodysplastic Syndrome (MDS) is a heterogenous disease which is almost incurable without an allogeneic hematopoietic cell transplantation (allo-HCT). Within the revised international scoring system (R-IPSS), MDS with poor and very poor cytogenetics have a much worse outcome after allo-HCT. The very poor cytogenetic subgroup refers to patients harboring more than 3 abnormalities and is therefore a highly heterogenous group. We have shown in acute myeloid leukemia (AML) that beyond complex karyotype, specific adverse cytogenetic features such as 7q abnormalities (abn7q), 5q abnormalities (abn5q), 17p abnormalities (abn17p) and monosomal karyotype (MK) worsen the outcomes after allo-HCT. We have therefore retrospectively reviewed MDS with very poor cytogenetics and studied the impact of adverse cytogenetic features on outcomes after transplant. METHODSWe selected MDS patients who underwent allo-HCT between 2001 and 2018 from a matched related or unrelated donor, for whom a full cytogenetic report was available in the EBMT registry. We then stratified them according to the presence of abn7q, abn5q, abn17p, MK and the number of abnormalities (≤5, 6-9 and ≥10). Graft-versus-host disease (GvHD) and relapse-free survival (GRFS) was defined as survival without grade II-IV acute GvHD, extensive chronic GvHD or relapse. RESULTSA total of 154 patients were identified in the registry. One hundred twenty-three patients (81%) had MDS with excess of blasts and 4 (3%) had secondary AML. Median age was 59 years (interquartile range (IQR), 51-64) and the median follow-up was 38 months (95% confidence interval (CI), 34-60). The time from diagnosis to allo-HCT was a median of 6 months (IQR, 4-8). Two thirds of patients received a reduced-intensity conditioning regimen (N = 103, 67%) and 87 patients had a matched unrelated donor (57%). Almost all patients were in first complete remission at time of transplant (N= 149, 97%). Regarding specific cytogenetic features, 87 patients had abn7q (57%), 99 abn5q (64%), 59 abn17p (38%) and 120 MK (78%) with considerable overlap between groups.The 2-year overall survival (OS) and progression-free survival (PFS) was 34% (95% CI 26-42%) and 24% (95% CI 17-31%), respectively. The 2-year cumulative incidence of relapse and non-relapse mortality (NRM) was 59% (95% CI 51-67%) and 18% (95% CI 12-24%), respectively. The cumulative incidence of grade II-IV acute GvHD and chronic GvHD was 33% (95% CI 25-40%) and 44% (95% CI 36-53%) by day 100 and 2 years respectively. The 2-year GRFS was 12% (95% CI 6-17%). The presence of abn5q was associated with a significantly decreased PFS of 17% (95% CI 9-25%) versus 36% (95% CI 23-49%); p=0.05) and GRFS (6% (95% CI 1-11%) versus 23% (95% CI 11-34%); p=0.04). The presence of abn7q was associated with significantly increased NRM (25% (15-34%) versus 9% (2-16%); p=0.02) which did not translate into OS. There were no specific cytogenetic features that had an independent impact on the cumulative incidence of relapse, but age over 55 years did increase the relapse risk (<55: 45% (95% CI 31-59%); 55-65: 65% (95% CI 54-77%); >65: 66% (95% CI 50-83%); p=0.03). A continuous effect was also observed (per decade increase: HR=1.24, 95%CI 1.02-1.52; p=0.03). Patients with an interval of more than 6 months from diagnosis to allo-HCT had almost double the OS (45% (95% CI 32-58%)) compared to patients with an interval less than 6 months (27% (95% CI 17-37%); p=0.04), however a continuous effect was not observed. CONCLUSIONMDS with very poor cytogenetics according to R-IPSS is a very bad group with dismal outcomes after allo-HCT. Within this high-risk group, specific adverse cytogenetic features such as the number of abnormalities, abn7q, abn5q, abn17p or MK did not stratify outcomes further, except for abn5q which was associated with a decreased PFS. Our results might be explained in part by the low number patients and by the over-representation of adverse features within this cohort. Despite that, advancing age was associated with increased relapse. Whilst allo-HCT remains the best therapeutic option for this very high-risk patient group, efforts should focus on post-transplant preemptive intervention strategies to prevent relapse. DisclosuresByrne: Incyte: Honoraria. Schroeder: Celgene: Honoraria, Other: Travel support, Research Funding. Blaise: Jazz Pharmaceuticals: Honoraria. Hayden: Jansen, Takeda: Other: Travel, Accomodation, Expenses; Amgen: Honoraria. Scheid: Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Honoraria; Roche: Consultancy; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees. Yakoub-Agha: Jazz Pharmaceuticals: Honoraria.

Allogeneic Hematopoietic Cell Transplantation for Acute Myeloid Leukemia with Hyperdiploid Complex Karyotype: A Study from the Acute Leukemia Working Party (ALWP) of the European Society for Blood and Marrow Transplantation (EBMT)

Introduction: Cytogenetics remains one of the most important prognostic factors in acute myeloid leukemia (AML) patients, even for outcomes after allogeneic hematopoietic cell transplantation (allo-HCT). Complex karyotype (CK) constitutes a cytogenetic category with a very adverse prognosis in this setting. However, CK is a heterogenous and loosely defined category which comprises a high diversity of cytogenetic subtypes, which is highly enriched with specific cytogenetic subtypes characterized by losses of chromosomal material at critical regions known to confer a poor prognosis per se, such as monosomal karyotype, del(7q)/-7, del(5q)/-5 or abnormalities leading to 17p region loss. On the contrary, rare AML cases characterized with only multiple numerical abnormalities known as pure hyperdiploid karyotype (HDK), have a controversial prognosis. We hypothesized that pure complex HDK AML has a distinct and much better prognosis after allo-HCT compared to non-HDK, CK AML.Methods: We selected from the EBMT registry adult patients with AML and a full cytogenetic report. HDK was defined by the presence of 49 chromosomes or more. Patients were then stratified by pure HDK (pHDK) and HDK with other cytogenetic abnormalities (HDK+), characterized by HDK and the presence of a prognostic-defining cytogenetic abnormality such as del(5q)/-5, del(7q)/-7, del(17p)/-17/i(17q), inv(3q21-26)/t(3;3)(q21;q26) or t(9;22). We included only first allo-HCT from a sibling or unrelated donor (UD) performed between 2000 and 2018.Results: A total of 236 patients were identified as having HDK. There were 95 pHDK and 141 HDK+. Median age at transplantation was 53 years (range, 18-74) and median follow-up was 43 months (range, 35-56). A diagnosis of secondary AML was reported in 48 patients (20%). At the time of allo-HCT, 180 patients (76%) were in first remission (CR1), and 56 were beyond CR1 (24%). Eighty-five (39%) patients received an allo-HCT from a sibling donor, with more matched unrelated donors (MUD) in HDK+ patients (p=0.02). Most patients (70%) had a Karnofsky performance status (KPS) score of more than 90% at the time of transplantation. A myeloablative conditioning regimen was administered in 46% of the patients. In vivo T-cell depletion was part of the regimen in 66% of the patients. The most frequent trisomies were trisomy 8, 21, 13, and 22.The 2-year probability of non-relapse mortality (NRM) was 26% for the entire cohort. The 2-year probability of LFS was 50% for pHDK and 31% for HDK+ (p=0.003). The 2-year probability of overall survival (OS) was 57% for pHDK and 36% for HDK+ (p=0.007). The 2-year cumulative incidence of relapse (RI) was 22% for pHDK and 44% for HDK+ (p=0.001) (Figure 1). The cumulative incidence of grade II-IV acute graft-versus-host disease (GvHD) and chronic GvHD was 34% and 33%, respectively, for the entire cohort. Finally, the 2-year probability of GvHD and relapse-free survival (GRFS) was 36% for pHDK and 21% for HDK+ (p=0.01). On multivariate analysis, pHDK remained associated with significantly better LFS, OS and GRFS and higher RI (all p-values<0.004). Age was associated with lower OS (p=0.05). Being in remission at the time of allo-HCT was associated with better LFS, OS and GRFS, and lower NRM and RI (all p-values<0.02). Secondary AML, donor type, KPS, and conditioning regimen intensity were not associated with any outcome in multivariate analysis.Conclusions: AML with pHDK has a better outcome after allo-HCT in terms of RI, LFS, OS and GRFS. pHDK AML constitutes probably a distinct cytogenetic entity from HDK+ or other non-hyperdiploid CK AML. CK remains a strong indication for allo-HCT, but the type of abnormalities included in CK significantly influences the outcome and should guide how to manage patients after allo-HCT in terms of immunosuppression withdrawal or prophylactic/preemptive post-transplant interventions such as use of hypomethylating agents or donor lymphocyte infusions. [Display omitted] DisclosuresLabopin: Jazz Pharmaceuticals: Honoraria. Ganser: Jazz Pharmaceuticals: Honoraria; Novartis: Honoraria; Celgene: Honoraria. Socie: Alexion: Research Funding. Forcade: Novartis: Other: travel grant. Chalandon: Incyte, BMS, Pfizer, Abbie, MSD, Roche, Novartis, Gilead, Amgen, Jazz, Astra Zenec: Other: Travel EXpenses, Accomodation; Incyte, BMS, Pfizer, Abbie, MSD, Roche, Novartis, Amgen: Other: Advisory Board; Incyte: Speakers Bureau. Yakoub-Agha: Jazz Pharmaceuticals: Honoraria. Kröger: Novartis: Research Funding; Riemser: Honoraria, Research Funding; Sanofi: Honoraria; Neovii: Honoraria, Research Funding; Jazz: Honoraria, Research Funding; Gilead/Kite: Honoraria; Celgene: Honoraria, Research Funding; AOP Pharma: Honoraria. Esteve: Jazz: Consultancy; Bristol Myers Squibb/Celgene: Consultancy; Abbvie: Consultancy; Novartis: Consultancy, Research Funding; Astellas: Consultancy; Pfizer: Consultancy; Novartis: Research Funding. Mohty: Sanofi: Honoraria, Research Funding; Pfizer: Honoraria; Novartis: Honoraria; Takeda: Honoraria; Jazz: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Gilead: Honoraria; Celgene: Honoraria, Research Funding; Bristol Myers Squibb: Honoraria; Astellas: Honoraria; Amgen: Honoraria; Adaptive Biotechnologies: Honoraria.

Cytogenetic aberrations in adult acute lymphoblastic leukemia-A population-based study.

Cytogenetic aberrations are recognized as important prognostic factors in adult acute lymphoblastic leukemia (ALL), but studies seldom include elderly patients. From the population‐based Swedish ALL Registry, we identified 728 patients aged 18–95 years, who were diagnosed with ALL 1997–2015 and had cytogenetic information. Registry data were complemented with original cytogenetic reports. BCR‐ABL1 was the most recurrent aberration, with a frequency of 26%, with additional cytogenetic alterations in 64%. KTM2A rearrangement was the second most frequent aberration found in 7%. Low hypodiploidy‐near triploidy and complex karyotype had negative impact, while t(1;19);TCF3‐PBX1 showed positive impact on overall survival. However, after correction for age only complex karyotype remained significant.

Prognostic significance of chromosomal abnormalities at relapse in children with relapsed acute myeloid leukemia: A retrospective cohort study of the Relapsed AML 2001/01 Study.

In addition to treatment response, cytogenetic and molecular aberrations are the most important prognostic factors in children with de novo acute myeloid leukemia (AML). However, little is known about cytogenetics at the time of relapse. This international study analyzed the prognostic value of cytogenetic profiles and karyotypic changes in pediatric relapsed AML in relation to the probability of event-free (pEFS) and overall survival (pOS). For this purpose, cytogenetic reports from all patients registered on the Relapsed AML 2001/01 Study were reviewed and classified. Cytogenetic information at relapse was available for 403 (71%) of 569 registered patients. Frequently detected aberrations at relapse were t(8;21)(q22;q22) (n = 60) and inv(16)(p13.1q22)/t(16;16)(p13.1;q22) (n = 24), both associated with relatively good outcome (4-year pOS 59% and 71%, respectively). Monosomy 7/7q-, t(9;11)(p22;q23), t(10;11)(p12;q23), and complex karyotypes were associated with poor outcomes (4-year pOS 17%, 19%, 22%, and 22%, respectively). Of 261 (65%) patients for whom cytogenetic data were reliable at both diagnosis and relapse, pEFS was inferior for patients with karyotypic instability (n = 128, 49%), but pOS was similar. Unstable karyotypes with both gain and loss of aberrations were associated with inferior outcome. Early treatment response, time to relapse, and cytogenetic profile at time of relapse were the most important prognostic factors, both outweighing karytoypic instability per se. The cytogenetic subgroup at relapse is an independent risk factor for (event-free) survival. Cytogenetic assessment at the time of relapse is of high importance and may contribute to improved risk-adapted treatment for children with relapsed AML.

Cytological Review and First Cytogenetic Report on Three Species of Family Macromiidae (Odonata: Anisoptera) from India

Cytological Review and First Cytogenetic Report on Three Species of Family Macromiidae (Odonata: Anisoptera) from India

Robust Parsing and Automated ELN Risk Classification for Acute Myeloid Leukemia

Introduction: Tumor karyotype is determined from cytogenetic analysis and is among the most valuable features for prognosis and therapy selection in many hematological malignancies. The International System for Human Cytogenetic Nomenclature (ISCN) standardizes the reporting of karyotypes. However, karyotype strings can be extremely complicated, sometimes leading to confusion in their interpretation by non-cytogeneticists. To improve the speed and accuracy of karyotype interpretation and classification, we developed an automated system to parse and interpret cytogenetics reports and have initially applied this to risk prediction in AML. Previous work in automated cytogenetics parsing (e.g. the CyDAS project Bradtke 2004) have not included inferred abnormalities (e.g. arm deletions inferred from isochromosomes and whole-arm translocations) or logic to categorize more general types of abnormalities (e.g. “any 17p abnormality”) which may have specific phenotypic significance or prognostic risk classifications, and require some level of both cytogenetic and programming expertise to utilize effectively.Methods: In previous work (Silgard, 2015), we developed a modular set of python scripts that process a batch of cytogenetics reports, identify and clean ISCN formulas, and parse ISCN into an efficient representation of cells and their clonal abnormalities as well as classify karyotypes according to Southwestern Oncology Group (SWOG) risk categories (Slovak, 2000). We extended this system to (1) effectively group abnormalities by types (e.g. translocation, deletion, duplication, inversions, etc.) and by the chromosome and arm affected, and (2) classify karyotypes according to the European Leukemia Net (ELN) risk categories (Döhner, 2017), and output salient abnormalities, risk categories, and text span references to the supporting evidence for interpretation. We classified each case according to ELN risk categories: favorable, unfavorable, or intermediate. Notable improvements upon the previous system include logic for inferred abnormalities (e.g. i(12)(q10) implies both a deletion of 12p as well as a duplication of 12q) as well as an optional minimum cell count to determine clonality. Complex karyotype and monosomal karyotype are also delineated.Results: Upon expert review of the automated parsing of 724 karyotype strings from 470 AML patients treated at the University of Washington/Fred Hutch Cancer Consortium between 1991 and 2016, automated ELN classification had an accuracy of 97.1%. Codification of chromosome arm specific abnormalities using 12p as a prototype (i.e. deletions, additions, translocations, duplications, inversions, and -12) collectively had micro-averaged sensitivity, specificity, and overall accuracy of 82.26%, 99.93%, and 99.68%; identifications of complex and monosomal karyotypes had sensitivity, specificity, and overall accuracy of 95.83%, 99.68%, 99.17% and 86.89%, 99.4%, 98.34%, respectively. The majority of the parsing errors were due either to typos in karyotype strings and non-standard nomenclature or to single cell count abnormalities that were assumed non-clonal.Conclusions: The automated karyotype parsing is an effective way to deliver condensed cytogenetic information to a more diverse audience of clinicians and researchers who lack either time or expertise to decipher complex karyotype strings or are unfamiliar with the updated risk stratification criteria for each disease. We have addressed any errors that arose from program defaults not associated with typos in the ISCN string and have included an optional clonality detection parameter to allow for some customization to individual lab reporting standards. Our next steps include extending the system to parse fluorescence in situ hybridization (FISH) nomenclature strings from cytogenetic lab reports, which can detect low-level or submicroscopic chromosomal abnormalities that cannot be detected by standard chromosomal analysis. We aim to provide the parsing and classification as an openly available web service for the broader community in the near future. DisclosuresNo relevant conflicts of interest to declare.

Complex Karyotype Predicts the Prognostics Impact of WBC Count in Untreated Mantle Cell Lymphoma and Is Associated with Shortened Survival Independent of Specific Cytogenetic Abnormalities

Complex Karyotype Predicts the Prognostics Impact of WBC Count in Untreated Mantle Cell Lymphoma and Is Associated with Shortened Survival Independent of Specific Cytogenetic Abnormalities

Allogeneic Stem Cell Transplantation for Acute Myeloid Leukemia with Monosomy 7 or Deletion 7q: A Study from the Acute Leukemia Working Party (ALWP) of the European Society of Blood and Marrow Transplantation (EBMT)

▪ INTRODUCTIONMonosomy 7 or deletion 7q (-7/7q-) is the most frequent high-risk cytogenetic feature reported in acute myeloid leukemia (AML) and is associated with a dismal outcome after chemotherapy alone. Allogeneic stem cell transplantation (SCT) appears to be the best consolidation strategy in these patients (pts), thereby significantly improving outcomes. Nevertheless, -7/7q- occurs frequently with other high-risk cytogenetic abnormalities such as complex karyotype (CK), monosomal karyotype (MK), monosomy 5 or deletion 5q (-5/5q-), 17p abnormalities (abn(17p)) or inversion/translocation of chromosome 3q26 (inv(3)). The presence of such abnormalities may further influence the outcomes of SCT in pts with -7/7q-. The purpose of this study was to evaluate the role of SCT in AML with -7/7q- in the context of additional cytogenetic abnormalities. METHODSWe selected adult pts with AML and -7/7q- reported to the EBMT registry with a complete cytogenetic report. We included only first SCT from a sibling or unrelated donor (UD) performed between 2000 and 2016. RESULTSA total of 1109 pts were identified. Median age at SCT was 52 year-old (range, 18-76) and median follow-up was 34 months (range, 0.7-193). A diagnosis of secondary AML was reported in 213 pts (19%). At the time of SCT, 702 patients (63%) were in first remission (CR1), 58 (5%) in subsequent remission and 349 (32%) had active disease. Four hundred ninety-six pts received SCT from a sibling donor (45%). Most pts had a Karnofsky's performance status (KPS) of more than 80% at the time of SCT (93%). A myeloablative conditioning regimen was administered in 50% of the pts. In vivo T-cell depletion was part of the regimen in 56% of the pts.The 2-year probability of leukemia-free survival (LFS) and overall survival (OS) were 30% and 36%, respectively. The 2-year probability of non-relapse mortality (NRM) was 20% and the 2-year cumulative incidence of relapse (RI) was 50%. The cumulative incidence of acute graft-versus-host disease (GvHD) was 31% and the 2-year cumulative incidence of chronic GvHD was 31%. The 2-year probability of GvHD and relapse-free survival (GRFS) was 21%. In multivariate analysis, age was not associated with any outcomes. Active disease was significantly associated with increased NRM and RI, which translated into worse LFS, OS and GRFS. Significant higher NRM was associated with UD. Secondary AML was associated with higher NRM and decreased OS. Better KPS correlated significantly with less NRM and better LFS, OS and GRFS.To evaluate the impact of additional cytogenetic abnormalities, we have been able to sort out 5 different groups within the entire cohort. The first group included 523 pts with -7/7q- with or without CK, but without any of the following chromosomal abnormalities: MK, -5/5q-, abn(17p) or inv(3). One hundred ninety-nine pts belonged to the second group that included pts with -7/7q- within MK but without -5/5q-, abn(17p) or inv(3). The third group included 151 pts with -7/7q- in association with -5/5q- but no abn(17p) or inv(3). Group 4 included 125 pts with -7/7q- and abn(17p) but without inv(3). Finally, 111 pts had inv(3) in addition to 7/7q- and were assigned to the fifth group. NRM was similar across all groups. The 2-year probability of LFS was 39.7% for group 1, 28.5% for group 2, 22.5% for group 3, 16.4% for group 4 and 13.7% for group 5 (p<0.001) (see figure). The 2-year probabilities of OS in the 5 groups were 47.7%, 34.9%, 28.2%, 15.9% and 19.7%, respectively (p<0.001). The corresponding 2-year probability of GRFS was 29.7% for group 1, 16.6% for group 2, 14.5% for group 3, 8.1% for group 4 and 8.9% for group 5 (p<0.001). Multivariate analysis confirmed those significant differences across groups. We observed comparable results when the analysis was focused on CR1 pts. CONCLUSIONSSCT in AML pts with -7/7q- provides durable response in one third of the pts. Disease status at the time of transplantation remains the strongest prognostic factor for poor outcomes. The presence of -7/7q- with or without CK in the absence of MK, -5/5q-, abn(17p) or inv(3) was associated with a better survival after SCT. On the contrary, addition of MK, -5/5q-, abn(17p) or inv(3) identifies a sub-group of pts that benefits less from SCT. In these pts, future efforts should focus on prevention of relapse by therapeutic modalities like early withdrawal of immunosuppression, administration of hypomethylating agents, donor lymphocytes infusion or others. [Display omitted] DisclosuresSocié:Alexion Pharmaceuticals, Inc.: Consultancy. Mohty:Sanofi: Honoraria, Speakers Bureau.

Prenatal Diagnosis of Radial Ray Defect Associated with Fanconi Anemia: a Case Report

AbstractFanconi anemia (FA) is a rare genetic disorder with multisystem involvement. Confirmatory genetic testing is possible by diagnostic clues on examination of the proband within the differential diagnosis. We describe a fetus with radial ray defect in a primigravida. Cytogenetic testing for breakages confirmed Fanconi anemia as the etiology. Molecular testing by next generation sequencing did not reveal a point change in any of the twenty-one genes known to be associated with FA. A confirmed fetal autopsy phenotype and the cytogenetic report allowed for the identification of a homozygous deletion of exon 4–6 in the FANCC gene on re-analysis of the molecular dataset. This case exemplifies the utility of a step wise approach to the diagnosis of prenatally diagnosed radial ray defects and the importance of genetic counseling and prenatal testing.

Immunophenotypic Lineage Assessment By Multiparameter Flow Cytometry Provides More Precise MDS Prognosis

Background: Mixed phenotype acute leukemia is a rare disease characterized by an expanded blast population exhibiting multiple lineage features. It is a diagnosis of exclusion, and we and others have observed that AML-MRC or therapy-related AML cases may also exhibit similar features. We therefore sought to determine whether multi-lineage expression is present in de-novo and therapy-related MDS and whether it has an impact on clinical outcomes. Methods: We reviewed pathology, flow cytometry, cytogenetic, and molecular reports from patients seen at Memorial Sloan Kettering Cancer Center between 1996 and 2020 and identified 472 patients diagnosed with MDS using a combination of custom natural language processing tools and manual review. Cox proportional hazards modeling was performed to assess the contribution of patient characteristics, pathology, flow cytometric, cytogenetic, and molecular characteristics to overall survival (OS). Fisher's exact testing was used to assess the association of individual features. Results: We found that an abnormal myeloid lineage signature was associated with poorer OS after adjusting for age, cytogenetics, and molecular features (HR=2.3, p&amp;lt;0.01). In contrast, an abnormal plasma cell signature was associated with better OS (HR=0.3, p&amp;lt;0.01) (Figure A). Other abnormal lineages did not contribute significantly to OS although there were relatively few cases with abnormal T-cell markers (n=19). Mutations in TP53, IDH1, and EZH2 were associated with poorer OS (TP53: HR=1.5, p&amp;lt;0.01; IDH1: HR=2.3, p&amp;lt;0.01, EZH2: HR=1.9, p&amp;lt;0.01) and mutations in SF3B1 and IDH2 were associated with better OS (SF3B1: HR=0.35, p&amp;lt;0.01; IDH2: HR=0.6, p=0.05) (Figure B). TP53 mutation was enriched among patients with intermediate and poor risk cytogenetic groups (OR=11.3, p&amp;lt;0.01), consistent with higher risk therapy-related disease. IDH2, TET2, and ASXL1, which have been associated with clonal hematopoiesis, were enriched in the good and intermediate risk cytogenetic groups (IDH2: OR=4.3; p=0.03, TET2: OR=3.7, p&amp;lt;0.01; ASXL1: OR=4.3, p&amp;lt;0.01), although only IDH2 had a significant association with OS. Interestingly, there was a significant association of plasma cell lineage abnormalities with SRSF2 mutation (OR=3.5, p=0.05), but SRSF2 mutation was not an independent contributor to the global survival model (Figure C). Conclusion: Routine flow cytometric and molecular assessment of diagnostic bone marrows can provide added prognostic value in MDS. Identification of an abnormal myeloid lineage is associated with higher risk disease, while identification of abnormal plasma cell features is associated with lower risk disease. SRSF2 mutation is also associated with abnormal plasma cell features, but does not contribute independently to OS. Abnormal T-cell features may also provide prognostic value, although assessment in a larger cohort will be necessary. We confirm previous findings indicating that TP53 mutation is associated with higher risk disease while SF3B1 mutation is associated with better outcomes characteristic of MDS-RARS. In addition, our data suggests that IDH1 and EZH2 are associated with poorer outcomes and that IDH2 is associated with lower risk disease. Figure 1 Disclosures Tallman: Bioline rx: Membership on an entity's Board of Directors or advisory committees; Delta Fly Pharma: Membership on an entity's Board of Directors or advisory committees; Amgen: Research Funding; Abbvie: Research Funding; Cellerant: Research Funding; Orsenix: Research Funding; ADC Therapeutics: Research Funding; BioSight: Membership on an entity's Board of Directors or advisory committees, Research Funding; Glycomimetics: Research Funding; Rafael: Research Funding; Oncolyze: Membership on an entity's Board of Directors or advisory committees; UpToDate: Patents &amp; Royalties; Novartis: Membership on an entity's Board of Directors or advisory committees; Roche: Membership on an entity's Board of Directors or advisory committees; Jazz Pharma: Membership on an entity's Board of Directors or advisory committees; Daiichi-Sankyo: Membership on an entity's Board of Directors or advisory committees; KAHR: Membership on an entity's Board of Directors or advisory committees; Rigel: Membership on an entity's Board of Directors or advisory committees. Levine:Morphosys: Consultancy; Astellas: Consultancy; Janssen: Consultancy; Lilly: Consultancy, Honoraria; Isoplexis: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; C4 Therapeutics: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Imago: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Loxo: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Qiagen: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Prelude Therapeutics: Research Funding; Gilead: Honoraria; Novartis: Consultancy; Amgen: Honoraria; Roche: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding. Xiao:Stemline Therapeutics: Research Funding. Glass:Gerson Lehman Group: Consultancy.

Abstract 2094: Improving cancer cytogenetic case review with a new machine learning system

Abstract A novel machine learning system trained on The Cancer Genome Atlas (TCGA) data has been designed to help with classification, prognostic measures, and monitoring treatment responses in cancer management. The utility of this system will be demonstrated using a set of retrospective samples. Cytogenetic analysis has long been utilized in clinical cancer care with conventional cytogenetic methods such as chromosomal banding and FISH still standard protocols for hematologic malignancies. With the advent of microarrays, smaller and more complex variants have been discovered in cancer samples but identifying the potential impact of many alterations such as copy number variation (CNV) and loss of heterozygosity (LOH) has not been fully exploited. A typical cancer cytogenetic report can list many tens of variants with unclear clinical implications. To bridge this gap and assist with determining the clinical implications of such alterations, we have developed a novel machine learning system that has been trained using data from The Cancer Genome Atlas (TCGA). The TCGA data has been processed using the SNP-FASST2 segmentation algorithm followed by manual review for ploidy adjustment yielding high quality regions of CNV and LOH for over 6000 cases across 29 cancer types. Our novel neural network used this processed data to arrange samples based on their CNV and LOH profile across a two-dimensional map. The proximity of one sample to another on this map corresponds to its similarity in terms of CNV and LOH profile. To apply this system in a clinical setting, we have designed a case review system that aligns a new case with the learned cancer map to provide information on the similarity of the case with ones in TCGA. This enables rapid verification of tumor type or detection of a different origin for the sample than the one reported. In addition, the system can create a prognostic score using clinical survival data for the samples in TCGA. Here we will demonstrate the utility of the system in classifying new cases against the learned cancer map and estimating prognostic measures. Citation Format: Megan Roytman, Viren Wasnikar, Paul An, Raja Kashevan, Shalini Verma, Soheil Shams. Improving cancer cytogenetic case review with a new machine learning system [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2094.

Machine Learning Classifiers Evaluation for Automatic Karyogram Generation from G-Banded Metaphase Images

This work proposes the evaluation of a set of algorithms of machine learning and the selection of the most appropriate one for the classification of segmented chromosomes images acquired using the Giemsa staining technique (G-banding). The evaluation and selection of the best classification algorithms was carried out over a dataset of 119 Q-banding chromosomes images, and the obtained results were then applied to a dataset of 24 G-band chromosomes images, manually classified by an expert of the Laboratory of Cytogenetic of the Children’s Hospital of Tamaulipas. The results of evaluation of 51 classifiers yielded that the best classification accuracy for the selected features was obtained by a backpropagation neural network. One of the main contributions of this study is the proposal of a two-stage classification scheme based on the best classifier found by the initial evaluation. In stage 1, chromosome images are classified into three major groups. In stage 2, the output of phase 1 is used as the input of a multiclass classifier. Using this scheme, 82% of the IGB bank samples and 88% of the samples of a bank of images obtained with a Q-band available in the literature consisting of 119 chromosome studies were successfully classified. The proposed work is a part of an desktop application that allows cytogeneticist to automatically generate cytogenetic reports.

The Glasgow Prognostic Score at Diagnosis Is a Predictor of Clinical Outcome in Patients with Multiple Myeloma Undergoing Autologous Haematopoietic Stem Cell Transplantation.

Background: Immunity and inflammatory response affect the tumour microenvironment and the progression of malignancies. Metabolic and inflammatory parameters and ratios of the peripheral blood correlate with outcome in cancer patients. There exist several established and validated inflammation-based scores of prognostic significances including the Glasgow Prognostic Score (GPS). Methods: In this retrospective, multicentre study, we investigated the prognostic capabilities of baseline GPS in patients with multiple myeloma (MM) undergoing autologous stem cell transplantation as a complementary resource for risk stratification. For GPS calculation, a C-reactive-protein (CRP) value of >10 mg/dL counts as one point and an albumin value of <35 g/L connotes another point, resulting in three different subgroups (group I: 0 points; group II: 1 point; and group III: 2 points). Patients with MM admitted to the participating institutions between January 2010 and July 2018 were screened, and established prognostic scores and ratios were assessed. Characteristics significantly associated with overall survival (OS) or progression-free survival (PFS), upon univariate analysis, were included in a Cox proportional hazards model. Results: Following initial assessment, we identified 224 fully evaluable patients who underwent autologous haematopoietic stem cell transplantation for multiple myeloma. A centralised review of pathology and cytogenetic reports was conducted, and a central hematopathology assessment was performed in 175 of 224 cases (78.1%). Proceeding to high-dose chemotherapy and subsequent autologous stem cell transplantation was the main inclusion criterion for all transplant-eligible patients in the study. The median age at diagnosis was 59 years (range: 35–76 years) with a median follow-up of 76 months. Multivariate analysis revealed neutrophil–platelet score (NPS) (HR = 0.528, 95% CI = 0.284–0.984) and B symptoms at primary diagnosis (HR = 1.838, 95% CI = 1.232–2.740) to be independent predictors of PFS while high-risk cytogenetic changes (HR = 2.358, 95% CI = 1.413–3.934, p = 0.001) could be identified as an independent predictor of OS, and GPS to be the only independent predictor of both OS and PFS (OS: HR = 2.127, 95% CI = 1.431–3.162, p < 0.0001 and PFS: HR = 1.405; 95% CI = 1.058–1.867, p = 0.019). Conclusions: Our data show that baseline GPS correlates with rates of relapse and refractory disease in MM patients undergoing autologous transplantation. In a multivariate analysis, these effects were proven to hold prognostic capabilities beyond and independent from established prognosticators. These results require further validation in a prospective setting.

Birth seasonality of childhood central nervous system tumors: Analysis of primary data from 16 Southern-Eastern European population-based registries.

Season of birth, a surrogate of seasonal variation of environmental exposures, has been associated with increased risk of several cancers. In the context of a Southern-Eastern Europe (SEE) consortium, we explored the potential association of birth seasonality with childhood (0-14 years) central nervous system (CNS) tumors. Primary CNS tumor cases (n = 6,014) were retrieved from 16 population-based SEE registries (1983-2015). Poisson regression and meta-analyses on birth season were performed in nine countries with available live birth data (n = 4,987). Subanalyses by birth month, age, gender and principal histology were also conducted. Children born during winter were at a slightly increased risk of developing a CNS tumor overall [incidence rate ratio (IRR): 1.06, 95% confidence intervals (CI): 0.99-1.14], and of embryonal histology specifically (IRR: 1.13, 95% CI: 1.01-1.27). The winter peak of embryonal tumors was higher among boys (IRR: 1.24, 95% CI: 1.05-1.46), especially during the first 4 years of life (IRR: 1.33, 95% CI: 1.03-1.71). In contrast, boys <5 years born during summer seemed to be at a lower risk of embryonal tumors (IRR: 0.73, 95% CI: 0.54-0.99). A clustering of astrocytomas was also found among girls (0-14 years) born during spring (IRR: 1.23, 95% CI: 1.03-1.46). Although the present exploratory results are by no means definitive, they provide some indications for age-, gender- and histology-related seasonal variations of CNS tumors. Expansion of registration and linkage with cytogenetic reports could refine if birth seasonality is causally associated with CNS tumors and shed light into the complex pathophysiology of this lethal disease.

Outcomes of allogeneic stem cell transplantation for patients with t(6:9) AML- A strong case for allogeneic stem cell transplantation in first complete remission.

Outcomes of allogeneic stem cell transplantation for patients with t(6:9) AML- A strong case for allogeneic stem cell transplantation in first complete remission.

Transplant Characteristics and Outcomes of Philadelphia (Ph)-like Acute Lymphoblastic Leukemia (ALL)

<h3>Background</h3> Ph-like ALL is a recently recognized high risk B-ALL subgroup, defined by a gene expression profile similar to Ph (+) ALL that activates tyrosine kinase or cytokine receptor signaling. Several studies have described inferior outcomes with conventional chemotherapy and although small series suggest that it is responsive to targeted therapies, stem cell transplant (SCT) remains the only potentially curative option. However, the SCT outcomes of Ph-like ALL are not well defined and it remains unknown whether SCT is able to overcome the adverse prognosis associated with it. <h3>Methods</h3> We retrospectively identified 77 adult patients with Ph (-) B-ALL that received a SCT at Memorial Sloan Kettering, 2008-2018, and reviewed their cytogenetic and molecular reports at diagnosis. Testing for Ph-like ALL is employed in an algorithmically driven approach at our institution including cytogenetics, chromosomal microarray and next generation sequencing (NGS). Ph-like ALL was defined by the presence of abnormalities including <i>ABL</i>-class fusions that phenocopy <i>BCR-ABL</i> (<i>ABL1, ABL2, CSF1R</i> and <i>PDGFRB</i>) or alterations of <i>CRFL2, JAK2</i> and <i>EPOR</i> that activate JAK/STAT signaling. We then analyzed the SCT outcomes of Ph-like patients and compared them to Ph (-) patients. <h3>Results</h3> A Ph-like signature was identified in 13 of 77 (16.9%) patients by NGS (n=7), cytogenetics (n=1), both NGS/cytogenetics (n=2) or microarray (n=3). Median age of all 13 patients was 42.7 (range 23.9-67.7) years and 6 (46.2%) patients were adolescents/young adults (<40 years). Ph-like abnormalities included mutations of <i>NRAS</i> (n=3), <i>JAK2</i> (n=2), <i>NF1</i> (n=2), <i>FLT3 ITD</i> (n=1), and <i>IL7R</i> (n=1), fusions involving <i>CRFL2</i> (n=3) or <i>PDGFRB</i> (n=1) and <i>ABL1</i> rearrangements (n=1). Three patients had concomitant <i>IKZF1</i> mutations. Most patients received myeloablative conditioning (n=8, 61.5%) and the most common donor type was matched unrelated (n=7, 53.8%) (Fig 1). At a median follow up of 17.3 (range 0.5-109.3) months, overall survival (OS) was comparable between the Ph-like and Ph (-) groups with one-year OS rates of 74% and 70% (p=0.534) respectively (Fig 2A). Causes of death in Ph-like patients were relapse (n=2) and infectious complications (n=1). One-year cumulative incidence of relapse was 32.7% in Ph-like vs 17.3% in Ph (-) patients, however it did not reach statistical significance (p=0.94, Fig 3). Among the 4 Ph-like patients who relapsed, 1 had refractory disease prior to SCT, 2 were in second remission and 1 in first remission. One-year disease free survival was also comparable between the 2 groups (67% for Ph-like vs 65% for Ph (-), p=0.719) (Fig 2B). Finally, acute GVHD rates by day 100 were 69.2% in Ph-like (n=9) vs 53.1% (n=34) in Ph (-) patients (p=0.3). <h3>Conclusions</h3> Our findings suggest that SCT overcomes the adverse prognosis associated with the Ph-like signature and should be incorporated in the treatment of patients with this disease entity.