Deletion In Arm Research Articles

PATH-64. UNDERSTANDING MECHANISTIC UNDERPINNINGS OF MOLECULAR SUBGROUPS OF MENINGIOMA

Abstract Meningiomas are the most common intracranial tumors. In the past, they were thought to be indolent and could be treated by resection. The current standard of care utilizes WHO histopathological grading to identify malignant potential. Our lab identified three molecular groups (MenG A, B, and C) using CNVs, methylation, and/or expression profiling with different biological characteristics. These groups were independently validated and predicted recurrence more reliably than WHO grade. MenG A is genomically stable but harbors tumors with point mutations, mainly in TRAF7, KLF4, and AKT1. On the other hand, MenG B and C tumors have chromosome 22q arm deletion or loss of merlin, the protein product of the NF2 gene. Moreover, MenG B is characterized by DNA hypomethylation, while MenG C tumors show DNA hypermethylation and have additional chromosomal losses, most notably in chromosome 1p. Lastly, while MenG A/B are indolent, MenG C – comprising approximately 28% of meningiomas – recur frequently and are refractory to radiotherapy and/or surgery. How can two groups of tumors with the same driver mutation behave so differently? Hence, our lab is interested in (1) what molecular pathway/factor(s) are necessary for becoming any meningioma, and (2) what mechanisms are critical for the aggressiveness of MenG C. Here, we investigate the role of TRAF7 in meningioma biology. Toward this end, we study interactors, modulators, and individual mutations in cell culture. In addition, we use published exome sequencing and expression data to reveal possible connections between chromatin state and individual genes. In conclusion, a variety of underlying mechanisms drive meningioma tumorigenicity and aggressiveness. Elucidating these mechanisms could provide future therapeutic targets for currently untreatable meningiomas.

CLINICAL CASE OF RARE SMITH-MAGENIS SYNDROME IN NEWBORN CHILD

Aim. The purpose of the work is a comprehensive analysis of chromosomal pathology based on own detection of a rare clinical case of Smith-Magenis syndrome in a newborn child, the results of which may be useful for the detection and prevention of hereditary diseases. Materials and methods. Based on the analysis of literature data, it was found that clinical cases of rare (SMS) in newborns occur with a frequency of 1 in 25,000–1:15,000. This syndrome is caused by a chromosomal rearrangement that leads to the loss of significant segments of one chromosome from the 17th pair of chromosomes. There is a deletion of genetic material in the region of chromosome 17 (17p11.2), which is why SMS is sometimes called 17p syndrome. In this work, the analysis of clinical symptoms and laboratory-instrumental examinations, the main of which are cytogenetic (karyotyping) and molecular genetic methods, were used to confirm the diagnosis of the disease. The results were obtained during the study of the biological material of the lymphocyte culture of the peripheral blood of the child, mother and father. As a result of the cytogenetic study of the child, the karyotype 46, ХУ, del(17) (p11.2p11.2) was established, that is, a male karyotype with an interstitial deletion in the short arm of chromosome 17 within the band 17p11.2. The mother's karyotype is 46, XX, no chromosomal abnormalities were detected. The father's karyotype is 46, XU, no chromosomal abnormalities were detected. A molecular genetic study of blood leukocytes was conducted to establish the presence of microdeletions/microduplications in the corresponding loci. The result of the study is rsa17p11.2(P245)x1. Chromosome imbalance was established in the form of RAI1, DRC3, LLGL1 gene deletion in the 17p11.2 region, which verifies Smith-Magenis syndrome. Conclusions. In the work, a comprehensive analysis of chromosomal pathology was carried out based on the own detection of a clinical case of a rare Smith-Magenis syndrome in a newborn child. A detailed anamnesis, clinical manifestations, a set of laboratory-instrumental studies, the main ones of which are cytogenetic (karyotyping) and molecular genetic methods, are used for targeted examination, verification of the diagnosis and assessment of disease manifestations. The biological material of the peripheral blood culture (lymphocytes, leukocytes) of the child and parents was used. The results of a comprehensive analysis of chromosomal pathology based on one's own clinical case of the rare Smith-Magenis syndrome in a child of the neonatal period can draw the attention of primary care physicians to the study of syndromes of hereditary diseases and, in the differential diagnosis of patients, direct them to a medical-genetic consultation for cyto- and molecular-genetic studies.

Analyzing the characteristics and prognostic outcomes for patients with myelodysplastic syndrome with Q-gene deletion.

e18526 Background: Myelodysplastic syndromes (MDS) are a group of hemopoietic disorders in which the bone marrow is deficient in producing healthy mature blood cells. MDS associated with a deletion in the long arm of chromosome 5Q is a rare occurrence, but considered a good prognosis in comparison to other subgroups of MDS. There has been limited focus directed towards this variant of the disease, especially concerning outcomes among different demographics. Methods: The National Cancer Institute’s Surveillance, Epidemiology, and End-Result (SEER) registry research database 17 (2000 -2020) was used to assess & compare the outcomes for this variant of MDS in adult & AYA pts. Univariate & multivariate analyses was performed and cox proportional hazards regression was used to assess prognostic outcomes. A two-sided pvalue ≤0.05 was considered significant. Results: Analysing (table) 2,323 pts identified, 98.92% (n= 2298) were adults ≥40yrs, and 1.08% (n= 25) were AYAs. AYAs comprised 32% Hispanic, 4% Non-Hispanic Asian or Pacific Islander (NHAPI), 16% Non-Hispanic Black (NHB), and 48% Non-Hispanic White (NHW). Compared to adults, AYAs had higher proportions of Hispanics and NHBs but fewer NHWs. AYAs showed longer average survival (57.7 vs 33 months) than older adults. Females generally had longer survival periods than males in both AYA (64.4 vs 49.1 months) & adult (37.2 vs 26.4 months) groups. Among adult racial groups, Non-Hispanic Black females had the poorest prognosis (29.6 months), while Hispanic males had the worst prognosis overall (21 months). Among AYAs, Hispanic females had the worst prognosis (4 months), followed by Hispanic males (24.2 months). Conclusions: Our study shows AYAs are less likely to die from MDS compared to adults ≥40. Hispanic females appear to have a worse outcome than males in both age groups & is independent of other analysed prognostic factors. More research is needed to examine other prognostic factors with the aim of improving survival outcomes. [Table: see text]

Abstract LB345: Correlating the blood immune repertoire and clinical features of del17p CLL patients

Abstract Introduction: Deletion in the short arm of chromosome 17 (del17p) is a strong, negative prognostic biomarker found in about eight percent of patients with untreated chronic lymphocytic leukemia (CLL). CLL patients with del17p exhibit resistance to therapy, accelerated disease progression, and global immunodeficiency. It is unclear the extent to which global immunodeficiency impacts disease course and therapy outcomes. The goal of this study was to document the blood immune repertoire of patients with untreated CLL who have del17p and associate with clinical features, time to first treatment (TFT), and overall survival (OS). Methods: Biobanked blood samples from treatment-naïve del17p CLL patients (n = 58) and age-matched controls (n = 5) were obtained. B cells and T cells were analyzed with comprehensive, cell type-specific flow cytometry panels and visualized with unbiased dimensionality reduction. Lab values were log-transformed and compared using t-tests and one-way ANOVAs. TFT was calculated from date of sample collection to date of first CLL-directed therapy or last known untreated date; OS was calculated from date of sample collection to death or last known alive status. Cox proportional hazards regression analyses (results reported as hazard ratio [HR] and 95% confidence interval [CI]) were employed to identify associations of lab values with OS and TFT. Results: Patients with del17p CLL had increased proportions of T regulatory cells (Tregs) among total CD4+ T cells compared to controls (CLL 11.1%, control 5.7%, p = 0.05). A higher proportion of CD8+ T cells was associated with longer TFT (HR 0.57, 95%CI 0.36-0.89); in contrast, higher proportions of TIGIT+ (HR 1.83, 95%CI 1.03-3.28) and TIM3+ conventional (non-Treg) CD4+ T cells were associated with shorter TFT (HR 1.70, 95%CI 1.02-2.84). A higher proportion of PD1+ CD8+ T cells was associated with shorter OS (HR 1.79, 95%CI 1.05-3.06), in addition to PD1+ conventional CD4+ T cell proportion (HR 2.21, 95%CI 1.06-4.60). CLL B cells expressed PD-1 and inducible T cell costimulator (ICOS) at significantly lower median fluorescence intensities (MFIs) than control B cells (p < 0.0001 for both). The CXCR5+ MFI (HR 1.0002, 95%CI 1.0001-1.003) and CD23+ MFI (HR 1.88, 95%CI 1.01-3.50) of CLL B cells were associated with shorter TFT. Discussion: In this cohort of treatment-naïve del17p CLL patients, we determined that patients with higher proportions of exhausted CD4+ and CD8+ T cell phenotypes had significantly shorter OS. Cytotoxic T cell proportion positively associated with TFT, whereas proportions of CD4+ T cell exhaustion phenotypes negatively associated with TFT. Higher CXCR5+ and CD23+ MFIs of CLL B cells also associated with shorter TFT. The preliminary findings from our study suggest that the blood immune repertoire has strong associations with clinically relevant outcomes such as time to first treatment and overall survival in patients with untreated del17p CLL. Citation Format: Ethan J. Katcher, Kim A. Gwin, Sameer A. Parikh, Kari G. Rabe, Petra K. Lothert, Preeti Trisal, Esteban Braggio, Susan L. Slager, Nicholas Strong, Daniel L. Van Dyke, Zhiquan Wang, C. Chris Huang, Anita K. Gandhi, Kay L. Medina, Neil E. Kay. Correlating the blood immune repertoire and clinical features of del17p CLL patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB345.

X chromosome rearrangement associated with premature ovarian insufficiency as diagnosed by molecular cytogenetic methods: a case report and review of the literature

BackgroundPremature ovarian insufficiency (POI) is a clinical condition characterized by ovarian dysfunction in women under 40. The etiology of most POI cases remains unidentified and is believed to be multifactorial, including factors such as autoimmunity, metabolism, infection, and genetics. POI exhibits significant genetic heterogeneity, and it can result from chromosomal abnormalities and monogenic defects.Case presentationThe study participant, a 33-year-old woman, presented with a history of irregular menstruation that commenced two years ago, progressing to prolonged menstrual episodes and eventual cessation. The participant exhibits a rearrangement of the X chromosome, characterized by heterozygosity duplication on the long arm and heterozygosity deletion on the short arm by whole exome sequencing(WES) combined with cell chromosome detection.ConclusionsThis study expands the spectrum of mutations associated with POI resulting from X chromosomal abnormalities. WES-Copy number variation analysis, in conjunction with chromosome karyotype analysis and other detection techniques, can provide a more comprehensive understanding of the genetic landscape underlying complex single or multi-system diseases.

Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories

The mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.

NCMP-05. INTRACTABLE HEADACHE IN NEWLY DIAGNOSED AML WITH MIGRAINES AND CHIARI MALFORMATION- UNVEILING A COMPLEX SYMPTOM

Abstract Acute Myeloid Leukemia (AML) involvement in central nervous system (CNS) is poorly understood in pathophysiology, with reported incidence rates ranging from 1-33% of patients with relapsed AML. CNS involvement is uncommon in the early stages of AML. FLT3-ITD, chromosome 11 abnormalities, and inv(16) cytogenetics are known to have more potential to invade the CNS. A 28-year-old woman with recently diagnosed AML (FLT D835 mutation with deletion in the long arm of chromosome 11) and migraines was admitted for HIDAC consolidation #3. On day two, she started experiencing headaches in the bifrontal and bitemporal regions associated with photophobia, phonophobia, and nausea. Treatment for status migrainous provided little relief. MRI brain showed progression of Chiari malformation (CM) with tonsillar herniation from 16 to 19 mm, which precluded a lumbar puncture. On day 4, she was noted to have grade III papilledema and bilateral cranial nerve IV palsy with non-enhancing patchy increased FLAIR signal in dorsal pons, bilateral cerebral and middle cerebellar peduncles, without diffuse restriction on imaging. The patient underwent sub-occipital craniotomy and C1 laminectomy for decompression for chiari. On day 5, she developed cranial nerve palsies involving nerves VII, IV, and XII. Lumbar puncture (LP) performed after decompression demonstrated elevated opening pressure and 98% abnormal myeloid blast population, confirming CNS involvement of AML. 4 days before starting intrathecal chemotherapy, the patient was found to be in asystole (unclear etiology). This case highlights the range of differential diagnoses for headaches in a patient with multiple comorbidities, including obesity, migraine, Chiari malformation with tonsillar herniation, and cancer. It underscores the necessity for proactive screening of CNS invasion in AML patients with high-risk mutations and neurological symptoms. Moreover, it emphasizes the need to consider CNS involvement in AML patients with headaches, even if standard imaging does not show typical signs of leptomeningeal spread.

Cost-minimisation analysis of chronic lymphocytic leukemia in Spain in the era of oral targeted therapies

ObjectiveChronic lymphocytic leukaemia places a considerable economic burden on the Spanish National Health System. This study estimated the direct costs of chronic lymphocytic leukaemia oral targeted therapies from 2011 to 2025, inclusive, in a scenario with fixed treatment oral targeted therapies and in a scenario without them. MethodThe clinical course of adult chronic lymphocytic leukaemia patients was represented by a Markov model with four health states: watchful waiting, first-line treatment, relapse, and death. The treatment pattern was defined according to patient type by disease status or situation, age, presence or absence of deletion in the short arm of chromosome 17, immunoglobulin heavy chain mutation status, and year of treatment. The treatment algorithm was simulated from 2011 to 2025, and included therapies funded by the Spanish National Health System and their use in routine clinical practice, validated by leading experts. A single treatment option was assumed for each type of patient and time period (the most widely option used at each time point). Direct costs were included: pharmacological, administration, tests performed, routine visits, hospitalizations, and adverse events. ResultsFrom 2011 to 2025, there would be a mean annual chronic lymphocytic leukaemia prevalence of 16,436 patients in the scenario without fixed treatment oral targeted therapies and 16,413 in the scenario with fixed treatment oral targeted therapies. In the same period, the total costs in the scenario without fixed treatment oral targeted therapies would be €4,676.7 million and in the scenario with fixed treatment oral targeted therapies they would be €4,111.8 million. Thus, the introduction of fixed treatment oral targeted therapies would entail a saving of €564.9 million (12.1% of the total cost of care of chronic lymphocytic leukaemia patients during the period assessed). In this period, the total cost per patient would decrease from €266,019 in the scenario without fixed treatment oral targeted therapies to €236,852 in the scenario with fixed treatment oral targeted therapies, representing a saving of €29,167 per patient. ConclusionsThis study estimates that, between 2011 and 2025, the introduction of fixed treatment oral targeted therapies for the treatment of chronic lymphocytic leukaemia would entail €564.9 million cost savings for the Spanish National Health System (12.1% of the total cost of care of chronic lymphocytic leukaemia patients during the period assessed).

Cognitive-Behavioral Profile in Pediatric Patients with Syndrome 5p-; Genotype-Phenotype Correlationships.

(1) Background: 5p minus Syndrome (S5p-) is a neurodevelopmental disorder caused by a deletion in the short arm of chromosome 5. Among the phenotypic characteristics of S5p-, the most characteristic and representative element is a monochromatic cry with a high-pitched tone reminiscent of a cat's meow. Individuals may also show great phenotypic heterogeneity and great genetic variability. Regarding cognitive-behavioral aspects of the syndrome, the studies are scarce and do not establish a general profile of the main cognitive-behavioral particularities that this syndrome presents. The main objective of this work was to describe the development profile of a cohort of 45 children with 5p minus Syndrome, concerning the biomedical, genetic, cognitive, and behavioral aspects. Establishing putative genotype-phenotype (cognitive-behavioral profiles) relationships in our cohort, from an interdisciplinary approach. (2) Methods: A selection of instruments of measures was selected for neuropsychological assessment (3) Results: In general, children with S5p- have a higher cognitive level than a communicative and motor level. Language difficulties, especially expressive ones, influence the frequency and severity of the most frequent behavioral problems in S5p. The most significant problem behavior of children with S5p-, especially girls, is self-harm. Compulsive behavior, limited preferences, and interest in monotony are significantly more frequent in subjects with better cognitive levels. We also find a significant correlation between the size of the loss of genetic material on 5p and the cognitive level of the subjects. (4) Conclusions: We described for the first time, the cognitive-behavioral profile of a cohort of minors with S5p-. Remarkably, it was found that language, especially of an expressive nature, modulates the most frequent behavioral aspects in subjects with lower cognitive levels, so it is essential to develop verbal or alternative communication strategies adjusted to these individuals.

Microdeletion 3q13.31 and Agenesis of the Corpus Callosum in a Patient with Intellectual Disability and Autism Spectrum Disorder: A Case Report

Total agenesis of the corpus callosum (ACC) is a rare condition characterized by the absence of corpus callosum formation during fetal development. It can occur in isolation or be associated with congenital syndromes, including the emerging microdeletion syndrome 3q13.31. This syndrome, caused by a deletion in the long arm of chromosome 3, presents with developmental delay, growth abnormalities, craniofacial dysmorphology, skeletal malformations, genital anomalies, and agenesis of the corpus callosum. The case of a 7½-year-old boy with microdeletion 3q13.31 is described, highlighting common clinical manifestations observed in this syndrome. The patient exhibited delayed psychomotor development, language delay, autism spectrum disorder, intellectual disability, facial dysmorphology, and agenesis of the corpus callosum. Comparison with existing literature showed similarities in features such as delayed development, language delays, intellectual disability, and brain anomalies. The 3q13.31 microdeletion syndrome encompasses a wide range of clinical phenotypes, and the identification of responsible genes contributes to understanding the condition, although treatment remains challenging.

Cytogenetic Analysis of Patients with Hematological Malignancies

With this study, we aim to summarize and assess the activity and performance of the Cytogenetic sector of the Laboratory of Medical Genetics—Varna, regarding the conventional cytogenetic analysis of bone marrow samples from patients with (onco)hematological diagnoses. Another purpose is to evaluate the tendencies noticed over a period of eleven years to draw conclusions and share our experience. We have performed the analysis with the G-banding technique on 2653 samples from patients of age 0–93 yr by the current European recommendations and the International System for Human Cytogenomic Nomenclature. The greater part of these samples (90.9%) was with an indication of a hematological malignancy, most commonly Acute myeloid leukemia, Myelodysplastic syndrome, Acute lymphoid leukemia, Chronic myeloid leukemia, and Multiple myeloma. Analysis was successful in 2215 (83.5%)—from those normal karyotypes were found in 1492 (67.4%) and pathology in 723 (32.6%). Regarding the latter, the most common were complex karyotypes (30.6%), Philadelphian chromosome (21.3%), trisomy 8 (5.9%), and deletion in the long arm of chromosome 5 (4.3%). Cytogenetic analysis is a method with great impact on the evaluation of many hematological malignancies and for this reason, it remains an essential part of routine assessment of these diseases. The disadvantages of it mainly in the field of oncohematological diseases, recognized by the scientific society and confirmed in our own experience, suggest a need for an additional genetic method to overcome these limitations.

PASTE: The Way Forward for Large DNA Insertions.

PASTE: The Way Forward for Large DNA Insertions.

Genetic analysis of Turner syndrome in Tunisian patients

Background/aim Turner syndrome (TS) is a rare sex chromosome abnormality in women, occurring in approximately one in 2500 live births, associated with a wide range of clinical stigmata of which short stature, ovarian dysgenesis, and dysmorphic features are the most frequent. Morbidity and mortality are clearly increased compared with the general population, and the average age at diagnosis is quite delayed. Even if the majority of females with TS have a non-mosaic 45,X karyotype, several karyotype variations exist, including short or long arm deletion, ring X isochromosome of the long arm, and 45,X 46,XX mosaicism. This explains the large phenotypic and genetic heterogeneities of TS, which make the diagnosis and especially the management increasingly difficult. We present in this work a genetic study of TS in the Tunisian population to establish a genotype–phenotype correlation, which would be of great help for the diagnosis and the care of patients. Patients and methods A total of 26 unrelated Tunisian girls were included in this study. All patients underwent a complete clinical and biochemical examination as well as karyotyping. The screening for the SRY gene was carried out by fluorescence in-situ hybridization or by PCR. Results Cytogenetic results showed a prevalence of the 45,X karyotype in 46% of patients and various proportions of the other karyotypes. However, genotype–phenotype correlation revealed several discrepancies regarding the major signs and the age at diagnosis. The comparison of the approaches used for the screening of the SRY gene showed that karyotyping is unable to detect low 45,X/46,XY mosaicism and that it is the PCR that would be able to do, eliciting its role to make a reliable diagnosis. Conclusion The karyotype alone is not sufficient to make a TS diagnosis in cases of weak mosaicism, and the great heterogeneity that reigns the syndrome elicits an epigenetic and transcriptomic exploration of several genes that recently seem to be involved in the disease.

ZDHHC15 as a candidate gene for autism spectrum disorder.

The phenotypic repercussion of ZDHHC15 haploinsufficiency is not well-known. This gene was initially suggested as a candidate for X-linked mental retardation, but such an association was later questioned. We studied a multiplex family with three members with autism spectrum disorder (ASD) by array CGH, karyotype, exome sequencing and X-chromosome inactivation patterns. Medical history interviews, cognitive and physical examinations, and sensory profiling were also assessed. The three family members with ASD (with normal cognitive abilities and an abnormal sensory profile) were the only carriers of a 1.7Mb deletion in the long arm of chromosome X, involving: ZDHHC15, MAGEE2, PBDC1, MAGEE1, MIR384 and MIR325. The normal chromosome X was preferentially inactivated in female carriers, and the whole exome sequencing of an affected family member did not reveal any additional genetic variant that could explain the phenotype. Thus, in the present family, ASD segregates with a deletion on chromosome X that includes ZDHHC15. Considering our results together with gene data (regarding function, expression, conservation and animal/cellular models), ZDHHC15 is a candidate gene for ASD. Emerging evidence also suggests that this gene could be associated with other neurodevelopmental disorders, with incomplete penetrance and variable expressivity.

Quantitative Cytogenetic Analysis with karyoParser Allows for More Precise Identification of Disease Biology, Clonal Evolution, and Etiology of Relapse in Acute Myeloid Leukemia

Introduction: Clinical risk assessment in AML relies on high quality cytogenetic data, often reported as a modal karyotype in International System for Human Cytogenomic Nomenclature format (ISCN). Here we show that quantitative assessment of clonal hierarchy is feasible for both internal and public datasets and reveals cytogenetic signatures reflective of disease biology both at diagnosis and relapse. Methods We built karyoParser as an R package to facilitate automated analysis. Using the ISCN string, it builds a quantitative clonal hierarchy for downstream analysis including automated AML assessment using leukNLP (Abstract id: 170203). To quantitatively assess relationships between different karyotypes, each alteration was assigned a value reflecting the degree of change. Translocations were assigned +3, full additions +1, full deletions -1, p arm additions +0.3, p arm deletions -0.3, q arm additions + 0.7, and q arm deletions -0.7. Hierarchical clustering was then performed on cases with cytogenetic abnormalities using Euclidean distance and Ward's method. Clusters were identified by cutting the dendrogram at a distance balancing intercluster homogeneity with intracluster heterogeneity. Cluster labels were assigned according to dominant cytogenetic features. Clinical annotation of prior MDS cases at Memorial Sloan Kettering (MSK) were obtained through a manually curated database. MPN cases were identified using a composite of JAK2/CALR/MPL mutation presence as well as leukNLP annotation. Prior treatment information and AML therapy were also obtained through leukNLP annotation. Clinical annotation of TCGA and Beat AML cases were obtained from the respective publications. Enrichment for these features and molecular features in specific clusters was assessed using a logistic regression model. The impact of diagnostic abnormal clone count was determined by Cox Proportional Hazards survival modeling. In the MSK cohort, response to therapy was obtained through leukNLP annotation and included complete response (CR), CR without minimal residual disease (CR MRD-), CR with incomplete count recovery (CRi), morphologic leukemia free state (MLFS), partial response (PR), and no response (NR). Patterns of clonal evolution were analyzed using a Cox Proportional Hazards event free survival model. Results We applied karyoParser to a dataset consisting of AML patients from MSK (N= 599), the public TCGA AML cohort (N=195) 5 and public Beat AML cohort (N=466). Unsupervised analysis revealed 14 clusters, 8 of which were defined by well characterized AML translocations (Figure 1). Clusters 6 and 7 were enriched for prior chemotherapy (p<0.01, p<0.01). Clusters 2, 7, and 8 were associated with prior MDS or MPN (p<0.01, p< 0.01, p=0.01). Cluster 4 was negatively correlated with prior malignancy (p<0.01). Clusters 7, 5, and 11 were significantly enriched for TP53 mutations, exhibiting the diverse modalities of AML progression following this mutation (p < 0.01). We also note a significant enrichment of SF3B1 in the inv(3) cluster (p < 0.01) which was only recently described in AML. In addition, we note enrichment of KIT mutations in t(8;21) and FLT3-ITD in APL (p < 0.01, p = 0.04), which have been previously described. We next sought to assess the impact of abnormal clones on clinical outcomes. In the combined cohort, increased abnormal clone count at diagnosis was associated with poorer overall survival (3 clones: HR: 3.2, p<0.01, 4+ clones: HR: 3.0, p <0.01). For the subset of patients at MSK with longitudinal data we found that depth of response was also influenced by abnormal clone count. Achievement of a CR decreased significantly with higher numbers of abnormal clones (p = 0.05) and NR increased (p < 0.01). CR MRD- also showed a trend toward decline with increasing abnormal clone count (p=0.10) (Figure 2). Time to relapse also differed based on the pattern of clonal evolution. Compared to normal karyotype cases, emergence of new clones had a significantly longer disease free interval (16.4 months; p=0.01) and relapse with an identical clone showed a trend toward a shorter interval (6.4 months; p=0.053). Conclusion Quantitative assessment of hierarchically structured karyotypes in AML fills a void in the analysis of AML biology. Using karyoParser, we show that joint analysis of both public and local datasets is feasible in a way that defines novel disease biology, prognosis, and patterns of relapse. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Reversal of Clinical Phenotype of Sotos Syndrome Due to Microduplication of NSD1 Gene.

Sotos syndrome is caused by heterozygous pathogenic variants or deletions in the long arm of chromosome 5 encompassing NSD1. The cardinal features of this condition are overgrowth, macrocephaly, and intellectual disability. Conversely, duplications leading to an extra copy of NSD1 result in a reverse phenotype that is observed in duplication/microduplication of the 5q region.An 11-y-old boy was referred to the genetics clinic in view of global developmental delay and general tonic-clonic seizures. Whole-exome sequencing revealed the presence of likely pathogenic copy number variation, a contiguous duplication of size ~4.11Mb spanning genomic location chr5: g.(?_171773956)_(175880045_?)dup. After validation by multiplex ligation-dependent probe amplification (MLPA) and phenotypic correlation, a diagnosis of reverse Sotos syndrome was confirmed. As far as the authors know, this is the first patient report of reverse Sotos syndrome from India. It highlights the peculiar presentation of this disorder as well as discusses the increasing potential of exome sequencing to screen for copy number variations (CNVs).

Endothelial Loss of ETS1 Impairs Coronary Vascular Development and Leads to Ventricular Non-Compaction.

Jacobsen syndrome is a rare chromosomal disorder caused by deletions in the long arm of human chromosome 11, resulting in multiple developmental defects including congenital heart defects. Combined studies in humans and genetically engineered mice implicate that loss of ETS1 (E26 transformation specific 1) is the cause of congenital heart defects in Jacobsen syndrome, but the underlying molecular and cellular mechanisms are unknown. To determine the role of ETS1 in heart development, specifically its roles in coronary endothelium and endocardium and the mechanisms by which loss of ETS1 causes coronary vascular defects and ventricular noncompaction. ETS1 global and endothelial-specific knockout mice were used. Phenotypic assessments, RNA sequencing, and chromatin immunoprecipitation analysis were performed together with expression analysis, immunofluorescence and RNAscope in situ hybridization to uncover phenotypic and transcriptomic changes in response to loss of ETS1. Loss of ETS1 in endothelial cells causes ventricular noncompaction, reproducing the phenotype arising from global deletion of ETS1. Endothelial-specific deletion of ETS1 decreased the levels of Alk1 (activin receptor-like kinase 1), Cldn5 (claudin 5), Sox18 (SRY-box transcription factor 18), Robo4 (roundabout guidance receptor 4), Esm1 (endothelial cell specific molecule 1) and Kdr (kinase insert domain receptor), 6 important angiogenesis-relevant genes in endothelial cells, causing a coronary vasculature developmental defect in association with decreased compact zone cardiomyocyte proliferation. Downregulation of ALK1 expression in endocardium due to the loss of ETS1, along with the upregulation of TGF (transforming growth factor)-β1 and TGF-β3, occurred with increased TGFBR2/TGFBR1/SMAD2 signaling and increased extracellular matrix expression in the trabecular layer, in association with increased trabecular cardiomyocyte proliferation. These results demonstrate the importance of endothelial and endocardial ETS1 in cardiac development. Delineation of the gene regulatory network involving ETS1 in heart development will enhance our understanding of the molecular mechanisms underlying ventricular and coronary vascular developmental defects and will lead to improved approaches for the treatment of patients with congenital heart disease.

Novel 12 Mb interstitial deletion of chromosome 8p11.22-p21.2: a case report

BackgroundThe deletion of a short arm fragment on chromosome 8 is a rare cause of Kallmann syndrome and spherocytosis due to deletion of the FGFR1 and ANK1 genes.Case presentationThis case study describes a 4-month-old child with growth and psychomotor retardation, auricle deformity, microcephaly, polydactyly, a heart abnormality, and feeding difficulties. An approximately 12.00 MB deletion was detected in the 8p11.22-p21.2 region of chromosome 8. After sequencing, we found that 65 protein genes had been deleted, including FGFR1, which resulted in Kallmann syndrome. There was no deletion of the ANK1 gene associated with spherocytosis, consistent with the phenotype.ConclusionThis patient is a new case of short arm deletion of chromosome 8, resulting in novel and previously unreported clinical features.

EP073: Interstitial deletion of 3q21 in a child with multiple congenital anomalies; Expanding the phenotype

Interstitial deletions in the long arm of chromosome 3 although relatively rare, have been reported to be associated with several congenital anomalies and developmental delays. Around eleven individuals with interstitial deletion spanning the region 3q21 have been reported with overlapping phenotype, including craniofacial dysmorphism, global developmental delay, skeletal manifestations, hypotonia, ophthalmological abnormalities, brain anomalies (mainly agenesis of corpus callosum), genitourinary tract anomalies, failure to thrive and microcephaly.

13q14 Deletion and Its Effect on Prognosis of Chronic Lymphocytic Leukemia.

Chronic lymphocytic leukemia (CLL) is the most common leukemia affecting adults. CLL results due to uncontrolled accumulation of B lymphocytes in the body with the clinical spectrum ranging from comparatively benign disease to an aggressive form. The disease pathogenesis lies in molecular genetics, the most common alteration being the deletion in the long arm of chromosome 13, at position 14 (13q14) region. This deletion leads to the loss of important microRNAs which are involved in maintaining the critical balance of the apoptosis mechanism of cell death of B lymphocytes. As such, the imbalance contributes towards B cells' immortality and, thus, CLL arises. This significant 13q14 deletion contributes to CLL's pathogenesis and paves the way for CLL treatment, hence affecting the prognosis of the affected patients.Furthermore, the size of deletion of the long arm of chromosome 13 (13q) has a remarkable effect on its prognosis and therapeutic intervention. The minimal deleted region (MDR)/small deletion or long 13q loss/mutation, and biallelic 13q deletion or monoallelic 13q deletion are commonly seen. 13q14 deletion is an initiating defect targeting tumor suppressor gene locus deleted in lymphocytic leukemia 2 (DLEU2))/microRNA15A (MIR15A)/microRNA 16-1 (MIR 16-1). Regarding CLL treatment, conventional therapy with alkylating agents has been used for a long time, which reported low- to non-existent complete remission rates and adverse events after prolonged use. Moreover, research into the 13q14 deletion has also provided new insights into the molecular genetics and pathways that interact in such a way, making it possible to transform healthy cells into malignant cells in an entirely new fashion with a complete disregard to its original form, resulting in CLL.