1p Deletions Research Articles

Genetic Analysis of Pheochromocytoma and Paraganglioma Complicating Cyanotic Congenital Heart Disease.

Pheochromocytoma and paraganglioma (PPGL) may appear as a complication of cyanotic congenital heart disease (CCHD-PPGL) with frequent EPAS1 mutations, suggesting a close link between EPAS1 mutations and tissue hypoxia in CCHD-PPGL pathogenesis. Our aim is to further investigate the role of EPAS1 mutations in the hypoxia-driven mechanism of CCHD-PPGL pathogenesis, particularly focusing on metachronous and/or multifocal CCHD-PPGL tumors. We performed whole-exome sequencing (WES) for somatic and germline mutations in 15 PPGL samples from 7 CCHD patients, including 3 patients with metachronous and/or multifocal tumors, together with an adrenal medullary hyperplasia (AMH) sample. We detected EPAS1 mutations in 15 out of 16 PPGL/AMH samples from 7 cases. Conspicuously, all EPAS1 mutations in each of 3 cases with multifocal or metachronous tumors were mutually independent and typical examples of parallel evolution, which is suggestive of strong positive selection of EPAS1-mutated clones. Compared to 165 The Cancer Genome Atlas non-CCHD-PPGL samples, CCHD-PPGL/AMH samples were enriched for 11p deletions (13/16) and 2p amplifications (4/16). Of particular note, the multiple metachronous PPGL tumors with additional copy number abnormalities developed 18 to 23 years after the resolution of hypoxemia, suggesting that CCHD-induced hypoxic environments are critical for positive selection of EPAS1 mutants in early life, but may no longer be required for development of PPGL in later life. Our results highlight a key role of activated hypoxia-inducible factor 2α due to mutated EPAS1 in positive selection under hypoxic environments, although hypoxemia itself may not necessarily be required for the EPAS1-mutated clones to progress to PPGL.

P-146 The first comprehensive genomic characterization of rectal squamous cell carcinoma

Rectal cancers represent 35% of colorectal cancers; 90% are adenocarcinomas while rectal squamous cell carcinomas represents 0.3% of them. Given its rarity, little is known concerning its pathogenesis, molecular profile and therapeutic management. The current treatment trend is to treat rectal squamous cell carcinoma by analogy with anal squamous cell carcinoma with definitive chemoradiotherapy setting aside surgery in case of local recurrence. We performed an in-depth genomic analysis (Next Generation Sequencing – 400 gene panel, Oncoscan, Human Papilloma Virus characterization) on 10 rectal squamous cell carcinoma samples and compared them in silico to those of anal squamous cell carcinoma and rectal adenocarcinoma. Rectal squamous cell carcinoma shows 100% HPV positivity. It has a similar mutational (PIK3CA, PTEN, TP53, ATM, BCL6, SOX2) and copy number variations profiles (3p deletion and 3q, 5p, 8q, 20p gain) to anal squamous cell carcinomas. PI3K/Akt/mTOR is the most commonly affected signaling pathway similarly to anal squamous cell carcinoma. In addition, common genomic alterations seen in rectal adenocarcinoma (FLT3, CDX2, GNAS BCL2, SMAD4, MALT1 mutations) were not found in these rectal squamous cases. This study presents the first comprehensive genomic characterization of rectal squamous cell carcinoma. We confirm the existence of this rare histology and its molecular similarity with anal squamous cell carcinoma. This molecular proximity confirms the adequacy of therapeutic management based on histology and not localization.

Chromosome 1 instability in multiple myeloma: Aberrant gene expression, pathogenesis, and potential therapeutic target.

Multiple myeloma (MM), the terminally differentiated B cells malignancy, is widely considered to be incurable since many patients have either developed drug resistance or experienced an eventual relapse. To develop precise and efficient therapeutic strategies, we must understand the pathogenesis of MM. Thus, unveiling the driver events of MM and its further clonal evolution will help us understand this complicated disease. Chromosome 1 instabilities are the most common genomic alterations that participate in MM pathogenesis, and these aberrations of chromosome 1mainly include copy number variations and structural changes. The chromosome 1q gains/amplifications and 1p deletions are the most frequent structural changes of chromosomes in MM. In this review, we intend to focus on the genes that are affected by chromosome 1 instability: some tumor suppressors were lost or down regulated in 1p deletions, and others that contributed to tumorigenesis were upregulated in 1q gains/amplifications. We have summarized their biological function as well as their roles in the MM pathogenesis, hoping to uncover potential novel therapeutical targets and promote the development of future therapeutic approaches.

Low-grade oncocytic tumor (LOT) - a new renal entity ready for a prime time: An updated review.

Low-grade oncocytic tumor (LOT) of kidney has been recently proposed as a new renal entity. LOT was identified in the spectrum of oncocytic renal tumors with overlapping features between oncocytoma and eosinophilic chromophobe renal cell carcinoma, or it has been labelled as one of those entities in prior studies and in practice. LOT is often a single, relatively small tumor, found in a non-syndromic setting, but rare examples of multiple LOTs or admixed with other tumors have been found in patients with tuberous sclerosis complex. LOT typically has solid architecture, and it is composed of eosinophilic cells, with round to oval 'low-grade' nuclei, lacking irregularities and showing focal perinuclear halos. Sharp transition into edematous stromal areas, with scattered or loosely arranged cells are frequently found. LOT has a consistent immunohistochemical profile with diffuse reactivity for cytokeratin 7 and absent (or rarely weak) expression for CD117, a profile different from oncocytoma and eosinophilic chromophobe renal cell carcinoma. Similarly, in contrast to those entities, it also lacks or shows only weak expression for FOXI1. Recent studies have shown that LOT has a molecular/genetic profile different from other renal tumors, with frequent alterations affecting the MTOR/TSC pathway genes. LOT demonstrates either disomic pattern or deletions of 19p13, 19q13 and 1p36, and lacks complete chromosomal losses or gains. In all published studies to date, LOT has shown benign behavior. In this review, we summarize the evidence from recently published studies, which strongly supports the conclusion that LOT is a distinct and unique renal entity.

Epigenetic and genomic profiling of chordoid meningioma: implications for clinical management

Chordoid meningioma is a morphological variant of meningioma designated as WHO grade 2. However, the recurrence rates varied widely in different case series, and to date, a unifying molecular genetic signature has not been identified. Among 1897 meningiomas resected at our institution, we identified 12 primary chordoid meningiomas from 12 patients. Histologically, all 12 cases had predominant (> 50%) chordoid morphology. Ten were otherwise grade 1, and two were also atypical. We performed DNA global methylation profile, copy number variation analysis, and targeted next-generation sequencing on 11 chordoid meningiomas, and compared to those of 51 non-chordoid, mostly high grade meningiomas. The chordoid meningiomas demonstrated a unique methylation profile in tSNE, UMAP, and hierarchical heatmap clustering analyses of the most differentially methylated CpGs. The most common copy number variation in chordoid meningioma was loss of 1p (7/11, 64%). Three chordoid meningiomas had 2p loss, which was significantly higher than the non-chordoid control cohort (27% vs 7.2%, p = 0.035). 22q loss was only seen in the two cases with additional atypical histological features. Chordoid meningiomas were enriched in mutations in chromatin remodeling genes EP400 (8/11,73%) KMT2C (4/11, 36%) and KMT2D (4/11, 36%), and showed low or absent NF2, TERT, SMO, and AKT1 mutations. Prognosis wise, only one case recurred. This case had atypical histology and high-grade molecular features including truncating NF2 mutation, 1p, 8p, 10, 14, 22q loss, and homozygous deletion of CDKN2A/B. Progression free survival of chordoid, otherwise grade 1 meningioma was comparable to non-chordoid WHO grade 1 meningioma (p = 0.75), and significantly better than chordoid WHO grade 2 meningioma (p = 0.019). Conclusion: the chordoid histology alone may not justify a universal WHO grade 2 designation. Screening for additional atypical histological or molecular genetic features is recommended.

Adapted whole‐body surveillance for von Hippel–Lindau‐associated tumors in 3p deletion syndrome with VHL deletion: A case report

Adapted whole‐body surveillance for von Hippel–Lindau‐associated tumors in 3p deletion syndrome with <i>VHL</i> deletion: A case report

Comprehensive analysis of chromosome 8 abnormalities and its prognostic value in patients with uveal melanoma

Introduction. Uveal melanoma ability to metastasize depends on a few prognostic factors. The genetic ones are considered to be the most significant. The role of disorders of the short arm of chromosome 8 (8p), as well as a combination of changes in 8p and the long arm of this chromosome (8q) in the development of metastatic lesions in this pathology remains insufficiently studied.The study objective – to evaluate the prognostic value of chromosome 8 abnormalities in patients with uveal melanoma.Materials and methods. We analyzed 2 retrospective groups of patients who underwent enucleation for uveal melanoma, statistically homogeneous in the main clinical parameters. Group 1 included patients without signs of metastases (n = 41) with an average follow-up period of 71 months, Group 2 included patients with detected metastases (n = 51) and an average follow-up period of 21 months Chromosome abnormalities were tested by multiplex ligation-dependent probe amplification.Results. Three- and five-year survival in patients with uveal melanoma without 8p deletion were 64 and 54 %, respectively; with 8p deletion significantly lower – 25 and 6 %, respectively. The same survival rates in patients with uveal melanoma with 8q amplification were 43 and 26 %, respectively, whereas in patients without 8q amplification they were significantly higher – 80 and 74 %, respectively. In patients with uveal melanoma harbouring both abnormalities, 3- and 5-year survival rates were 26 and 7 %, whereas isolated 8q amplification was associated with 47 and 35 % survival, respectively. These survival rates differ greatly and significantly: hazard ratio 3,26 (95 % confidence interval 1,86–5,69) and 6,89 (95 % confidence interval 2,67–17,73), respectively (р &lt;0,0001).Conclusion. The findings support comprehensive evaluation of chromosome 8 abnormalities as a substantial part of uveal melanoma prognostication. 8q amplification, 8p deletion, combination of these abnormalities and its role in uveal melanoma malignity should be further discovered. Further research in this direction is needed.

Genomic and Metabolic Hallmarks of SDH- and FH-deficient Renal Cell Carcinomas

BackgroundSuccinate dehydrogenase-deficient and fumarate hydratase-deficient renal cell carcinomas (SDHRCC and FHRCC) are rare kidney cancers driven by loss of TCA cycle enzymes. ObjectiveTo define and compare the genomic and metabolomic hallmarks of SDHRCC and FHRCC. Design, setting, and participantsWe analyzed SDHRCC and FHRCC tumors with either immunohistochemical evidence of loss of protein expression or genomically confirmed biallelic inactivation of SDHA/B/C/D/AF2 or FH. Outcome measurements and statistical analysisSomatic alterations were identified using clinical pipelines, with allele-specific copy number alterations (CNAs) identified using FACETS. Mass spectrometry–based metabolomic profiling was performed on available SDHRCC and FHRCC tumors. Results and limitationsTumors were analyzed for 42 patients (25 FHRCC, 17 SDHRCC). In the germline analysis, 16/17 SDHRCCs harbored a germline alteration in SDHB, whereas only 17/22 FHRCCs had pathogenic germline FH variants. SDHRCCs had a lower mutation burden (p = 0.02) and CNA burden (p = 0.0002) than FHRCCs. All SDHRCCs presented with deletion of chromosome 1p (overlapping SDHB), whereas FHRCCs demonstrated high but not ubiquitous loss of 1q (FH locus). Both SDHRCCs and FHRCCs exhibited significant idiopathic accumulation of the metabolite guanine. FHRCC tumors had elevated levels of urea cycle metabolites (argininosuccinate, citrulline, and fumarate), whereas SDHRCC tumors had elevation of numerous acylcarnitines. These characteristic metabolic changes allowed identification of a previously unrecognized SDH-deficient RCC. ConclusionsDespite sharing similar genetic etiology, SDHRCC and FHRCC represent distinct molecular entities with unique genetic and metabolic abnormalities. Patient summaryKidney cancers driven by loss of the gene encoding either the succinate dehydrogenase or fumarate hydratase enzyme are rare. We sought to define and compare the genetic and metabolic features of these cancer entities.

Characterization of a rare mosaic unbalanced translocation of t(3;12) in a patient with neurodevelopmental disorders

BackgroundUnbalanced translocations may be de novo or inherited from one parent carrying the balanced form and are usually present in all cells. Mosaic unbalanced translocations are extremely rare with a highly variable phenotype depending on the tissue distribution and level of mosaicism. Mosaicism for structural chromosomal abnormalities is clinically challenging for diagnosis and counseling due to the limitation of technical platforms and complex mechanisms, respectively. Here we report a case with a tremendously rare maternally-derived mosaic unbalanced translocation of t(3;12), and we illustrate the unreported complicated mechanism using single nucleotide polymorphism (SNP) array, fluorescence in situ hybridization (FISH), and chromosome analyses.Case presentationAn 18-year-old female with a history of microcephaly, pervasive developmental disorder, intellectual disability, sensory integration disorder, gastroparesis, and hypotonia presented to our genetics clinic. She had negative karyotype by parental report but no other genetic testing performed previously. SNP microarray analysis revealed a complex genotype including 8.4 Mb terminal mosaic duplication on chromosome 3 (3p26.3->3p26.1) with the distal 5.7 Mb involving two parental haplotypes and the proximal 2.7 Mb involving three parental haplotypes, and a 6.1 Mb terminal mosaic deletion on chromosome 12 (12p13.33->12p13.31) with no evidence for a second haplotype. Adjacent to the mosaic deletion is an interstitial mosaic copy-neutral region of homozygosity (1.9 Mb, 12p13.31). The mother of this individual was confirmed by chromosome analysis and FISH that she carries a balanced translocation, t(3;12)(p26.1;p13.31).ConclusionTaken together, the proband, when at the stage of a zygote, likely carried the derivative chromosome 12 from this translocation, and a postzygotic mitotic recombination event occurred between the normal paternal chromosome 12 and maternal derivative chromosome 12 to “correct” the partial 3p trisomy and partial deletion of 12p. To the best of our knowledge, it is the first time to report the mechanism utilizing a combined cytogenetic and cytogenomic approach, and we believe it expands our knowledge of mosaic structural chromosomal disorders and provides new insight into clinical management and genetic counseling.

Interstitial deletions of chromosome 1p: novel 1p31.3p22.2 microdeletion in a newborn with craniosynostosis, coloboma and cleft palate, and review of the genomic and phenotypic profiles

BackgroundRearrangements of unstable DNA sequences may alter the structural integrity or the copy number of dose-sensitive genes, resulting in copy number variations. They may lead more frequently to deletions, in addition to duplications and/or inversions, which are the underlying pathogenic mechanism of a group of conditions known as genomic disorders (or also contiguous gene syndromes). Interstitial deletions of the short arm of chromosome 1 are rare, and only about 30 patients have been reported. Their clinical features are variable, in respect of the extent of the deleted region. They include global developmental delay, central nervous system (CNS) malformations, craniosynostosis, dysmorphic face, ocular defects, cleft palate, urinary tract anomalies and hand/foot abnormalities.Case presentationHereby, we report on an Italian female newborn with craniosynostosis, facial dysmorphisms including bilateral microphthalmia and coloboma, cleft palate, and a severe global developmental and growth delay, associated to a 1p31.3p22.2 deletion of 20.7 Mb. This was inherited from the healthy mother, who was carrier of a smaller (2.6 Mb) deletion included within the centromeric region (1p22.3p22.2) of the same rearrangement, in addition to a translocation between chromosomes 1p and 4q. The deleted region of the proband contains about ninety genes. We focus on the genotype–phenotype correlations.ConclusionsThe results of the present study further confirm that microdeletions at 1p31.3 constitute a contiguous gene syndrome. It is hard to establish whether the critical rearrangement of such syndrome may involve the centromeric band p22.3p22.2, or more likely do not, also in light of the genomic profile of the healthy mother of our patient. Neonatologists and pediatricians should take into consideration 1p31 microdeletion in cases of developmental and growth delay associated to craniosynostosis, peculiar facial dysmorphisms, cleft palate and hand/foot abnormalities. The present report provides new data about 1p31 microdeletion syndrome, in view of a better characterization of its genomic and phenotypic profile.

NCAPG as a Novel Prognostic Biomarker in Glioma.

BackgroundNon-SMC condensin I complex subunit G (NCAPG) is expressed in various human cancers, including gliomas. However, its biological function in glioma remains unclear. The present study was designed to determine the biological functions of NCAPG in glioma and to evaluate the association of NCAPG expression with glioma progression.MethodsClinical data on patients with glioma were obtained from The Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), the Gene Expression Omnibus (GEO), and the Rembrandt and Gravendeel databases. The correlations among NCAPG expression, pathological characteristics, and clinical outcome were evaluated. In addition, the correlations of NCAPG expression with immune cell infiltration and glioma progression were analyzed.ResultsNCAPG expression was higher in gliomas than in adjacent normal tissues. Higher expression of NCAPG in gliomas correlated with poorer prognosis, unfavorable histological features, absence of mutations in the isocitrate dehydrogenase gene (IDH), absence of chromosome 1p and 19q deletions, and responses to chemoradiotherapy. Univariate and multivariate Cox analysis demonstrated, in addition to patient age, tumor grade, absence of IDH mutations, and absence of chromosome 1p and 19q deletions, NCAPG expression was independently prognostic of overall survival, disease-free survival, and progression-free survival in patients with glioma. In addition, high expression of NCAPG correlated with tumor infiltration of B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells. Gene set enrichment analysis (GSEA) indicated that high NCAPG expression was associated with cell proliferation and immune response-related signaling pathways. NCAPG knockdown in glioma cell lines significantly reduced cell survival, proliferation, and migration.ConclusionNCAPG expression correlates with glioma progression and immune cell infiltration, suggesting that NCAPG expression may be a useful prognostic biomarker for glioma.

Improved Uveal Melanoma Copy Number Subtypes Including an Ultra-High-Risk Group.

PurposeTo evaluate the clinical relevance of low-frequency copy number aberrations (CNAs) in uveal melanoma (UM) and to discern residual genomic and clinical heterogeneity within established molecular subtypes based on genome-wide CNA profiling of 921 primary tumors.DesignRetrospective single-center case series.ParticipantsPatients with primary UM referred for genetic testing between 2008 and 2016 (n = 921). The Cancer Genome Atlas cohort with clinical outcome data available (n = 70) was used to validate findings.MethodsGenome-wide CNAs were generated for primary tumors from 921 patients and for 19 metastatic UM (mUM) in the liver. Of the 921 patients, metastatic outcome was known for 678 patients with a median time to metastasis of 4.5 years. The primary tumors were processed on the Affymetrix arrays SNP-5.0 (n = 140), SNP-6.0 (n = 359), or CytoScanHD (n = 422), and the metastatic tumors on the CytoScanHD array (n = 19). Recurrent CNAs were identified, and the prognostic effect of individual CNAs and multiple CNA clustering strategies, including more specific molecular subgroups with rare CNAs, were evaluated.Main Outcome MeasuresCNA recurrence, and effect of CNAs and derived molecular subtypes on metastatic-free survival.ResultsGenomic profiling revealed CNAs associated with risk of metastasis and demonstrated a strong association between chromosomal instability and patient prognosis. Using standard prognostic CNAs, 6 clusters were detected, and inclusion of chromosome 16q deletion revealed an additional cluster. Of these 7 genomic clusters, 5 patient groups showed distinct rates of metastasis, indicating that different genomic patterns can have similar patient outcomes. A small group of patients with a significantly higher rate of metastasis was characterized by monosomy 3, 8q amplification, and deletion of 1p or 16q. Although this ultra–high-risk group accounts for only 7% of this cohort, 88% demonstrated metastasis within 4 years, compared with 45% in the second-highest risk group.ConclusionsThese results suggest that 1p and 16q deletion should be incorporated in clinical assays to assess prognosis at diagnosis and to guide enrollment in clinical trials for adjuvant therapies.

FISH analyses for 1p and 19q status on gliomas: Reporting an 8 years' experience from a tertiary care center in the Middle East

Diffuse gliomas are the most common primary malignancies of the central nervous system (CNS). The 2016 edition of the World Health Organization (WHO) classification of CNS tumors opted to integrate current molecular data with the traditional histologic diagnosis in the definition of the disease. This integrated diagnosis offers a greater level of objectivity and helps in establishing more definitive diagnoses for tumors that may have been controversial on histology alone. The classification of gliomas may require FISH technique to identify chromosomal abnormalities. FISH is commonly used to identify 1p/19q codeletion, but many challenges are encountered in the process. In this study, we review the FISH results for 1p/19q codeletion of n = 85 diffuse glioma samples examined at a tertiary care center in the Middle East over a period of 8 years. We also conduct a literature review to study the potential role of DNA-microarray in the identification of 1p/19q deletions. Glioblastoma (GBM), WHO grade IV is the most common glioma type identified (n = 24; 29%). All oligodendrogliomas show 1p/19q codeletion (26/26) while 12.5% of GBMs have 1p/19q codeletion (3/24). Isolated 1p deletions are only identified in one case of diffuse astrocytoma, WHO grade II. Isolated 19q deletions are identified in oligoastrocytoma, anaplastic astrocytoma, and glioblastoma. FISH is the most commonly used technique to diagnose oligodendroglioma because it is a simple, effective, and accessible technique in settings with limited resources. However, the optimization process remains highly variable between laboratories. Microarray is a more objective technique that can provide more information about the genetic alterations of the tumor for better diagnosis and sub-classification of diffuse glioma types.

Renal cell carcinoma with leiomyomatous stroma: A case report and a review of the literature of a provisional entity distinct from conventional renal cell carcinoma

Renal Cell Carcinoma with Leiomyomatous Stroma (RCCLMS) is a rare renal cancer with indolent behavior and favorable prognosis. We present a case of rare renal cell carcinoma with leiomyomatous stroma in a 49-year-old male, with an incidental finding of a 1.6 cm renal nodule on MRI scan. The patient underwent partial nephrectomy of the left kidney and subsequent histological examination showed an epithelial tumor composed of clear cell cytoplasm with low grade nuclear features, surrounded by an abundant smooth muscle stroma composed of fascicles of spindle cells. Immunohistochemistry revealed the positive reaction of tumor cells for CK7, CD10, CAIX, vimentin and desmin; negative for AMACR. Molecular testing via FISH study shows lack of 3p deletion. Final diagnosis of RCCLMS was made. The aim of this case report is to highlight the importance of awareness of this disease as well as to differentiate RCCLMS from other renal cancers with less favorable prognosis and higher degree of malignancy like clear cell renal cell carcinoma. Keywords: renal cell carcinoma; leiomyomatous stroma; kidney.

SH2D4A downregulation due to loss of chromosome 8p is associated with poor prognosis and low T cell infiltration in colorectal cancer.

Colorectal cancer (CRC) develops through chromosomal instability (CIN) or microsatellite instability (MSI) due to deficient mismatch-repair (dMMR). We aimed to characterise novel cancer-associated genes that are downregulated upon malignant transformation in microsatellite stable (MSS) CRCs, which typically exhibit CIN with proficient mismatch-repair (pMMR). Comprehensive screening was conducted on adenomas, MSI/MSS CRCs and cell lines, followed by copy number analysis, and their genetic and prognostic relevance was confirmed in microarray and RNA-seq cohorts (n = 3262, in total). Immunohistochemistry for SH2D4A was performed in 524 specimens of adenoma, carcinoma in situ and dMMR/pMMR CRC. The functional role of SH2D4A was investigated using CRC cell lines. A set of 11 genes, including SH2D4A, was downregulated during the adenoma-carcinoma sequence in MSS/CIN CRCs, mainly due to chromosome 8p deletions, and their negative prognostic impact was validated in independent cohorts. All adenomas were SH2D4A positive, but a subset of CRCs (5.3%) lacked SH2D4A immunohistochemical staining, correlating with poor prognosis and scarce T cell infiltration. SH2D4A depletion did not affect cell proliferation or IL-6-induced STAT3 phosphorylation. Our findings suggest that downregulation of multiple genes on chromosome 8p, including SH2D4A, cooperatively contribute to tumorigenesis, resulting in the immune cold tumour microenvironment and poor prognosis.

Abstract 17250: Novel Association Of Left Ventricular Outflow Tract Obstructions With Chromosome 5p Deletions

Case Presentation: Patient 1: Female infant diagnosed with Cri du Chat Syndrome (CdCS) (Fig. 1A), hypoplastic left heart syndrome variant (Fig. 1 B), duodenal atresia (Fig. 1 E, F), IUGR. Chromosomal microarray (CMA) showed a 4.3 Mb deletion at 5p15.33 (Fig. 1A) and a 32.2 Mb duplication of 5q32. Dysmorphisms including hypertelorism, low set ears, and micrognathia were noted. Echocardiogram showed a hypoplastic left ventricle, mitral valve dysplasia (Fig. 1B), dysplastic aortic valve (Fig. 1C), interrupted aortic arch (Fig. 1D). Patient 2: Male infant prenatally diagnosed with aortic valve stenosis, aortic arch hypoplasia (Fig. 1H, I), and IUGR. Multiple dysmorphic features including microcephaly, hypertelorism, down slanting palpebral fissures, and abnormal distal extremities. CMA revealed a large deletion at 5p13.33-p13.2 (Fig 1G). He underwent aortic valvuloplasty complicated by development of a posterior left ventricular wall pseudoaneurysm (Fig. 1J). He later underwent arch reconstruction. At 2 months of age, he was diagnosed with obstructive jaundice requiring a biliary drain (Fig.1K, L). He had been gaining weight and height steadily (Fig.1M, N). We identified 5 more patients with 5p deletions and left outflow tract obstructions (LVOTO) from the Cytogenomics of Cardiovascular Malformations Consortium (Table 1). Discussion: CdCS is the most common 5p deletion syndrome and is associated with mild congenital heart defects in 15-30% of individuals. There is no reported association between LVOTO and 5p deletions. These 7 patients did not all share the same deletions and had high mortality. Further studies are needed to better understand possible genetic etiologies.

Outcomes Among Primary Refractory Multiple Myeloma Patients in the Era of Monoclonal Antibodies: The Yale Experience

Introduction: Multiple myeloma (MM) is an incurable yet highly heterogeneous disease of clonal plasma cells. The role of induction therapy is to achieve a complete response, thereby reducing the number of malignant plasma cells in the bone marrow. Partial responses or less are considered suboptimal and are associated with poorer outcomes. Following the approval of monoclonal antibody (mAb) therapies in MM, little is known of their effect on primary refractory and suboptimal responses in real-world populations.Methods: This retrospective cohort study included patients with clinical MM who were diagnosed and treated within the Yale New Haven Health System between 2009-2019. Our primary aim was to evaluate the overall survival (OS) in patients with primary refractory (PriRef) or suboptimal responding disease compared to those who achieved at least a very good partial response (≥VGPR). PriRef disease was assessed following three months of induction therapy, and was defined as a partial response, stable disease, or progressive disease based on International Myeloma Working Group (IMWG) criteria. A stricter cutoff of less than a VGPR was chosen for our definition of PriRef, because deeper responses, including MRD-negative status, have demonstrated increasingly important prognostic value. Descriptive statistics and OS analysis were performed with 2-tailed contingency χ²-tests, t-tests, Kaplan Meier, and log-rank tests using GraphPad Prism v8.Results: 246 patients (pts) with adequate response data following 3 months of induction therapy were identified. Clinical features included median age at diagnosis of 61 years (range, 34-92), 26.8% of whom were 70 years or older, 54.9% male, 63.4% Caucasian, 24.3% Black or African American, and 11% Hispanic. 46.8% had International Staging System (ISS) stage II or III disease and 41.1% had Revised International Staging System (R-ISS) stage II or III disease. 33.3% of patients had high-risk cytogenetics, which was defined as a del17/17p, t(4:14), t(4;16), t(4;20), gain or amplification of 1q, deletion of 1p, and chromosome 1 translocations. 81.7% of this cohort received a triplet or quadruplet induction regimen. The majority of patients received triplet induction regimens that included immunomodulatory and proteasome inhibitor combinations, and only two patients were prescribed quadruplet therapy. 44.7% of patients received autologous stem cell transplant (ASCT) at some point in their treatment course, with 79.1% (87/110) in the upfront setting and 20.9% (23/110) having delayed ASCT (Table 1).In this cohort, 122 pts (49.6%) achieved ≥VGPR and 124 pts (50.4%) were PriRef. There were no significant differences in the baseline demographics, ISS, R-ISS, or cytogenetic characteristics between ≥VGPR and PriRef. PriRef patients were less likely to have been treated with at least a triplet induction regimen than ≥VGPR (74.2% vs. 89.3%, p <0.01), and they were also less likely to have undergone ASCT (37.1% % vs. 52.5%, p = 0.02). When the two cohorts were stratified by upfront versus delayed ASCT, PriRef pts still demonstrated lower rates of ASCT in both settings, but the differences were not statistically significant (Table 1). There was no significant difference in OS between PriRef and ≥VGPR pts. Median OS for PriRef was 102.9 months compared to 114.9 months in ≥VGPR (p = 0.27) (Figure 1). Out of the 124 PriRef pts, 78 (62.9%) went on to receive subsequent lines of therapy. 39.7% of these PriRef pts received a mAb, such as daratumumab, elotuzumab or isatuximab, in the 2 nd or 3 rd line setting. When stratified by whether they received mAb therapy, median OS of PriRef pts who did not receive a mAb was 86.6 months, whereas median OS was not reached for the PriRef pts who received a mAb (p=0.98) (Figure 2).Conclusions: Our cohort analysis showed that early primary refractoriness to induction in newly diagnosed MM patients was not associated with a lower overall survival, despite lower utilization of triplet regimens and ASCT. Treatment with monoclonal antibodies in the 2 nd and 3 rd line setting may explain this finding. Since the approval of mAbs for myeloma, OS appears to be beneficially impacted. However, the effect of this class of therapy is yet to be fully appreciated in the real-world setting. Therefore, longer follow up data is needed to better assess the true impact of monoclonal antibodies on primary refractory multiple myeloma patients. [Display omitted] DisclosuresNeparidze: GlaxoSmithKline: Research Funding; Janssen: Research Funding; Eidos Therapeutics: Membership on an entity's Board of Directors or advisory committees.

FISH and WGS in Newly Diagnosed and Relapsed/Refractory Multiple Myeloma - WGS Will Affect Future Treatment Decisions

Background:FISH is the gold standard for genetic characterization and risk stratification of multiple myeloma (MM) at diagnosis. Retrospective studies have shown the potential of whole genome sequencing (WGS) to gain new insights into MM genetics. With respect to clinical application, we prospectively performed FISH and WGS in parallel in patients (pts) with newly diagnosed MM (NDMM) and relapsed/refractory MM (RRMM) to evaluate advantages and limitations.Patients and methods:From bone marrow (BM) samples of 280 MM pts CD138+ cells were enriched by MACS. In 100 pts (30 NDMM, 70 RRMM) FISH (del(1p32), del(13q), del(17p), t(4;14), t(11;14), t(14;16), t(14;20), t(6;14), 1q gain, MYC rearrangement (MYCr) and trisomies 3, 5, 9) and WGS were performed. WGS: 150bp paired-end sequences were generated on NovaSeq 6000 (Illumina); median coverage 104x. Single nucleotide variants (SNV) were called with Strelka software, copy number variations (CNV) with GATK4 and structural variants (SV) with Manta. Technical artefacts and germline calls were reduced by a tumor/unmatched normal workflow with genomic DNA from a mix of anonymous donors. Variants with global population frequency >0.5% (gnomAD) were excluded.Results:In 100/280 (36%) MM pts WGS could be performed in parallel to FISH in this cohort with a low median BM plasma cell infiltration (PCI) of 6% (range 1-95%). Likelihood of DNA yields sufficient for WGS increased with higher PCI (23% (1-95%) vs 3% (1-50%) in 100 pts with WGS vs 180 pts without sufficient DNA).Comparison of FISH and WGS results for 100 pts showed 100% concordance for recurrent SV (table 1): t(11;14) in 29%, t(4;14) in 17% and t(14;16) in 5%. No pts harbored a t(14;20) but in one case FISH indicated another alteration of MAFB and WGS revealed MAFB rearranged to FAM46C resulting in an elevated MAFB expression.Due to heterogeneous breakpoints FISH is less reliable for the detection of MYCr than WGS (24/42 (57%) detected by FISH vs 40/42 (95%) by WGS). Partners of MYC included IGH (n=10), FAM46C (n=4), IGK (n=3), IGL (n=3), FOXO3 (n=2) and IRF4 (n=1). Rare IGH rearrangements with partner genes such as IRF1, IRF4, ZBTB38 and ZFP36L1 were observed in 11 pts all identified by WGS, but only 8 (73%) were detected by FISH.Total frequencies of CNV were del(13q) in 50%, del(17p) in 29%, del(1p32) in 22%, 1q gains in 61% and hyperdiploidy in 36%. WGS detected 95% of CNV (details table 1). CNV that were missed by WGS included one del(17p) and were all identified in small subclones with a median clone size of 10% (6-25%) in FISH.Tetraploid MM, potentially harboring adverse prognostic implication, was identified in 11 pts by FISH but not in WGS.However, in 97 pts WGS depicted additional SV and CNV compared to FISH. This includes aberrations of prognostic significance such as a TP53 deletion that was located adjacent to a 451kb gain on 17p. The FISH probe encompassing TP53 confirmed the 17p gain but masked the TP53 deletion. Also 1p deletions, which have been described to be a negative prognostic factor, were found more frequently by WGS with 24 pts harboring a del(1p) other than del(1p32) (locus evaluated by FISH) which was detected in 22 pts by both methods. Furthermore, as WGS cannot only detect SV and CNV but also SNV, WGS allows screening for potentially clinically exploitable drug targets, e.g. BRAF V600E mutation (5 pts in our cohort) or resistance associated mutations such as in cereblon for immunomodulatory compounds (CRBN mutation in 3 pts) as well as biallelic events in TP53 (del(17p)+TP53 mutation), detected in 15 of our pts suggesting worst prognosis for affected pts. WGS in RRMM can shed light on the genetic background of relapses. Of note, homozygous del(16p) inducing loss of the treatment target were first described using our dataset in two patients with acquired resistance toward anti-BCMA CAR T cells or bispecific antibody therapy.Conclusions:FISH is the preferred approach in pts with BM PCI <10% and for the detection of clones <15% or variant ploidy levels. WGS is superior to FISH regarding the identification of biallelic events and rearrangements with heterogeneous breakpoints and rare partners. But even more, WGS can address various questions in follow up in terms of increase of complexity, target specific therapy, therapy failure and relapse. Thus, WGS allows a holistic insight into the genetics of MM and provides crucial information for clinical decision making. [Display omitted] DisclosuresKern: MLL Munich Leukemia Laboratory: Other: Part ownership. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Einsele: Janssen, Celgene/BMS, Amgen, GSK, Sanofi: Consultancy, Honoraria, Research Funding. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership.

The Impact of gain1q on Mutational Structure and Clonal Evolution in a Uniformly Treated High-Risk Series of Patients at First Relapse

The Impact of gain1q on Mutational Structure and Clonal Evolution in a Uniformly Treated High-Risk Series of Patients at First Relapse

Uterine cellular leiomyomas are characterized by common HMGA2 aberrations, followed by chromosome 1p deletion and MED12 mutation: morphological, molecular, and immunohistochemical study of 52 cases.

Cellular leiomyoma (CL) represents an uncommon variant of uterine leiomyoma with limited data concerning its immunohistochemical and molecular profile. We performed a comprehensive analysis of 52 CL cases all of which were analyzed immunohistochemically. Molecular analysis was possible in 32 cases with sufficient DNA, and 38 cases with sufficient RNA. The immunohistochemical results showed a high expression of smooth muscle markers (calponin (100%), desmin (100%), smooth muscle actin (98.1%), caldesmon (96.1%), transgelin (96.1%), smooth muscle myosin heavy chain (86.5%), and smoothelin (61.5%)). Concerning markers of endometrial stromal differentiation, the expression of CD10 was observed in 65.4% cases (42.2% with H-score > 50), and IFITM1 in 36.5% cases (1.9% with H-score > 50). 36.5% showed HMGA2 overexpression at the IHC level, associated with increased mRNA expression in 14/14 cases. The rearrangement of the HMGA2 gene was detected in 13.2%. Chromosome 1p deletion was found in 19.3%, while 9.4% of tumors showed a pathogenic mutation in the MED12 gene. In conclusion, CL is immunohistochemically characterized by a high expression of "smooth muscle" markers commonly associated with a co-expression of "endometrial stromal" markers, where IFITM1 shows superior performance compared to CD10 regarding its specificity for differentiation from endometrial stromal tumors. The sensitivity of smoothelin in CL seems rather low, but no data is available to assess its specificity. On a molecular level, the most common mutually exclusive aberration in CL affects HMGA2, followed by chromosome 1p deletions and MED12 mutations.