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Matched Paired Primary and Recurrent Meningiomas Points to Cell-Death Program Contributions to Genomic and Epigenomic Instability along Tumor Progression. Cancers (Basel) 2022; 14:cancers14164008. [PMID: 36011000 PMCID: PMC9406329 DOI: 10.3390/cancers14164008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Meningioma (MN) is an important cause of disability, and predictive tools for estimating the risk of recurrence are still scarce. The need for objective and cost-effective techniques addressed to this purpose is well known. In this study, we present methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as a friendly method for deepening the understanding of the mechanisms underlying meningioma progression. A large follow-up allowed us to obtain 50 samples, which included the primary tumor of 20 patients in which half of them are suffering one recurrence and the other half are suffering more than one. We histologically characterized the samples and performed MS-MLPA assays validated by FISH to assess their copy number alterations (CNA) and epigenetic status. Interestingly, we determined the increase in tumor instability with higher values of CNA during the progression accompanied by an increase in epigenetic damage. We also found a loss of HIC1 and the hypermethylation of CDKN2B and PTEN as independent prognostic markers. Comparison between grade 1 and higher primary MN's self-evolution pointed to a central role of GSTP1 in the first stages of the disease. Finally, a high rate of alterations in genes that are related to apoptosis and autophagy, such as DAPK1, PARK2, BCL2, FHIT, or VHL, underlines an important influence on cell-death programs through different pathways.
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Nagarajan PP, Tora MS, Neill SG, Federici T, Texakalidis P, Donsante A, Canoll P, Lei K, Boulis NM. Lentiviral-Induced Spinal Cord Gliomas in Rat Model. Int J Mol Sci 2021; 22:12943. [PMID: 34884748 PMCID: PMC8657985 DOI: 10.3390/ijms222312943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022] Open
Abstract
Intramedullary spinal cord tumors are a rare and understudied cancer with poor treatment options and prognosis. Our prior study used a combination of PDGF-B, HRAS, and p53 knockdown to induce the development of high-grade glioma in the spinal cords of minipigs. In this study, we evaluate the ability of each vector alone and combinations of vectors to produce high-grade spinal cord gliomas. Eight groups of rats (n = 8/group) underwent thoracolumbar laminectomy and injection of lentiviral vector in the lateral white matter of the spinal cord. Each group received a different combination of lentiviral vectors expressing PDGF-B, a constitutively active HRAS mutant, or shRNA targeting p53, or a control vector. All animals were monitored once per week for clinical deficits for 98 days. Tissues were harvested and analyzed using hematoxylin and eosin (H&E) and immunohistochemical (IHC) staining. Rats injected with PDGF-B+HRAS+sh-p53 (triple cocktail) exhibited statistically significant declines in all behavioral measures (Basso Beattie Bresnahan scoring, Tarlov scoring, weight, and survival rate) over time when compared to the control. Histologically, all groups except the control and those injected with sh-p53 displayed the development of tumors at the injection site, although there were differences in the rate of tumor growth and the histopathological features of the lesions between groups. Examination of immunohistochemistry revealed rats receiving triple cocktail displayed the largest and most significant increase in the Ki67 proliferation index and GFAP positivity than any other group. PDGF-B+HRAS also displayed a significant increase in the Ki67 proliferation index. Rats receiving PDGF-B alone and PDGF-B+ sh-p53 displayed more a significant increase in SOX2-positive staining than in any other group. We found that different vector combinations produced differing high-grade glioma models in rodents. The combination of all three vectors produced a model of high-grade glioma more efficiently and aggressively with respect to behavioral, physiological, and histological characteristics than the rest of the vector combinations. Thus, the present rat model of spinal cord glioma may potentially be used to evaluate therapeutic strategies in the future.
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Affiliation(s)
- Purva P. Nagarajan
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
| | - Muhibullah S. Tora
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Stewart G. Neill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Thais Federici
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
| | - Pavlos Texakalidis
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
| | - Anthony Donsante
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA;
| | - Kecheng Lei
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
| | - Nicholas M. Boulis
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA; (P.P.N.); (M.S.T.); (T.F.); (P.T.); (A.D.)
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Lim-Fat MJ, Dietrich J. Myelopathies from Neoplasms. Semin Neurol 2021; 41:291-302. [PMID: 34030192 DOI: 10.1055/s-0041-1725948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Benign and malignant tumors can be an important cause of myelopathy. Patients may present with a wide range of neurologic symptoms including back and neck pain, weakness, sensory abnormalities, and bowel and bladder dysfunction. Management can be challenging depending on the location and underlying biology of the tumor. Neuroimaging of the spine is an important component of diagnostic evaluation and patient management both during initial evaluation and when monitoring after treatment. This article provides a systematic and practical review of neoplasms that can cause myelopathy. Unique imaging and biological features of distinct tumors are discussed, and their management strategies are reviewed.
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Affiliation(s)
- Mary Jane Lim-Fat
- Division of Neurology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Jorg Dietrich
- Division of Neuro-Oncology, Department of Neurology, Massachusetts General Hospital Cancer Center, Boston, MA
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Grade III intradural extramedullary anaplastic ependymoma managed with near-complete resection and adjuvant radiotherapy: a case report. Spinal Cord Ser Cases 2021; 7:1. [PMID: 33468988 DOI: 10.1038/s41394-020-00367-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/05/2020] [Accepted: 11/13/2020] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Of the 23 cases of spinal intradural-extramedullary ependymomas which have been reported to date, 11 were diagnosed as anaplastic. Here we present a very rare case of a thoracic intradural-extramedullary (not intramedullary) anaplastic ependymoma in an adult along with a literature review. CASE PRESENTATION A 29-year-old man presented with rapidly progressive gait disturbance, a sensory-deficit below the trunk and urination disorders that had begun a few months earlier. Magnetic resonance imaging of his thoracic spine revealed a dorsal-located intradural-extramedullary tumor at T4-5. The rapid deterioration of his symptoms within several months led him to refer to our department for surgery. Within one month the size of tumor increased to involve the T4-6 level, consequently worsening his gait disturbance. He underwent surgery and tumor mass was resected. However, there was leptomeningeal dissemination of the tumor cells on the surface of cord. A near-total resection was therefore achieved. Histopathology revealed the resected specimen had immunoreactivity for EMA/Vimentin/CD56/CD99/S-100/GFAP, with a Ki-67 index of ~35%. These factors led to the diagnosis of anaplastic ependymoma. Seven weeks postoperatively he received adjuvant radiotherapy to the whole brain and the whole spinal cord. He recovered as an independent ambulator without recurrence 1 year postoperatively. DISCUSSION Because of their rarity, there are no clear treatment or adjuvant therapy guidelines for spinal anaplastic ependymoma. Adjuvant radiotherapy to the whole brain and spinal cord was necessarily indicated after near-total resection. Although the patient's condition has not recurred 1 year after surgery, careful and serial follow-up is necessary for this individual.
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Algattas H, Abou-Al-Shaar H, Mendelson M, Arnold GL, Felker J, Meade J, Greene S. Familial Cerebral Cavernous Malformation Syndrome with Concomitant Fourth Ventricular Ependymoma: True Association or Mere Coincidence? Cancer Genet 2020; 244:36-39. [PMID: 32434131 DOI: 10.1016/j.cancergen.2020.04.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/02/2020] [Accepted: 04/15/2020] [Indexed: 11/27/2022]
Abstract
Familial cerebral cavernous malformation syndromes are most commonly caused by mutations in one of three genes. The overlap of these genetic malformations with other acquired neoplastic lesions and congenital malformations is still under investigation. To the best of our knowledge, the concurrent occurrence of familial cavernous malformations and ependymoma has not been previously reported in the literature. Herein, we describe a patient with familial cerebral cavernous malformation syndrome and posterior fossa ependymoma. A 17-year-old asymptomatic male was referred to our outpatient neurosurgery clinic after genetic testing identified a familial KRIT1 (CCM1) mutation. The patient's sister had presented with a seizure disorder previously; multiple cavernous malformations were discovered, and a symptomatic large cavernous malformation required a craniotomy for resection. Two years later, she was diagnosed with follicular thyroid cancer due to HRAS (c.182A>G) mutation. The patient and his sister were found to have a novel germline KRIT1 disease-causing variant (c.1739deletion, p.ASN580Ilefs*2) and a variant of uncertain significance, potentially pathogenic (c.1988 A>G, p.Asn663Ser) in cis in CCM1 (KRIT1), of paternal inheritance. Due to the presence of genetic abnormalities, the patient underwent screening imaging of his neuraxis. Multiple cavernous malformations were identified, as was an incidental fourth ventricular mass. Resection of the fourth ventricular lesion was performed, and histopathological examination was consistent with ependymoma. We report a unique case of posterior fossa ependymoma in an individual with a familial cerebral cavernous malformation syndrome and a novel genetic abnormality in KRIT1. The association of these two findings may be valuable in determining a potential genetic association between the two pathologies and elucidating the pathogenesis of both cavernous malformations and ependymomas.
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Affiliation(s)
- Hanna Algattas
- Department of Neurological Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Hussam Abou-Al-Shaar
- Department of Neurological Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Michael Mendelson
- Department of Neurological Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Georgianne L Arnold
- Department of Pediatrics, Division of Genetics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - James Felker
- Department of Pediatrics, Division of Hematology/Oncology, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Julia Meade
- Department of Pediatrics, Division of Hematology/Oncology, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Stephanie Greene
- Department of Neurological Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA.
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Wang L, Zhang C, Xie Y, Jiang W, Huang J, Guo S, Xu F, Wang J. Detecting the long non‑coding RNA signature related to spinal cord ependymal tumor subtype using a genome‑wide methylome analysis approach. Mol Med Rep 2019; 20:1531-1540. [PMID: 31257484 PMCID: PMC6625447 DOI: 10.3892/mmr.2019.10388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/30/2019] [Indexed: 11/16/2022] Open
Abstract
Ependymoma is a type of intramedullary tumor that tends to occur in the adult spinal cord. Ependymoma affects the nervous system and has significant impacts on the quality of life, and it may lead to mortality. Previous studies have performed molecular classification of spinal cord ependymal tumors at the DNA methylation level. However, the DNA methylation status of non-coding regions in spinal cord ependymal tumors remains unclear. In the present study, a genome-wide methylome method was used to characterize the DNA methylation landscape of long non-coding RNAs (lncRNAs) in spinal cord ependymal tumor samples. The present study identified lncRNA signatures associated with tumor subtypes based on the methylation status of lncRNA promoters. The present results suggested that the identified lncRNA signatures were associated with cancer- or nervous system-related protein-coding genes. The majority of the identified lncRNAs was hypomethylated, and may have a role in spinal cord development. The present findings suggested that detection of tumor subtype-specific lncRNAs may facilitate the identification of novel diagnostic and therapeutic strategies to treat patients with spinal cord ependymal tumor.
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Affiliation(s)
- Li Wang
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Chi Zhang
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yujie Xie
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Wei Jiang
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Juan Huang
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Shengmin Guo
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Fangyuan Xu
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jianxiong Wang
- Rehabilitation Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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Halliday D, Emmanouil B, Vassallo G, Lascelles K, Nicholson J, Chandratre S, Anand G, Wasik M, Pretorius P, Evans DG, Parry A, Axon P, Gair J, Smyth C, Afridi SK, Obholzer R, Everett V, Jarvis N, Henshaw K, Hanemann CO, Howard W, May A, Redman C, Rattihalli R, Tomkins H. Trends in phenotype in the English paediatric neurofibromatosis type 2 cohort stratified by genetic severity. Clin Genet 2019; 96:151-162. [DOI: 10.1111/cge.13551] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 04/03/2019] [Accepted: 04/07/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Dorothy Halliday
- Oxford Centre for Genomic MedicineOxford University Hospitals NHS Trust Oxford UK
- Oxford NF2 Unit, Oxford University Hospitals NHS Trust Oxford UK
| | - Beatrice Emmanouil
- Oxford NF2 Unit, Oxford University Hospitals NHS Trust Oxford UK
- Oxford Brookes University, Faculty of Health and Life Sciences, Department of Psychology, Health and Professional Development Oxford UK
| | - Grace Vassallo
- Department of Paediatric NeurologyCentral Manchester University Hospitals NHS Foundation Trust Manchester UK
| | - Karine Lascelles
- Department of Paediatric NeurologyGuy's and St Thomas' NHS Foundation Trust London UK
| | - James Nicholson
- Department of Paediatric OncologyCambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Saleel Chandratre
- Department of Paediatric NeurologyOxford University Hospitals NHS Foundation Trust Oxford UK
| | - Geetha Anand
- Department of PaediatricsOxford University Hospitals NHS Foundation Trust Oxford UK
| | - Martin Wasik
- Department of OphthalmologyOxford University Hospitals NHS Foundation Trust Oxford UK
| | - Pieter Pretorius
- Depatment of NeuroradiologyOxford University Hospitals NHS Foundation Trust Oxford UK
| | - D. Gareth Evans
- Genomic Medicine, Division of Evolution and Genomic Sciences, MAHSCUniversity of Manchester, St Mary's Hospital Manchester UK
| | - Allyson Parry
- Oxford NF2 Unit, Oxford University Hospitals NHS Trust Oxford UK
- Department of NeurosciencesOxford University Hospitals NHS Foundation Trust Oxford UK
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Is NF2 a Key Player of the Differentially Expressed Gene Between Spinal Cord Ependymoma and Intracranial Ependymoma? World Neurosurg 2018; 118:e906-e917. [PMID: 30031196 DOI: 10.1016/j.wneu.2018.07.096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Although intracranial and spinal ependymomas are histopathologically similar, the molecular landscape is heterogeneous. An urgent need exists to identify differences in the genomic profiles to tailor treatment strategies. In the present study, we delineated differential gene expression patterns between intracranial and spinal ependymomas. METHODS We searched the Gene Expression Omnibus database using the term "ependymoma" and analyzed the raw gene expression profiles of 292 ependymomas (31 spinal and 261 intracranial). The gene expression data were analyzed to find differentially expressed genes (DEGs) between 2 regions. The fold change (FC) and false discovery rate (FDR) were used to assess DEGs after gene integration (|log2FC|>2; FDR P < 0.01). Enrichment and pathway analysis was also performed. RESULTS A total of 201 genes (105 upregulated and 96 downregulated) were significant DEGs in the data sets. The underexpression of NF2 in spinal ependymomas was statistically significant (FDR P = 7.91 × 10-9). However, the FC of NF2 did not exceed the cutoff value (log2FC, -1.2). The top 5 ranked upregulated genes were ARX, HOXC6, HOXA9, HOXA5, and HOXA3, which indicated that spinal ependymomas frequently demonstrate overexpression of HOX family genes, which play fundamental roles in specifying anterior/posterior body patterning. Moreover, the gene ontology enrichment analysis specified "anterior/posterior pattern specification" and "neuron migration" in spinal and intracranial ependymomas, respectively. CONCLUSIONS The most substantial magnitude of DEGs in ependymoma might be HOX genes. However, whether the differential expression of these genes is the cause or consequence of the disease remains to be elucidated in a larger prospective study.
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Miller CA, Dahiya S, Li T, Fulton RS, Smyth MD, Dunn GP, Rubin JB, Mardis ER. Resistance-promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002444. [PMID: 29440180 PMCID: PMC5880262 DOI: 10.1101/mcs.a002444] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022] Open
Abstract
As in other brain tumors, multiple recurrences after complete resection and irradiation of supratentorial ependymoma are common and frequently result in patient death. This standard-of-care treatment was established in the pregenomic era without the ability to evaluate the effect that mutagenic therapies may exert on tumor evolution and in promoting resistance, recurrence, and death. We seized a rare opportunity to characterize treatment effects and the evolution of a single patient's ependymoma across four recurrences after different therapies. A combination of high-depth whole-genome and exome-based DNA sequencing of germline and tumor specimens, RNA sequencing of tumor specimens, and advanced computational analyses were used. Treatment with radiation and chemotherapies resulted in a substantial increase in mutational burden and diversification of the tumor subclonal architecture without eradication of the founding clone. Notable somatic alterations included a MEN1 driver, several epigenetic modifiers, and therapy-induced mutations that impacted multiple other cancer-relevant pathways and altered the neoantigen landscape. These genomic data provided new mechanistic insights into the genesis of ependymoma and pathways of resistance. They also revealed that radiation and chemotherapy were significant forces in shaping the increased subclonal complexity of each tumor recurrence while also failing to eradicate the founding clone. This raises the question of whether standard-of-care treatments have similar consequences in other patients with ependymoma and other types of brain tumors. If so, the perspective obtained by real-time genomic characterization of a tumor may be essential for making effective patient-specific and adaptive clinical decisions.
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Affiliation(s)
- Christopher A Miller
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Sonika Dahiya
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Tiandao Li
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Matthew D Smyth
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, and The Ohio State University College of Medicine, Columbus, Ohio 43205, USA
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