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Kristopher T. Kahle, David Kozono, Kimberly Ng, Grace Hsieh, Pascal O. Zinn, Masayuki Nitta and Clark C. Chen

variation, transcriptional profiles, epigenetic modifications, and DNA sequence alterations. This approach has the potential to identify common alterations in oncogenes and tumor suppressors for further functional analysis and to uncover oncogene addiction pathways that can be targeted. 7 , 21 For example, Yan et al., 36 by sequencing 20,661 protein-coding genes, determining the presence of amplifications and deletions using high-density oligonucleotide arrays, and performing gene expression analyses using next-generation sequencing technologies in 22 human GBM samples

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Paul A. Northcott, James T. Rutka and Michael D. Taylor

human embryonic stem cells . Genome Res 18 : 610 – 621 , 2008 111 Morozova O , Marra MA : Applications of next-generation sequencing technologies in functional genomics . Genomics 92 : 255 – 264 , 2008 112 Morozova O , Marra MA : From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors . Biochem Cell Biol 86 : 81 – 91 , 2008 113 Mortazavi A , Williams BA , McCue K , Schaeffer L , Wold B : Mapping and quantifying mammalian transcriptomes by RNASeq . Nat

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explore cancer cell vulnerabilities Kristopher T. Kahle 1, 2, 3, 4 M.D., Ph.D. David Kozono 5, 6 M.D., Ph.D. Kimberly Ng 6 B.S. Grace Hsieh 6 B.A. Pascal O. Zinn 6 M.D. Masayuki Nitta 6 M.D., Ph.D. Clark C. Chen 6, 7 M.D., Ph.D. 1 2010 28 1 E5 10.3171/2009.10.FOCUS09212 2009.10.FOCUS09212 Genomics of medulloblastoma: from Giemsa-banding to next-generation sequencing in 20 years Paul A. Northcott 1, 2, 3 M.Sc. James T. Rutka 1, 3 M.D., Ph.D. Michael D. Taylor 1, 2, 3 M.D., Ph.D. 1 2010 28 1 E6 10.3171/2009.10.FOCUS09218 0280006 Genetic basis of Parkinson disease

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Martin H. Pham, Gabriel Zada, Gina M. Mosich, Thomas C. Chen, Steven L. Giannotta, Kai Wang and William J. Mack

available surgical and radiation treatment paradigms. The authors present a systematic review of the genes currently associated with the development, progression, and recurrence of meningiomas. The article then provides a brief discussion of potential future avenues of research and targeted therapeutic paradigms employing novel genetic techniques such as next-generation sequencing data analysis and high throughput genomics. Genetics Tumor Suppressor Genes Tumor suppressor genes are those that encode proteins whose function is to inhibit the development of

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Discovering neurosurgery: new frontiers

The 2011 AANS Presidential Address

James T. Rutka

therapy. The Cancer Genome Atlas, led by the National Cancer Institute, is a multiinstitutional consortium aimed at improving our understanding of cancer through genomic characterization and high-throughput, next-generation sequencing technologies. Luckily for neurosurgeons and our patients, one of the first tumors to be sequenced by The Cancer Genome Atlas was GBM. 12 , 47 Has there been tangible progress that has benefited our patients in neurooncology? I would argue that there have been several discoveries that have paved the way toward improved patient diagnosis

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Daniel D. Cavalcanti, M. Yashar S. Kalani, Nikolay L. Martirosyan, Justin Eales, Robert F. Spetzler and Mark C. Preul

and their transplantation into an immunodeficient animal, as has been recently described for hemangiomas, 36 may allow both the study of human forms of CCMs and a robust model for imaging and drug trials. Another exciting frontier of research is the sequencing of the entire genome of patients afflicted with CCM by using next-generation sequencing technology. Obtaining the full genomic profile of patients with multiple CCMs will provide further mechanistic clues about the role of other genes and gene regulatory machinery, such as small RNAs, in the pathogenesis of

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Shih-Shan Lang, Eric L. Zager, Thomas M. Coyne, Raj Nangunoori, J. Bruce Kneeland and Katherine L. Nathanson

presentation of multiple hybrid nerve sheath tumors. The development of the hybrid tumors, with conserved morphological features, in multiple locations at an early age is strongly suggestive of an underlying germline mutation, which we have not detected using current methods. This case likely represents a previously uncharacterized syndrome. Unique individuals similar to the one described herein represent an opportunity for the identification of novel susceptibility genes associated with hybrid nerve sheath tumors. With the advent of next-generation sequencing, such

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Ibrahim Hussain, Jean Anderson Eloy, Peter W. Carmel and James K. Liu

Craniopharyngiomas are benign intracranial tumors that arise in the suprasellar and intrasellar region in children and adults. They are associated with calcification on neuroimaging, endocrinopathies, vision problems, and recurrence following subtotal resection. Molecular studies into their genetic basis have been limited, and therefore targeted medical therapies for this tumor have eluded physicians. With the discovery of aberrant Wnt/β-catenin pathway signaling in the pathogenesis of the most common subtype of craniopharyngioma (adamantinomatous), the identification of candidate genes and proteins implicated in this cascade provide attractive targets for future therapies. The recent development of a genetically engineered animal model of this tumor may also serve as a platform for evaluating potential therapies prior to clinical trials in humans. Advances in understanding the molecular pathogenesis of tumor recurrence have also been made, providing clues to develop adjuvant and neoadjuvant therapies to couple with tumor resection for optimal response rates. Finally, advances in genomic technologies and next-generation sequencing will underlie the translation of these genetic and molecular studies from the bench to clinical practice. In this review, the authors present an analysis of the molecular oncogenesis of craniopharyngioma and current directions in the development of novel therapies for these morbid, yet poorly understood brain tumors.

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Shuhan He, Martin H. Pham, Matthew Pease, Gabriel Zada, Steven L. Giannotta, Kai Wang and William J. Mack

studies. For example, the ChIP-sequencing (ChIP-seq) technique, which combines chromatin immune-precipitation with next-generation sequencing, can be used to examine histone modification patterns given antibodies for the specific modifications. Similarly, 3C, 4C, 5C, Hi-C and ChIA-PET techniques, 18 , 20 , 82 were specifically developed for interrogating higher-order chromosomal structures between regulatory elements and target genes that may be located far away (even in different chromosomes). These techniques were becoming increasingly popular in molecular genetics

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Ibrahim Hussain, Qasim Husain, Soly Baredes, Jean Anderson Eloy, Robert W. Jyung and James K. Liu

and time efficiency of next-generation sequencing platforms. This approach will also allow more comprehensive cataloging of potential imprinting modifiers associated with SDHD and SDHAF2 mutations in familial paraganglioma syndromes, as well as a better understanding of the genomic landscape in individuals who develop SHN-PG sporadically. Coupled with individualized genetic signatures, advances in CT, MRI, and nuclear imaging may also have an impact on the way individuals with paragangliomas are managed. Earlier detection of high-risk asymptomatic tumors may