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Molecular Diagnostics for Neurological Disorders

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Applications of Biotechnology in Neurology

Abstract

Molecular diagnosis can be defined as the clinical application of molecular technologies to elucidate, diagnose, and monitor human diseases. Molecular technologies incorporate the use of nucleic acids (DNA and RNA) as well as recombinant antibodies. Proteomic technologies are also applied to molecular diagnosis, justifying the term “proteodiagnostics.” More than 500 molecular diagnostic systems have been developed to date. This article describes the basic principles of these technologies and their application to the diagnosis of neurologic disorders. The College of American Pathologists has used the term “molecular pathology” for molecular diagnostics, and as an extension of this, the application for neurologic disorders can be considered as “molecular neuropathology.” Imaging technologies have been refined to the molecular level and the term “molecular brain imaging” is suggested.

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References

  • Aguilar J, Urday-Cornejo V, Donabedian S, et al. Staphylococcus aureus meningitis: case series and literature review. Medicine (Baltimore) 2010;89:117–25.

    Article  Google Scholar 

  • Alfonso Y, Fraga J, Jiménez N, et al. Detection of Toxoplasma gondii in cerebrospinal fluid from AIDS patients by nested PCR and rapid identification of type I allele at B1 gene by RFLP analysis. Exp Parasitol 2009;122:203–7.

    Article  PubMed  CAS  Google Scholar 

  • Bennett J, Hahn SH. Clinical molecular diagnosis of Wilson disease. Semin Liver Dis 2011;31:233–8.

    Article  PubMed  CAS  Google Scholar 

  • Bergallo M, Costa C, Margio S, Sidoti F, Terlizzi ME, Cavallo R. Development of a multiplex PCR for detection and typing of major human herpesviruses in cerebrospinal fluid. Can J Microbiol 2007;53:1117–22.

    Article  PubMed  CAS  Google Scholar 

  • Beroukhim R, Getz G, Nghiemphu L, et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A 2007;104:20007–12.

    Article  PubMed  CAS  Google Scholar 

  • Bertram L, Lill CM, Tanzi RE. The genetics of Alzheimer disease: back to the future. Neuron 2010;68:270–81.

    Article  PubMed  CAS  Google Scholar 

  • Boaretti M, Scalet G, Fontana R. A two-year prospective study of clinical criteria and PCR assay of cerebrospinal fluid for the diagnosis of viral infections of the central nervous system. New Microbiol 2008;31:445–50.

    PubMed  Google Scholar 

  • Bras JM, Singleton AB. Exome sequencing in Parkinson's disease. Clin Genet 2011;80:104–9.

    Article  PubMed  CAS  Google Scholar 

  • Bredel M, Scholtens DM, Harsh GR, et al. A network model of a cooperative genetic landscape in brain tumors. JAMA 2009;302:261–275.

    Article  PubMed  CAS  Google Scholar 

  • Bredel M, Scholtens DM, Yadav AK, et al. NFKBIA deletion in glioblastomas. N Engl J Med 2011;364:627–37.

    Article  PubMed  CAS  Google Scholar 

  • Burgunder JM, Finsterer J, Szolnoki Z, et al. EFNS guidelines on the molecular diagnosis of channelopathies, epilepsies, migraine, stroke, and dementias. Eur J Neurol 2010;17:641–8

    Article  PubMed  Google Scholar 

  • Burgunder JM, Schöls L, Baets J, et al. EFNS guidelines for the molecular diagnosis of neurogenetic disorders: motoneuron, peripheral nerve and muscle disorders. Eur J Neurol 2011;18:207–17.

    Article  PubMed  Google Scholar 

  • Camacho-Vanegas O, Narla G, Teixeira MS, et al. Functional inactivation of the KLF6 tumor suppressor gene by loss of heterozygosity and increased alternative splicing in glioblastoma. Int J Cancer 2007;121:1390–5.

    Article  PubMed  CAS  Google Scholar 

  • Chandramuki A, Lyashchenko K, Kumari HB, et al. Detection of antibody to Mycobacterium tuberculosis protein antigens in the cerebrospinal fluid of patients with tuberculous meningitis. J Infect Dis 2002;186:678–83.

    Article  PubMed  CAS  Google Scholar 

  • Colmenero JD, Queipo-Ortuno MI, Reguera JM, et al. Real time polymerase chain reaction: a new powerful tool for the diagnosis of neurobrucellosis. J Neurol Neurosurg Psychiatry 2005;76:1025–7.

    Article  PubMed  CAS  Google Scholar 

  • Crespo I, Vital AL, Nieto AB, et al. Detailed Characterization of Alterations of Chromosomes 7, 9, and 10 in Glioblastomas as Assessed by Single-Nucleotide Polymorphism Arrays. J Mol Diagn 2011;13: 634–47.

    Article  PubMed  CAS  Google Scholar 

  • del Gaudio D, Yang Y, Boggs BA, et al. Molecular diagnosis of Duchenne/Becker muscular dystrophy: enhanced detection of dystrophin gene rearrangements by oligonucleotide array-comparative genomic hybridization. Hum Mutat 2008;29:1100–7.

    Article  PubMed  Google Scholar 

  • Douglas TA, Tamburro D, Fredolini C, et al. The use of hydrogel microparticles to sequester and concentrate bacterial antigens in a urine test for Lyme disease. Biomaterials 2011;32:1157–66.

    Article  PubMed  CAS  Google Scholar 

  • Dreyfuss JM, Johnson MD, Park PJ. Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. Mol Cancer 2009;8:71.

    Article  PubMed  Google Scholar 

  • Duffy KJ, Littrell J, Locke A, Sherman SL, Olivier M. A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay. Nucleic Acids Res 2008;36:e145.

    Article  PubMed  Google Scholar 

  • Eberlin LS, Norton I, Dill AL, et al. Classifying human brain tumors by lipid imaging with mass spectrometry. Cancer Res 2012;72:645–54.

    Article  PubMed  CAS  Google Scholar 

  • Ehrich M, Deciu C, Zwiefelhofer T, et al. Noninvasive detection of fetal trisomy 21 by sequencing of DNA in maternal blood: a study in a clinical setting. Am J Obst Gynecol 2011;204:205.e1-11.

    Article  Google Scholar 

  • El Hallani S, Ducray F, Idbaih A, et al. TP53 codon 72 polymorphism is associated with age at onset of glioblastoma. Neurology 2009;72:332–6.

    Article  PubMed  Google Scholar 

  • Falk M, Vojtiskova M, Lukas Z, Kroupova I, Froster U. Simple procedure for automatic detection of unstable alleles in the myotonic dystrophy and Huntington's disease loci. Genet Test 2006;10:85–97.

    Article  PubMed  CAS  Google Scholar 

  • Felsberg J, Rapp M, Loeser S, et al. Prognostic significance of molecular markers and extent of resection in primary glioblastoma patients. Clin Cancer Res 2009;15:6683–93.

    Article  PubMed  CAS  Google Scholar 

  • Franzen-Rohl E, Tiveljung-Lindell A, Grillner L, Aurelius E. Increased detection rate in diagnosis of herpes simplex virus type 2 meningitis by real-time PCR of cerebrospinal fluid. Evaluation of a large and clinically well-characterized material. J Clin Microbiol 2007;45:2516–20.

    Article  PubMed  Google Scholar 

  • Gaeta A, Verzaro S, Cristina LM, Mancini C, Nazzari C. Diagnosis of neurological herpesvirus infections: real time PCR in cerebral spinal fluid analysis. New Microbiol 2009;32:333–40.

    PubMed  CAS  Google Scholar 

  • Gasser T, Finsterer J, Baets J, et al. EFNS guidelines on the molecular diagnosis of ataxias and spastic paraplegias. Eur J Neurol 2010;17:179–88.

    Article  PubMed  CAS  Google Scholar 

  • Goldman S, Pirotte BJ. Brain tumors. Methods Mol Biol 2011;727:291–315.

    Article  PubMed  Google Scholar 

  • Graham BH. Diagnostic challenges of mitochondrial disorders: complexities of two genomes. Methods Mol Biol 2012;837:35–46.

    Article  PubMed  CAS  Google Scholar 

  • Gusella JF, Wexler NS, Conneally PM, et al. A polymorphic DNA marker genetically linked to Huntington's disease. Nature 1983;306:234–8.

    Article  PubMed  CAS  Google Scholar 

  • Halmøy A, Johansson S, Winge I, et al. Attention-deficit/hyperactivity disorder symptoms in offspring of mothers with impaired serotonin production. Arch Gen Psychiatry 2010;67:1033–43.

    Article  PubMed  Google Scholar 

  • Harrington AT, Creutzfeldt CJ, Sengupta DJ, Hoogestraat DR, Zunt JR, Cookson BT. Diagnosis of neurocysticercosis by detection of Taenia solium DNA using a global DNA screening platform. Clin Infect Dis 2009;48:86–90.

    Article  PubMed  CAS  Google Scholar 

  • Hernandez M, Gonzalez LM, Fleury A, et al. Neurocysticercosis: detection of Taenia solium DNA in human cerebrospinal fluid using a semi-nested PCR based on HDP2. Ann Trop Med Parasitol 2008;102:317–23.

    Article  PubMed  CAS  Google Scholar 

  • Hirose Y, Sasaki H, Miwa T, et al. Whole genome analysis from microdissected tissue revealed adult supratentorial grade II-III gliomas are divided into clinically relevant subgroups by genetic profile. Neurosurgery 2011;69:376–90.

    Article  PubMed  Google Scholar 

  • Horbinski C, Miller CR, Perry A. Gone FISHing: clinical lessons learned in brain tumor molecular diagnostics over the last decade. Brain Pathol 2011;21:57–73.

    Article  PubMed  Google Scholar 

  • Intergroup Radiation Therapy Oncology Group Trial 9402; Cairncross G, Berkey B, Shaw E, et al. Phase III trial of chemotherapy plus radiotherapy compared with radiotherapy alone for pure and mixed anaplastic oligodendroglioma: Intergroup Radiation Therapy Oncology Group Trial 9402. J Clin Oncol 2006;24:2707–14.

    Google Scholar 

  • Jain KK. Application of laser capture microdissection to proteomics. Methods Enzymol 2002;356:157–67.

    Article  PubMed  CAS  Google Scholar 

  • Jain KK. DNA Sequencing. Jain PharmaBiotech Publications, Basel, Switzerland, 2012a.

    Google Scholar 

  • Jain KK. Molecular Diagnostics. Jain PharmaBiotech Publications, Basel, Switzerland, 2012.

    Google Scholar 

  • Jain KK. Molecular Diagnostics. Jain PharmaBiotech Publications, Basel, Switzerland, 2012.

    Google Scholar 

  • Jensen R, Lee J. Predicting outcomes of patients with intracranial meningiomas using molecular markers of hypoxia, vascularity, and proliferation. Neurosurgery 2012;71:146–56.

    Article  PubMed  Google Scholar 

  • Jones DT, Jäger N, Kool M, et al. Dissecting the genomic complexity underlying medulloblastoma. Nature 2012;doi:10.1038/nature11284.

  • Kalman L, Leonard J, Gerry N, et al. Quality assurance for Duchenne and Becker muscular dystrophy genetic testing: development of a genomic DNA reference material panel. J Mol Diagn 2011;13:167–74.

    Article  PubMed  CAS  Google Scholar 

  • Kanerva M, Mannonen L, Piiparinen H, Peltomaa M, Vaheri A, Pitkaranta A. Search for Herpesviruses in cerebrospinal fluid of facial palsy patients by PCR. Acta Otolaryngol 2007;127:775–9.

    Article  PubMed  CAS  Google Scholar 

  • Kennerson ML, Warburton T, Nelis E, et al. Mutation scanning the GJB1 gene with high-resolution melting analysis: implications for mutation scanning of genes for Charcot-Marie-Tooth disease. Clin Chem 2007;53:349–52.

    Article  PubMed  CAS  Google Scholar 

  • Kool M, Koster J, Bunt J, et al. Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features. PLoS One 2008;3:e3088.

    Article  PubMed  Google Scholar 

  • Kouwenhoven MC, Gorlia T, Kros JM, et al. Molecular analysis of anaplastic oligodendroglial tumors in a prospective randomized study: a report from EORTC study 26951. Neuro Oncol 2009;11:737–46.

    Article  PubMed  Google Scholar 

  • Leveque N, Van Haecke A, Renois F, Boutolleau D, Talmud D, Andreoletti L. Rapid virological diagnosis of central nervous system infections by use of a multiplex reverse transcription-PCR DNA microarray. J Clin Microbiol 2011;49:3874–9.

    Article  PubMed  CAS  Google Scholar 

  • Lionel AC, Crosbie J, Barbosa N, et al. Rare copy number variation discovery and cross-disorder comparisons identify risk genes for ADHD. Sci Transl Med 2011;3:95ra75.

    Article  PubMed  CAS  Google Scholar 

  • Lupski JR, Reid JG, Gonzaga-Jauregui C, et al. Whole-Genome Sequencing in a Patient with Charcot-Marie-Tooth Neuropathy. NEJM 2010;362:1181–91.

    Article  PubMed  CAS  Google Scholar 

  • Magri F, Del Bo R, D'Angelo MG, et al. Clinical and molecular characterization of a cohort of patients with novel nucleotide alterations of the Dystrophin gene detected by direct sequencing. BMC Med Genet 2011;12:37.

    Article  PubMed  CAS  Google Scholar 

  • Martinez R, Schackert G, Esteller M. Hypermethylation of the proapoptotic gene TMS1/ASC: prognostic importance in glioblastoma multiforme. J Neurooncol 2007;82:133–9.

    Article  PubMed  CAS  Google Scholar 

  • Matilla-Dueñas A, Corral-Juan M, Volpini V, Sanchez I. The spinocerebellar ataxias: clinical aspects and molecular genetics. Adv Exp Med Biol 2012;724:351–74.

    Article  PubMed  Google Scholar 

  • Morikawa S, Harahap IS, Kaszynski RH, et al. Diagnosis of Spinal Muscular Atrophy Via High-Resolution Melting Analysis Symmetric Polymerase Chain Reaction Without Probe: A Screening Evaluation for SMN1 Deletions and Intragenic Mutations. Genet Test Mol Biomarkers 2011;15:677–84.

    Article  PubMed  CAS  Google Scholar 

  • Nagdev KJ, Kashyap RS, Deshpande PS, Purohit HJ, Taori GM, Daginawala HF. Determination of PCR efficiency for diagnosis of tuberculous meningitis in Chelex-100 extracted DNA samples. Int J Tuberc Lung Dis 2010;14:1032–8.

    PubMed  CAS  Google Scholar 

  • Parra E, Castañeda E, Moreno J. Identification of Haemophilus influenzae, Streptococcus pneumoniae and Neisseria meningitidis by polymerase chain reaction. Biomedica 2007;27:454–60.

    PubMed  Google Scholar 

  • Parsons DW, Jones S, Zhang X, et al. An integrated genomic analysis of human glioblastoma multiforme. Science 2008;321:1807–12.

    Article  PubMed  CAS  Google Scholar 

  • Parsons DW, Li M, Zhang X, Jones S, et al. The genetic landscape of the childhood cancer medulloblastoma. Science 2011;331:435–9.

    Article  PubMed  CAS  Google Scholar 

  • Persson A, Bergström T, Lindh M, Namvar L, Studahl M. Varicella-zoster virus CNS disease--viral load, clinical manifestations and sequels. J Clin Virol 2009;46:249–53.

    Article  PubMed  CAS  Google Scholar 

  • Pinto D, Pagnamenta AT, Klei L, et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 2010;466:368–72.

    Article  PubMed  CAS  Google Scholar 

  • Plagnol V, Nalls MA, Bras J, et al. A two-stage meta-analysis identifies several new loci for Parkinson’s disease. PLoS Genet 2011;7(6):e1002142.

    Article  CAS  Google Scholar 

  • Pugh TJ, Weeraratne SD, Archer TC, et al. Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature 2012; doi:10.1038/nature11329.

  • Reitman ZJ, Jin G, Karoly ED, et al. Profiling the effects of isocitrate dehydrogenase 1 and 2 mutations on the cellular metabolome. Proc Natl Acad Sci U S A 2011;108:3270–5.

    Article  PubMed  CAS  Google Scholar 

  • Reuser AJJ, Verheijen FW, Kroos MA, et al. Enzymatic and molecular strategies to diagnose Pompe disease. Expert Opin Med Diagn 2010;4:79–89.

    Article  CAS  Google Scholar 

  • Richards M, Coppée F, Thomas N, et al. Facioscapulohumeral muscular dystrophy (FSHD): an enigma unravelled? Hum Genet 2012;131:325–40.

    Article  PubMed  CAS  Google Scholar 

  • Robinson G, Parker M, Kranenburg TA, et al. Novel mutations target distinct subgroups of medulloblastoma. Nature 2012;doi:10.1038/nature11213.

  • Sehbani L, Kabamba-Mukadi B, Vandenbroucke AT, Bodeus M, Goubau P. Specific and quantitative detection of human polyomaviruses BKV and JCV by LightCycler real-time PCR. J Clin Virol 2006;36:159–62.

    Article  PubMed  CAS  Google Scholar 

  • Simon M, Boström JP, Hartmann C. Molecular genetics of meningiomas: from basic research to potential clinical applications. Neurosurgery 2007;60:787–98.

    Article  PubMed  Google Scholar 

  • Sonneville R, Klein I, de Broucker T, Wolff M. Post-infectious encephalitis in adults: diagnosis and management. J Infect 2009;58:321–8.

    Article  PubMed  CAS  Google Scholar 

  • Szerlip NJ, Pedraz A, Chakravarty D, et al. Intratumoral heterogeneity of receptor tyrosine kinases EGFR and PDGFRA amplification in glioblastoma defines subpopulations with distinct growth factor response. Proc Natl Acad Sci U S A 2012;109:3041–6.

    Article  PubMed  CAS  Google Scholar 

  • Takahashi T, Nakayama T, Tamura M, et al. Nested PCR for assessing the clinical course of tuberculous meningitis. Neurology 2005;64:1789–93.

    Article  PubMed  CAS  Google Scholar 

  • Tassone F, Pan R, Amiri K, Taylor AK, Hagerman PJ. A rapid polymerase chain reaction-based screening method for identification of all expanded alleles of the fragile X (FMR1) gene in newborn and high-risk populations. J Mol Diagn 2008;10:43–9.

    Article  PubMed  CAS  Google Scholar 

  • Tchirkov A, Rolhion C, Kemeny JL, et al. Clinical implications of quantitative real-time RT-PCR analysis of hTERT gene expression in human gliomas. Br J Cancer 2003;88:516–20.

    Article  PubMed  CAS  Google Scholar 

  • Veiseh M, Gabikian P, Bahrami SB, et al. Tumor paint: a chlorotoxin:cy5.5 bioconjugate for intraoperative visualization of cancer foci. Cancer Res 2007;67:6882–8.

    Article  PubMed  CAS  Google Scholar 

  • von Einsiedel RW, Samorei IW, Pawlita M, Zwissler B, Deubel M, Vinters HV. New JC virus infection patterns by in situ PCR in brains of acquired immunodeficiency syndrome patients with progressive multifocal leukoencephalopathy. J Neurovirol 2004;10:1–11.

    Article  Google Scholar 

  • Vranova V, Necesalova E, Kuglik P, et al. Screening of genomic imbalances in glioblastoma multiforme using high-resolution comparative genomic hybridization. Oncol Rep 2007;17:457–64.

    PubMed  CAS  Google Scholar 

  • Walker C, du Plessis DG, Joyce KA, et al. Molecular pathology and clinical characteristics of oligodendroglial neoplasms. Ann Neurol 2005;57:855–65.

    Article  PubMed  CAS  Google Scholar 

  • Wang H, Wang H, Zhang W, Fuller GN. Overexpression of IGFBP5, but not IGFBP3, correlates with the histologic grade of human diffuse glioma: a tissue microarray and immunohistochemical study. Technol Cancer Res Treat 2006;5:195–9.

    PubMed  CAS  Google Scholar 

  • Wong LJ, Scaglia F, Graham BH, Craigen WJ. Current molecular diagnostic algorithm for mitochondrial disorders. Mol Genet Metab 2010;100:111–7.

    Article  PubMed  CAS  Google Scholar 

  • Wu CH, Fallini C, Ticozzi N, et al. Mutations in the profilin 1 gene cause familial amyotrophic lateral sclerosis. Nature 2012 July 15;doi:10.1038/nature11280.

  • Yadav AK, Renfrow JJ, Scholtens DM, et al. Monosomy of chromosome 10 associated with dysregulation of epidermal growth factor signaling in glioblastomas. JAMA 2009;302:276–89.

    Article  PubMed  CAS  Google Scholar 

  • Yan H, Parsons DW, Jin G. IDH1 and IDH2 mutations in gliomas. N Engl J Med 2009;360:765–73.

    Article  PubMed  CAS  Google Scholar 

  • Yanoov-Sharav M, Leshinsky-Silver E, Cohen S, et al. Genetic Counseling and Testing for FSHD (Facioscapulohumeral Muscular Dystrophy) in the Israeli Population. J Genet Couns 2012;21:557–63.

    Article  PubMed  Google Scholar 

  • Zhang SJ, Endo S, Saito T, et al. Primary malignant lymphoma of the brain: frequent abnormalities and inactivation of p14 tumor suppressor gene. Cancer Sci 2005;96:38–41.

    Article  PubMed  CAS  Google Scholar 

  • Zhu H, Acquaviva J, Ramachandran P, et al. Oncogenic EGFR signaling cooperates with loss of tumor suppressor gene functions in gliomagenesis. Proc Natl Acad Sci U S A 2009a;106:2712–6.

    Article  PubMed  CAS  Google Scholar 

  • Zhu YN, Lu SM, You JF, Zhu B, Yu MY. Novel real-time PCR assay for rapid prenatal diagnosis of Down syndrome: a prospective study of 563 amniocytes. Clin Biochem 2009;42:672–5.

    Article  PubMed  CAS  Google Scholar 

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Jain, K.K. (2013). Molecular Diagnostics for Neurological Disorders. In: Applications of Biotechnology in Neurology. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-272-8_5

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