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  1. Article ; Online: Clinical Evaluation of IDH Mutation Status in Formalin-Fixed Paraffin-Embedded Tissue in Gliomas.

    Nelson, Ernest J / Gubbiotti, Maria A / Carlin, Alicia M / Nasrallah, MacLean P / Van Deerlin, Vivianna M / Herlihy, Sarah E

    Molecular diagnosis & therapy

    2023  Volume 27, Issue 3, Page(s) 371–381

    Abstract: Background and objective: Determination of isocitrate dehydrogenase (IDH) 1/2 mutational status is crucial for a glioma diagnosis. It is common for IDH mutational status to be determined via a two-step algorithm that utilizes immunohistochemistry ... ...

    Abstract Background and objective: Determination of isocitrate dehydrogenase (IDH) 1/2 mutational status is crucial for a glioma diagnosis. It is common for IDH mutational status to be determined via a two-step algorithm that utilizes immunohistochemistry studies for IDH1 R132H, the most frequent variant, followed by next-generation sequencing studies for immunohistochemistry-negative or immunohistochemistry-equivocal cases. The objective of this study was to evaluate adding a rapid real-time polymerase chain reaction (RT-PCR) assay to the testing algorithm.  METHODS: We validated a modified, commercial, qualitative, RT-PCR assay with the ability to detect 14 variants in IDH1/2 in formalin-fixed paraffin-embedded glioma tumor specimens. The assay was validated using 51 tumor formalin-fixed paraffin-embedded specimens. During clinical implementation of this assay, 48 brain tumor specimens were assessed for IDH result concordance and turnaround time to result.
    Results: Concordance between the RT-PCR and sequencing and IHC studies was 100%. This RT-PCR assay also showed concordant results with IHC for IDH1 R132H for 11 of the 12 (92%) tumor specimens with IDH mutations. The RT-PCR assay yielded faster results (average 2.6 days turnaround time) in comparison to sequencing studies (17.9 days), with complete concordance.
    Conclusions: In summary, we report that this RT-PCR assay can reliably be performed on formalin-fixed paraffin-embedded specimens and has a faster turnaround time than sequencing assays and can be clinically implemented for determination of IDH mutation status for patients with glioma.
    MeSH term(s) Humans ; Paraffin Embedding ; Isocitrate Dehydrogenase/genetics ; Glioma/genetics ; Brain Neoplasms/genetics ; Mutation ; Formaldehyde
    Chemical Substances Isocitrate Dehydrogenase (EC 1.1.1.41) ; Formaldehyde (1HG84L3525)
    Language English
    Publishing date 2023-01-23
    Publishing country New Zealand
    Document type Journal Article
    ZDB-ID 2232796-4
    ISSN 1179-2000 ; 1177-1062
    ISSN (online) 1179-2000
    ISSN 1177-1062
    DOI 10.1007/s40291-022-00638-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5202: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  2. Article ; Online: GPNMB Biomarker Levels in GBA1 Carriers with Lewy Body Disorders.

    Brody, Eliza M / Seo, Yunji / Suh, EunRan / Amari, Noor / Hartstone, Whitney G / Skrinak, R Tyler / Zhang, Hanwen / Diaz-Ortiz, Maria E / Weintraub, Daniel / Tropea, Thomas F / Van Deerlin, Vivianna M / Chen-Plotkin, Alice S

    Movement disorders : official journal of the Movement Disorder Society

    2024  

    Abstract: Background: The GPNMB single-nucleotide polymorphism rs199347 and GBA1 variants both associate with Lewy body disorder (LBD) risk. GPNMB encodes glycoprotein nonmetastatic melanoma protein B (GPNMB), a biomarker for GBA1-associated Gaucher's disease.: ...

    Abstract Background: The GPNMB single-nucleotide polymorphism rs199347 and GBA1 variants both associate with Lewy body disorder (LBD) risk. GPNMB encodes glycoprotein nonmetastatic melanoma protein B (GPNMB), a biomarker for GBA1-associated Gaucher's disease.
    Objective: The aim of this study was to determine whether GPNMB levels (1) differ in LBD with and without GBA1 variants and (2) associate with rs199347 genotype.
    Methods: We quantified GPNMB levels in plasma and cerebrospinal fluid (CSF) from 124 individuals with LBD with one GBA1 variant (121 plasma, 14 CSF), 631 individuals with LBD without GBA1 variants (626 plasma, 41 CSF), 9 neurologically normal individuals with one GBA1 variant (plasma), and 2 individuals with two GBA1 variants (plasma). We tested for associations between GPNMB levels and rs199347 or GBA1 status.
    Results: GPNMB levels associate with rs199347 genotype in plasma (P = 0.022) and CSF (P = 0.007), but not with GBA1 status.
    Conclusions: rs199347 is a protein quantitative trait locus for GPNMB. GPNMB levels are unaltered in individuals carrying one GBA1 variant. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
    Language English
    Publishing date 2024-04-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 607633-6
    ISSN 1531-8257 ; 0885-3185
    ISSN (online) 1531-8257
    ISSN 0885-3185
    DOI 10.1002/mds.29773
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  3. Article: Cytoarchitectonic gradients of laminar degeneration in behavioral variant frontotemporal dementia.

    Ohm, Daniel T / Xie, Sharon X / Capp, Noah / Arezoumandan, Sanaz / Cousins, Katheryn A Q / Rascovsky, Katya / Wolk, David A / Van Deerlin, Vivianna M / Lee, Edward B / McMillan, Corey T / Irwin, David J

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Behavioral variant frontotemporal dementia (bvFTD) is a clinical syndrome primarily caused by either tau (bvFTD-tau) or TDP-43 (bvFTD-TDP) proteinopathies. We previously found lower cortical layers and dorsolateral regions accumulate greater tau than TDP- ...

    Abstract Behavioral variant frontotemporal dementia (bvFTD) is a clinical syndrome primarily caused by either tau (bvFTD-tau) or TDP-43 (bvFTD-TDP) proteinopathies. We previously found lower cortical layers and dorsolateral regions accumulate greater tau than TDP-43 pathology; however, patterns of laminar neurodegeneration across diverse cytoarchitecture in bvFTD is understudied. We hypothesized that bvFTD-tau and bvFTD-TDP have distinct laminar distributions of pyramidal neurodegeneration along cortical gradients, a topologic order of cytoarchitectonic subregions based on increasing pyramidal density and laminar differentiation. Here, we tested this hypothesis in a frontal cortical gradient consisting of five cytoarchitectonic types (i.e., periallocortex, agranular mesocortex, dysgranular mesocortex, eulaminate-I isocortex, eulaminate-II isocortex) spanning anterior cingulate, paracingulate, orbitofrontal, and mid-frontal gyri in bvFTD-tau (n=27), bvFTD-TDP (n=47), and healthy controls (HC; n=32). We immunostained all tissue for total neurons (NeuN; neuronal-nuclear protein) and pyramidal neurons (SMI32; non-phosphorylated neurofilament) and digitally quantified NeuN-immunoreactivity (ir) and SMI32-ir in supragranular II-III, infragranular V-VI, and all I-VI layers in each cytoarchitectonic type. We used linear mixed-effects models adjusted for demographic and biologic variables to compare SMI32-ir between groups and examine relationships with the cortical gradient, long-range pathways, and clinical symptoms. We found regional and laminar distributions of SMI32-ir expected for HC, validating our measures within the cortical gradient framework. While SMI32-ir loss was not related to the cortical gradient in bvFTD-TDP, SMI32-ir progressively decreased along the cortical gradient of bvFTD-tau and included greater SMI32-ir loss in supragranular eulaminate-II isocortex in bvFTD-tau vs bvFTD-TDP (
    Language English
    Publishing date 2024-04-09
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.05.588259
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Validation of a Long-Read PCR Assay for Sensitive Detection and Sizing of C9orf72 Hexanucleotide Repeat Expansions.

    Suh, EunRan / Grando, Kaitlyn / Van Deerlin, Vivianna M

    The Journal of molecular diagnostics : JMD

    2018  Volume 20, Issue 6, Page(s) 871–882

    Abstract: A hexanucleotide GGGGCC repeat expansion in C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal degeneration. Accurate determination and quantitation of the repeat length is critical in both clinical and research ... ...

    Abstract A hexanucleotide GGGGCC repeat expansion in C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal degeneration. Accurate determination and quantitation of the repeat length is critical in both clinical and research settings. However, because of the complexity of the C9orf72 expansion with high GC content, large size of repeats, and high rate of insertions/deletions (indels) and sequence variations in the flanking regions, molecular genetic analysis of the locus is challenging. To improve the performance characteristics for clinical testing, we evaluated a commercially available long-read C9orf72 PCR assay for research use only, AmplideX PCR/CE C9orf72 assay (AmplideX-C9), and compared its performance with our existing laboratory-developed C9orf72 expansion procedure. Overall, in comparison to the laboratory-developed C9orf72 expansion procedure, AmplideX-C9 demonstrated a more efficient workflow, greater PCR efficiency for sizing of repeat expansions, and improved peak amplitude with lower DNA input and higher analytic sensitivity. This, in turn, permitted detection of indels in the 3' downstream of the repeat expansion region in expanded alleles, showed a higher success rate with formalin-fixed, paraffin-embedded tissue specimens, and facilitated the assessment of repeat mosaicism. In summary, AmplideX-C9 will not only help to improve clinical testing for C9orf72-associated amyotrophic lateral sclerosis and frontotemporal degeneration but will also be a valuable research tool to better characterize the complexity of expansions and study the effects of indels/sequence variations in the flanking region.
    MeSH term(s) Alleles ; Base Sequence ; C9orf72 Protein/genetics ; DNA/genetics ; DNA Repeat Expansion/genetics ; Humans ; INDEL Mutation/genetics ; Limit of Detection ; Mosaicism ; Polymerase Chain Reaction/methods ; Reproducibility of Results
    Chemical Substances C9orf72 Protein ; DNA (9007-49-2)
    Language English
    Publishing date 2018-08-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Validation Study
    ZDB-ID 2000060-1
    ISSN 1943-7811 ; 1525-1578
    ISSN (online) 1943-7811
    ISSN 1525-1578
    DOI 10.1016/j.jmoldx.2018.07.001
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    Zs.A 5146: Show issues Location:
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  5. Article ; Online: Alzheimer's Disease and Frontotemporal Dementia: The Current State of Genetics and Genetic Testing Since the Advent of Next-Generation Sequencing.

    Goldman, Jill S / Van Deerlin, Vivianna M

    Molecular diagnosis & therapy

    2018  Volume 22, Issue 5, Page(s) 505–513

    Abstract: The advent of next-generation sequencing has changed genetic diagnostics, allowing clinicians to test concurrently for phenotypically overlapping conditions such as Alzheimer's disease (AD) and frontotemporal dementia (FTD). However, to interpret genetic ...

    Abstract The advent of next-generation sequencing has changed genetic diagnostics, allowing clinicians to test concurrently for phenotypically overlapping conditions such as Alzheimer's disease (AD) and frontotemporal dementia (FTD). However, to interpret genetic results, clinicians require an understanding of the benefits and limitations of different genetic technologies, such as the inability to detect large repeat expansions in such diseases as C9orf72-associated FTD and amyotrophic lateral sclerosis. Other types of mutations such as large deletions or duplications and triple repeat expansions may also go undetected. Additionally, the concurrent testing of multiple genes or the whole exome increases the likelihood of discovering variants of unknown significance. Our goal here is to review the current knowledge about the genetics of AD and FTD and suggest up-to-date guidelines for genetic testing for these dementias. Despite the improvements in diagnosis due to biomarkers testing, AD and FTD can have overlapping symptoms. When used appropriately, genetic testing can elucidate the diagnosis and specific etiology of the disease, as well as provide information for the family and determine eligibility for clinical trials. Prior to ordering genetic testing, clinicians must determine the appropriate genes to test, the types of mutations that occur in these genes, and the best type of genetic test to use. Without this analysis, interpretation of genetic results will be difficult. Patients should be counseled about the benefits and limitations of different types of genetic tests so they can make an informed decision about testing.
    MeSH term(s) Algorithms ; Alzheimer Disease/diagnosis ; Alzheimer Disease/genetics ; Frontotemporal Dementia/diagnosis ; Frontotemporal Dementia/genetics ; Genetic Association Studies/methods ; Genetic Counseling ; Genetic Predisposition to Disease ; Genetic Testing/methods ; Genomics/methods ; Humans ; Practice Patterns, Physicians'
    Language English
    Publishing date 2018-07-03
    Publishing country New Zealand
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 2232796-4
    ISSN 1179-2000 ; 1177-1062
    ISSN (online) 1179-2000
    ISSN 1177-1062
    DOI 10.1007/s40291-018-0347-7
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    Zs.A 5202: Show issues Location:
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  6. Article ; Online: TMEM106B deficiency impairs cerebellar myelination and synaptic integrity with Purkinje cell loss.

    Feng, Tuancheng / Luan, Lin / Katz, Isabel Iscol / Ullah, Mohammed / Van Deerlin, Vivianna M / Trojanowski, John Q / Lee, Edward B / Hu, Fenghua

    Acta neuropathologica communications

    2022  Volume 10, Issue 1, Page(s) 33

    Abstract: TMEM106B, a type II lysosomal transmembrane protein, has recently been associated with brain aging, hypomyelinating leukodystrophy, frontotemporal lobar degeneration (FTLD) and several other brain disorders. TMEM106B is critical for proper lysosomal ... ...

    Abstract TMEM106B, a type II lysosomal transmembrane protein, has recently been associated with brain aging, hypomyelinating leukodystrophy, frontotemporal lobar degeneration (FTLD) and several other brain disorders. TMEM106B is critical for proper lysosomal function and TMEM106B deficiency leads to myelination defects, FTLD related pathology, and motor coordination deficits in mice. However, the physiological and pathological functions of TMEM106B in the brain are still not well understood. In this study, we investigate the role of TMEM106B in the cerebellum, dysfunction of which has been associated with FTLD and other brain disorders. We found that TMEM106B is ubiquitously expressed in neurons in the cerebellum, with the highest levels in the Purkinje neurons. Aged TMEM106B-deficient mice show significant loss of Purkinje neurons specifically in the anterior lobe of the cerebellum. Increased microglia and astrocyte activation, as well as an accumulation of ubiquitinated proteins, p62 and TDP-43 were also detected in the cerebellum of aged TMEM106B deficient mice. In the young mice, myelination defects and a significant loss of synapses between Purkinje and deep cerebellar nuclei neurons were observed. Interestingly, TMEM106B deficiency causes distinct lysosomal phenotypes in different types of neurons and glia in the cerebellum and frontal cortex. In humans, TMEM106B rs1990622 risk allele (T/T) is associated with increased Purkinje neuron loss. Taken together, our studies support that TMEM106B regulates lysosomal function in a cell-type-specific manner and TMEM106B is critical for maintaining synaptic integrity and neural functions in the cerebellum.
    MeSH term(s) Animals ; Brain Diseases/genetics ; Frontotemporal Dementia/genetics ; Frontotemporal Lobar Degeneration/pathology ; Membrane Proteins/genetics ; Mice ; Nerve Tissue Proteins/genetics ; Purkinje Cells/pathology
    Chemical Substances Membrane Proteins ; Nerve Tissue Proteins ; Tmem106b protein, mouse
    Language English
    Publishing date 2022-03-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2715589-4
    ISSN 2051-5960 ; 2051-5960
    ISSN (online) 2051-5960
    ISSN 2051-5960
    DOI 10.1186/s40478-022-01334-7
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  7. Article ; Online: The genetics and neuropathology of neurodegenerative disorders: perspectives and implications for research and clinical practice.

    Van Deerlin, Vivianna M

    Acta neuropathologica

    2012  Volume 124, Issue 3, Page(s) 297–303

    MeSH term(s) Brain/pathology ; Genetic Predisposition to Disease ; Humans ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/pathology ; Research
    Language English
    Publishing date 2012-08-09
    Publishing country Germany
    Document type Editorial ; Introductory Journal Article
    ZDB-ID 1079-0
    ISSN 1432-0533 ; 0001-6322
    ISSN (online) 1432-0533
    ISSN 0001-6322
    DOI 10.1007/s00401-012-1032-2
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    Ui II Zs.188: Show issues Location:
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  8. Article ; Online: Correction to: Isoform-specific patterns of tau burden and neuronal degeneration in MAPT-associated frontotemporal lobar degeneration.

    Giannini, Lucia A A / Ohm, Daniel T / Rozemuller, Annemieke J M / Dratch, Laynie / Suh, EunRan / van Deerlin, Vivianna M / Trojanowski, John Q / Lee, Edward B / van Swieten, John C / Grossman, Murray / Seelaar, Harro / Irwin, David J

    Acta neuropathologica

    2023  Volume 145, Issue 5, Page(s) 711

    Language English
    Publishing date 2023-03-17
    Publishing country Germany
    Document type Published Erratum
    ZDB-ID 1079-0
    ISSN 1432-0533 ; 0001-6322
    ISSN (online) 1432-0533
    ISSN 0001-6322
    DOI 10.1007/s00401-023-02556-2
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    Ui II Zs.188: Show issues Location:
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  9. Article ; Online: Correction: APOE and TREM2 regulate amyloid-responsive microglia in Alzheimer's disease.

    Nguyen, Aivi T / Wang, Kui / Hu, Gang / Wang, Xuran / Miao, Zhen / Azevedo, Joshua A / Suh, EunRan / Van Deerlin, Vivianna M / Choi, David / Roeder, Kathryn / Li, Mingyao / Lee, Edward B

    Acta neuropathologica

    2023  Volume 146, Issue 4, Page(s) 661

    Language English
    Publishing date 2023-08-17
    Publishing country Germany
    Document type Published Erratum
    ZDB-ID 1079-0
    ISSN 1432-0533 ; 0001-6322
    ISSN (online) 1432-0533
    ISSN 0001-6322
    DOI 10.1007/s00401-023-02620-x
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  10. Article: Glucocerebrosidase activity and lipid levels are related to protein pathologies in Parkinson's disease.

    Leyns, Cheryl E G / Prigent, Alice / Beezhold, Brenna / Yao, Lihang / Hatcher, Nathan G / Tao, Peining / Kang, John / Suh, EunRan / Van Deerlin, Vivianna M / Trojanowski, John Q / Lee, Virginia M Y / Kennedy, Matthew E / Fell, Matthew J / Henderson, Michael X

    NPJ Parkinson's disease

    2023  Volume 9, Issue 1, Page(s) 74

    Abstract: Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are progressive neurodegenerative diseases characterized by the accumulation of misfolded α-synuclein in the form of Lewy pathology. While most cases are sporadic, there are rare genetic ... ...

    Abstract Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are progressive neurodegenerative diseases characterized by the accumulation of misfolded α-synuclein in the form of Lewy pathology. While most cases are sporadic, there are rare genetic mutations that cause disease and more common variants that increase incidence of disease. The most prominent genetic mutations for PD and DLB are in the GBA1 and LRRK2 genes. GBA1 mutations are associated with decreased glucocerebrosidase activity and lysosomal accumulation of its lipid substrates, glucosylceramide and glucosylsphingosine. Previous studies have shown a link between this enzyme and lipids even in sporadic PD. However, it is unclear how the protein pathologies of disease are related to enzyme activity and glycosphingolipid levels. To address this gap in knowledge, we examined quantitative protein pathology, glucocerebrosidase activity and lipid substrates in parallel from 4 regions of 91 brains with no neurological disease, idiopathic, GBA1-linked, or LRRK2-linked PD and DLB. We find that several biomarkers are altered with respect to mutation and progression to dementia. We found mild association of glucocerebrosidase activity with disease, but a strong association of glucosylsphingosine with α-synuclein pathology, irrespective of genetic mutation. This association suggests that Lewy pathology precipitates changes in lipid levels related to progression to dementia.
    Language English
    Publishing date 2023-05-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2819218-7
    ISSN 2373-8057
    ISSN 2373-8057
    DOI 10.1038/s41531-023-00517-w
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