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Trait Loci Map** and CSF Proteome

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Cerebrospinal Fluid (CSF) Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2044))

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Abstract

Recent advance in high-throughput proteome analysis has enabled genome-wide and proteome-wide analyses of associations between single nucleotide polymorphisms and protein expression levels. Protein quantitative trait locus (pQTL) studies using cerebrospinal fluid (CSF) and DNA samples may provide valuable insights into the genetic basis and molecular mechanisms regulating protein expression in the central nervous system. In this chapter, we describe a step-by-step procedures of CSF collection and pQTL analysis, by using PLINK and R software.

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Author information

Authors and Affiliations

  1. Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan

    Daimei Sasayama, Kotaro Hattori & Hiroshi Kunugi

  2. Department of Psychiatry, Shinshu University School of Medicine, Nagano, Japan

    Daimei Sasayama

  3. Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan

    Kotaro Hattori

Authors
  1. Daimei Sasayama
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  2. Kotaro Hattori
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  3. Hiroshi Kunugi
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Corresponding author

Correspondence to Daimei Sasayama .

Editor information

Editors and Affiliations

  1. Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain

    Enrique Santamaría

  2. Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain

    Joaquín Fernández-Irigoyen

1 Electronic Supplementary Materials

Supplementary File 1

Sample (3615 kb)

Supplementary File 2

Sample (1 kb)

Supplementary File 3

CSF protein (TXT 19 kb)

Supplementary File 4

Covariate (TXT 1 kb)

Supplementary File 5

Gene location (TXT 691 bytes)

Supplementary File 6

SNP position (TXT 150 kb)

Supplementary File 7

Cis pqtl (TXT 7 kb)

Supplementary File 8

Trans pqtl (TXT 50 kb)

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Sasayama, D., Hattori, K., Kunugi, H. (2019). Trait Loci Map** and CSF Proteome. In: Santamaría, E., Fernández-Irigoyen, J. (eds) Cerebrospinal Fluid (CSF) Proteomics. Methods in Molecular Biology, vol 2044. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9706-0_24

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  • DOI: https://doi.org/10.1007/978-1-4939-9706-0_24

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9705-3

  • Online ISBN: 978-1-4939-9706-0

  • eBook Packages: Springer Protocols

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