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BMC Med Genomics. 2016 Aug 12;9 Suppl 1:30. doi: 10.1186/s12920-016-0190-9.

Integration of bioinformatics and imaging informatics for identifying rare PSEN1 variants in Alzheimer's disease.

Author information

1
Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA. knho@iupui.edu.
2
Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA. knho@iupui.edu.
3
Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA. knho@iupui.edu.
4
Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
5
Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA.
6
Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA.
7
Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA.
8
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
9
Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
10
Department of Neurology, Mayo Clinic Minnesota, Rochester, MN, USA.
11
Department of Radiology, Mayo Clinic Minnesota, Rochester, MN, USA.
12
Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
13
Departments of Radiology, Medicine, and Psychiatry, University of California-San Francisco, San Francisco, CA, USA.
14
Department of Veterans Affairs Medical Center, San Francisco, CA, USA.
15
Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
16
The Institute for Neuroimaging and Informatics and Laboratory of Neuro Imaging, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
17
Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA. asaykin@iupui.edu.
18
Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA. asaykin@iupui.edu.
19
Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA. asaykin@iupui.edu.
20
Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA. asaykin@iupui.edu.

Abstract

BACKGROUND:

Pathogenic mutations in PSEN1 are known to cause familial early-onset Alzheimer's disease (EOAD) but common variants in PSEN1 have not been found to strongly influence late-onset AD (LOAD). The association of rare variants in PSEN1 with LOAD-related endophenotypes has received little attention. In this study, we performed a rare variant association analysis of PSEN1 with quantitative biomarkers of LOAD using whole genome sequencing (WGS) by integrating bioinformatics and imaging informatics.

METHODS:

A WGS data set (N = 815) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort was used in this analysis. 757 non-Hispanic Caucasian participants underwent WGS from a blood sample and high resolution T1-weighted structural MRI at baseline. An automated MRI analysis technique (FreeSurfer) was used to measure cortical thickness and volume of neuroanatomical structures. We assessed imaging and cerebrospinal fluid (CSF) biomarkers as LOAD-related quantitative endophenotypes. Single variant analyses were performed using PLINK and gene-based analyses of rare variants were performed using the optimal Sequence Kernel Association Test (SKAT-O).

RESULTS:

A total of 839 rare variants (MAF < 1/√(2 N) = 0.0257) were found within a region of ±10 kb from PSEN1. Among them, six exonic (three non-synonymous) variants were observed. A single variant association analysis showed that the PSEN1 p. E318G variant increases the risk of LOAD only in participants carrying APOE ε4 allele where individuals carrying the minor allele of this PSEN1 risk variant have lower CSF Aβ1-42 and higher CSF tau. A gene-based analysis resulted in a significant association of rare but not common (MAF ≥ 0.0257) PSEN1 variants with bilateral entorhinal cortical thickness.

CONCLUSIONS:

This is the first study to show that PSEN1 rare variants collectively show a significant association with the brain atrophy in regions preferentially affected by LOAD, providing further support for a role of PSEN1 in LOAD. The PSEN1 p. E318G variant increases the risk of LOAD only in APOE ε4 carriers. Integrating bioinformatics with imaging informatics for identification of rare variants could help explain the missing heritability in LOAD.

KEYWORDS:

Gene-based association of rare variants; Imaging genetics; PSEN1; Whole genome sequencing

PMID:
27535542
PMCID:
PMC4989889
DOI:
10.1186/s12920-016-0190-9
[Indexed for MEDLINE]
Free PMC Article

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