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Item Integration of bioinformatics and imaging informatics for identifying rare PSEN1 variants in Alzheimer's disease(BioMed Central, 2016-08-12) Nho, Kwangsik; Horgusluoglu, Emrin; Kim, Sungeun; Risacher, Shannon L.; Kim, Dokyoon; Foroud, Tatiana; Aisen, Paul S.; Peterson, Ronald C.; Jack Jr., Clifford R.; Shaw, Leslie M.; Trojanowski, John Q.; Weiner, Michael W.; Green, Robert C.; Toga, Arthur W.; Saykin, Andrew J.; Department of Radiology and Imaging Sciences, IU School of MedicineBACKGROUND: 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.Item Widespread white matter and conduction defects in PSEN1-related spastic paraparesis(Elsevier, 2016-11) Soosman, Steffan K.; Joseph-Mathurin, Nelly; Braskie, Meredith N.; Bordelon, Yvette M.; Wharton, David; Casado, Maria; Coppola, Giovanni; McCallum, Holly; Nuwer, Marc; Coutin-Churchman, Pedro; Apostolova, Liana G.; Benzinger, Tammie; Ringman, John M.; Neurology, School of MedicineThe mechanisms underlying PSEN1 mutation-associated spastic paraparesis (SP) are not clear. We compared diffusion and volumetric magnetic resonance measures between 3 persons with SP associated with the A431E mutation and 7 symptomatic persons with PSEN1 mutations without SP matched for symptom duration. We performed amyloid imaging and central motor and somatosensory conduction studies in one subject with SP. We found decreases in fractional anisotropy and increases in mean diffusivity in widespread white matter areas including the corpus callosum, occipital, parietal, and frontal lobes in PSEN1 mutation carriers with SP. Volumetric measures were not different and amyloid imaging showed low signal in sensorimotor cortex and other areas in a single subject with SP. Electrophysiological studies demonstrated both slowed motor and sensory conduction in the lower extremities in this same subject. Our results suggest that SP in carriers of the A431E PSEN1 mutation is a manifestation of widespread white matter abnormalities not confined to the corticospinal tract that is at most indirectly related to the mutation’s effect on APP processing and amyloid deposition.