Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

Risk for late-onset Alzheimer's disease (LOAD), the most prevalent dementia, is partially driven by genetics. To identify LOAD risk loci, we performed a large genome-wide association meta-analysis of clinically diagnosed LOAD (94,437 individuals). We confirm 20 previous LOAD risk loci and identify five new genome-wide loci (IQCK, ACE, ADAM10, ADAMTS1, and WWOX), two of which (ADAM10, ACE) were identified in a recent genome-wide association (GWAS)-by-familial-proxy of Alzheimer's or dementia. Fine-mapping of the human leukocyte antigen (HLA) region confirms the neurological and immune-mediated disease haplotype HLA-DR15 as a risk factor for LOAD. Pathway analysis implicates immunity, lipid metabolism, tau binding proteins, and amyloid precursor protein (APP) metabolism, showing that genetic variants affecting APP and Aβ processing are associated not only with early-onset autosomal dominant Alzheimer's disease but also with LOAD. Analyses of risk genes and pathways show enrichment for rare variants (P = 1.32 × 10-7), indicating that additional rare variants remain to be identified. We also identify important genetic correlations between LOAD and traits such as family history of dementia and education.

Nuclear-Mitochondrial interactions influence susceptibility to HIV-associated neurocognitive impairment

HIV-associated neurocognitive impairment (NCI) is a term established to capture a wide spectrum of HIV related neurocognitive deficits ranging in severity from asymptomatic to dementia. The genetic underpinnings of this complex phenotype are incompletely understood. Mitochondrial function has long been thought to play a role in neurodegeneration, along with iron metabolism and transport. In this work, we aimed to characterize the interplay of mitochondrial DNA (mtDNA) haplogroup and nuclear genetic associations to NCI phenotypes in the CHARTER cohort, encompassing 1025 individuals of European-descent, African-descent, or admixed Hispanic. We first employed a polygenic modeling approach to investigate the global effect of previous marginally associated nuclear SNPs, and to examine how the polygenic effect of these SNPs is influenced by mtDNA haplogroups. We see evidence of a significant interaction between nuclear SNPs en masse and mtDNA haplogroups within European-descent and African-descent individuals. Subsequently, we performed an analysis of each SNP by mtDNA haplogroup, and detected significant interactions between two nuclear SNPs (rs17160128 and rs12460243) and European haplogroups. These findings, which require validation in larger cohorts, indicate a potential new role for nuclear-mitochondrial DNA interactions in susceptibility to NCI and shed light onto the pathophysiology of this neurocognitive phenotype.

Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network

Genetic variation can affect drug response in multiple ways, although it remains unclear how rare genetic variants affect drug response. The electronic Medical Records and Genomics (eMERGE) Network, collaborating with the Pharmacogenomics Research Network, began eMERGE‐PGx, a targeted sequencing study to assess genetic variation in 82 pharmacogenes critical for implementation of “precision medicine.” The February 2015 eMERGE‐PGx data release includes sequence‐derived data from ∼5,000 clinical subjects. We present the variant frequency spectrum categorized by variant type, ancestry, and predicted function. We found 95.12% of genes have variants with a scaled Combined Annotation‐Dependent Depletion score above 20, and 96.19% of all samples had one or more Clinical Pharmacogenetics Implementation Consortium Level A actionable variants. These data highlight the distribution and scope of genetic variation in relevant pharmacogenes, identifying challenges associated with implementing clinical sequencing for drug treatment at a broader level, underscoring the importance for multifaceted research in the execution of precision medicine.

Elevation of IgA levels in the non-insulin-dependent (type II) diabetic patient

Serum immunoglobulin (G, A, M) levels were performed on 66 patients with non-insulin-dependent (type II) diabetes mellitus (NIDDM). When compared with 30 age-matched normal controls and 32 hospitalized controls there was no significant difference between the mean IgG and IgM levels. The IgA levels were significantly higher (P less than 0.005) in the diabetic group when compared with both control groups. This is true regardless of age, sex, duration of disease, and type of treatment (insulin/diet or oral hypoglycemic agents and/or diet). Thirty-six percent of the diabetic patients' IgA levels exceeded the mean +/- 2 SD of the normal control group. There were no significant differences in immunoglobulin levels between insulin-treated and non-insulin-treated diabetic groups. Since diabetic patients may have a number of secondary diseases, attempts were made to correlate the most common of these (acute and/or chronic bacterial infections, hypertension, arteriosclerotic heart disease, and diabetic neuropathy) with elevated IgA levels. Only IgA levels of diabetic patients with infections versus diabetic patients without infections were significantly different (P less than 0.05). However, IgA levels of uninfected diabetic patients remained significantly higher than those of normal controls (P less than 0.005), hospitalized controls (P less than 0.01), and hospitalized controls with bacterial infections (P less than 0.005). Possible reasons for the isolated elevations of IgA are discussed.

An evaluation of a C-reactive protein assay using a rate immunonephelometric procedure

By using 20 repetitive assays at three levels of C-reactive protein control serum, within-run and day-to-day precision of a rate immunonephelometric system was established. The precision was excellent in each case. Linearity of the system between 1.8 and 20 mg/dl was established at a coefficient of correlation of 0.999 by using serial dilutions of C-reactive protein control serum. When the immunonephelometric assay was compared with electroimmunodiffusion and radial immunodiffusion assays, coefficients of correlation of 0.986 and 0.993, respectively, were obtained. The lower limit of sensitivity of the immunonephelometric assay was 1.8 mg/dl. The relationship of clinical significance to the performance of the C-reactive protein test system using rate immunonephelometry is discussed.