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author:("goat, Alison")
1.  Alzheimer’s Disease Risk Polymorphisms Regulate Gene Expression in the ZCWPW1 and the CELF1 Loci 
PLoS ONE  2016;11(2):e0148717.
Late onset Alzheimer’s disease (LOAD) is a genetically complex and clinically heterogeneous disease. Recent large-scale genome wide association studies (GWAS) have identified more than twenty loci that modify risk for AD. Despite the identification of these loci, little progress has been made in identifying the functional variants that explain the association with AD risk. Thus, we sought to determine whether the novel LOAD GWAS single nucleotide polymorphisms (SNPs) alter expression of LOAD GWAS genes and whether expression of these genes is altered in AD brains. The majority of LOAD GWAS SNPs occur in gene dense regions under large linkage disequilibrium (LD) blocks, making it unclear which gene(s) are modified by the SNP. Thus, we tested for brain expression quantitative trait loci (eQTLs) between LOAD GWAS SNPs and SNPs in high LD with the LOAD GWAS SNPs in all of the genes within the GWAS loci. We found a significant eQTL between rs1476679 and PILRB and GATS, which occurs within the ZCWPW1 locus. PILRB and GATS expression levels, within the ZCWPW1 locus, were also associated with AD status. Rs7120548 was associated with MTCH2 expression, which occurs within the CELF1 locus. Additionally, expression of several genes within the CELF1 locus, including MTCH2, were highly correlated with one another and were associated with AD status. We further demonstrate that PILRB, as well as other genes within the GWAS loci, are most highly expressed in microglia. These findings together with the function of PILRB as a DAP12 receptor supports the critical role of microglia and neuroinflammation in AD risk.
doi:10.1371/journal.pone.0148717
PMCID: PMC4769299  PMID: 26919393
2.  Rarity of the Alzheimer Disease–Protective APP A673T Variant in the United States 
JAMA neurology  2015;72(2):209-216.
IMPORTANCE
Recently, a rare variant in the amyloid precursor protein gene (APP) was described in a population from Iceland. This variant, in which alanine is replaced by threonine at position 673 (A673T), appears to protect against late-onset Alzheimer disease (AD). We evaluated the frequency of this variant in AD cases and cognitively normal controls to determine whether this variant will significantly contribute to risk assessment in individuals in the United States.
OBJECTIVE
To determine the frequency of the APP A673T variant in a large group of elderly cognitively normal controls and AD cases from the United States and in 2 case-control cohorts from Sweden.
DESIGN, SETTING, AND PARTICIPANTS
Case-control association analysis of variant APP A673T in US and Swedish white individuals comparing AD cases with cognitively intact elderly controls. Participants were ascertained at multiple university-associated medical centers and clinics across the United States and Sweden by study-specific sampling methods. They were from case-control studies, community-based prospective cohort studies, and studies that ascertained multiplex families from multiple sources.
MAIN OUTCOMES AND MEASURES
Genotypes for the APP A673T variant were determined using the Infinium HumanExome V1 Beadchip (Illumina, Inc) and by TaqMan genotyping (Life Technologies).
RESULTS
The A673T variant genotypes were evaluated in 8943 US AD cases, 10 480 US cognitively normal controls, 862 Swedish AD cases, and 707 Swedish cognitively normal controls. We identified 3 US individuals heterozygous for A673T, including 1 AD case (age at onset, 89 years) and 2 controls (age at last examination, 82 and 77 years). The remaining US samples were homozygous for the alanine (A673) allele. In the Swedish samples, 3 controls were heterozygous for A673T and all AD cases were homozygous for the A673 allele. We also genotyped a US family previously reported to harbor the A673T variant and found a mother-daughter pair, both cognitively normal at ages 72 and 84 years, respectively, who were both heterozygous for A673T; however, all individuals with AD in the family were homozygous for A673.
CONCLUSIONS AND RELEVANCE
The A673T variant is extremely rare in US cohorts and does not play a substantial role in risk for AD in this population. This variant may be primarily restricted to Icelandic and Scandinavian populations.
doi:10.1001/jamaneurol.2014.2157
PMCID: PMC4324097  PMID: 25531812
3.  Genetic studies of plasma analytes identify novel potential biomarkers for several complex traits 
Scientific Reports  2016;6:18092.
Genome-wide association studies of 146 plasma protein levels in 818 individuals revealed 56 genome-wide significant associations (28 novel) with 47 analytes. Loci associated with plasma levels of 39 proteins tested have been previously associated with various complex traits such as heart disease, inflammatory bowel disease, Type 2 diabetes, and multiple sclerosis. These data suggest that these plasma protein levels may constitute informative endophenotypes for these complex traits. We found three potential pleiotropic genes: ABO for plasma SELE and ACE levels, FUT2 for CA19-9 and CEA plasma levels, and APOE for ApoE and CRP levels. We also found multiple independent signals in loci associated with plasma levels of ApoH, CA19-9, FetuinA, IL6r, and LPa. Our study highlights the power of biological traits for genetic studies to identify genetic variants influencing clinically relevant traits, potential pleiotropic effects, and complex disease associations in the same locus.
doi:10.1038/srep18092
PMCID: PMC4698720
4.  ALS onset is influenced by the burden of rare variants in known ALS genes 
Annals of neurology  2014;77(1):100-113.
Objective
To define the genetic landscape of amyotrophic lateral sclerosis (ALS) and assess the contribution of possible oligogenic inheritance, we aimed to comprehensively sequence 17 known ALS genes in 391 ALS patients from the United States.
Methods
Targeted pooled-sample sequencing was used to identify variants in 17 ALS genes. Fragment size analysis was used to define ATXN2 and C9ORF72 expansion sizes. Genotype-phenotype correlations were made with individual variants and total burden of variants. Rare variant associations for risk of ALS were investigated at both the single variant and gene level.
Results
64.3% of familial and 27.8% of sporadic subjects carried potentially pathogenic novel or rare coding variants identified by sequencing or an expanded repeat in C9ORF72 or ATXN2. 3.8% of subjects had variants in more than one ALS gene, and these individuals had disease onset ten years earlier (p=0.0046) than subjects with variants in a single gene. The number of potentially pathogenic coding variants did not influence disease duration or site of onset.
Interpretation
Rare and potentially pathogenic variants in known ALS genes are present in over 25% of apparently sporadic and 64% of familial patients, significantly higher than previous reports using less comprehensive sequencing approaches. A significant number of subjects carried variants in more than one gene, which influenced the age of symptom onset and supports oligogenic inheritance as relevant to disease pathogenesis.
doi:10.1002/ana.24306
PMCID: PMC4293318  PMID: 25382069
5.  Peroxisome proliferator-activated receptors α and γ are linked with alcohol consumption in mice and withdrawal and dependence in humans 
Background
Peroxisome proliferator-activated receptor (PPAR) agonists reduce voluntary ethanol consumption in rat models and are promising therapeutics in the treatment of drug addictions. We studied the effects of different classes of PPAR agonists on chronic ethanol intake and preference in mice with a genetic predisposition for high alcohol consumption and then examined human genome wide association data for polymorphisms in PPAR genes in alcohol-dependent subjects.
Methods
Two different behavioral tests were used to measure intake of 15% ethanol in C57BL/6J male mice: 24-hour two-bottle choice and limited access (3-hour) two-bottle choice, drinking in the dark. We measured the effects of pioglitazone (10 and 30 mg/kg), fenofibrate (50 and 150 mg/kg), GW0742 (10 mg/kg), tesaglitazar (1.5 mg/kg) and bezafibrate (25 and 75 mg/kg) on ethanol intake and preference. Fenofibric acid, the active metabolite of fenofibrate, was quantified in mouse plasma, liver, and brain by LC-MS/MS. Data from a human genome wide association study (GWAS) completed in the Collaborative Study on the Genetics of Alcoholism (COGA) was then used to analyze the association of single nucleotide polymorphisms (SNPs) in different PPAR genes (PPARA, PPARD, PPARG, and PPARGC1A) with two phenotypes: DSM-IV alcohol dependence (AD) and the DSM-IV criterion of withdrawal.
Results
Activation of two isoforms of PPARs, α and γ, reduced ethanol intake and preference in the two different consumption tests in mice. However, a selective PPARδ agonist or a pan agonist for all three PPAR isoforms did not decrease ethanol consumption. Fenofibric acid, the active metabolite of the PPARα agonist fenofibrate, was detected in liver, plasma, and brain after 1 or 8 days of oral treatment. The GWAS from COGA supported an association of SNPs in PPARA and PPARG with alcohol withdrawal and PPARGC1A with AD but found no association for PPARD with either phenotype.
Conclusions
We provide convergent evidence using both mouse and human data for specific PPARs in alcohol action. Reduced ethanol intake in mice and the genetic association between AD or withdrawal in humans highlight the potential for repurposing FDA-approved PPARα or PPARγ agonists for the treatment of AD.
doi:10.1111/acer.12610
PMCID: PMC4308472  PMID: 25516156
two-bottle choice; C57BL/6J; pioglitazone; fenofibrate; fenofibric acid; tesaglitazar; GWAS
6.  Alzheimer's disease risk genes and mechanisms of disease pathogenesis 
Biological psychiatry  2014;77(1):43-51.
Here, we review the genetic risk factors for late onset Alzheimer's disease (AD) and their role in AD pathogenesis. Recent advances in our understanding of the human genome, namely technological advances in methods to analyze millions of polymorphisms in thousands of subjects, have revealed new genes associated with AD risk: ABCA7, BIN1, CASS4, CD33, CD2AP, CELF1, CLU, CR1, DSG2, EPHA1, FERMT2, HLA-DRB5-DBR1, INPP5D, MS4A, MEF2C, NME8, PICALM, PTK2B, SLC24H4 RIN3, SORL1, ZCWPW1. Emerging technologies to analyze the entire genome in large datasets have also revealed coding variants that increase AD risk: PLD3 and TREM2. We review the relationship between these AD risk genes and the cellular and neuropathological features of AD. Together, understanding the mechanisms underlying the association of these genes with risk for disease will provide the most meaningful targets for therapeutic development to date.
doi:10.1016/j.biopsych.2014.05.006
PMCID: PMC4234692  PMID: 24951455
Alzheimer's disease; amyloid precursor protein; genome wide association studies; endocytosis; immune response; cholesterol metabolism
7.  SUCLG2 identified as both a determinator of CSF Aβ1–42 levels and an attenuator of cognitive decline in Alzheimer's disease 
Human Molecular Genetics  2014;23(24):6644-6658.
Cerebrospinal fluid amyloid-beta 1–42 (Aβ1–42) and phosphorylated Tau at position 181 (pTau181) are biomarkers of Alzheimer's disease (AD). We performed an analysis and meta-analysis of genome-wide association study data on Aβ1–42 and pTau181 in AD dementia patients followed by independent replication. An association was found between Aβ1–42 level and a single-nucleotide polymorphism in SUCLG2 (rs62256378) (P = 2.5×10−12). An interaction between APOE genotype and rs62256378 was detected (P = 9.5 × 10−5), with the strongest effect being observed in APOE-ε4 noncarriers. Clinically, rs62256378 was associated with rate of cognitive decline in AD dementia patients (P = 3.1 × 10−3). Functional microglia experiments showed that SUCLG2 was involved in clearance of Aβ1–42.
doi:10.1093/hmg/ddu372
PMCID: PMC4240204  PMID: 25027320
8.  Association of Long Runs of Homozygosity With Alzheimer Disease Among African American Individuals 
JAMA neurology  2015;72(11):1313-1323.
IMPORTANCE
Mutations in known causal Alzheimer disease (AD) genes account for only 1% to 3% of patients and almost all are dominantly inherited. Recessive inheritance of complex phenotypes can be linked to long (>1-megabase [Mb]) runs of homozygosity (ROHs) detectable by single-nucleotide polymorphism (SNP) arrays.
OBJECTIVE
To evaluate the association between ROHs and AD in an African American population known to have a risk for AD up to 3 times higher than white individuals.
DESIGN, SETTING, AND PARTICIPANTS
Case-control study of a large African American data set previously genotyped on different genome-wide SNP arrays conducted from December 2013 to January 2015. Global and locus-based ROH measurements were analyzed using raw or imputed genotype data. We studied the raw genotypes from 2 case-control subsets grouped based on SNP array: Alzheimer’s Disease Genetics Consortium data set (871 cases and 1620 control individuals) and Chicago Health and Aging Project–Indianapolis Ibadan Dementia Study data set (279 cases and 1367 control individuals). We then examined the entire data set using imputed genotypes from 1917 cases and 3858 control individuals.
MAIN OUTCOMES AND MEASURES
The ROHs larger than 1 Mb, 2 Mb, or 3 Mb were investigated separately for global burden evaluation, consensus regions, and gene-based analyses.
RESULTS
The African American cohort had a low degree of inbreeding (F ~ 0.006). In the Alzheimer’s Disease Genetics Consortium data set, we detected a significantly higher proportion of cases with ROHs greater than 2 Mb (P = .004) or greater than 3 Mb (P = .02), as well as a significant 114-kilobase consensus region on chr4q31.3 (empirical P value 2 = .04; ROHs >2 Mb). In the Chicago Health and Aging Project–Indianapolis Ibadan Dementia Study data set, we identified a significant 202-kilobase consensus region on Chr15q24.1 (empirical P value 2 = .02; ROHs >1 Mb) and a cluster of 13 significant genes on Chr3p21.31 (empirical P value 2 = .03; ROHs >3 Mb). A total of 43 of 49 nominally significant genes common for both data sets also mapped to Chr3p21.31. Analyses of imputed SNP data from the entire data set confirmed the association of AD with global ROH measurements (12.38 ROHs >1 Mb in cases vs 12.11 in controls; 2.986 Mb average size of ROHs >2 Mb in cases vs 2.889 Mb in controls; and 22% of cases with ROHs >3 Mb vs 19% of controls) and a gene-cluster on Chr3p21.31 (empirical P value 2 = .006-.04; ROHs >3 Mb). Also, we detected a significant association between AD and CLDN17 (empirical P value 2 = .01; ROHs >1 Mb), encoding a protein from the Claudin family, members of which were previously suggested as AD biomarkers.
CONCLUSIONS AND RELEVANCE
To our knowledge, we discovered the first evidence of increased burden of ROHs among patients with AD from an outbred African American population, which could reflect either the cumulative effect of multiple ROHs to AD or the contribution of specific loci harboring recessive mutations and risk haplotypes in a subset of patients. Sequencing is required to uncover AD variants in these individuals.
doi:10.1001/jamaneurol.2015.1700
PMCID: PMC4641052  PMID: 26366463
9.  Genetic Influences on Alcohol Use across Stages of Development: GABRA2 and Longitudinal Trajectories of Drunkenness from Adolescence to Young Adulthood 
Addiction biology  2013;19(6):1055-1064.
Longitudinal analyses allow us to understand how genetic risk unfolds across development, in a way that is not possible with cross-sectional analyses of individuals at different ages. This has received little attention in genetic association analyses. In this study, we test for genetic effects of GABRA2, a gene previously associated with alcohol dependence, on trajectories of drunkenness from age 14 to 25. We use data from 1070 individuals who participated in the prospective sample of the Collaborative Study on the Genetics of Alcoholism (COGA), in order to better understand the unfolding of genetic risk across development. Piecewise linear growth models were fit to model the influence of genotype on rate of increase in drunkenness from early adolescence to young adulthood (14–18 years), the change in drunkenness during the transition to adulthood (18–19 years), and the rate of change in drunkenness across young adulthood (≥ 19 years). Variation in GABRA2 was associated with an increase in drunkenness that occurred at the transition between adolescence and adulthood. The genotypic effect was more pronounced in females. These analyses illustrate the importance of longitudinal data to characterize how genetic effects unfold across development. The findings suggest that transitions across important developmental periods may alter the relative importance of genetic effects on patterns of alcohol use. The findings also suggest the importance of considering gender when evaluating genetic effects on drinking patterns in males and females.
doi:10.1111/adb.12066
PMCID: PMC3783626  PMID: 23692184
alcohol; COGA; GABRA2; genetic association; longitudinal; trajectories
10.  APOE ε4 Genotype Predicts Memory for Everyday Activities 
The apolipoprotein E (ApoE) ε4 allele is associated with neuropathological buildup of amyloid in the brain, and with lower performance on some laboratory measures of memory in some populations. In two studies, we tested whether ApoE genotype affects memory for everyday activities. In Study 1, participants aged 20-79 years old (n = 188) watched movies of actors engaged in daily activities and completed memory tests for the activities in the movies. In Study 2, cognitively healthy and demented older adults (n = 97) watched and remembered similar movies, and also underwent structural MRI scanning. All participants provided saliva samples for genetic analysis. In both samples we found that, in older adults, ApoE ε4 carriers demonstrated worse everyday memory performance than did ε4 non-carriers. In Study 2, ApoE ε4 carriers had smaller MTL volumes, and MTL volume mediated the relationship between ApoE genotype and everyday memory performance. These everyday memory tasks measure genetically-determined cognitive decline that can occur prior to a clinical diagnosis of dementia. Further, these tasks are easily administered and may be a useful clinical tool in identifying ε4 carriers who may be at risk for MTL atrophy and further cognitive decline that is a common characteristic of the earliest stages of Alzheimer's disease.
doi:10.1080/13825585.2015.1020916
PMCID: PMC4537694  PMID: 25754878
everyday memory; APOE; episodic memory; aging; Alzheimer's disease
11.  Coding variants in TREM2 increase risk for Alzheimer's disease 
Human Molecular Genetics  2014;23(21):5838-5846.
The triggering receptor expressed on myeloid 2 (TREM2) is an immune phagocytic receptor expressed on brain microglia known to trigger phagocytosis and regulate the inflammatory response. Homozygous mutations in TREM2 cause Nasu–Hakola disease, a rare recessive form of dementia. A heterozygous TREM2 variant, p.R47H, was recently shown to increase Alzheimer’'s disease (AD) risk. We hypothesized that if TREM2 is truly an AD risk gene, there would be additional rare variants in TREM2 that substantially affect AD risk. To test this hypothesis, we performed pooled sequencing of TREM2 coding regions in 2082 AD cases and 1648 cognitively normal elderly controls of European American descent. We identified 16 non-synonymous variants, six of which were not identified in previous AD studies. Two variants, p.R47H [P = 9.17 × 10−4, odds ratio (OR) = 2.63 (1.44–4.81)] and p.R62H [P = 2.36 × 10−4, OR = 2.36 (1.47–3.80)] were significantly associated with disease risk in single-variant analyses. Gene-based tests demonstrate variants in TREM2 are genome-wide significantly associated with AD [PSKAT-O = 5.37 × 10−7; OR = 2.55 (1.80–3.67)]. The association of TREM2 variants with AD is still highly significant after excluding p.R47H [PSKAT-O = 7.72 × 10−5; OR = 2.47 (1.62–3.87)], indicating that additional TREM2 variants affect AD risk. Genotyping in available family members of probands suggested that p.R47H (P = 4.65 × 10−2) and p.R62H (P = 6.87 × 10−3) were more frequently seen in AD cases versus controls within these families. Gel electrophoresis analysis confirms that at least three TREM2 transcripts are expressed in human brains, including one encoding a soluble form of TREM2.
doi:10.1093/hmg/ddu277
PMCID: PMC4189899  PMID: 24899047
12.  Two rare AKAP9 variants are associated with Alzheimer disease in African Americans 
Background
Less is known about the genetic basis of Alzheimer disease (AD) in African Americans (AAs) than in non-Hispanic whites.
Methods
Whole exome sequencing (WES) was performed on seven AA AD cases. Disease association with potentially AD-related variants from WES was assessed in an AA discovery cohort of 422 cases and 394 controls. Replication was sought in an AA sample of 1,037 cases and 1,869 controls from the Alzheimer Disease Genetics Consortium (ADGC).
Results
Forty-four SNPs from WES passed filtering criteria and were successfully genotyped, Nominally significant (p<0.05) association to AD was observed with two African-descent specific AKAP9 SNPs in tight linkage disequilibrium: rs144662445 (p=0.014) and rs149979685 (p=0.037). These associations were replicated in the ADGC sample (rs144662445: p=0.0022, odds ratio [OR]=2.75; rs149979685: p=0.0022, OR=3.61).
Conclusions
Because AKAP9 was not previously linked to AD risk, this study indicates a potential new disease mechanism.
doi:10.1016/j.jalz.2014.06.010
PMCID: PMC4253055  PMID: 25172201
whole-exome sequencing; late-onset Alzheimer disease; rare variant; genetic association; African American; AKAP9
13.  An ADH1B variant and peer drinking in progression to adolescent drinking milestones: Evidence of a gene-by-environment interaction 
Background
Adolescent drinking is an important public health concern, one that is influenced by both genetic and environmental factors. The functional variant rs1229984 in alcohol dehydrogenase 1B (ADH1B) has been associated at a genome-wide level with alcohol use disorders in diverse adult populations. However, few data are available regarding whether this variant influences early drinking behaviors and whether social context moderates this effect. This study examines the interplay between rs1229984 and peer drinking in the development of adolescent drinking milestones.
Methods
1,550 European and African American individuals who had a full drink of alcohol before age 18 were selected from a longitudinal study of youth as part of the Collaborative Study on the Genetics of Alcoholism (COGA). Cox proportional hazards regression, with GxE product terms in the final models, was used to study two primary outcomes during adolescence: age of first intoxication and age of first DSM-5 alcohol use disorder symptom.
Results
The minor A allele of rs1229984 was associated with a protective effect for first intoxication (HR=0.56, 95% CI 0.41–0.76) and first DSM-5 symptom (HR=0.45, 95% CI 0.26–0.77) in the final models. Reporting that most or all best friends drink was associated with a hazardous effect for first intoxication (HR=1.81, 95% CI 1.62–2.01) and first DSM-5 symptom (HR=2.17, 95% 1.88–2.50) in the final models. Furthermore, there was a significant GxE interaction for first intoxication (p=.002) and first DSM-5 symptom (p=.01). Among individuals reporting none or few best friends drinking, the ADH1B variant had a protective effect for adolescent drinking milestones, but for those reporting most or all best friends drinking, this effect was greatly reduced.
Conclusions
Our results suggest that the risk factor of best friends drinking attenuates the protective effect of a well-established ADH1B variant for two adolescent drinking behaviors. These findings illustrate the interplay between genetic and environmental factors in the development of drinking milestones during adolescence.
doi:10.1111/acer.12524
PMCID: PMC4256939  PMID: 25257461
Gene-Environment Interaction; Adolescent; Alcohol Dehydrogenase; Peer drinking
14.  Effects upon in vivo nicotine metabolism reveal functional variation in FMO3 associated with cigarette consumption 
Pharmacogenetics and genomics  2013;23(2):62-68.
Background
Flavin-containing monooxygenases (FMO) catalyze the metabolism of nucleophilic heteroatom containing drugs and xenobiotics including nicotine. Rare mutations in FMO3 are responsible for defective N-oxygenation of dietary trimethylamine leading to trimethylaminuria, and common genetic variation in FMO3 has been linked to interindividual variability in metabolic function that may be substrate specific.
Methods
A genetic model of CYP2A6 function is used as a covariate to reveal functional polymorphism in FMO3 that indirectly influences the ratio of deuterated nicotine metabolized to cotinine following oral administration. The association is tested between FMO3 haplotype and cigarette consumption in a set of nicotine dependent smokers.
Results
FMO3 haplotype, based on all common coding variants in Europeans, significantly predicts nicotine metabolism and accounts for approximately 2% of variance in the apparent percent of nicotine metabolized to cotinine. The metabolic ratio is not associated with FMO2 haplotype or an FMO1 expression quantitative trait locus (eQTL). Cross validation demonstrates calculated FMO3 haplotype parameters to be robust and significantly improve the predictive nicotine metabolism model over CYP2A6 genotype alone. Functional classes of FMO3 haplotypes, as determined by their influence on nicotine metabolism to cotinine, are also significantly associated with cigarettes per day (CPD) in nicotine dependent European Americans (n=1,025, p=0.04), and significantly interact (p=0.016) with CYP2A6 genotype to predict CPD.
Conclusion
These findings suggest that common polymorphisms in FMO3 influence nicotine clearance, and that these genetic variants in turn influence cigarette consumption.
doi:10.1097/FPC.0b013e32835c3b48
PMCID: PMC4583063  PMID: 23211429
15.  Beyond Cigarettes Per Day. A Genome-Wide Association Study of the Biomarker Carbon Monoxide 
Rationale: The CHRNA5-CHRNA3-CHRNB4 locus is associated with self-reported smoking behavior and also harbors the strongest genetic associations with chronic obstructive pulmonary disease (COPD) and lung cancer. Because the associations with lung disease remain after adjustment for self-reported smoking behaviors, it has been asserted that CHRNA5-CHRNA3-CHRNB4 variants increase COPD and lung cancer susceptibility independently of their effects on smoking.
Objectives: To compare the genetic associations of exhaled carbon monoxide (CO), a biomarker of current cigarette exposure, with self-reported smoking behaviors.
Methods: A total of 1,521 European American and 247 African American current smokers recruited into smoking cessation studies were assessed for CO at intake before smoking cessation. DNA samples were genotyped using the Illumina Omni2.5 microarray. Genetic associations with CO and smoking behaviors (cigarettes smoked per day, Fagerstrom test for nicotine dependence) were studied.
Measurements and Main Results: Variants in the CHRNA5-CHRNA3-CHRNB4 locus, including rs16969968, a nonsynonymous variant in CHRNA5, are genomewide association study–significantly associated with CO (β = 2.66; 95% confidence interval [CI], 1.74–3.58; P = 1.65 × 10−8), and this association remains strong after adjusting for smoking behavior (β = 2.18; 95% CI, 1.32–3.04; P = 7.47 × 10−7). The correlation between CO and cigarettes per day is statistically significantly lower (z = 3.43; P = 6.07 × 10−4) in African Americans (r = 0.14; 95% CI, 0.02–0.26; P = 0.003) than in European-Americans (r = 0.36; 95% CI, 0.31–0.40; P = 0.0001).
Conclusions: Exhaled CO, a biomarker that is simple to measure, captures aspects of cigarette smoke exposure in current smokers beyond the number of cigarettes smoked per day. Behavioral measures of smoking are therefore insufficient indices of cigarette smoke exposure, suggesting that genetic associations with COPD or lung cancer that persist after adjusting for self-reported smoking behavior may still reflect genetic effects on smoking exposure.
doi:10.1513/AnnalsATS.201401-010OC
PMCID: PMC4214060  PMID: 25072098
smoking; nicotine; chronic obstructive pulmonary disease; lung cancer; nicotinic receptor
16.  Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families* 
Drug and alcohol dependence  2014;142:56-62.
Background
The age at onset of alcohol dependence (AD) is a critical moderator of genetic associations for alcohol dependence. The present study evaluated whether single nucleotide polymorphisms (SNPs) can influence the age at onset of AD in large high-risk families from the Collaborative Study on the Genetics of Alcoholism (COGA).
Methods
Genomewide SNP genotyping was performed in 1788 regular drinkers from 118 large European American families densely affected with alcoholism. We used a genome-wide Cox proportional hazards regression model to test for association between age at onset of AD and SNPs.
Results
This family-based analysis identified an intergenic SNP, rs2168784 on chromosome 3 that showed strong evidence of association (p= 5 × 10−9) with age at onset of AD among regular drinkers. Carriers of the minor allele of rs2168784 had 1.5 times the hazard of AD onset as compared with those homozygous for the major allele. By the age of 20 years, nearly 30% of subjects homozygous for the minor allele were alcohol dependent while only 19% of those homozygous for the major allele were. We also identified intronic SNPs in the ADP-ribosylation factor like 15 (ARL15) gene on chromosome 5 (P = 1.11 × 10−8) and the UTP20 small subunit (UTP20) gene on chromosome 12 (P = 4.32 × 10−8) that were associated with age at onset of AD.
Conclusions
This extended family based genome-wide cox-proportional hazards analysis identified several loci that might be associated with age at onset of AD.
doi:10.1016/j.drugalcdep.2014.05.023
PMCID: PMC4127128  PMID: 24962325
GWAS; alcohol dependence; age at onset; survival analysis; SNP
17.  Positive Selection on Loci Associated with Drug and Alcohol Dependence 
PLoS ONE  2015;10(8):e0134393.
Much of the evolution of human behavior remains a mystery, including how certain disadvantageous behaviors are so prevalent. Nicotine addiction is one such phenotype. Several loci have been implicated in nicotine related phenotypes including the nicotinic receptor gene clusters (CHRNs) on chromosomes 8 and 15. Here we use 1000 Genomes sequence data from 3 populations (Africans, Asians and Europeans) to examine whether natural selection has occurred at these loci. We used Tajima’s D and the integrated haplotype score (iHS) to test for evidence of natural selection. Our results provide evidence for strong selection in the nicotinic receptor gene cluster on chromosome 8, previously found to be significantly associated with both nicotine and cocaine dependence, as well as evidence selection acting on the region containing the CHRNA5 nicotinic receptor gene on chromosome 15, that is genome wide significant for risk for nicotine dependence. To examine the possibility that this selection is related to memory and learning, we utilized genetic data from the Collaborative Studies on the Genetics of Alcoholism (COGA) to test variants within these regions with three tests of memory and learning, the Wechsler Adult Intelligence Scale (WAIS) Block Design, WAIS Digit Symbol and WAIS Information tests. Of the 17 SNPs genotyped in COGA in this region, we find one significantly associated with WAIS digit symbol test results. This test captures aspects of reaction time and memory, suggesting that a phenotype relating to memory and learning may have been the driving force behind selection at these loci. This study could begin to explain why these seemingly deleterious SNPs are present at their current frequencies.
doi:10.1371/journal.pone.0134393
PMCID: PMC4536217  PMID: 26270548
18.  Alzheimer’s Disease Genetics: From the bench to the clinic 
Neuron  2014;83(1):11-26.
Alzheimer’s disease (AD) is a clinically heterogeneous neurodegenerative disease with a strong genetic component. Several genes have been associated with AD risk for nearly twenty years. However, it was not until the recent technological advances that allow for the analysis of millions of polymorphisms in thousands of subjects that we have been able to advance our understanding of the genetic complexity of AD susceptibility. Genome wide association studies and whole exome and whole genome sequencing have revealed more than twenty loci associated with AD risk. These studies have provided insights into the molecular pathways that are altered in AD pathogenesis, which have, in turn, provided insight into novel therapeutic targets.
doi:10.1016/j.neuron.2014.05.041
PMCID: PMC4120741  PMID: 24991952
Alzheimer’s disease; genome wide association studies; whole exome sequencing; whole genome sequencing; APP; PSEN1; PSEN2; APOE; CLU; PICALM; CR1; BIN1; CD33; MS4A4A; MS4A6A; CD2AP; EPHA1; ABCA7; CASS4; CELF1; DSG2; FERMT2; HLA-DRB5-DRB1; INPP5D; MEF2C; NME8; PTK2B; SLC24A4; RIN3; SORL1; ZCWPW1; TREM2; PLD3; C9ORF72; MAPT; GRN; ADAM10
19.  Using genetic information from candidate gene and genome-wide association studies in risk prediction for alcohol dependence 
Addiction biology  2013;19(4):708-721.
Family-based and genome-wide association studies (GWAS) of alcohol dependence (AD) have reported numerous associated variants. The clinical validity of these variants for predicting AD compared to family history information has not been reported. Using the Collaborative Study on the Genetics of Alcoholism (COGA) and the Study of Addiction: Genes and Environment (SAGE) GWAS samples, we examined the aggregate impact of multiple single nucleotide polymorphisms (SNPs) on risk prediction. We created genetic sum scores by adding risk alleles associated in discovery samples, and then tested the scores for their ability to discriminate between cases and controls in validation samples. Genetic sum scores were assessed separately for SNPs associated with AD in candidate gene studies and SNPs from GWAS analyses that met varying p-value thresholds. Candidate gene sum scores did not exhibit significant predictive accuracy. Family history was a better classifier of case-control status, with a significant area under the receiver operating characteristic curve (AUC) of 0.686 in COGA and 0.614 in SAGE. SNPs that met less stringent p-value thresholds of 0.01 to 0.50 in GWAS analyses yielded significant AUC estimates, ranging from mean estimates of 0.549 for SNPs with p < 0.01 to 0.565 for SNPs with p < 0.50. This study suggests that SNPs currently have limited clinical utility, but there is potential for enhanced predictive ability with better understanding of the large number of variants that might contribute to risk.
doi:10.1111/adb.12035
PMCID: PMC3664249  PMID: 23362995
clinical validity; genetic risk prediction; polygenic risk score; psychiatric genetic counseling; receiver operating characteristic curve analysis
20.  Missense variant in TREML2 protects against Alzheimer’s Disease 
Neurobiology of aging  2013;35(6):1510.e19-1510.e26.
TREM and TREM-like receptors are a structurally similar protein family encoded by genes clustered on chromosome 6p21.11. Recent studies have identified a rare coding variant (p.R47H) in TREM2 that confers a high risk for Alzheimer’s disease (AD). In addition, common SNPs in this genomic region are associated with cerebrospinal fluid (CSF) biomarkers for AD and a common intergenic variant found near the TREML2 gene has been identified to be protective for AD. However, little is known about the functional variant underlying the latter association or its relationship with the p.R47H. Here, we report comprehensive analyses using whole-exome sequencing data, CSF biomarker analyses, meta-analyses (16,254 cases and 20,052 controls) and cell-based functional studies to support the role of the TREML2 coding missense variant p.S144G (rs3747742) as a potential driver of the meta-analysis AD-associated GWAS signal. Additionally, we demonstrate that the protective role of TREML2 in AD is independent of the role of TREM2 gene as a risk factor for AD.
doi:10.1016/j.neurobiolaging.2013.12.010
PMCID: PMC3961557  PMID: 24439484
21.  Variants in PPP3R1 and MAPT are associated with more rapid functional decline in Alzheimer’s disease: The Cache County Dementia Progression Study 
Background
SNPs located in the gene encoding the regulatory subunit of the protein phosphatase 2B (PPP3R1, rs1868402) and the microtubule-associated protein tau (MAPT, rs3785883) gene were recently associated with higher cerebrospinal fluid (CSF) tau levels in samples from the Knight Alzheimer’s Disease Research Center at Washington University (WU) and Alzheimer’s Disease Neuroimaging Initiative (ADNI). In these same samples these SNPs were also associated with faster functional decline, or progression of Alzheimer’s disease (AD) as measured by the Clinical Dementia Rating sum of boxes scores (CDR-sb). We attempted to validate the latter association in an independent, population-based sample of incident AD cases from the Cache County Dementia Progression Study (DPS).
Methods
All 92 AD cases from the DPS with a global CDR-sb ≤ 1 (mild) at initial clinical assessment who were later assessed on CDR-sb data on at least two other time points were genotyped at the 2 SNPs of interest (rs1868402 and rs3785883). We used linear mixed models to estimate associations between these SNPs and CDR-sb trajectory. All analyses were performed using Proc Mixed in SAS.
Results
While we observed no association between rs3785883 or rs1868402 alone and change in CDR-sb (p>0.10), there was a significant association between a combined genotype model and change in CDR-sb: carriers of the high-risk genotypes at both loci progressed more than 2.9 times faster than non-carriers (p=0.015). When data from DPS were combined with previously published data from WU and ADNI, change in CDR-sb was 30% faster for each copy of the high-risk allele at rs3785883 (p=0.0082) and carriers of both high-risk genotypes at both loci progressed six times faster (p<0.0001) than all others combined.
Conclusions
We replicate a previous report by Cruchaga et al that specific variations in rs3785883 and rs1868402 are associated with accelerated progression of AD. Further characterization of this association will provide a better understanding of how genetic factors influence the rate of progression of Alzheimer’s disease and could provide novel insights into preventative and therapeutic strategies.
doi:10.1016/j.jalz.2013.02.010
PMCID: PMC3809344  PMID: 23727081
Alzheimer’s disease; genetics; association; rate of progression; PPP3R1; MAPT
22.  Multiple distinct CHRNB3-CHRNA6 variants are genetic risk factors for nicotine dependence in African Americans and European Americans 
Addiction (Abingdon, England)  2014;109(5):814-822.
Aims
Studies have shown association between common variants in the α6–β3 nicotinic receptor subunit gene cluster and nicotine dependence in European Ancestry populations. We investigate whether this generalizes to African Americans, whether the association is specific to nicotine dependence, and whether this region contains additional genetic contributors to nicotine dependence.
Design
We examined consistency of association across studies and race between the α6β3 nicotinic receptor subunit locus and nicotine, alcohol, marijuana, and cocaine dependence in three independent studies.
Setting
United States of America
Participants
European Americans and African Americans from three case control studies of substance dependence.
Measurements
Subjects were evaluated using the Semi-Structured Assessment for the Genetics of Alcoholism. Nicotine dependence was determined using the Fagerström Test for Nicotine Dependence.
Findings
rs13273442 was significantly associated to nicotine dependence across all three studies in both ancestry groups (OR=0.75, p=5.8 × 10−4 European Americans; OR=0.80, p=0.05 African Americans). No other substance dependence was consistently associated to this variant in either group. Another SNP in the region, rs4952, remains modestly associated with nicotine dependence in the combined data after conditioning on rs13273442.
Conclusions
The common variant rs13273442 in the CHRNB3-CHNRA6 region is significantly associated to nicotine dependence in European Americans and African Americans across studies recruited for nicotine, alcohol, and cocaine dependence. Although these data are modestly powered for other substances, our results provide no evidence that correlates of rs13273442 represent a general substance dependence liability. Additional variants likely account for some of the association of this region to nicotine dependence.
doi:10.1111/add.12478
PMCID: PMC3984604  PMID: 24401102
23.  Ptau-Aβ42 ratio as a continuous trait for biomarker discovery for early stage Alzheimer’s disease in multiplex immunoassay panels of Cerebrospinal fluid 
Biological psychiatry  2014;75(9):723-731.
Background
Identification of the physiological changes that occur during the early stages of Alzheimer’s disease (AD) may provide critical insights for the diagnosis, prognosis and treatment of disease. Cerebrospinal fluid (CSF) biomarkers are a rich source of information that reflect the brain proteome.
Methods
We applied a novel approach to screen a panel of ~190 CSF analytes quantified by multiplex immunoassay and detected common associations in the Knight- Alzheimer’s Disease Research Center (ADRC;N=311) and the Alzheimer’s Disease Neuroimaging Initiative (ADNI;N=293) cohorts. CSF ptau181-Aβ42 ratio was used as a continuous trait, rather than case control status in these analyses.
Results
We demonstrate the ptau181-Aβ42 ratio has more statistical power than traditional modeling approaches and that the levels of CSF Fatty Acid Binding Protein (H-FABP) and 12 other correlated analytes increase as the disease progresses. These results were validated using the traditional case control status model. Stratification of our dataset demonstrated that increases in these analytes occur very early in the disease course and were apparent even in non-demented individuals with AD pathology (low ptau181, low Aβ42) compared to pathology-negative elderly control subjects (low ptau181, high Aβ42). FABP-Aβ42 ratio demonstrates a similar hazard ratio for disease conversion to ptau181-Aβ42 even though the overlap in classification is incomplete suggesting that FABP contributes independent information as a predictor
Conclusions
Our results clearly indicate that the approach presented here can be employed to correctly identify novel biomarkers for AD, and that CSF H-FABP levels start to increase at very early stages of the disease.
doi:10.1016/j.biopsych.2013.11.032
PMCID: PMC4007142  PMID: 24548642
Alzheimer’s disease; Biomarkers; cerebrospinal fluid (CSF); Ptau-Aβ42 ratio; Heart Fatty Acid binding protein; Brain Proteome - Rules Based Medicine Discovery Multi-Analyte Profile 1.0
24.  TREM2 is associated with increased risk for Alzheimer’s disease in African Americans 
Background
TREM2 encodes for triggering receptor expressed on myeloid cells 2 and has rare, coding variants that associate with risk for late-onset Alzheimer’s disease (LOAD) in Caucasians of European and North-American origin. This study evaluated the role of TREM2 in LOAD risk in African-American (AA) subjects. We performed exonic sequencing and validation in two independent cohorts of >800 subjects. We selected six coding variants (p.R47H, p.R62H, p.D87N, p.E151K, p.W191X, and p.L211P) for case–control analyses in a total of 906 LOAD cases vs. 2,487 controls.
Results
We identified significant LOAD risk association with p.L211P (p = 0.01, OR = 1.27, 95%CI = 1.05-1.54) and suggestive association with p.W191X (p = 0.08, OR = 1.35, 95%CI = 0.97-1.87). Conditional analysis suggests that p.L211P, which is in linkage disequilibrium with p.W191X, may be the stronger variant of the two, but does not rule out independent contribution of the latter. TREM2 p.L211P resides within the cytoplasmic domain and p.W191X is a stop-gain mutation within the shorter TREM-2V transcript. The coding variants within the extracellular domain of TREM2 previously shown to confer LOAD risk in Caucasians were extremely rare in our AA cohort and did not associate with LOAD risk.
Conclusions
Our findings suggest that TREM2 coding variants also confer LOAD risk in AA, but implicate variants within different regions of the gene than those identified for Caucasian subjects. These results underscore the importance of investigating different ethnic populations for disease risk variant discovery, which may uncover allelic heterogeneity with potentially diverse mechanisms of action.
Electronic supplementary material
The online version of this article (doi:10.1186/s13024-015-0016-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s13024-015-0016-9
PMCID: PMC4426167  PMID: 25886450
LOAD; African-American; TREM2; Coding variants; Case–control
25.  The TREM2 variant p.R47H is a risk factor for sporadic amyotrophic lateral sclerosis 
JAMA neurology  2014;71(4):449-453.
Importance
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease in which microglia play a significant and active role. Recently, a rare missense variant (p.R47H) in the microglial activating gene TREM2 was found to increase the risk of several neurodegenerative diseases, including Alzheimer’s disease. Whether the p.R47H variant is a risk factor for ALS is not currently known.
Objective
To determine if p.R47H (rs75932628) in TREM2 is a risk factor for ALS and assess whether TREM2 expression is dysregulated in disease.
Design, setting, and participants
923 sporadic ALS subjects and 1854 normal controls self-reported as non-Hispanic white were collected from ALS clinics in the United States and genotyped for the p.R47H variant in TREM2. Clinical data was obtained on ALS subjects for genotype/phenotype correlations. Expression of TREM2 was measured by quantitative PCR and compared in spinal cord from 18 ALS subjects, 12 neurologically normal controls, as well as from wildtype and transgenic SOD1G93A mice.
Main outcome measures
Minor allele frequency of rs75932628 and relative expression of TREM2.
Results
The TREM2 variant p. R47H was more common in subject with ALS than in controls and is therefore a significant risk factor for ALS (OR=2.40; 95%CI=1.29-4.15; p=4.1×10-3). Furthermore, TREM2 expression was increased in spinal cords from ALS patients and SOD1G93A mice (p=2.8×10-4, p=2.8×10-9 respectively), confirming dysregulated TREM2 in disease. TREM2 expression in human spinal cord was negatively correlated with survival (p=0.04), but not other phenotypic aspects of disease.
Conclusion and relevance
This study demonstrates that the TREM2 p.R47H variant is a potent risk factor for sporadic amyotrophic lateral sclerosis. These findings identify the first genetic influence on neuro-inflammation in ALS and highlight the TREM2 signaling pathway as a therapeutic target in ALS and other neurodegenerative diseases.
doi:10.1001/jamaneurol.2013.6237
PMCID: PMC4087113  PMID: 24535663

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