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Article ; Online: Correction to: Large‑scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease.

Bandres-Ciga, S / Saez-Atienzar, S / Kim, J J / Makarious, M B / Faghri, F / Diez-Fairen, M / Iwaki, H / Leonard, H / Botia, J / Ryten, M / Hernandez, D / Gibbs, J R / Ding, J / Gan-Or, Z / Noyce, A / Pihlstrom, L / Torkamani, A / Soltis, A R / Dalgard, C L /

Scholz, S W / Traynor, B J / Ehrlich, D / Scherzer, C R / Bookman, M / Cookson, M / Blauwendraat, C / Nalls, M A / Singleton, A B

Acta neuropathologica

2021 Volume 142, Issue 1, Page(s) 223–224

Language	English
Publishing date	2021-05-04
Publishing country	Germany
Document type	Published Erratum
ZDB-ID	1079-0
ISSN	1432-0533 ; 0001-6322
ISSN (online)	1432-0533
ISSN	0001-6322
DOI	10.1007/s00401-021-02309-z
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Article ; Online: Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease.

Scholz, S W / Traynor, B J / Ehrlich, D / Scherzer, C R / Bookman, M / Cookson, M / Blauwendraat, C / Nalls, M A / Singleton, A B

Acta neuropathologica

2020 Volume 140, Issue 3, Page(s) 341–358

Abstract: Polygenic inheritance plays a central role in Parkinson disease (PD). A priority in elucidating PD etiology lies in defining the biological basis of genetic risk. Unraveling how risk leads to disruption will yield disease-modifying therapeutic targets ... ...

Abstract	Polygenic inheritance plays a central role in Parkinson disease (PD). A priority in elucidating PD etiology lies in defining the biological basis of genetic risk. Unraveling how risk leads to disruption will yield disease-modifying therapeutic targets that may be effective. Here, we utilized a high-throughput and hypothesis-free approach to determine biological processes underlying PD using the largest currently available cohorts of genetic and gene expression data from International Parkinson's Disease Genetics Consortium (IPDGC) and the Accelerating Medicines Partnership-Parkinson's disease initiative (AMP-PD), among other sources. We applied large-scale gene-set specific polygenic risk score (PRS) analyses to assess the role of common variation on PD risk focusing on publicly annotated gene sets representative of curated pathways. We nominated specific molecular sub-processes underlying protein misfolding and aggregation, post-translational protein modification, immune response, membrane and intracellular trafficking, lipid and vitamin metabolism, synaptic transmission, endosomal-lysosomal dysfunction, chromatin remodeling and apoptosis mediated by caspases among the main contributors to PD etiology. We assessed the impact of rare variation on PD risk in an independent cohort of whole-genome sequencing data and found evidence for a burden of rare damaging alleles in a range of processes, including neuronal transmission-related pathways and immune response. We explored enrichment linked to expression cell specificity patterns using single-cell gene expression data and demonstrated a significant risk pattern for dopaminergic neurons, serotonergic neurons, hypothalamic GABAergic neurons, and neural progenitors. Subsequently, we created a novel way of building de novo pathways by constructing a network expression community map using transcriptomic data derived from the blood of PD patients, which revealed functional enrichment in inflammatory signaling pathways, cell death machinery related processes, and dysregulation of mitochondrial homeostasis. Our analyses highlight several specific promising pathways and genes for functional prioritization and provide a cellular context in which such work should be done.
MeSH term(s)	Community Networks ; Dopaminergic Neurons/metabolism ; Gene Expression Profiling/methods ; Genetic Predisposition to Disease/genetics ; Humans ; Lysosomes/metabolism ; Mitochondria/metabolism ; Multifactorial Inheritance/physiology ; Parkinson Disease/metabolism
Language	English
Publishing date	2020-06-29
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1079-0
ISSN	1432-0533 ; 0001-6322
ISSN (online)	1432-0533
ISSN	0001-6322
DOI	10.1007/s00401-020-02181-3
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Article ; Online: Extended tracts of homozygosity identify novel candidate genes associated with late-onset Alzheimer's disease.

Nalls, M A / Guerreiro, R J / Simon-Sanchez, J / Bras, J T / Traynor, B J / Gibbs, J R / Launer, L / Hardy, J / Singleton, A B

Neurogenetics

2009 Volume 10, Issue 3, Page(s) 183–190

Abstract: Large tracts of extended homozygosity are more prevalent in outbred populations than previously thought. With the advent of high-density genotyping platforms, regions of extended homozygosity can be accurately located allowing for the identification of ... ...

Abstract	Large tracts of extended homozygosity are more prevalent in outbred populations than previously thought. With the advent of high-density genotyping platforms, regions of extended homozygosity can be accurately located allowing for the identification of rare recessive risk variants contributing to disease. We compared measures of extended homozygosity (greater than 1 Mb in length) in a population of 837 late-onset Alzheimer's disease (LOAD) cases and 550 controls. In our analyses, we identify one homozygous region on chromosome 8 that is significantly associated with LOAD after adjusting for multiple testing. This region contains seven genes from which the most biologically plausible candidates are STAR, EIF4EBP1, and ADRB3. We also compared the total numbers of homozygous runs and the total length of these runs between cases and controls, showing a suggestive difference in these measures (p-values 0.052-0.062). This research suggests a recessive component to the etiology of LOAD.
MeSH term(s)	Age of Onset ; Alzheimer Disease/genetics ; Chromosomes, Human, Pair 8 ; Genetic Predisposition to Disease ; Genetics, Population ; Genome, Human ; Genotype ; Humans ; Molecular Sequence Data ; Sequence Analysis, DNA
Language	English
Publishing date	2009-03-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1339887-8
ISSN	1364-6753 ; 1364-6745
ISSN (online)	1364-6753
ISSN	1364-6745
DOI	10.1007/s10048-009-0182-4
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Article ; Online: Somatic, positive and negative domains of the Center for Epidemiological Studies Depression (CES-D) scale: a meta-analysis of genome-wide association studies.

Demirkan, A / Lahti, J / Direk, N / Viktorin, A / Lunetta, K L / Terracciano, A / Nalls, M A / Tanaka, T / Hek, K / Fornage, M / Wellmann, J / Cornelis, M C / Ollila, H M / Yu, L / Smith, J A / Pilling, L C / Isaacs, A / Palotie, A / Zhuang, W V /

Zonderman, A / Faul, J D / Sutin, A / Meirelles, O / Mulas, A / Hofman, A / Uitterlinden, A / Rivadeneira, F / Perola, M / Zhao, W / Salomaa, V / Yaffe, K / Luik, A I / Liu, Y / Ding, J / Lichtenstein, P / Landén, M / Widen, E / Weir, D R / Llewellyn, D J / Murray, A / Kardia, S L R / Eriksson, J G / Koenen, K / Magnusson, P K E / Ferrucci, L / Mosley, T H / Cucca, F / Oostra, B A / Bennett, D A / Paunio, T / Berger, K / Harris, T B / Pedersen, N L / Murabito, J M / Tiemeier, H / van Duijn, C M / Räikkönen, K

Psychological medicine

2016 Volume 46, Issue 8, Page(s) 1613–1623

Abstract: Background: Major depressive disorder (MDD) is moderately heritable, however genome-wide association studies (GWAS) for MDD, as well as for related continuous outcomes, have not shown consistent results. Attempts to elucidate the genetic basis of MDD ... ...

Abstract	Background: Major depressive disorder (MDD) is moderately heritable, however genome-wide association studies (GWAS) for MDD, as well as for related continuous outcomes, have not shown consistent results. Attempts to elucidate the genetic basis of MDD may be hindered by heterogeneity in diagnosis. The Center for Epidemiological Studies Depression (CES-D) scale provides a widely used tool for measuring depressive symptoms clustered in four different domains which can be combined together into a total score but also can be analysed as separate symptom domains. Method: We performed a meta-analysis of GWAS of the CES-D symptom clusters. We recruited 12 cohorts with the 20- or 10-item CES-D scale (32 528 persons). Results: One single nucleotide polymorphism (SNP), rs713224, located near the brain-expressed melatonin receptor (MTNR1A) gene, was associated with the somatic complaints domain of depression symptoms, with borderline genome-wide significance (p discovery = 3.82 × 10-8). The SNP was analysed in an additional five cohorts comprising the replication sample (6813 persons). However, the association was not consistent among the replication sample (p discovery+replication = 1.10 × 10-6) with evidence of heterogeneity. Conclusions: Despite the effort to harmonize the phenotypes across cohorts and participants, our study is still underpowered to detect consistent association for depression, even by means of symptom classification. On the contrary, the SNP-based heritability and co-heritability estimation results suggest that a very minor part of the variation could be captured by GWAS, explaining the reason of sparse findings.
MeSH term(s)	Depression/genetics ; Depression/physiopathology ; Depression/psychology ; Depressive Disorder, Major/genetics ; Depressive Disorder, Major/physiopathology ; Depressive Disorder, Major/psychology ; Genome-Wide Association Study ; Humans ; Polymorphism, Single Nucleotide ; Receptor, Melatonin, MT1/genetics ; Somatoform Disorders/genetics ; Somatoform Disorders/physiopathology ; Somatoform Disorders/psychology
Chemical Substances	MTNR1A protein, human ; Receptor, Melatonin, MT1
Language	English
Publishing date	2016-03-21
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	217420-0
ISSN	1469-8978 ; 0033-2917
ISSN (online)	1469-8978
ISSN	0033-2917
DOI	10.1017/S0033291715002081
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Article ; Online: Admixture mapping of ankle-arm index: identification of a candidate locus associated with peripheral arterial disease.

Scherer, M L / Nalls, M A / Pawlikowska, L / Ziv, E / Mitchell, G / Huntsman, S / Hu, D / Sutton-Tyrrell, K / Lakatta, E G / Hsueh, W-C / Newman, A B / Tandon, A / Kim, L / Kwok, P-Y / Sung, A / Li, R / Psaty, B / Reiner, A P / Harris, T

Journal of medical genetics

2009 Volume 47, Issue 1, Page(s) 1–7

Abstract: Background: Peripheral arterial disease (PAD) is associated with significant morbidity and mortality, and has a higher prevalence in African Americans than Caucasians. Ankle-arm index (AAI) is the ratio of systolic blood pressure in the leg to that in ... ...

Abstract	Background: Peripheral arterial disease (PAD) is associated with significant morbidity and mortality, and has a higher prevalence in African Americans than Caucasians. Ankle-arm index (AAI) is the ratio of systolic blood pressure in the leg to that in the arm, and, when low, is a marker of PAD. Methods: The authors used an admixture mapping approach to search for genetic loci associated with low AAI. Using data from 1040 African American participants in the observational, population based Health, Aging, and Body Composition Study who were genotyped at 1322 single nucleotide polymorphisms (SNPs) that are informative for African versus European ancestry and span the entire genome, we estimated genetic ancestry in each chromosomal region and then tested the association between AAI and genetic ancestry at each locus. Results: The authors found a region of chromosome 11 that reaches its peak between 80 and 82 Mb associated with low AAI (p<0.001 for rs12289502 and rs9665943, both within this region). 753 African American participants in the observational, population based Cardiovascular Health Study were genotyped at rs9665943 to test the reproducibility of this association, and this association was also statistically significant (odds ratio (OR) for homozygous African genotype 1.59, 95% confidence interval (CI) 1.12 to 2.27). Another candidate SNP (rs1042602) in the same genomic region was tested in both populations, and was also found to be significantly associated with low AAI in both populations (OR for homozygous African genotype 1.89, 95% CI 1.29 to 2.76). Conclusion: This study identifies a novel region of chromosome 11 representing an area with a potential candidate gene associated with PAD in African Americans.
MeSH term(s)	African Americans/genetics ; Aged ; Ankle Brachial Index ; Chromosome Mapping ; Chromosomes, Human, Pair 11/genetics ; Female ; Genetic Loci ; Genotype ; Humans ; Male ; Odds Ratio ; Peripheral Vascular Diseases/epidemiology ; Peripheral Vascular Diseases/genetics ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2009-07-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	220881-7
ISSN	1468-6244 ; 0022-2593
ISSN (online)	1468-6244
ISSN	0022-2593
DOI	10.1136/jmg.2008.064808
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Article: Somatic, positive and negative domains of the Center for Epidemiological Studies Depression (CES-D) scale

NABEC / UKBEC / Demirkan, A. / Lahti, J. / Direk, N. / Viktorin, A. / Lunetta, K. L. / Terracciano, A. / Nalls, M. A. / Tanaka, T. / Hek, K. / Fornage, M. / Wellmann, J. / Cornelis, M. C. / Ollila, H. M. / Yu, L. / Smith, J. A. / Pilling, L. C. / Isaacs, A. /

Palotie, A. / Zhuang, W. V. / Zonderman, A. / Faul, J. D. / Sutin, A. / Meirelles, O. / Mulas, A. / Hofman, A. / Uitterlinden, A. / Rivadeneira, F. / Perola, M. / Zhao, W. / Salomaa, V. / Yaffe, K. / Luik, A. I. / Liu, Y. / Ding, J. / Lichtenstein, P. / Landén, M. / Widen, E. / Weir, D. R. / Llewellyn, D. J. / Murray, A. / Kardia, S. L. R. / Eriksson, J. G. / Koenen, K. / Magnusson, P. K. E. / Ferrucci, L. / Mosley, T. H. / Cucca, F. / Oostra, B. A. / Bennett, D. A. / Paunio, T. / Berger, K. / Harris, T. B. / Pedersen, N. L. / Murabito, J. M. / Tiemeier, H. / van Duijn, C. M. / Räikkönen, K.

Psychological Medicine

A meta-analysis of genome-wide association studies

2016 Volume 46, Issue 8, Page(s) 1613–1623

Abstract: Examined the role of genetic factors in susceptibility to depression. Major depressive disorder (MDD) is moderately heritable, however genome-wide association studies (GWAS) for MDD, as well as for related continuous outcomes, have not shown consistent ... ...

Title translation	Somatische, positive und negative Bereiche des Zentrums für epidemiologische Studien Depression (CES-D) Skala: Eine Meta-Analyse der genomweiten Assoziationsstudien
Abstract	Examined the role of genetic factors in susceptibility to depression. Major depressive disorder (MDD) is moderately heritable, however genome-wide association studies (GWAS) for MDD, as well as for related continuous outcomes, have not shown consistent results. Attempts to elucidate the genetic basis of MDD may be hindered by heterogeneity in diagnosis. The Center for Epidemiological Studies Depression (CES-D) scale provides a widely used tool for measuring depressive symptoms clustered in four different domains which can be combined together into a total score but also can be analyzed as separate symptom domains. A meta-analysis of GWAS of the CES-D symptom clusters was performed which included 12 cohorts with the 20- or 10-item CES-D scale (32,528 persons). Initial screening was done with the Mini-Mental State Examination. Results showed one single nucleotide polymorphism (SNP), rs713224, located near the brain-expressed melatonin receptor (MTNR1A) gene, was associated with the somatic complaints domain of depression symptoms, with borderline genome-wide significance (p(discovery) = 3.82 x 10(-8)). The SNP was analyzed in an additional five cohorts comprising the replication sample (6,813 persons). However, the association was not consistent among the replication sample (p(discovery+replication) = 1.10 x 10(-6)) with evidence of heterogeneity. Despite the effort to harmonize the phenotypes across cohorts and participants, this study is still underpowered to detect consistent association for depression, even by means of symptom classification. On the contrary, the SNP-based heritability and co-heritability estimation results suggest that a very minor part of the variation could be captured by GWAS, explaining the reason for sparse findings.
Keywords	Erblichkeit ; Genom ; Genome ; Heritability ; Major Depression ; Phenotypes ; Phänotypen ; Rating Scales ; Rating-Skalen ; Symptome ; Symptoms
Language	English
Document type	Article
ZDB-ID	217420-0
ISSN	1469-8978 ; 0033-2917
ISSN (online)	1469-8978
ISSN	0033-2917
DOI	10.1017/S0033291715002081
Database	PSYNDEX

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Article ; Online: Is the adiposity-associated FTO gene variant related to all-cause mortality independent of adiposity? Meta-analysis of data from 169,551 Caucasian adults.

Zimmermann, E / Ängquist, L H / Mirza, S S / Zhao, J H / Chasman, D I / Fischer, K / Qi, Q / Smith, A V / Thinggaard, M / Jarczok, M N / Nalls, M A / Trompet, S / Timpson, N J / Schmidt, B / Jackson, A U / Lyytikäinen, L P / Verweij, N / Mueller-Nurasyid, M / Vikström, M /

Marques-Vidal, P / Wong, A / Meidtner, K / Middelberg, R P / Strawbridge, R J / Christiansen, L / Kyvik, K O / Hamsten, A / Jääskeläinen, T / Tjønneland, A / Eriksson, J G / Whitfield, J B / Boeing, H / Hardy, R / Vollenweider, P / Leander, K / Peters, A / van der Harst, P / Kumari, M / Lehtimäki, T / Meirhaeghe, A / Tuomilehto, J / Jöckel, K-H / Ben-Shlomo, Y / Sattar, N / Baumeister, S E / Smith, G Davey / Casas, J P / Houston, D K / März, W / Christensen, K / Gudnason, V / Hu, F B / Metspalu, A / Ridker, P M / Wareham, N J / Loos, R J F / Tiemeier, H / Sonestedt, E / Sørensen, T I A

Obesity reviews : an official journal of the International Association for the Study of Obesity

2015 Volume 16, Issue 4, Page(s) 327–340

Abstract: Previously, a single nucleotide polymorphism (SNP), rs9939609, in the FTO gene showed a much stronger association with all-cause mortality than expected from its association with body mass index (BMI), body fat mass index (FMI) and waist circumference ( ... ...

Abstract	Previously, a single nucleotide polymorphism (SNP), rs9939609, in the FTO gene showed a much stronger association with all-cause mortality than expected from its association with body mass index (BMI), body fat mass index (FMI) and waist circumference (WC). This finding implies that the SNP has strong pleiotropic effects on adiposity and adiposity-independent pathological pathways that leads to increased mortality. To investigate this further, we conducted a meta-analysis of similar data from 34 longitudinal studies including 169,551 adult Caucasians among whom 27,100 died during follow-up. Linear regression showed that the minor allele of the FTO SNP was associated with greater BMI (n = 169,551; 0.32 kg m(-2) 95% CI 0.28-0.32, P < 1 × 10(-32) ), WC (n = 152,631; 0.76 cm; 0.68-0.84, P < 1 × 10(-32) ) and FMI (n = 48,192; 0.17 kg m(-2) 0.13-0.22, P = 1.0 × 10(-13) ). Cox proportional hazard regression analyses for mortality showed that the hazards ratio (HR) for the minor allele of the FTO SNPs was 1.02 (1.00-1.04, P = 0.097), but the apparent excess risk was eliminated after adjustment for BMI and WC (HR: 1.00; 0.98-1.03, P = 0.662) and for FMI (HR: 1.00; 0.96-1.04, P = 0.932). In conclusion, this study does not support that the FTO SNP is associated with all-cause mortality independently of the adiposity phenotypes.
MeSH term(s)	Adiposity/genetics ; Alpha-Ketoglutarate-Dependent Dioxygenase FTO ; Body Mass Index ; Genetic Predisposition to Disease ; Genetic Variation ; Genome-Wide Association Study ; Humans ; Obesity/genetics ; Obesity/mortality ; Observational Studies as Topic ; Polymorphism, Single Nucleotide ; Proteins/genetics ; Waist Circumference
Chemical Substances	Proteins ; Alpha-Ketoglutarate-Dependent Dioxygenase FTO (EC 1.14.11.33) ; FTO protein, human (EC 1.14.11.33)
Language	English
Publishing date	2015-03-05
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2147980-X
ISSN	1467-789X ; 1467-7881
ISSN (online)	1467-789X
ISSN	1467-7881
DOI	10.1111/obr.12263
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Article ; Online: Common genetic variation near the connexin-43 gene is associated with resting heart rate in African Americans: a genome-wide association study of 13,372 participants.

Deo, R / Nalls, M A / Avery, C L / Smith, J G / Evans, D S / Keller, M F / Butler, A M / Buxbaum, S G / Li, G / Miguel Quibrera, P / Smith, E N / Tanaka, T / Akylbekova, E L / Alonso, A / Arking, D E / Benjamin, E J / Berenson, G S / Bis, J C / Chen, L Y /

Chen, W / Cummings, S R / Ellinor, P T / Evans, M K / Ferrucci, L / Fox, E R / Heckbert, S R / Heiss, G / Hsueh, W C / Kerr, K F / Limacher, M C / Liu, Y / Lubitz, S A / Magnani, J W / Mehra, R / Marcus, G M / Murray, S S / Newman, A B / Njajou, O / North, K E / Paltoo, D N / Psaty, B M / Redline, S S / Reiner, A P / Robinson, J G / Rotter, J I / Samdarshi, T E / Schnabel, R B / Schork, N J / Singleton, A B / Siscovick, D / Soliman, E Z / Sotoodehnia, N / Srinivasan, S R / Taylor, H A / Trevisan, M / Zhang, Z / Zonderman, A B / Newton-Cheh, C / Whitsel, E A

Heart rhythm

2012 Volume 10, Issue 3, Page(s) 401–408

Abstract: Background: Genome-wide association studies have identified several genetic loci associated with variation in resting heart rate in European and Asian populations. No study has evaluated genetic variants associated with heart rate in African Americans.!# ...

Abstract	Background: Genome-wide association studies have identified several genetic loci associated with variation in resting heart rate in European and Asian populations. No study has evaluated genetic variants associated with heart rate in African Americans. Objective: To identify novel genetic variants associated with resting heart rate in African Americans. Methods: Ten cohort studies participating in the Candidate-gene Association Resource and Continental Origins and Genetic Epidemiology Network consortia performed genome-wide genotyping of single nucleotide polymorphisms (SNPs) and imputed 2,954,965 SNPs using HapMap YRI and CEU panels in 13,372 participants of African ancestry. Each study measured the RR interval (ms) from 10-second resting 12-lead electrocardiograms and estimated RR-SNP associations using covariate-adjusted linear regression. Random-effects meta-analysis was used to combine cohort-specific measures of association and identify genome-wide significant loci (P≤2.5×10(-8)). Results: Fourteen SNPs on chromosome 6q22 exceeded the genome-wide significance threshold. The most significant association was for rs9320841 (+13 ms per minor allele; P = 4.98×10(-15)). This SNP was approximately 350 kb downstream of GJA1, a locus previously identified as harboring SNPs associated with heart rate in Europeans. Adjustment for rs9320841 also attenuated the association between the remaining 13 SNPs in this region and heart rate. In addition, SNPs in MYH6, which have been identified in European genome-wide association study, were associated with similar changes in the resting heart rate as this population of African Americans. Conclusions: An intergenic region downstream of GJA1 (the gene encoding connexin 43, the major protein of the human myocardial gap junction) and an intragenic region within MYH6 are associated with variation in resting heart rate in African Americans as well as in populations of European and Asian origin.
MeSH term(s)	Adult ; Black or African American/genetics ; Aged ; Arrhythmias, Cardiac/ethnology ; Arrhythmias, Cardiac/genetics ; Arrhythmias, Cardiac/physiopathology ; Connexin 43/genetics ; Connexin 43/metabolism ; Electrocardiography ; Female ; Genetic Variation ; Genome-Wide Association Study/methods ; Genotype ; Heart Rate ; Humans ; Male ; Meta-Analysis as Topic ; Middle Aged ; Polymorphism, Single Nucleotide ; Rest/physiology ; United States/epidemiology
Chemical Substances	Connexin 43
Language	English
Publishing date	2012-11-24
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Multicenter Study ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2229357-7
ISSN	1556-3871 ; 1547-5271
ISSN (online)	1556-3871
ISSN	1547-5271
DOI	10.1016/j.hrthm.2012.11.014
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Article ; Online: A novel Alzheimer disease locus located near the gene encoding tau protein.

Jun, G / Ibrahim-Verbaas, C A / Vronskaya, M / Lambert, J-C / Chung, J / Naj, A C / Kunkle, B W / Wang, L-S / Bis, J C / Bellenguez, C / Harold, D / Lunetta, K L / Destefano, A L / Grenier-Boley, B / Sims, R / Beecham, G W / Smith, A V / Chouraki, V / Hamilton-Nelson, K L /

Ikram, M A / Fievet, N / Denning, N / Martin, E R / Schmidt, H / Kamatani, Y / Dunstan, M L / Valladares, O / Laza, A R / Zelenika, D / Ramirez, A / Foroud, T M / Choi, S-H / Boland, A / Becker, T / Kukull, W A / van der Lee, S J / Pasquier, F / Cruchaga, C / Beekly, D / Fitzpatrick, A L / Hanon, O / Gill, M / Barber, R / Gudnason, V / Campion, D / Love, S / Bennett, D A / Amin, N / Berr, C / Tsolaki, Magda / Buxbaum, J D / Lopez, O L / Deramecourt, V / Fox, N C / Cantwell, L B / Tárraga, L / Dufouil, C / Hardy, J / Crane, P K / Eiriksdottir, G / Hannequin, D / Clarke, R / Evans, D / Mosley, T H / Letenneur, L / Brayne, C / Maier, W / De Jager, P / Emilsson, V / Dartigues, J-F / Hampel, H / Kamboh, M I / de Bruijn, R F A G / Tzourio, C / Pastor, P / Larson, E B / Rotter, J I / O'Donovan, M C / Montine, T J / Nalls, M A / Mead, S / Reiman, E M / Jonsson, P V / Holmes, C / St George-Hyslop, P H / Boada, M / Passmore, P / Wendland, J R / Schmidt, R / Morgan, K / Winslow, A R / Powell, J F / Carasquillo, M / Younkin, S G / Jakobsdóttir, J / Kauwe, J S K / Wilhelmsen, K C / Rujescu, D / Nöthen, M M / Hofman, A / Jones, L / Haines, J L / Psaty, B M / Van Broeckhoven, C / Holmans, P / Launer, L J / Mayeux, R / Lathrop, M / Goate, A M / Escott-Price, V / Seshadri, S / Pericak-Vance, M A / Amouyel, P / Williams, J / van Duijn, C M / Schellenberg, G D / Farrer, L A

Molecular psychiatry

2015 Volume 21, Issue 1, Page(s) 108–117

Abstract: APOE ɛ4, the most significant genetic risk factor for Alzheimer disease (AD), may mask effects of other loci. We re-analyzed genome-wide association study (GWAS) data from the International Genomics of Alzheimer's Project (IGAP) Consortium in APOE ɛ4+ ( ... ...

Abstract	APOE ɛ4, the most significant genetic risk factor for Alzheimer disease (AD), may mask effects of other loci. We re-analyzed genome-wide association study (GWAS) data from the International Genomics of Alzheimer's Project (IGAP) Consortium in APOE ɛ4+ (10 352 cases and 9207 controls) and APOE ɛ4- (7184 cases and 26 968 controls) subgroups as well as in the total sample testing for interaction between a single-nucleotide polymorphism (SNP) and APOE ɛ4 status. Suggestive associations (P<1 × 10(-4)) in stage 1 were evaluated in an independent sample (stage 2) containing 4203 subjects (APOE ɛ4+: 1250 cases and 536 controls; APOE ɛ4-: 718 cases and 1699 controls). Among APOE ɛ4- subjects, novel genome-wide significant (GWS) association was observed with 17 SNPs (all between KANSL1 and LRRC37A on chromosome 17 near MAPT) in a meta-analysis of the stage 1 and stage 2 data sets (best SNP, rs2732703, P=5·8 × 10(-9)). Conditional analysis revealed that rs2732703 accounted for association signals in the entire 100-kilobase region that includes MAPT. Except for previously identified AD loci showing stronger association in APOE ɛ4+ subjects (CR1 and CLU) or APOE ɛ4- subjects (MS4A6A/MS4A4A/MS4A6E), no other SNPs were significantly associated with AD in a specific APOE genotype subgroup. In addition, the finding in the stage 1 sample that AD risk is significantly influenced by the interaction of APOE with rs1595014 in TMEM106B (P=1·6 × 10(-7)) is noteworthy, because TMEM106B variants have previously been associated with risk of frontotemporal dementia. Expression quantitative trait locus analysis revealed that rs113986870, one of the GWS SNPs near rs2732703, is significantly associated with four KANSL1 probes that target transcription of the first translated exon and an untranslated exon in hippocampus (P ⩽ 1.3 × 10(-8)), frontal cortex (P ⩽ 1.3 × 10(-9)) and temporal cortex (P⩽1.2 × 10(-11)). Rs113986870 is also strongly associated with a MAPT probe that targets transcription of alternatively spliced exon 3 in frontal cortex (P=9.2 × 10(-6)) and temporal cortex (P=2.6 × 10(-6)). Our APOE-stratified GWAS is the first to show GWS association for AD with SNPs in the chromosome 17q21.31 region. Replication of this finding in independent samples is needed to verify that SNPs in this region have significantly stronger effects on AD risk in persons lacking APOE ɛ4 compared with persons carrying this allele, and if this is found to hold, further examination of this region and studies aimed at deciphering the mechanism(s) are warranted.
MeSH term(s)	Alzheimer Disease/genetics ; Apolipoprotein E4/genetics ; Chromosomes, Human, Pair 17 ; Genome-Wide Association Study ; Humans ; Polymorphism, Single Nucleotide ; tau Proteins/genetics
Chemical Substances	Apolipoprotein E4 ; MAPT protein, human ; tau Proteins
Language	English
Publishing date	2015-03-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1330655-8
ISSN	1476-5578 ; 1359-4184
ISSN (online)	1476-5578
ISSN	1359-4184
DOI	10.1038/mp.2015.23
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genome-wide meta-analyses of smoking behaviors in African Americans.

David, S P / Hamidovic, A / Chen, G K / Bergen, A W / Wessel, J / Kasberger, J L / Brown, W M / Petruzella, S / Thacker, E L / Kim, Y / Nalls, M A / Tranah, G J / Sung, Y J / Ambrosone, C B / Arnett, D / Bandera, E V / Becker, D M / Becker, L / Berndt, S I /

Bernstein, L / Blot, W J / Broeckel, U / Buxbaum, S G / Caporaso, N / Casey, G / Chanock, S J / Deming, S L / Diver, W R / Eaton, C B / Evans, D S / Evans, M K / Fornage, M / Franceschini, N / Harris, T B / Henderson, B E / Hernandez, D G / Hitsman, B / Hu, J J / Hunt, S C / Ingles, S A / John, E M / Kittles, R / Kolb, S / Kolonel, L N / Le Marchand, L / Liu, Y / Lohman, K K / McKnight, B / Millikan, R C / Murphy, A / Neslund-Dudas, C / Nyante, S / Press, M / Psaty, B M / Rao, D C / Redline, S / Rodriguez-Gil, J L / Rybicki, B A / Signorello, L B / Singleton, A B / Smoller, J / Snively, B / Spring, B / Stanford, J L / Strom, S S / Swan, G E / Taylor, K D / Thun, M J / Wilson, A F / Witte, J S / Yamamura, Y / Yanek, L R / Yu, K / Zheng, W / Ziegler, R G / Zonderman, A B / Jorgenson, E / Haiman, C A / Furberg, H

Translational psychiatry

2012 Volume 2, Page(s) e119

Abstract: The identification and exploration of genetic loci that influence smoking behaviors have been conducted primarily in populations of the European ancestry. Here we report results of the first genome-wide association study meta-analysis of smoking behavior ...

Abstract	The identification and exploration of genetic loci that influence smoking behaviors have been conducted primarily in populations of the European ancestry. Here we report results of the first genome-wide association study meta-analysis of smoking behavior in African Americans in the Study of Tobacco in Minority Populations Genetics Consortium (n = 32,389). We identified one non-coding single-nucleotide polymorphism (SNP; rs2036527[A]) on chromosome 15q25.1 associated with smoking quantity (cigarettes per day), which exceeded genome-wide significance (β = 0.040, s.e. = 0.007, P = 1.84 × 10(-8)). This variant is present in the 5'-distal enhancer region of the CHRNA5 gene and defines the primary index signal reported in studies of the European ancestry. No other SNP reached genome-wide significance for smoking initiation (SI, ever vs never smoking), age of SI, or smoking cessation (SC, former vs current smoking). Informative associations that approached genome-wide significance included three modestly correlated variants, at 15q25.1 within PSMA4, CHRNA5 and CHRNA3 for smoking quantity, which are associated with a second signal previously reported in studies in European ancestry populations, and a signal represented by three SNPs in the SPOCK2 gene on chr10q22.1. The association at 15q25.1 confirms this region as an important susceptibility locus for smoking quantity in men and women of African ancestry. Larger studies will be needed to validate the suggestive loci that did not reach genome-wide significance and further elucidate the contribution of genetic variation to disparities in cigarette consumption, SC and smoking-attributable disease between African Americans and European Americans.
MeSH term(s)	Adult ; African Americans/genetics ; Aged ; Chromosomes, Human, Pair 10/genetics ; Chromosomes, Human, Pair 15/genetics ; Female ; Genetic Loci/genetics ; Genetic Predisposition to Disease/genetics ; Genetic Variation/genetics ; Genome-Wide Association Study ; Genotype ; Humans ; Male ; Middle Aged ; Nerve Tissue Proteins/genetics ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Proteoglycans/genetics ; Receptors, Nicotinic/genetics ; Smoking/genetics ; Statistics as Topic
Chemical Substances	CHRNA5 protein, human ; Nerve Tissue Proteins ; Proteoglycans ; Receptors, Nicotinic ; SPOCK2 protein, human
Language	English
Publishing date	2012-05-22
Publishing country	United States
Document type	Journal Article ; Meta-Analysis
ZDB-ID	2609311-X
ISSN	2158-3188 ; 2158-3188
ISSN (online)	2158-3188
ISSN	2158-3188
DOI	10.1038/tp.2012.41
Database	MEDical Literature Analysis and Retrieval System OnLINE

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