TY - JOUR. T1 - A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer. AU - Olama, Ali Amin Al. AU - Kote-Jarai, Zsofia. AU - Berndt, Sonja I.. AU - Conti, David V.. AU - Schumacher, Fredrick. AU - Han, Ying. AU - Benlloch, Sara. AU - Hazelett, Dennis J.. AU - Wang, Zhaoming. AU - Saunders, Ed. AU - Leongamornlert, Daniel. AU - Lindstrom, Sara. AU - Jugurnauth-Little, Sara. AU - Dadaev, Tokhir. AU - Tymrakiewicz, Malgorzata. AU - Stram, Daniel O.. AU - Rand, Kristin. AU - Wan, Peggy. AU - Stram, Alex. AU - Sheng, Xin. AU - Pooler, Loreall C.. AU - Park, Karen. AU - Xia, Lucy. AU - Tyrer, Jonathan. AU - Kolonel, Laurence N.. AU - Marchand, Loic Le. AU - Hoover, Robert N.. AU - Machiela, Mitchell J.. AU - Yeager, Merideth. AU - Burdette, Laurie. AU - Chung, Charles C.. AU - Hutchinson, Amy. AU - Yu, Kai. AU - Goh, Chee. AU - Ahmed, Mahbubl. AU - Govindasami, Koveela. AU - Guy, Michelle. AU - Tammela, Teuvo L.J.. AU - Auvinen, Anssi. AU - Wahlfors, ...
Complete information for BMIQ14 gene (Genetic Locus), Body Mass Index QTL14, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
Complete information for CMR1A gene (Genetic Locus), Cardiomyopathy, Restrictive 1A (Autosomal Dominant), including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
[Identification of changes in gene loci potentially associated with cervical cancer using NotI microarrays].: The investigation of the cancer-associated structu
TY - JOUR. T1 - 12 new susceptibility loci for prostate cancer identified by genome-wide association study in Japanese population. AU - Takata, Ryo. AU - Takahashi, Atsushi. AU - Fujita, Masashi. AU - Momozawa, Yukihide. AU - Saunders, Edward J.. AU - Yamada, Hiroki. AU - Maejima, Kazuhiro. AU - Nakano, Kaoru. AU - Nishida, Yuichiro. AU - Hishida, Asahi. AU - Matsuo, Keitaro. AU - Wakai, Kenji. AU - Yamaji, Taiki. AU - Sawada, Norie. AU - Iwasaki, Motoki. AU - Tsugane, Shoichiro. AU - Sasaki, Makoto. AU - Shimizu, Atsushi. AU - Tanno, Kozo. AU - Minegishi, Naoko. AU - Suzuki, Kichiya. AU - Matsuda, Koichi. AU - Kubo, Michiaki. AU - Inazawa, Johji. AU - Egawa, Shin. AU - Haiman, Christopher A.. AU - Ogawa, Osamu. AU - Obara, Wataru. AU - Kamatani, Yoichiro. AU - Akamatsu, Shusuke. AU - Nakagawa, Hidewaki. PY - 2019/12/1. Y1 - 2019/12/1. N2 - Genome-wide association studies (GWAS) have identified ~170 genetic loci associated with prostate cancer (PCa) risk, but most of them were identified in ...
Genome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining similar to 14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprising 15,748 breast cancer cases and 18,084 controls together with 46,785 cases and 42,892 controls from 41 studies genotyped on a 211,155-marker custom array (iCOGS). Analyses were restricted to women of European ancestry. We generated genotypes for more than 11 million SNPs by imputation using the 1000 Genomes Project reference panel, and we identified 15 new loci associated with breast cancer at P , 5 x 10(-8). Combining association analysis with ChIP-seq chromatin binding data in mammary cell lines and ChIA-PET chromatin interaction data from ENCODE, we identified likely target genes in two regions: SETBP1 at 18q12.3 and RNF115 and PDZK1 at 1q21.1. One association appears to be driven by an amino acid ...
The present study aimed to discover novel susceptibility loci associated with risk of rheumatoid arthritis (RA).We performed a new genome-wide association study (GWAS) in Chinese subjects (1027 RA cases and 2879 controls) and further conducted an expanded meta-analysis with previous GWAS summary data and replication studies. The functional roles of the associated loci were interrogated using publicly available databases. Dual-luciferase reporter and cytokine assay were also used for exploring variant function.We identified five new susceptibility loci (IL12RB2, BOLL-PLCL1, CCR2, TCF7 and IQGAP1; pmeta ,5.00E-08) with same effect direction in each study cohort. The sensitivity analyses showed that the genetic association of at least three loci was reliable and robust. All these lead variants are expression quantitative trait loci and overlapped with epigenetic marks in immune cells. Furthermore, genes within the five loci are genetically associated with risk of other autoimmune diseases, and ...
GWAS has enormously contributed to the identification of susceptibility genes for T2D and many other complex disorders. The discovery of new susceptibility loci in GWAS of different ethnic groups emphasizes the need for conducting more GWAS in populations of diverse ethnic groups. Our study also shows the potential of identifying new signals through GWAS in population of different ethnicity. In this study, we performed a GWAS in Indians and identified a new signal for T2D on chromosome 2q21.. The strongest signal on newly identified locus 2q21 mapped to TMEM163. The association of TMEM163 variants (rs6723108 and rs998451) with reduced fasting plasma insulin levels and HOMA-IR indicates that it might modulate susceptibility to T2D by affecting insulin secretion. Previously, rs6723108 has also been suggested to be associated with waist circumference. These data indicate the biological relevance of the identified locus with T2D. TMEM163 encodes a synaptic vesicle membrane protein with six putative ...
Bei, J.-X., Jia, W.-H., Feng, B.-J., Chen, L.-Z., Feng, Q.-S., Kang, T., Liu, J., Zeng, Y.-X., Li, Y., Low, H.-Q., Zhou, G., Zhang, H., He, F., Tai, E.S., Liu, E.T. (2010). A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci. Nature Genetics 42 (7) : 599-603. [email protected] Repository. https://doi.org/10.1038/ng. ...
Genome-wide association studies (GWAS) have identified approximately 100 breast cancer risk loci. Translating these findings into a greater understanding of the mechanisms that influence disease risk requires identification of the genes or non-coding RNAs that mediate these associations. Here, we use Capture Hi-C (CHi-C) to annotate 63 loci; we identify 110 putative target genes at 33 loci. To assess the support for these target genes in other data sources we test for associations between levels of expression and SNP genotype (eQTLs), disease-specific survival (DSS), and compare them with somatically mutated cancer genes. 22 putative target genes are eQTLs, 32 are associated with DSS and 14 are somatically mutated in breast, or other, cancers. Identifying the target genes at GWAS risk loci will lead to a greater understanding of the mechanisms that influence breast cancer risk and prognosis ...
by Barbara Stranger, Qiyuan Li, Ji-Heui Seo, Aaron McKenna, Itsik Peer, Thomas LaFramboise, Myles Brown, Svitlana Tyekucheva, Matthew L. Freedman Germline determinants of gene expression in tumors are infrequently studied due to the complexity of transcript regulation caused by somatically acquired alterations. We performed expression quantitative trait locus (eQTL)-based analyses using the multi-level information provided in The Cancer Genome Atlas (TCGA). Of the factors we measured, cis-acting eQTLs accounted for 1.2% of the total variation of tumor gene expression, while somatic copy-number alteration and CpG methylation accounted for 7.3% and 3.3%, respectively. eQTL analyses of 15 previously reported breast cancer risk loci resulted in the discovery of three variants that are significantly associated with transcript levels (false discovery rate [FDR] < 0.1). Our trans-based analysis identified an additional three risk loci to act through ESR1, MYC, and KLF4. These findings provide a more ...
Erdmann J, Grosshennig A, Braund PS, König IR, Hengstenberg C, Hall AS, Linsel-Nitschke P, Kathiresan S, Wright B, Trégouët DA, Cambien F, Bruse P, Aherrahrou Z, Wagner AK, Stark K, Schwartz SM, Salomaa V, Elosua R, Melander O, Voight BF, ODonnell CJ, Peltonen L, Siscovick DS, Altshuler D, Merlini PA, Peyvandi F, Bernardinelli L, Ardissino D, Schillert A, Blankenberg S, Zeller T, Wild P, Schwarz DF, Tiret L, Perret C, Schreiber S, El Mokhtari NE, Schäfer A, März W, Renner W, Bugert P, Klüter H, Schrezenmeir J, Rubin D, Ball SG, Balmforth AJ, Wichmann HE, Meitinger T, Fischer M, Meisinger C, Baumert J, Peters A, Ouwehand WH, Deloukas P, Thompson JR, Ziegler A, Samani NJ, Schunkert H, ...
Lambert, Jean-Charles, Ibrahim-Verbaas, Carla A., Harold, Denise, Naj, Adam C., Sims, Rebecca, Bellenguez, Céline, Jun, Gyungah, DeStefano, Anita L., Bis, Joshua C., Beecham, Gary W., Grenier-Boley, Benjamin, Russo, Giancarlo, Thornton-Wells, Tricia A., Denning, Nicola, Smith, Albert V., Chouraki, Vincent, Thomas, Charlene, Ikram, M. Arfan, Zelenika, Diana, Vardarajan, Badri N., Kamatani, Yoichiro, Lin, Chiao-Feng, Gerrish, Amy, Schmidt, Helena, Kunkle, Brian, Dunstan, Melanie, Ruiz, Agustin, Bihoreau, Marie-Thérèse, Choi, Seung-Hoan, Reitz, Christiane, Pasquier, Florence, Hollingworth, Paul, Ramirez, Alfredo, Hanon, Olivier, Fitzpatrick, Annette L., Buxbaum, Joseph D., Campion, Dominique, Crane, Paul K, Baldwin, Clinton, Becker, Tim, Gudnason, Vilmundur, Cruchaga, Carlos, Craig, David, Amin, Najaf, Berr, Claudine, Lopez, Oscar L., De Jager, Philip L., Deramecourt, Vincent, Johnston, Janet A., Evans, Denis, Lovestone, Simon, Letenneur, Luc, Morón, Francisco J., Rubinsztein, David C., ...
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|p|Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P | 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-wi|/p| …
There is mounting evidence that endometriosis is inherited as a complex trait, like diabetes or asthma. This implies there are environmental factors, such as dioxin, that are interacting with multiple genetic susceptibility loci to produce the phenotype. The Oxford Endometriosis Gene OXEGENE study, an international collaborative project seeks...
Like GRCh37, the updated reference assembly provides alternate sequence representation for variant regions in the form of alternate loci (alt loci) scaffolds. The alt loci are stand-alone, accessioned sequences for which chromosomal context is provided via alignment to the reference chromosomes. All alternate loci include at least one anchor sequence, a component also found on the reference chromosomes, to ensure these alignments are of high quality. Alt loci belong to alternate loci assembly units: the assembly unit ALT_REF_LOCI_1 contains the first alternate sequence representation for any genomic locus, ALT_REF_LOCI_2 contains the second alternate sequence representation and so forth. GRCh38 contains 261 alt loci scaffolds, in 35 alternate assembly units. 72 of these alternate loci were previously available as NOVEL patches to GRCh37. The LRC/KIR complex on chr. 19 has the largest number of alternate sequence representations (35), followed by the MHC on chr. 6 (7 ...
Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis. PLoS Med. 2017 Sep; 14(9):e1002383 ...
Researchers unearthed 75 risk loci, 42 of them new, and nominated candidate genes for each. A polygenic risk score based on all variants predicted AD risk with high accuracy.. ...
This article, which contained no data, represents a departure from McClintocks previous published work, which had been based primarily on empirical data collected during research. It demonstrated again her fascination with the fundamental theoretical and philosophical problems of genetics ...
Using the Immunochip custom SNP array, which was designed for dense genotyping of 186 loci identified through genome-wide association studies (GWAS), we analyzed 11,475 individuals with rheumatoid arthritis (cases) of European ancestry and 15,870 controls for 129,464 markers. We combined these data in a meta-analysis with GWAS data from additional independent cases (n = 2,363) and controls (n = 17,872). We identified 14 new susceptibility loci, 9 of which were associated with rheumatoid arthritis overall and five of which were specifically associated with disease that was positive for anticitrullinated peptide antibodies, bringing the number of confirmed rheumatoid arthritis risk loci in individuals of European ancestry to 46. We refined the peak of association to a single gene for 19 loci, identified secondary independent effects at 6 loci and identified association to low-frequency variants at 4 loci. Bioinformatic analyses generated strong hypotheses for the causal SNP at seven loci. This ...
TY - JOUR. T1 - Genome-wide pooling approach identifies SPATA5 as a new susceptibility locus for alopecia areata. AU - Forstbauer, Lina M. AU - Brockschmidt, Felix F. AU - Moskvina, Valentina. AU - Herold, Christine. AU - Redler, Silke. AU - Herzog, Alexandra. AU - Hillmer, Axel M. AU - Meesters, Christian. AU - Heilmann, Stefanie. AU - Albert, Florian. AU - Alblas, Margrieta. AU - Hanneken, Sandra. AU - Eigelshoven, Sibylle. AU - Giehl, Kathrin A. AU - Jagielska, Dagny. AU - Blume-Peytavi, Ulrike. AU - Garcia Bartels, Natalie. AU - Kuhn, Jennifer. AU - Hennies, Hans Christian. AU - Goebeler, Matthias. AU - Jung, Andreas. AU - Peitsch, Wiebke K. AU - Kortüm, Anne-Katrin. AU - Moll, Ingrid. AU - Kruse, Roland. AU - Lutz, Gerhard. AU - Wolff, Hans. AU - Blaumeiser, Bettina. AU - Böhm, Markus. AU - Kirov, George. AU - Becker, Tim. AU - Nöthen, Markus M. AU - Betz, Regina C. PY - 2012/3. Y1 - 2012/3. N2 - Alopecia areata (AA) is a common hair loss disorder, which is thought to be a ...
Dendrobium huoshanense (Orchidaceae) is a perennial herb and a widely used medicinal plant in Traditional Chinese medicine (TCM) endemic to Huoshan County town in Anhui province in Southeast China. A microsatellite-enriched genomic DNA library of D. huoshanense was developed and screened to identify marker loci. Eleven polymorphic loci were isolated and analyzed by screening 25 individuals collected from a natural population. The number of alleles per locus ranged from 2 to 5. The observed and expected heterozygosities ranged from 0.227 to 0.818 and from 0.317 to 0.757, respectively. Two loci showed significant deviations from Hardy-Weinberg equilibrium and four of the pairwise comparisons of loci revealed linkage disequilibrium (p < 0.05). These microsatellite loci were cross-amplified for five congeneric species and seven loci can be amplified in all species. These simple sequence repeats (SSR) markers are useful in genetic studies of D. huoshanense and other related species and in conservation
Genome-wide association studies (GWASs) have identified a number of genetic risk loci associated with systemic sclerosis (SSc) and Crohns disease (CD), some of which confer susceptibility to both diseases. In order to identify new risk loci shared between these two immune-mediated disorders, we performed a cross-disease meta-analysis including GWAS data from 5,734 SSc patients, 4,588 CD patients and 14,568 controls of European origin. We identified 4 new loci shared between SSc and CD, IL12RB2, IRF1/SLC22A5, STAT3 and an intergenic locus at 6p21.31. Pleiotropic variants within these loci showed opposite allelic effects in the two analysed diseases and all of them showed a significant effect on gene expression. In addition, an enrichment in the IL-12 family and type I interferon signaling pathways was observed among the set of SSc-CD common genetic risk loci. In conclusion, through the first cross-disease meta-analysis of SSc and CD, we identified genetic variants with pleiotropic effects on two ...
Background:Crohns disease (CD) is an intractable inflammatory bowel disease of unknown cause. Recent genome-wide association studies of CD in Korean and Japanese populations suggested marginal sharing of susceptibility loci between Caucasian and Asian populations. As the 7 identified loci altogethe
Read Isolation and characterization of twelve polymorphic microsatellite loci in the buff-throated partridge (Tetraophasis szechenyii), Russian Journal of Genetics on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
We genotyped 2,861 cases of primary biliary cirrhosis (PBC) from the UK PBC Consortium and 8,514 UK population controls across 196,524 variants within 186 known autoimmune risk loci. We identified 3 loci newly associated with PBC (at P|5×10(-8)), increasing the number of known susceptibility loci …
Levine DM., Ek WE., Zhang R., Liu X., Onstad L., Sather C., Lao-Sirieix P., Gammon MD., Corley DA., Shaheen NJ., Bird NC., Hardie LJ., Murray LJ., Reid BJ., Chow W-H., Risch HA., Nyrén O., Ye W., Liu G., Romero Y., Bernstein L., Wu AH., Casson AG., Chanock SJ., Harrington P., Caldas I., Debiram-Beecham I., Caldas C., Hayward NK., Pharoah PD., Fitzgerald RC., Macgregor S., Whiteman DC., Vaughan TL ...
TY - JOUR. T1 - Association analysis identifies 65 new breast cancer risk loci. AU - Michailidou, Kyriaki. AU - Lindström, Sara. AU - Dennis, Joe. AU - Beesley, Jonathan. AU - Hui, Shirley. AU - Kar, Siddhartha. AU - Lemaçon, Audrey. AU - Soucy, Penny. AU - Glubb, Dylan. AU - Rostamianfar, Asha. AU - Bolla, Manjeet K. AU - Wang, Qin. AU - Tyrer, Jonathan. AU - Dicks, Ed. AU - Lee, Andrew. AU - Wang, Zhaoming. AU - Allen, Jamie. AU - Keeman, Renske. AU - Eilber, Ursula. AU - French, Juliet D. AU - Qing Chen, Xiao. AU - Fachal, Laura. AU - McCue, Karen. AU - McCart Reed, Amy E. AU - Ghoussaini, Maya. AU - Carroll, Jason S. AU - Jiang, Xia. AU - Finucane, Hilary. AU - Adams, Marcia. AU - Adank, Muriel A. AU - Ahsan, Habibul. AU - Aittomäki, Kristiina. AU - Anton-Culver, Hoda. AU - Antonenkova, Natalia N. AU - Arndt, Volker. AU - Aronson, Kristan J. AU - Arun, Banu. AU - Auer, Paul L. AU - Bacot, François. AU - Barrdahl, Myrto. AU - Baynes, Caroline. AU - Beckmann, Matthias W. AU - Behrens, ...
Few genome-wide association studies (GWAS) account for environmental exposures, like smoking, potentially impacting the overall trait variance when investigating the genetic contribution to obesity-related traits. Here, we use GWAS data from 51,080 current smokers and 190,178 nonsmokers (87% European descent) to identify loci influencing BMI and central adiposity, measured as waist circumference and waist-to-hip ratio both adjusted for BMI. We identify 23 novel genetic loci, and 9 loci with convincing evidence of gene-smoking interaction (GxSMK) on obesity-related traits. We show consistent direction of effect for all identified loci and significance for 18 novel and for 5 interaction loci in an independent study sample. These loci highlight novel biological functions, including response to oxidative stress, addictive behaviour, and regulatory functions emphasizing the importance of accounting for environment in genetic analyses. Our results suggest that tobacco smoking may alter the genetic ...
TY - JOUR. T1 - Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. AU - Estrada, K.. AU - Styrkarsdottir, U.. AU - Evangelou, E.. AU - Hsu, Y.H.. AU - Duncan, E.L.. AU - Ntzani, E.E.. AU - Oei, L.. AU - Albagha, O.M.E.. AU - Amin, N.. AU - Kemp, J.P.. AU - Koller, D.L.. AU - Li, G.. AU - Liu, C.T.. AU - Minster, R.L.. AU - Moayyeri, A.. AU - Vandenput, L.. AU - Willner, D.. AU - Xiao, S.M.. AU - Yerges-Armstrong, L.M.. AU - Zheng, H.F.. AU - Alonso, N.. AU - Eriksson, J.. AU - Kammerer, C.M.. AU - Kaptoge, S.K.. AU - Leo, P.J.. AU - Thorleifsson, G.. AU - Wilson, S.G.. AU - Wilson, J.F.. AU - Aalto, V.. AU - Alen, M.. AU - Aragaki, A.K.. AU - Aspelund, T.. AU - Center, J.R.. AU - Dailiana, Z.. AU - Duggan, DJ. AU - Garcia, M.. AU - Garcia-Giralt, N.. AU - Giroux, S.. AU - Hallmans, G.. AU - Hocking, L.J.. AU - Husted, L.B.. AU - Jameson, K.A.. AU - Khusainova, R.. AU - Kim, G.S.. AU - Kooperberg, C.. AU - Koromila, T.. AU - ...
Kar, SP, Beesley, J, Al Olama, AA, Michailidou, K, Tyrer, J, Kote-Jarai, ZA, Lawrenson, K, Lindstrom, S, Ramus, SJ, Thompson, DJ et al, Kibel, AS, Dansonka-Mieszkowska, A, Michael, A, Dieffenbach, AK, Gentry-Maharaj, A, Whittemore, AS, Wolk, A, Monteiro, A, Peixoto, A, Kierzek, A, Cox, A, Rudolph, A, Gonzalez-Neira, A, Wu, AH, Lindblom, A, Swerdlow, A, Ziogas, A, Ekici, AB, Burwinkel, B, Karlan, BY, Nordestgaard, BG, Blomqvist, C, Phelan, C, McLean, C, Pearce, CL, Vachon, C, Cybulski, C, Slavov, C, Stegmaier, C, Maier, C, Ambrosone, CB, Hogdall, CK, Teerlink, CC, Kang, D, Tessier, DC, Schaid, DJ, Stram, DO, Cramer, DW, Neal, DE, Eccles, D, Flesch-Janys, D, Edwards, DRV, Wokozorczyk, D, Levine, DA, Yannoukakos, D, Sawyer, EJ, Bandera, EV, Poole, EM, Goode, EL, Khusnutdinova, E, Hogdall, E, Song, F, Bruinsma, F, Heitz, F, Modugno, F, Hamdy, FC, Wiklund, F, Giles, GG, Olsson, H, Wildiers, H, Ulmer, H-U, Pandha, H, Risch, HA, Darabi, H, Salvesen, HB, Nevanlinna, H, Gronberg, H, Brenner, H, Brauch, ...
Patterns of biodiversity and evolutionary processes controlling them are still poorly studied in desert biomes. Fine-scale markers could help answer some of the pressing research questions for desert biomes and Sahara in particular. Such markers are available for some large mammals and crocodiles, but not for small vertebrates. Here we present a battery of microsatellite loci developed for Agama boulengeri, a promising model to study evolutionary and demographic processes in the Sahara-Sahel. Loci were selected by sequencing enriched DNA libraries with 454 pyrosequencing. A total of 23 polymorphic loci were successfully amplified in four multiplex reactions. Cross-amplification of the microsatellite loci in A. agama and A. boueti was partially successful. These markers are a promising tool for assessing genetic diversity, gene-flow dynamics and demographic patterns in this group. Given the genus Agama is distributed throughout Africa, results presented here might also facilitate studies in other ...
Figure 2 The American Journal of Human Genetics , DOI: ( /j.ajhg ) Copyright © 2013 The American Society of Human Genetics Terms and Conditions Terms and Conditions
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Genome-Wide Association Analysis of Existing Data Sets for Arthritis and Musculoskeletal and Skin Diseases (R01) PAR-08-123. NIAMS
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Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer. AP Klein;B Wolpin;H Risch;R Stolzenberg-Solomon;E Mocci;M Zhang;O Obazee;E Childs;J Hoskins;A Jermusyk;J Zhong;F Chen;D Albanes;G Andreotti;A Arslan;A Babic;W Bamlet;L Beane-Freeman;S Berndt;A Blackford;M Borges;A Borgida;P Bracci;L Brais;P Brennan;H Brenner;B Bueno-de-Mesquita;J Buring;D Campa;G Capurso;G Cavestro;K Chaffee;C Chung;S Cleary;M Cotterchio;F Dijk;E Duell;L Foretova;C Fuchs;N Funel;S Gallinger;JM Gaziano;M Gazouli;G Giles;E Giovannucci;M Goggins;G Goodman;P Goodman;T Hackert;P Hartge;M Hasan;P Hegyi;K Helzlsouer;J Herman;I Holcatova;E Holly;R Hoover;R Hung;E Jacobs;K Jamroziak;V Janout;R Kaaks;K-T Khaw;EA Klein;M Kogevinas;C Kooperberg;M Kulke;J Kupcinskas;R Kurtz;D Laheru;S Landi;R Lawlor;I-M Lee;L LeMarchand;L Lu;N Malats;A Mambrini;S Mannisto;R Milne;B Mohelnikova-Duchonova;R Neale;J Neoptolemos;A Oberg;S Olson;I Orlow;C Pasquali;A Patel;U Peters;R Pezzilli;M Porta;F Real;N Rothman;G Scelo;H ...
Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals) and took forward 348 SNPs into follow-up (additional 137,052 individuals) in a total of 94 studies. Seven loci displayed significant sex-difference ( ...
SwePub titelinformation: Genome-wide association analysis identifies novel blood pressure loci and offers biological insights into cardiovascular risk
In jlim-1.0.2/examples, we provide the following dataset: - MS/MS-indexSNP.tsv Master file containing the list of index SNPs of known GWAS hits to run JLIM. As an example, we include two GWAS hits and ImmunoChip intervals covering them (chr1:160697074-160933065 and chr12:57626582-58488667). The GWAS hits are originally from IMSGC. Nature Genetics 2013. - MS/ Summary statistics of association to Multiple Sclerosis as primary trait. A separate summary statistic file is provided for each interval listed in the indexSNP file. The data are originally from IMSGC. Nature Genetics 2013. - LCL/ eQTLs in Lymphoblastoid cell lines (LCL) as secondary trait. A separate directory is provided for each interval listed in the indexSNP file. For each interval, two files are provided for each gene to be analyzed: summary association file (.assoc.linear.gz) and permutation file (.mperm.dump.all.gz), which are both generated by plink. In addition, plink ped file (LCL.ped.gz) is provided to calculate in-sample LD ...
The deeper understanding of non-coding RNAs has recently changed the dogma of molecular biology assuming protein-coding genes as unique functional …
Warren, H. R., E. Evangelou, C. P. Cabrera, H. Gao, M. Ren, B. Mifsud, I. Ntalla, et al. 2017. Genome-wide association analysis identifies novel blood pressure loci and offers biological insights into cardiovascular risk. Nature genetics 49 (3): 403-415. doi:10.1038/ng.3768. http://dx.doi.org/10.1038/ng.3768 ...
Oncotarget | https://doi.org/10.18632/oncotarget.14200 Jianjun Yu, Yan Liu, Zhaojian Gong, Shanshan Zhang, Can Guo, Xiayu Li, Yanyan Tang, Liting Yang, Yi He, Fang Wei, Yumin Wang, Qianjin Liao, Wenling Zhang,...
Later, a systematic search of the 65,000 felons in the Arizona database revealed that there were 122 pairs that matched at 9 of 13 loci. Twenty pairs matched at 10 loci. When I heard about this, I wondered if the F.B.I. is totally off its rocker when it comes to the probabilities it gives about DNA matches. Is it possible that the F.B.I. is right about the statistics it cites, and that there could be 122 nine-out-of-13 matches in Arizonas database? Perhaps surprisingly, the answer turns out to be yes. Lets say that the chance of any two individuals matching at any one locus is 7.5 percent. In reality, the frequency of a match varies from locus to locus, but I think 7.5 percent is pretty reasonable. For instance, with a 7.5 percent chance of matching at each locus, the chance that any 2 random people would match at all 13 loci is about 1 in 400 trillion. If you choose exactly 9 loci for 2 random people, the chance that they will match all 9 is 1 in 13 billion. Those are the sorts of numbers the ...
Characterization of the Duplex-comb locus by genetic mapping and whole genome sequencing.(A) The genomic region to which the Duplex-comb locus was mapped to; ad
Average locus differences in mutability related to protein class: a hypothesis.: Substantially less genetic variation has been recognized in studies of the pr
Unusual comQXPA-like loci.(A) Non-canonical unusual com system is present in B. cereus VD102, B. cereus BAG4X12 1, B. cereus MSX A1 and L. fusiformis ZC1. Note
TY - JOUR. T1 - Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. AU - Rioux, John D.. AU - Xavier, Ramnik J.. AU - Taylor, Kent D.. AU - Silverberg, Mark S.. AU - Goyette, Philippe. AU - Huett, Alan. AU - Green, Todd. AU - Kuballa, Petric. AU - Barmada, M. Michael. AU - Datta, Lisa. AU - Shugart, Yin Yao. AU - Griffiths, Anne M.. AU - Targan, Stephan R.. AU - Ippoliti, Andrew F.. AU - Bernard, Edmond Jean. AU - Mei, Ling. AU - Nicolae, Dan L.. AU - Regueiro, Miguel. AU - Schumm, L. Philip. AU - Steinhart, A. Hillary. AU - Rotter, Jerome I.. AU - Duerr, Richard H.. AU - Cho, Judy H.. AU - Daly, Mark J.. AU - Brant, Steven R.. PY - 2007/5. Y1 - 2007/5. N2 - We present a genome-wide association study of ileal Crohn disease and two independent replication studies that identify several new regions of association to Crohn disease. Specifically, in addition to the previously established CARD15 and IL23R associations, we ...
TY - JOUR. T1 - A genome-wide association study reveals that variants within the HLA region are associated with risk for nonobstructive azoospermia. AU - Zhao, Han. AU - Xu, Jianfeng. AU - Zhang, Haobo. AU - Sun, Jielin. AU - Sun, Yingpu. AU - Wang, Zhong. AU - Liu, Jiayin. AU - Ding, Qiang. AU - Lu, Shaoming. AU - Shi, Rong. AU - You, Li. AU - Qin, Yingying. AU - Zhao, Xiaoming. AU - Lin, Xiaoling. AU - Li, Xiao. AU - Feng, Junjie. AU - Wang, Li. AU - Trent, Jeffrey M.. AU - Xu, Chengyan. AU - Gao, Ying. AU - Zhang, Bo. AU - Gao, Xuan. AU - Hu, Jingmei. AU - Chen, Hong. AU - Li, Guangyu. AU - Zhao, Junzhao. AU - Zou, Shuhua. AU - Jiang, Hong. AU - Hao, Cuifang. AU - Zhao, Yueran. AU - Ma, Jinglong. AU - Zheng, S. Lilly. AU - Chen, Zi Jiang. PY - 2012/5/4. Y1 - 2012/5/4. N2 - A genome-wide association study of Han Chinese subjects was conducted to identify genetic susceptibility loci for nonobstructive azoospermia (NOA). In the discovery stage, 802 azoospermia cases and 1,863 controls were ...
Common variants in 94 loci have been associated with breast cancer including 15 loci with genome-wide significant associations (P,5 x 10(-8)) with oestrogen receptor (ER)-negative breast cancer and BRCA1-associated breast cancer risk. In this study, to identify new ER-negative susceptibility loci, we performed a meta-analysis of 11 genome-wide association studies (GWAS) consisting of 4,939 ER-negative cases and 14,352 controls, combined with 7,333 ER-negative cases and 42,468 controls and 15,252 BRCA1 mutation carriers genotyped on the iCOGS array. We identify four previously unidentified loci including two loci at 13q22 near KLF5, a 2p23.2 locus near WDR43 and a 2q33 locus near PPIL3 that display genome-wide significant associations with ER-negative breast cancer. In addition, 19 known breast cancer risk loci have genome-wide significant associations and 40 had moderate associations (P,0.05) with ER-negative disease. Using functional and eQTL studies we implicate TRMT61B and WDR43 at 2p23.2 and ...
Montserrat Garcia-Closas and colleagues report a genome-wide association study for bladder cancer. They identify three new susceptibility loci on chromosomes 22q13.1, 19q12 and 2q37.1. We conducted a multi-stage, genome-wide association study of bladder cancer with a primary scan of 591,637 SNPs in 3,532 affected individuals (cases) and 5,120 controls of European descent from five studies followed by a replication strategy, which included 8,382 cases and 48,275 controls from 16 studies. In a combined analysis, we identified three new regions associated with bladder cancer on chromosomes 22q13.1, 19q12 and 2q37.1: rs1014971, (P = 8 × 10−12) maps to a non-genic region of chromosome 22q13.1, rs8102137 (P = 2 × 10−11) on 19q12 maps to CCNE1 and rs11892031 (P = 1 × 10−7) maps to the UGT1A cluster on 2q37.1. We confirmed four previously identified genome-wide associations on chromosomes 3q28, 4p16.3, 8q24.21 and 8q24.3, validated previous candidate associations for the GSTM1 deletion (P = 4 × 10
We genotyped 2,861 cases of primary biliary cirrhosis (PBC) from the UK PBC Consortium and 8,514 UK population controls across 196,524 variants within 186 known autoimmune risk loci. We identified 3 loci newly associated with PBC (at P|5×10(-8)), increasing the number of known susceptibility loci to 25. The most associated variant at 19p12 is a low-frequency nonsynonymous SNP in TYK2, further implicating JAK-STAT and cytokine signaling in disease pathogenesis. An additional five loci contained nonsynonymous variants in high linkage disequilibrium (LD; r2|0.8) with the most associated variant at the locus. We found multiple independent common, low-frequency and rare variant association signals at five loci. Of the 26 independent non-human leukocyte antigen (HLA) signals tagged on the Immunochip, 15 have SNPs in B-lymphoblastoid open chromatin regions in high LD (r2|0.8) with the most associated variant. This study shows how data from dense fine-mapping arrays coupled with functional genomic data can be
The oval squid Sepioteuthis lessoniana is one of the most economically important squid species in Japan; however, its population structure is poorly understood due to the lack of hypervariable markers. Such information is critical for managing sustainable fisheries, as well as for ensuring the existence of wild S. lessoniana stocks. Eleven candidate microsatellite loci were isolated from a small insert genomic DNA library. Polymorphisms in these 11 loci were screened in 24 wild individuals. The number of alleles per locus was found to range from 5 to 19 alleles, and the observed heterozygosity ranged from 0.292 to 0.958. No evidence for linkage disequilibrium was detected among all the loci. The genotypic proportions conformed to Hardy-Weinberg equilibrium, except at one locus. In conclusion, these polymorphic microsatellite loci may be used to develop a genetic framework to manage S. lessoniana in the future.
Indians undergoing socioeconomic and lifestyle transitions will be maximally affected by epidemic of type 2 diabetes (T2D). We conducted a two-stage genome-wide association study of T2D in 12,535 Indians, a less explored but high-risk group. We identified a new type 2 diabetes-associated locus at 2q21, with the lead signal being rs6723108 (odds ratio 1.31; P = 3.32 × 10−9). Imputation analysis refined the signal to rs998451 (odds ratio 1.56; P = 6.3 × 10−12) within TMEM163 that encodes a probable vesicular transporter in nerve terminals. TMEM163 variants also showed association with decreased fasting plasma insulin and homeostatic model assessment of insulin resistance, indicating a plausible effect through impaired insulin secretion. The 2q21 region also harbors RAB3GAP1 and ACMSD; those are involved in neurologic disorders. Forty-nine of 56 previously reported signals showed consistency in direction with similar effect sizes in Indians and previous studies, and 25 of them were also ...
article{7553dae4-0464-42ca-8c45-78d32d2b97af, abstract = {We performed a meta-analysis of 14 genome-wide association studies of coronary artery disease (CAD) comprising 22,233 individuals with CAD (cases) and 64,762 controls of European descent followed by genotyping of top association signals in 56,682 additional individuals. This analysis identified 13 loci newly associated with CAD at P < 5 x 10(-8) and confirmed the association of 10 of 12 previously reported CAD loci. The 13 new loci showed risk allele frequencies ranging from 0.13 to 0.91 and were associated with a 6% to 17% increase in the risk of CAD per allele. Notably, only three of the new loci showed significant association with traditional CAD risk factors and the majority lie in gene regions not previously implicated in the pathogenesis of CAD. Finally, five of the new CAD risk loci appear to have pleiotropic effects, showing strong association with various other human diseases or traits.}, author = {Schunkert, Heribert and ...
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Schizophrenia is an idiopathic mental disorder with a heritable component and a substantial public health impact. We conducted a multi-stage genome-wide association study (GWAS) for schizophrenia beginning with a Swedish national sample (5,00 cases and 6,243 controls) followed by meta-analysis with previous schizophrenia GWAS (8,832 cases and 2,067 controls) and finally by replication of SNPs in 68 genomic regions in independent samples (7,43 cases, 9,762 controls and 58 parent-offspring trios). We identified 22 loci associated at genome-wide significance; 3 of these are new, and was previously implicated in bipolar disorder. Examination of candidate genes at these loci suggests the involvement of neuronal calcium signaling. We estimate that 8,300 independent, mostly common SNPs (95% credible interval of 6,300-0,200 SNPs) contribute to risk for schizophrenia and that these collectively account for at least 32% of the variance
Purpose: Refractive error is the most common eye disorder worldwide, and a prominent cause of blindness. Myopia affects over 30% of Caucasian populations, and up to 80% of Asians. We aimed to identify multiple genetic loci that explain the genetic architecture of refractive error.. Methods: The Consortium for Refractive Error and Myopia (CREAM) conducted genome-wide meta-analyses including 37,382 individuals from 27 Caucasian studies, and 8,376 from 5 Asian cohorts. Identified variants were used for genetic risk score assessment.. Results: We identified 16 new loci for refractive error in Caucasians, of which 10 were shared with Asians. Combined analysis revealed 8 additional new loci. The new loci include genes with function in neurotransmission (GRIA4), ion channels (KCNQ5), retinoic acid metabolism (RDH5), extracellular matrix remodeling (LAMA2, BMP2), and eye development (SIX6, PRSS56). We also confirmed previously reported associations with GJD2 (top SNP rs524952; Pcombined=1.44x10-15) and ...
Image_6_Genome-Wide Association Studies Reveal Genomic Regions Associated With the Response of Wheat (Triticum aestivum L.) to Mycorrhizae Under Drought Stress Conditions.pdf
Seagrasses are one of the most productive and economically important habitats in the coastal zone, but they are disappearing at an alarming rate, with more than half the worlds seagrass area lost since the 1990s. They now face serious threat from climate change, and there is much current speculation over whether they will survive the coming decades. The future of seagrasses depends on their ability to recover and adapt to environmental change-i.e. their resilience. Key to this, is understanding the role that genetic diversity plays in the resilience of this highly clonal group of species. To investigate population structure, genetic diversity, mating system (sexual versus asexual reproduction) and patterns of connectivity, we isolated and characterised 23 microsatellite loci using next generation sequencing for the Australian seagrass species, Zostera muelleri (syn. Z. capricorni), which is regarded as a globally significant congeneric species. Loci were tested for levels of variation based ...
An experimental procedure using biotin-labelled probes and streptavidin-bound magnetic beads (FIASCO) was used to produce a microsatellite-enriched library for the collembolan Orchesella villosa. PCR primers were successfully constructed for seven loci containing, respectively, five pure, one interrupted, and one compound dinucleotide microsatellite repeats. As a preliminary test of their variability, we investigated 15 individuals from 5 locations inside a dismissed mining area in southern Tuscany. All microsatellite loci showed high levels of polymorphism. The mean number of different alleles at each locus across populations was 10.1 and observed heterozygosity per locus was 0.13-0.86. Only 2 out of the 7 loci appeared to be in Hardy-Weinberg equilibrium. The potential application of these loci to test the effects of environmental contamination on the genetic structure of exposed populations is discussed.. ...
More than 20 genetic loci have been associated with risk for Alzheimers disease (AD), but reported genome-wide significant loci do not account for all the estimated heritability and provide little information about underlying biological mechanisms. Genetic studies using intermediate quantitative traits such as biomarkers, or endophenotypes, benefit from increased statistical power to identify variants that may not pass the stringent multiple test correction in case-control studies. Endophenotypes also contain additional information helpful for identifying variants and genes associated with other aspects of disease, such as rate of progression or onset, and provide context to interpret the results from genome-wide association studies (GWAS). We conducted GWAS of amyloid beta (Aβ42), tau, and phosphorylated tau (ptau181) levels in cerebrospinal fluid (CSF) from 3146 participants across nine studies to identify novel variants associated with AD. Five genome-wide significant loci (two novel) were ...
The genome-wide association study (GWAS) publications listed here include a primary GWAS analysis, defined as array-based genotyping and analysis of 100,000+ pre-QC SNPs selected to tag variation across the genome and without regard to gene content. GWAS data from published studies which are incorporated into new GWAS analyses are eligible, provided they meet the other criteria. Studies imputing sequencing data to genotyping arrays are eligible as long as the arrays include sufficient genome-wide coverage so that the post-imputation analysis meets the definition of a GWAS analysis, as described above. Customized gene-based arrays without a clearly described GWAS backbone, including those selected to replicate published GWAS findings (e.g., Metabochip, Immunochip, etc.) are not eligible. Publications are organized from most to least recent date of publication, indexing from online publication if available. Studies are identified through weekly PubMed literature searches, daily NIH-distributed ...
The genome-wide association study (GWAS) publications listed here include a primary GWAS analysis, defined as array-based genotyping and analysis of 100,000+ pre-QC SNPs selected to tag variation across the genome and without regard to gene content. GWAS data from published studies which are incorporated into new GWAS analyses are eligible, provided they meet the other criteria. Studies imputing sequencing data to genotyping arrays are eligible as long as the arrays include sufficient genome-wide coverage so that the post-imputation analysis meets the definition of a GWAS analysis, as described above. Customized gene-based arrays without a clearly described GWAS backbone, including those selected to replicate published GWAS findings (e.g., Metabochip, Immunochip, etc.) are not eligible. Publications are organized from most to least recent date of publication, indexing from online publication if available. Studies are identified through weekly PubMed literature searches, daily NIH-distributed ...
Candidate gene and genome-wide association studies (GWAS) have identified 15 independent genomic regions associated with bladder cancer risk. In search for additional susceptibility variants, we followed up on four promising single-nucleotide polymorphisms (SNPs) that had not achieved genome-wide significance in 6911 cases and 11 814 controls (rs6104690, rs4510656, rs5003154 and rs4907479, P | 1 × 10(-6)), using additional data from existing GWAS datasets and targeted genotyping for studies that did not have GWAS data. In a combined analysis, which included data on up to 15 058 cases and 286 270 controls, two SNPs achieved genome-wide statistical significance: rs6104690 in a gene desert at 20p12.2 (P = 2.19 × 10(-11)) and rs4907479 within the MCF2L gene at 13q34 (P = 3.3 × 10(-10)). Imputation and fine-mapping analyses were performed in these two regions for a subset of 5551 bladder cancer cases and 10 242 controls. Analyses at the 13q34 region suggest a single signal marked by rs4907479. In contrast
The shrimp Nematocarcinus lanceopes Bate, 1888 is found in the deep sea around Antarctica and sub-Antarctic islands. Previous studies on mitochondrial data and species distribution models provided evidence for a homogenous circum-Antarctic population of N. lanceopes. However, to analyze the fine-scale population genetic structure and to examine influences of abiotic environmental conditions on population composition and genetic diversity, a set of fast evolving nuclear microsatellite markers is required. We report the isolation and characterization of nine polymorphic microsatellite markers from the Antarctic deep-sea shrimp species Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). Microsatellite markers were screened in 55 individuals from different locations around the Antarctic continent. All markers were polymorphic with 9 to 25 alleles per locus. The observed heterozygosity ranged from 0.545 to 0.927 and the expected heterozygosity from 0.549 to 0.934. The reported markers provide a novel
The SSR enriched library was constructed from the genotype TMV2 following by modified method of Fischer and Bachmann [23]. This library was enriched for CA and CT SSR repeat motifs. From this library, 3,072 clones were picked from 32 96-well plates. Hybridization of these clones with digoxigenin-labeled SSR probes (CA and CT) provided 720 (23.4%) putatively positive clones. Sequencing of these clones indicated the insert size in the range of 50 bp to 792 bp with an average size of 309 bp. Majority of clones (43.9%) contained the insert of moderate size (200 bp-400 bp) while 34.6% clones contained small inserts (50 bp-200 bp) and 21.5% clones contained inserts of , 500 bp.. Analysis of sequence data mentioned above with Tandem Repeat Finder (TRF) had 490 (68%) clones which contained one or more SSRs. The efficiency of the enrichment procedure for the constructed library was higher as compared to other SSR isolation studies of groundnut. Like the present study, 61% of clones were found to contain ...
Thirteen new microsatellite loci were isolated and tested on two land snail species, Trochulus villosus and T. sericeus (Pulmonata: Hygromiidae), resulting in a set of eight polymorphic markers for each species. The expected heterozygosity was high for all loci and species (between 0.616 and 0.944). Such levels of variability will allow detailed insights into the population genetic structure of some Trochulus species.
Only two genome-wide significant loci associated with longevity have been identified so far, probably because of insufficient sample sizes of centenarians, whose genomes may harbor genetic variants associated with health and longevity. Here we report a genome-wide association study (GWAS) of Han Chinese with a sample size 2.7 times the largest previously published GWAS on centenarians. We identified 11 independent loci associated with longevity replicated in Southern-Northern regions of China, including two novel loci (rs2069837-IL6; rs2440012-ANKRD20A9P) with genome-wide significance and the rest with suggestive significance (P | 3.65 × 10−5). Eight independent SNPs overlapped across Han Chinese, European and U.S. populations, and APOE and 5q33.3 were replicated as longevity loci. Integrated analysis indicates four pathways (starch, sucrose and xenobiotic metabolism; immune response and inflammation; MAPK; calcium signaling) highly associated with longevity (P ≤ 0.006) in Han Chinese. The
Microsatellite markers from a transcriptome sequence library were initially isolated, and their genetic variation was characterized in a wild population of the mud crab (Scylla paramamosain). We then tested the association between these microsatellite markers and the growth performance of S. paramamosain. A total of 129 polymorphic microsatellite markers were identified, with an observed heterozygosity ranging from 0.19 to 1.00 per locus, an expected heterozygosity ranging from 0.23 to 0.96 per locus, and a polymorphism information content (PIC) ranging from 0.21 to 0.95 per locus. Of these microsatellite markers, 30 showed polymorphism in 96 full-sib individuals of a first generation family. Statistical analysis indicated that three microsatellite markers were significantly associated with 12 growth traits of S. paramamosain. Of these three markers, locus Scpa36 was significantly associated with eight growth traits, namely, carapace length, abdomen width (AW), body height (BH), fixed finger length of
Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q , 0.05). Loci influencing fasting insulin concentration showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional analysis of these newly discovered loci will further improve our understanding of glycemic control ...
Most genome-wide association studies have been of European individuals, even though most genetic variation in humans is seen only in non-European samples. To search for novel loci associated with blood lipid levels and clarify the mechanism of action at previously identified lipid loci, we used an exome array to examine protein-coding genetic variants in 47,532 East Asian individuals. We identified 255 variants at 41 loci that reached chip-wide significance, including 3 novel loci and 14 East Asian-specific coding variant associations. After a meta-analysis including >300,000 European samples, we identified an additional nine novel loci. Sixteen genes were identified by protein-altering variants in both East Asians and Europeans, and thus are likely to be functional genes. Our data demonstrate that most of the low-frequency or rare coding variants associated with lipids are population specific, and that examining genomic data across diverse ancestries may facilitate the identification of ...
Author Summary We conducted a large genome-wide association study (GWAS) of Parkinsons disease (PD) with over 3,400 cases and 29,000 controls (the largest single PD GWAS cohort to date). We report two novel genetic associations and replicate a total of twenty previously described associations, showing that there are now many solid genetic factors underlying PD. We also estimate that genetic factors explain at least one-fourth of the variation in PD liability, of which currently discovered factors only explain a small fraction (6%-7%). Together, these results expand the set of genetic factors discovered to date and imply that many more associations remain to be found. Unlike traditional studies, participation in this study took place completely online, using a collection of cases recruited primarily via PD mailing lists and controls derived from the customer base of the personal genetics company 23andMe. Our study thus illustrates the ability of web-based methods for enrollment and data collection to
The vast majority of breast cancer-associated variants identified by genome-wide association studies (GWAS) are located to non-protein coding genomic regions. Although some have been shown to regulate the expression of specific genes, novel approaches to elucidate the in vivo mechanisms underlying such breast cancer susceptibility loci are needed. The gene desert located on human chromosomal band 8q24, proximal to MYC and PVT1, and distal to FAM84B, harbors 2 common, low-penetrance breast cancer variants. We generated a megadeletion mouse model lacking 430 Kb of sequence orthologous to the breast cancer-associated locus of the 8q24 gene desert. Homozygous megadeletion mice are viable, fertile, lactate sufficiently to nourish their pups, but maintain a 10% lower body weight mainly due to decreased adiposity. We found that the mutation altered mammary gland development, resulting in less branch points, terminal end buds and altered luminal/basal ratio. Using a reciprocal mammary gland ...
We identified two new genomic loci associated with paediatric obesity on chromosomes 1q43-q44 and 8p23.1 by a meta-analysis of two GWAS for early onset extreme obesity with a total 2,258 individuals of European origin. In addition, we confirmed the three known loci FTO, MC4R and TMEM18 using a hypothesis-free step-wise design. Leaving the hypothesis-free approach and focussing on known GWAS-based candidate markers, we were able to substantiate another four loci (NEGR1, SEC16B, BDNF and BCDIN3D) of the 16 obesity loci previously detected in GWAS [6], [9], [13], [14]. Thus, we demonstrate that the currently known major common variants related to obesity overlap to a substantial degree between children and adults confirming previous observations for FTO, MC4R, TMEM18, NEGR1 [2], [6], [14] and extending this observation to SEC16B, BDNF and BCDIN3D; [13], [14]. As our meta-analysis includes data from Meyre et al. [9] an independent well-powered replication of NPC1, MAF and PTER was not possible ...
Access to high-quality and safe food is a basic need in our community and, consequently, the European Union has defined maximum residue levels (MRLs) for a number of antibacterial compounds. However, despite the obvious demand for quantitative multi-residue detection methods that can be carried out on a rout
With the detailed genomic information that is now becoming available, we have a plethora of data that allows researchers to address questions in a variety of areas. Genome-wide association studies (GWAS) have become a vital approach to identify candidate regions associated with complex diseases in
The present study deals with the assessment of genetic diversity using microsatellite marker in the fish Labeo gonius from Nanak Sagar and Dhaura reservoirs of Uttarakhand having different morpho-edhaphic features and self- recruiting populations of this fish. These reservoirs are distantly located and distinctly separated without any connection having negligible possibility of gene exchange with each other. Total 12 cross amplified microsatellite primers after using software Primer-BLAST and Primer-3 were screened in all 100 DNA samples of fish collected from both the reservoirs. 12 cross amplified microsatellite primers were screened and successfully amplified. After PCR amplification of microsatellite loci and performing native PAGE using amplified DNA samples as above, POP GENE Version 1.32 was used to calculate Neis observed heterozygosity, expected heterozygosity, Neis genetic diversity, Fixation index (Fis) and Shannons information index (SI) and genetic variability indices viz. Gene flow(Nm),
Skol, A. D., Scott, L. J., Abecasis, G. R. and Boehnke, M. (2007), Optimal designs for two-stage genome-wide association studies. Genet. Epidemiol., 31: 776-788. doi: 10.1002/gepi.20240 ...
The igvR package provides easy programmic access in R to the web-based javascript library igv.js in order to create and display genome tracks in its richly interactive web browser visual interface. I am grateful to Jim Robinson, Douglass Turner and colleagues for their fine work.. We introduce igvR via a case study of genetic variants associated with Alzheimers Disease as described in the 2014 Nature Genetics paper. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimers disease1. Theses 11 loci bring the total susceptibility loci count to 20, of which MEF2C is one. We focus on a 1 megabase region surrounding the MEF2C gene which contains 208 variants whose presence is associated with the expression of MEF2C in 17,008 Alzheimers disease cases and 37,154 controls. Interestingly, these variants do not occur in coding regions of the gene. Some possible insight into their function - of a highly speculative and preliminary sort - is provided by this case study. We ...
SHETE, SANJAY... A Genome-Wide Association Study Identifies Two Novel Susceptible Regions for Squamous Cell Carcinoma of the Head and Neck. Cancer Research 80 n.12 p. 2451-2460 JUN 15 2020. Journal article.
Genome-wide meta-analyses of breast, ovarian, and prostate cancer association studies identify multiple new susceptibility loci shared by at least two cancer types
Zeng, C., Guo, X., Long, J., Kuchenbaecker, K.B., Droit, A., Michailidou, K., Ghoussaini, M., Kar, S., Freeman, A., Hopper, J.L., Milne, R.L., Bolla, M.K., Wang, Q., Dennis, J., Agata, S., Ahmed, S., Aittomaki, K., Andrulis, I.L., Anton-Culver, H., Antonenkova, N.N., Arason, A., Arndt, V., Arun, B.K., Arver, B., Bacot, F., Barrowdale, D., Baynes, C., Beeghly-Fadiel, A., Benitez, J., Bermisheva, M., Blomqvist, C., Blot, W.J., Bogdanova, N.V., Bojesen, S.E., Bonanni, B., Borresen-Dale, A.-L., Brand, J.S., Brauch, H., Brennan, P., Brenner, H., Broeks, A., Brüning, T., Burwinkel, B., Buys, S.S., Cai, Q., Caldes, T., Campbell, I., Carpenter, J., Chang-Claude, J., Choi, J.Y., Claes, K.B.M., Clarke, C., Cox, A., Cross, S.S., Czene, K., Daly, M.B., de la Hoya, M., De Leeneer, K., Devilee, P., Diez, O., Domchek, S.M., Doody, M.M., Dorfling, C.M., Dörk, T., Dos Santos Silva, I., Dumont, M., Dwek, M., Dworniczak, B., Egan, K.M., Eilber, U., Einbeigi, Z., Ejlertsen, B., Ellis, S., Frost, D., Lalloo, F., ...
Authors: Kunkle BW, Grenier-Boley B, Sims R, Bis JC, Damotte V, Naj AC, Boland A, Vronskaya M, van der Lee SJ, Amlie-Wolf A, Bellenguez C, Frizatti A, Chouraki V, Martin ER, Sleegers K, Badarinarayan N, Jakobsdottir J, Hamilton-Nelson KL, Moreno-Grau S, Olaso R, Raybould R, Chen Y, Kuzma AB, Hiltunen M, Morgan T, Ahmad S, Vardarajan BN, Epelbaum J, Hoffmann P, Boada M, Beecham GW, Garnier JG, Harold D, Fitzpatrick AL, Valladares O, Moutet ML, Gerrish A, Smith AV, Qu L, Bacq D, Denning N, Jian X, Zhao Y, Del Zompo M, Fox NC, Choi SH, Mateo I, Hughes JT, Adams HH, Malamon J, Sanchez-Garcia F, Patel Y, Brody JA, Dombroski BA, Naranjo MCD, Daniilidou M, Eiriksdottir G, Mukherjee S, Wallon D, Uphill J, Aspelund T, Cantwell LB, Garzia F, Galimberti D, Hofer E, Butkiewicz M, Fin B, Scarpini E, Sarnowski C, Bush WS, Meslage S, Kornhuber J, White CC, Song Y, Barber RC, Engelborghs S, Sordon S, Voijnovic D, Adams PM, Vandenberghe R, Mayhaus M, Cupples LA, Albert MS, De Deyn PP, Gu W, Himali JJ, Beekly D, ...
Chauhan G., Arnold CR., Chu AY., Fornage M., Reyahi A., Bis JC., Havulinna AS., Sargurupremraj M., Smith AV., Adams HHH., Choi SH., Pulit SL., Trompet S., Garcia ME., Manichaikul A., Teumer A., Gustafsson S., Bartz TM., Bellenguez C., Vidal JS., Jian X., Kjartansson O., Wiggins KL., Satizabal CL., Xue F., Ripatti S., Liu Y., Deelen J., den Hoed M., Bevan S., Hopewell JC., Malik R., Heckbert SR., Rice K., Smith NL., Levi C., Sharma P., Sudlow CLM., Nik AM., Cole JW., Schmidt R., Meschia J., Thijs V., Lindgren A., Melander O., Grewal RP., Sacco RL., Rundek T., Rothwell PM., Arnett DK., Jern C., Johnson JA., Benavente OR., Wassertheil-Smoller S., Lee J-M., Wong Q., Aparicio HJ., Engelter ST., Kloss M., Leys D., Pezzini A., Buring JE., Ridker PM., Berr C., Dartigues J-F., Hamsten A., Magnusson PK., Traylor M., Pedersen NL., Lannfelt L., Lindgren L., Lindgren CM., Morris AP., Jimenez-Conde J., Montaner J., Radmanesh F., Slowik A., Woo D., Hofman A., Koudstaal PJ., Portegies MLP., Uitterlinden AG., de ...
A genome-wide association study on hundreds of thousands of women with or without breast cancer implicated 32 new risk loci, including sites associated with specific subtypes.
Non-coding RNAs constitute almost 98% of the human genome. Long non-coding RNA (lnc RNA) is a large class of this family where the RNA sequences are more than 200 nucleotides long and do not encode for proteins.
TY - JOUR. T1 - IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes. AU - Momozawa, Yukihide. AU - Dmitrieva, Julia. AU - Theatre, Emilie. AU - Deffontaine, Valerie. AU - Rahmouni, Souad. AU - Charloteaux, Benoit. AU - Crins, Francois. AU - Docampo, Elisa. AU - Elansary, Mahmoud. AU - Gori, Ann-Stephan. AU - Lecut, Christelle. AU - Mariman, Rob. AU - Mni, Myriam. AU - Oury, Cecile. AU - Altukhov, Ilya. AU - Alexeev, Dmitry. AU - Aulchenko, Yuri. AU - Amininejad, Leila. AU - Bouma, Gerd. AU - Hoentjen, Frank. AU - Lowenberg, Mark. AU - Oldenburg, Bas. AU - Pierik, Marieke J.. AU - vander Meulen-de Jong, Andrea E.. AU - van der Woude, C. Janneke. AU - Visschedijk, Marijn C.. AU - Lathrop, Mark. AU - Hugot, Jean-Pierre. AU - Weersma, Rinse K.. AU - De Vos, Martine. AU - Franchimont, Denis. AU - Vermeire, Severine. AU - Kubo, Michiaki. AU - Louis, Edouard. AU - Georges, Michel. AU - Abraham, Clara. AU - Achkar, Jean-Paul. AU - Ahmad, Tariq. AU - ...