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Tilhou N, Kissing Kucek L, Carr B, Douglas J, Englert J, Ali S, Raasch J, Bhamidimarri S, Mirsky S, Monteros MJ, Hayes R, Riday H. Pooled DNA sequencing in hairy vetch ( Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence. FRONTIERS IN PLANT SCIENCE 2024; 15:1384596. [PMID: 38638346 PMCID: PMC11024373 DOI: 10.3389/fpls.2024.1384596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Introduction Hairy vetch (Vicia villosa Roth) is a promising legume cover crop, but its use is limited by high rates of pod dehiscence and seed dormancy. Methods We used phenotypically contrasting pooled DNA samples (n=24 with 29-74 individuals per sample) from an ongoing cover crop breeding program across four environments (site-year combinations: Maryland 2020, Maryland 2022, Wisconsin 2021, Wisconsin 2022) to find genetic associations and genomic prediction accuracies for pod dehiscence and seed dormancy. We also combined pooled DNA sample genetic association results with the results of a prior genome-wide association study. Results and discussion Genomic prediction resulted in positive predictive abilities for both traits between environments and with an independent dataset (0.34-0.50), but reduced predictive ability for DNA pools with divergent seed dormancy in the Maryland environments (0.07-0.15). The pooled DNA samples found six significant (false discovery rate q-value<0.01) quantitative trait loci (QTL) for seed dormancy and four significant QTL for pod dehiscence. Unfortunately, the minor alleles of the pod dehiscence QTL increased the rate of pod dehiscence and are not useful for marker-assisted selection. When combined with a prior association study, sixteen seed dormancy QTL and zero pod dehiscence QTL were significant. Combining the association studies did not increase the detection of useful QTL.
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Affiliation(s)
- Neal Tilhou
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - Lisa Kissing Kucek
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - Brandon Carr
- United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), James E. “Bud” Smith Plant Materials Center, Knox City, TX, United States
| | - Joel Douglas
- United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), Central National Technology Support Center, Fort Worth, TX, United States
| | - John Englert
- United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), National Plant Materials Program, Washington, DC, United States
| | - Shahjahan Ali
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - John Raasch
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | | | - Steven Mirsky
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Maria J. Monteros
- Bayer Crop Science, North America (NA) Breeding, Chesterfield, MO, United States
| | - Ryan Hayes
- Forage Seed and Cereal Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Corvallis, OR, United States
| | - Heathcliffe Riday
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
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Vargas Jurado N, Kuehn LA, Keele JW, Lewis RM. Accuracy of GEBV of sires based on pooled allele frequency of their progeny. G3-GENES GENOMES GENETICS 2021; 11:6321233. [PMID: 34510188 DOI: 10.1093/g3journal/jkab231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 11/12/2022]
Abstract
Despite decreasing genotyping costs, in some cases individually genotyping animals is not economically feasible (e.g., in small ruminants). An alternative is to pool DNA, using the pooled allele frequency (PAF) to garner information on performance. Still, the use of PAF for prediction (estimation of genomic breeding values; GEBVs) has been limited. Two potential sources of error on accuracy of GEBV of sires, obtained from PAF of their progeny themselves lacking pedigree information, were tested: (i) pool construction error (unequal contribution of DNA from animals in pools), and (ii) technical error (variability when reading the array). Pooling design (random, extremes, K-means), pool size (5, 10, 25, 50, and 100 individuals), and selection scenario (random, phenotypic) also were considered. These factors were tested by simulating a sheep population. Accuracy of GEBV-the correlation between true and estimated values-was not substantially affected by pool construction or technical error, or selection scenario. A significant interaction, however, between pool size and design was found. Still, regardless of design, mean accuracy was higher for pools of 10 or less individuals. Mean accuracy of GEBV was 0.174 (SE 0.001) for random pooling, and 0.704 (SE 0.004) and 0.696 (SE 0.004) for extreme and K-means pooling, respectively. Non-random pooling resulted in moderate accuracy of GEBV. Overall, pooled genotypes can be used in conjunction with individual genotypes of sires for moderately accurate predictions of their genetic merit with little effect of pool construction or technical error.
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Affiliation(s)
| | - Larry A Kuehn
- Genetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE 68933, USA
| | - John W Keele
- Genetics, Breeding, and Animal Health Research Unit, U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE 68933, USA
| | - Ronald M Lewis
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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Canut MI, Villa O, Kudsieh B, Mattlin H, Banchs I, González JR, Armengol L, Casaroli-Marano RP. MLIP genotype as a predictor of pharmacological response in primary open-angle glaucoma and ocular hypertension. Sci Rep 2021; 11:1583. [PMID: 33452295 PMCID: PMC7810753 DOI: 10.1038/s41598-020-80954-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/24/2020] [Indexed: 11/20/2022] Open
Abstract
Predicting the therapeutic response to ocular hypotensive drugs is crucial for the clinical treatment and management of glaucoma. Our aim was to identify a possible genetic contribution to the response to current pharmacological treatments of choice in a white Mediterranean population with primary open-angle glaucoma (POAG) or ocular hypertension (OH). We conducted a prospective, controlled, randomized, partial crossover study that included 151 patients of both genders, aged 18 years and older, diagnosed with and requiring pharmacological treatment for POAG or OH in one or both eyes. We sought to identify copy number variants (CNVs) associated with differences in pharmacological response, using a DNA pooling strategy of carefully phenotyped treatment responders and non-responders, treated for a minimum of 6 weeks with a beta-blocker (timolol maleate) and/or prostaglandin analog (latanoprost). Diurnal intraocular pressure reduction and comparative genome wide CNVs were analyzed. Our finding that copy number alleles of an intronic portion of the MLIP gene is a predictor of pharmacological response to beta blockers and prostaglandin analogs could be used as a biomarker to guide first-tier POAG and OH treatment. Our finding improves understanding of the genetic factors modulating pharmacological response in POAG and OH, and represents an important contribution to the establishment of a personalized approach to the treatment of glaucoma.
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Affiliation(s)
- María I Canut
- Centro de Oftalmología Barraquer, Instituto Universitario Barraquer (UAB), Barcelona, Spain
| | - Olaya Villa
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Spain
| | | | - Heidi Mattlin
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Spain
| | - Isabel Banchs
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Spain
| | - Juan R González
- Barcelona Institute for Global Health (ISGlobal) and Centro de Investigación Biomédica en Red en Epidemiologia Y Salud Pública (CIBERESP), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lluís Armengol
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Spain.
| | - Ricardo P Casaroli-Marano
- Department of Surgery, School of Medicine and Health Sciences and Hospital Clinic de Barcelona (IDIBAPS), University of Barcelona, Calle Sabino de Arana 1 (2nd floor, Ophthalmology), 08028, Barcelona, Spain. .,Institute of Biomedical Research Sant Pau (IIB-Sant Pau, SGR1113) and Barcelona Tissue Bank (BST), Barcelona, Spain.
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Identification of novel alleles associated with insulin resistance in childhood obesity using pooled-DNA genome-wide association study approach. Int J Obes (Lond) 2017; 42:686-695. [PMID: 29188820 PMCID: PMC5984073 DOI: 10.1038/ijo.2017.293] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 10/05/2017] [Accepted: 11/09/2017] [Indexed: 02/07/2023]
Abstract
Background: Recently, we witnessed great progress in the discovery of genetic variants associated with obesity and type 2 diabetes (T2D), especially in adults. Much less is known regarding genetic variants associated with insulin resistance (IR). We hypothesized that novel IR genes could be efficiently detected in a population of obese children and adolescents who may not exhibit comorbidities and other confounding factors. Objectives: This study aimed to determine whether a genome-wide association study (GWAS), using a DNA-pooling approach, could identify novel genes associated with IR. Subjects: The pooled-DNA GWAS analysis included Slovenian obese children and adolescents with and without IR matched for body mass index, gender and age. A replication study was conducted in another independent cohort with or without IR. Methods: For the pooled-DNA GWAS, we used HumanOmni5-Quad SNP array (Illumina). Allele frequency distributions were compared with modified t-tests and χ2-tests and ranked using PLINK. Top single nucleotide polymorphisms (SNPs) were validated using individual genotyping by high-resolution melting analysis and TaqMan assay. Results: We identified five top-ranking SNPs from the pooled-DNA GWAS analysis within the ECE1, IL1R2, GNPDA1, HLA-J and PYGB loci. All except SNP rs9261108 (HLA-J locus) were confirmed in the validation phase using individual genotyping. The SNP rs2258617 within PYGB remained statistically significant for both recessive and additive models in both cohorts and in a merged analysis of both cohorts and present the strongest novel candidate gene for IR. Conclusion: We report for the first time a pooled-DNA GWAS approach to identify five novel SNPs or genes for IR in a paediatric population. The four loci confirmed in the second validation phase study warrant further studies, especially the strongest SNP rs2258617 within PYGB, and provide targets for further basic research of IR mechanisms and for the development of potential new IR and T2D therapies.
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Fowdar JY, Grealy R, Lu Y, Griffiths LR. A genome-wide association study of essential hypertension in an Australian population using a DNA pooling approach. Mol Genet Genomics 2016; 292:307-324. [PMID: 27866268 DOI: 10.1007/s00438-016-1274-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/10/2016] [Indexed: 01/11/2023]
Abstract
Despite the success of genome-wide association studies (GWAS) in detecting genetic loci involved in complex traits, few susceptibility genes have been detected for essential hypertension (EH). We aimed to use pooled DNA GWAS approach to identify and validate novel genomic loci underlying EH susceptibility in an Australian case-control population. Blood samples and questionnaires detailing medical history, blood pressure, and prescribed medications were collected for 409 hypertensives and 409 age-, sex- and ethnicity-matched normotensive controls. Case and control DNA were pooled in quadruplicate and hybridized to Illumina 1 M-Duo arrays. Allele frequencies agreed with those reported in reference data and known EH association signals were represented in the top-ranked SNPs more frequently than expected by chance. Validation showed that pooled DNA GWAS gave reliable estimates of case and control allele frequencies. Although no markers reached Bonferroni-corrected genome-wide significance levels (5.0 × 10-8), the top marker rs34870220 near ASGR1 approached significance (p = 4.32 × 10-7), as did several candidate loci (p < 1 × 10-6) on chromosomes 2, 4, 6, 9, 12, and 17. Four markers (located in or near genes NHSL1, NKFB1, GLI2, and LRRC10) from the top ten ranked SNPs were individually genotyped in pool samples and were tested for association between cases and controls using the χ 2 test. Of these, rs1599961 (NFKB1) and rs12711538 (GLI2) showed significant difference between cases and controls (p < 0.01). Additionally, four top-ranking markers within NFKB1 were found to be in LD, suggesting a single strong association signal for this gene.
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Affiliation(s)
- Javed Y Fowdar
- School of Medical Science, Griffith University, Gold Coast, Australia
| | - Rebecca Grealy
- School of Medical Science, Griffith University, Gold Coast, Australia
| | - Yi Lu
- Genetic Epidemiology Department, Queensland Institute of Medical Research, Brisbane, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, Brisbane, QLD, 4059, Australia.
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Janicki PK, Alexander GM, Eckert J, Postula M, Schwartzman RJ. Analysis of Common Single Nucleotide Polymorphisms in Complex Regional Pain Syndrome: Genome Wide Association Study Approach and Pooled DNA Strategy. PAIN MEDICINE 2016; 17:2344-2352. [PMID: 28025368 DOI: 10.1093/pm/pnw133] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVE The objective of this study was to use a genome-wide association (GWAS) approach and pooled DNA strategy to search for new genomic loci associated with complex regional pain syndrome (CRPS). DESIGN The study cohort consisted of 230 patients with established diagnosis of CRPS. The control group consisted of 230 age- and gender-matched subjects without chronic pain. We tested the association of common single nucleotide polymorphisms (SNPs), genotyped using a high-density microarray platform, with CRPS phenotype. This was followed by individual genotyping of the most significant SNPs identified in the microarray genomic scan, in both original discovery (N = 115) and independent verification (N = 115) groups of patients with CRPS, as well as in the appropriate matched control subjects. RESULTS The results of our study provide no support for the initial hypothesis of the existence of an association between any investigated genomic targets (including GWAS for all genomic loci available on the microarray, and focused scan of the HLA locus on chromosome 6) and CRPS phenotype. CONCLUSIONS Despite the fact that we interrogated about 83% of all of common SNPs in the human genome, we did not find evidence that any of the investigated common SNPs may be associated with CRPS phenotype.
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Affiliation(s)
- Piotr K Janicki
- *Department of Anesthesiology and Perioperative Medicine, Penn State Hershey College of Medicine, Hershey, Pennsylvania
| | | | - Jill Eckert
- *Department of Anesthesiology and Perioperative Medicine, Penn State Hershey College of Medicine, Hershey, Pennsylvania
| | - Marek Postula
- *Department of Anesthesiology and Perioperative Medicine, Penn State Hershey College of Medicine, Hershey, Pennsylvania
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Rahman A, Hellicar A, Smith D, Henshall JM. Allele frequency calibration for SNP based genotyping of DNA pools: A regression based local-global error fusion method. Comput Biol Med 2015; 61:48-55. [PMID: 25863000 DOI: 10.1016/j.compbiomed.2015.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 02/16/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND The costs associated with developing high density microarray technologies are prohibitive for genotyping animals when there is low economic value associated with a single animal (e.g. prawns). DNA pooling is an attempt to address this issue by combining multiple DNA samples prior to genotyping. Instead of genotyping the DNA samples of the individuals, a mixture of DNA samples (i.e. the pool) from the individuals is genotyped only once. This greatly reduces the cost of genotyping. Pooled samples are subject to greater genotyping inaccuracies than individual samples. Wrong genotyping will lead to wrong biological conclusions. It is thus required to calibrate the resulting genotypes (allele frequencies). METHODS We present a regression based approach to translate raw array output to allele frequency. During training, few pools and the individuals that constitute the pools are genotyped. Given the genotypes of individuals that constitute the pool, we compute the true allele frequency. We then train a regression algorithm to produce a mapping between the raw array outputs to the true allele frequency. We test the algorithm using pool samples withheld from the training set. During prediction, we use this map to genotype pools with no prior knowledge of the individuals constituting the pools. RESULTS AND DISCUSSION After data quality control we have available a dataset comprised of 912 pools. We estimate allele frequency using three approaches: the raw data, a commonly used piecewise linear transformation, and the proposed local-global learner fusion method. The resulting RMS errors for the three approaches are 0.135, 0.120, and 0.080 respectively.
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Affiliation(s)
- Ashfaqur Rahman
- Digital Productivity Flagship, CSIRO, Hobart, Tasmania, Australia.
| | - Andrew Hellicar
- Digital Productivity Flagship, CSIRO, Hobart, Tasmania, Australia
| | - Daniel Smith
- Digital Productivity Flagship, CSIRO, Hobart, Tasmania, Australia
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Shi M, Umbach DM, Weinberg CR. Disentangling pooled triad genotypes for association studies. Ann Hum Genet 2014; 78:345-56. [PMID: 24962618 DOI: 10.1111/ahg.12073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 05/05/2014] [Indexed: 11/30/2022]
Abstract
Association studies that genotype affected offspring and their parents (triads) offer robustness to genetic population structure while enabling assessments of maternal effects, parent-of-origin effects, and gene-by-environment interaction. We propose case-parents designs that use pooled DNA specimens to make economical use of limited available specimens. One can markedly reduce the number of genotyping assays required by randomly partitioning the case-parent triads into pooling sets of h triads each and creating three pools from every pooling set, one pool each for mothers, fathers, and offspring. Maximum-likelihood estimation of relative risk parameters proceeds via log-linear modeling using the expectation-maximization algorithm. The approach can assess offspring and maternal genetic effects and accommodate genotyping errors and missing genotypes. We compare the power of our proposed analysis for testing offspring and maternal genetic effects to that based on a difference approach and that of the gold standard based on individual genotypes, under a range of allele frequencies, missing parent proportions, and genotyping error rates. Power calculations show that the pooling strategies cause only modest reductions in power if genotyping errors are low, while reducing genotyping costs and conserving limited specimens.
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Affiliation(s)
- Min Shi
- Biostatistics Branch, NIEHS, NIH, DHHS, Research Triangle Park, NC, USA
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Earp MA, Kelemen LE, Magliocco AM, Swenerton KD, Chenevix-Trench G, Lu Y, Hein A, Ekici AB, Beckmann MW, Fasching PA, Lambrechts D, Despierre E, Vergote I, Lambrechts S, Doherty JA, Rossing MA, Chang-Claude J, Rudolph A, Friel G, Moysich KB, Odunsi K, Sucheston-Campbell L, Lurie G, Goodman MT, Carney ME, Thompson PJ, Runnebaum IB, Dürst M, Hillemanns P, Dörk T, Antonenkova N, Bogdanova N, Leminen A, Nevanlinna H, Pelttari LM, Butzow R, Bunker CH, Modugno F, Edwards RP, Ness RB, du Bois A, Heitz F, Schwaab I, Harter P, Karlan BY, Walsh C, Lester J, Jensen A, Kjær SK, Høgdall CK, Høgdall E, Lundvall L, Sellers TA, Fridley BL, Goode EL, Cunningham JM, Vierkant RA, Giles GG, Baglietto L, Severi G, Southey MC, Liang D, Wu X, Lu K, Hildebrandt MAT, Levine DA, Bisogna M, Schildkraut JM, Iversen ES, Weber RP, Berchuck A, Cramer DW, Terry KL, Poole EM, Tworoger SS, Bandera EV, Chandran U, Orlow I, Olson SH, Wik E, Salvesen HB, Bjorge L, Halle MK, van Altena AM, Aben KKH, Kiemeney LA, Massuger LFAG, Pejovic T, Bean YT, Cybulski C, Gronwald J, Lubinski J, Wentzensen N, Brinton LA, Lissowska J, Garcia-Closas M, Dicks E, Dennis J, Easton DF, Song H, Tyrer JP, Pharoah PDP, Eccles D, Campbell IG, Whittemore AS, McGuire V, Sieh W, Rothstein JH, Flanagan JM, Paul J, Brown R, Phelan CM, Risch HA, McLaughlin JR, Narod SA, Ziogas A, Anton-Culver H, Gentry-Maharaj A, Menon U, Gayther SA, Ramus SJ, Wu AH, Pearce CL, Pike MC, Dansonka-Mieszkowska A, Rzepecka IK, Szafron LM, Kupryjanczyk J, Cook LS, Le ND, Brooks-Wilson A. Genome-wide association study of subtype-specific epithelial ovarian cancer risk alleles using pooled DNA. Hum Genet 2014; 133:481-97. [PMID: 24190013 PMCID: PMC4063682 DOI: 10.1007/s00439-013-1383-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022]
Abstract
Epithelial ovarian cancer (EOC) is a heterogeneous cancer with both genetic and environmental risk factors. Variants influencing the risk of developing the less-common EOC subtypes have not been fully investigated. We performed a genome-wide association study (GWAS) of EOC according to subtype by pooling genomic DNA from 545 cases and 398 controls of European descent, and testing for allelic associations. We evaluated for replication 188 variants from the GWAS [56 variants for mucinous, 55 for endometrioid and clear cell, 53 for low-malignant potential (LMP) serous, and 24 for invasive serous EOC], selected using pre-defined criteria. Genotypes from 13,188 cases and 23,164 controls of European descent were used to perform unconditional logistic regression under the log-additive genetic model; odds ratios (OR) and 95 % confidence intervals are reported. Nine variants tagging six loci were associated with subtype-specific EOC risk at P < 0.05, and had an OR that agreed in direction of effect with the GWAS results. Several of these variants are in or near genes with a biological rationale for conferring EOC risk, including ZFP36L1 and RAD51B for mucinous EOC (rs17106154, OR = 1.17, P = 0.029, n = 1,483 cases), GRB10 for endometrioid and clear cell EOC (rs2190503, P = 0.014, n = 2,903 cases), and C22orf26/BPIL2 for LMP serous EOC (rs9609538, OR = 0.86, P = 0.0043, n = 892 cases). In analyses that included the 75 GWAS samples, the association between rs9609538 (OR = 0.84, P = 0.0007) and LMP serous EOC risk remained statistically significant at P < 0.0012 adjusted for multiple testing. Replication in additional samples will be important to verify these results for the less-common EOC subtypes.
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Affiliation(s)
- Madalene A Earp
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada,
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Rohrer GA, Rempel LA, Miles JR, Keele JW, Wiedmann RT, Vallet JL. Identifying genetic loci controlling neonatal passive transfer of immunity using a hybrid genotyping strategy. Anim Genet 2014; 45:340-9. [DOI: 10.1111/age.12131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2013] [Indexed: 11/28/2022]
Affiliation(s)
- G. A. Rohrer
- USDA; Agricultural Research Service; U.S. Meat Animal Research Center; PO Box 166 Clay Center NE 68933 USA
| | - L. A. Rempel
- USDA; Agricultural Research Service; U.S. Meat Animal Research Center; PO Box 166 Clay Center NE 68933 USA
| | - J. R. Miles
- USDA; Agricultural Research Service; U.S. Meat Animal Research Center; PO Box 166 Clay Center NE 68933 USA
| | - J. W. Keele
- USDA; Agricultural Research Service; U.S. Meat Animal Research Center; PO Box 166 Clay Center NE 68933 USA
| | - R. T. Wiedmann
- USDA; Agricultural Research Service; U.S. Meat Animal Research Center; PO Box 166 Clay Center NE 68933 USA
| | - J. L. Vallet
- USDA; Agricultural Research Service; U.S. Meat Animal Research Center; PO Box 166 Clay Center NE 68933 USA
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Cormier C, Mfuna Endam L, Filali-Mouhim A, Boisvert P, Boulet LP, Boulay ME, Vallée-Smedja S, Bossé Y, Desrosiers M. A pooling-based genomewide association study identifies genetic variants associated with Staphylococcus aureus colonization in chronic rhinosinusitis patients. Int Forum Allergy Rhinol 2014; 4:207-15. [PMID: 24431132 DOI: 10.1002/alr.21276] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 11/11/2013] [Accepted: 12/05/2013] [Indexed: 11/07/2022]
Abstract
BACKGROUND Staphylococcus aureus (S. aureus) has been implicated in the pathogenesis of chronic rhinosinusitis (CRS). However, host factors contributing to susceptibility to S. aureus colonization in CRS remain unknown. We wish to investigate, using a pooled genomewide association study (pGWAS), single-nucleotide polymorphisms (SNPs) associated with S. aureus carriage in CRS patients. METHODS An existing population of 408 CRS patients and 190 controls was prospectively recruited for genetic association studies. All CRS patients had an endoscopic swab culture as part of phenotyping. A pGWAS compared DNA pools from patients with and without S. aureus colonization using the Illumina HumanHap 1M BeadChip, which interrogates 1 million SNPs. Top-ranked SNPs associated with S. aureus colonization were selected according to biallelic differences and silhouette rank, and confirmed by individual genotyping using the Sequenom platform. PLINK software was used for genetic association tests. Ingenuity pathway analysis was used to identify canonical and signaling pathways enriched for genes neighboring associated SNPs, as well as identification of the underlying biological mechanisms. RESULTS Thirty-nine top priority SNPs were selected for individual genotyping. Out of 39 SNPs, 23 were associated (p < 0.05) with S. aureus colonization in CRS patients. These SNPs are located within or near 21 genes reported to be implicated in several diseases, endocytic internalization, and bacterial recognition. CONCLUSION These results suggest novel host genetic factors influencing susceptibility to S. aureus colonization in CRS. Identifying implicated mechanisms may offer new insights into pathogenesis of CRS.
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Affiliation(s)
- Chantale Cormier
- Department of Otolaryngology, Hôtel-Dieu Hospital, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
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12
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Mfuna Endam L, Filali-Mouhim A, Boisvert P, Boulet LP, Bossé Y, Desrosiers M. Genetic variations in taste receptors are associated with chronic rhinosinusitis: a replication study. Int Forum Allergy Rhinol 2014; 4:200-6. [PMID: 24415641 DOI: 10.1002/alr.21275] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 11/12/2013] [Accepted: 12/03/2013] [Indexed: 12/16/2022]
Abstract
BACKGROUND Recent evidence implicates polymorphisms of the bitter taste receptor TAS2R38 as defining characteristics in respiratory innate defense that may contribute to the complex genetic and environmental interactions predisposing to chronic rhinosinusitis (CRS). The purpose of this study was to (1) verify whether identified polymorphisms associated with respiratory infection in taste receptors replicate within our existing population of patients with CRS and (2) identify other taste receptors potentially associated with CRS. METHODS Pooling-based genomewide association studies (pGWAS) were previously performed on 2 populations of Canadian CRS patients (genetics of chronic rhinosinusitis 1, refractory CRS [GCRS1]; and genetics of chronic rhinosinusitis 2, CRS with nasal polyposis [GCRS2]) using the Illumina HumanHap 1-M chip. The pGWAS data were screened for polymorphisms in taste receptor genes. Single-nucleotide polymorphisms (SNPs) were considered replicated when the allele frequency differences were ≥10% in cases compared to controls. RESULTS The previously identified TAS2R38 coding SNP rs10246939 (I296V) was associated with CRS in both populations. The difference in allele frequency in cases compared to control subjects was 11% in GCRS1 and 15% in GCRS2. In addition, 3 previously undescribed missense variants were associated with CRS in our populations: 1 in the TAS2R13 gene (rs1015443), and the others in the TAS2R49 gene (rs12226920, rs12226919). CONCLUSION This study replicates previous work which showed that the coding SNP rs10246939 in the TAS2R38 gene is associated with CRS. Moreover, the results suggest that other taste receptors may be implicated in CRS. Further studies using individual genotyping and sequencing, and functional studies will provide more information about the implication of these genetic variants in CRS.
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Affiliation(s)
- Leandra Mfuna Endam
- Department of Otolaryngology, Hôtel-Dieu Hospital, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
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Ozerov M, Vasemägi A, Wennevik V, Diaz-Fernandez R, Kent M, Gilbey J, Prusov S, Niemelä E, Vähä JP. Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification. PLoS One 2013; 8:e82434. [PMID: 24358184 PMCID: PMC3864958 DOI: 10.1371/journal.pone.0082434] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 10/24/2013] [Indexed: 01/26/2023] Open
Abstract
Genetic stock identification (GSI) using molecular markers is an important tool for management of migratory species. Here, we tested a cost-effective alternative to individual genotyping, known as allelotyping, for identification of highly informative SNPs for accurate genetic stock identification. We estimated allele frequencies of 2880 SNPs from DNA pools of 23 Atlantic salmon populations using Illumina SNP-chip. We evaluated the performance of four common strategies (global F ST, pairwise F ST, Delta and outlier approach) for selection of the most informative set of SNPs and tested their effectiveness for GSI compared to random sets of SNP and microsatellite markers. For the majority of cases, SNPs selected using the outlier approach performed best followed by pairwise F ST and Delta methods. Overall, the selection procedure reduced the number of SNPs required for accurate GSI by up to 53% compared with randomly chosen SNPs. However, GSI accuracy was more affected by populations in the ascertainment group rather than the ranking method itself. We demonstrated for the first time the compatibility of different large-scale SNP datasets by compiling the largest population genetic dataset for Atlantic salmon to date. Finally, we showed an excellent performance of our top SNPs on an independent set of populations covering the main European distribution range of Atlantic salmon. Taken together, we demonstrate how combination of DNA pooling and SNP arrays can be applied for conservation and management of salmonids as well as other species.
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Affiliation(s)
- Mikhail Ozerov
- Kevo Subarctic Research Institute, University of Turku, Turku, Finland
| | - Anti Vasemägi
- Department of Biology, Division of Genetics and Physiology, University of Turku, Turku, Finland
- Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, Tartu, Estonia
| | - Vidar Wennevik
- Research group Population Genetics and Ecology, Institute of Marine Research, Bergen, Norway
| | | | - Matthew Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - John Gilbey
- Freshwater Laboratory, Marine Scotland, Faskally, Pitlochry, United Kingdom
| | - Sergey Prusov
- Freshwater Resources Laboratory, Knipovitch Polar Research Institute of Marine Fisheries and Oceanography, Murmansk, Russia
| | - Eero Niemelä
- Finnish Game and Fisheries Research Institute, Oulu, Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute, University of Turku, Turku, Finland
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Rahmani M, Earp MA, Ramezani Tehrani F, Ataee M, Wu J, Treml M, Nudischer R, P-Behnami S, Perry JRB, Murabito JM, Azizi F, Brooks-Wilson A. Shared genetic factors for age at natural menopause in Iranian and European women. Hum Reprod 2013; 28:1987-94. [PMID: 23592221 DOI: 10.1093/humrep/det106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
STUDY QUESTION Do differences in heritable genetic factors explain some of the difference in age at natural menopause (ANM) among populations? SUMMARY ANSWER One single nucleotide polymorphism (SNP)-ANM association (rs16991615) detected in European women was replicated in Iranian women. WHAT IS KNOWN ALREADY Genetics plays an important role in ANM, and well-powered genome-wide association studies (GWAS) of ANM performed in European women have discovered many statistically significant SNP-ANM associations. Average ANM varies by ethnicity, and population-specific differences in ANM-associated alleles may in part explain these differences. STUDY DESIGN, SIZE, DURATION After quality control procedures, 97 SNPs were analyzed in genotype data of 828 Iranian women who experienced natural menopause. SNP genotyping data were used to perform linear regression analyses with ANM as a quantitative trait. Study participants were drawn from the population-based Tehran Lipid and Glucose Study based in Tehran, Iran. This study was performed between February 2009 and March 2012. PARTICIPANTS/MATERIALS, SETTING AND METHODS Based on an ANM-GWAS literature review, eight SNPs at four loci previously associated with ANM in European women were tested for replication in Iranian women. Linear regression analyses were performed including (n = 828) and excluding (n = 783) women who experience premature ovarian failure (ANM before 40 years of age). In addition, to search for novel population-specific ANM risk alleles, a pool-based GWAS was performed using this collection of Iranian women. Two DNA pools were constructed and compared: an 'early' ANM pool (lower 20(th) percentile of menopause ages, 40-45 years, n = 165) and a 'late' ANM pool (upper 20(th) percentile of menopause ages, 54-65 years, n = 187). Each DNA pool was assayed on four Illumina Human1M-Duo arrays, and allele-based tests of association were used to rank SNPs. One hundred and two highly ranked SNPs were chosen for individual genotyping by Sequenom MassARRAY and association analysis in the Iranian women. MAIN RESULTS AND THE ROLE OF CHANCE One SNP-ANM association previously detected in European women was replicated in Iranian women (rs16991615; β = 1.07, standard error (SE): 0.49, P = 0.02). SNPs at the previously reported 19q13.42 and 6p24.2 loci also approached statistical significance and had consistent SNP effects (magnitude and direction) in Iranian women (rs1172822; β = -0.39, SE: 0.22, P = 0.08; and rs2153157, β = 0.41, SE: 0.21, P = 0.05). We found little evidence for novel SNP-ANM associations in Iranian women; no SNP selected based on the pool-based GWAS achieved genome-wide significance. LIMITATIONS, REASONS FOR CAUTION Due to small sample size this study was powered to reliably detect only moderate-to-large SNP effect sizes. This limited our ability to replicate many of the previously reported SNP-ANM risk alleles and to discover novel SNP-ANM associations' specific to the Iranian population. In performing our pool-based GWAS, a reduction in power was introduced relative to a conventional GWAS. WIDER IMPLICATIONS OF THE FINDINGS Our results imply that European and Iranian women share ANM-associated genetic variants. Our study was underpowered but for all SNPs tested the direction of the effect was consistent with data from the European study. Therefore, we anticipate that many (if not all) of the ANM-associated SNPs discovered in European women will replicate in Iranian women upon genotyping a sufficient number of women. Our data do not support the hypothesis that population-specific SNP-ANM associations explain population-specific differences in the mean ANM.
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Affiliation(s)
- Maziar Rahmani
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC, Canada
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Ozerov M, Vasemägi A, Wennevik V, Niemelä E, Prusov S, Kent M, Vähä JP. Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.). BMC Genomics 2013; 14:12. [PMID: 23324082 PMCID: PMC3575319 DOI: 10.1186/1471-2164-14-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 01/02/2013] [Indexed: 12/13/2022] Open
Abstract
Background New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS). However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salar L.) populations using an Illumina SNP-chip. Results In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF) close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r > 0.99) between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals) can provide accurate allele frequency estimates for a given sample. Conclusions Despite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost-efficient identification of informative markers for discrimination of populations at various geographical scales, as well as identification of loci controlling ecologically and economically important traits.
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Affiliation(s)
- Mikhail Ozerov
- Kevo Subarctic Research Institute, University of Turku, Turku 20014, Finland
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