1
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Pipal KV, Mamtani M, Patel AA, Jaiswal SG, Jaisinghani MT, Kulkarni H. Susceptibility Loci for Type 2 Diabetes in the Ethnically Endogamous Indian Sindhi Population: A Pooled Blood Genome-Wide Association Study. Genes (Basel) 2022; 13:1298. [PMID: 35893037 PMCID: PMC9331904 DOI: 10.3390/genes13081298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 12/10/2022] Open
Abstract
Type 2 diabetes (T2D) is a complex metabolic derangement that has a strong genetic basis. There is substantial population-specificity in the association of genetic variants with T2D. The Indian urban Sindhi population is at a high risk of T2D. The genetic basis of T2D in this population is unknown. We interrogated 28 pooled whole blood genomes of 1402 participants from the Diabetes In Sindhi Families In Nagpur (DISFIN) study using Illumina's Global Screening Array. From a total of 608,550 biallelic variants, 140 were significantly associated with T2D after adjusting for comorbidities, batch effects, pooling error, kinship status and pooling variation in a random effects multivariable logistic regression framework. Of the 102 well-characterized genes that these variants mapped onto, 70 genes have been previously reported to be associated with T2D to varying degrees with known functional relevance. Excluding open reading frames, intergenic non-coding elements and pseudogenes, our study identified 22 novel candidate genes in the Sindhi population studied. Our study thus points to the potential, interesting candidate genes associated with T2D in an ethnically endogamous population. These candidate genes need to be fully investigated in future studies.
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Affiliation(s)
- Kanchan V. Pipal
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
| | - Manju Mamtani
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
- M&H Research, LLC, San Antonio, TX 78249, USA
| | - Ashwini A. Patel
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
| | - Sujeet G. Jaiswal
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
| | - Manisha T. Jaisinghani
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
| | - Hemant Kulkarni
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
- M&H Research, LLC, San Antonio, TX 78249, USA
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2
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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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3
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Li J, Lee M, Davis BW, Lamichhaney S, Dorshorst BJ, Siegel PB, Andersson L. Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken. Mol Biol Evol 2021; 37:2477-2486. [PMID: 32344431 PMCID: PMC7475036 DOI: 10.1093/molbev/msaa093] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Feathered leg is a trait in domestic chickens that has undergone intense selection by fancy breeders. Previous studies have shown that two major loci controlling feathered leg are located on chromosomes 13 and 15. Here, we present genetic evidence for the identification of candidate causal mutations at these loci. This was accomplished by combining classical linkage mapping using an experimental cross segregating for feathered leg and high-resolution identical-by-descent mapping using whole-genome sequence data from 167 samples of chicken with or without feathered legs. The first predicted causal mutation is a single-base change located 25 kb upstream of the gene for the forelimb-specific transcription factor TBX5 on chromosome 15. The second is a 17.7-kb deletion located ∼200 kb upstream of the gene for the hindlimb-specific transcription factor PITX1 on chromosome 13. These mutations are predicted to activate TBX5 and repress PITX1 expression, respectively. The study reveals a remarkable convergence in the evolution of the feathered-leg phenotype in domestic chickens and domestic pigeons, as this phenotype is caused by noncoding mutations upstream of the same two genes. Furthermore, the PITX1 causal variants are large overlapping deletions, 17.7 kb in chicken and 44 kb in pigeons. The results of the present study are consistent with the previously proposed model for pigeon that feathered leg is caused by reduced PITX1 expression and ectopic expression of TBX5 in hindlimb buds resulting in a shift of limb identity from hindlimb to more forelimb-like identity.
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Affiliation(s)
- Jingyi Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX.,Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - MiOk Lee
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Sangeet Lamichhaney
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ben J Dorshorst
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Paul B Siegel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX.,Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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4
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González-Ruiz S, Strillacci MG, Durán-Aguilar M, Cantó-Alarcón GJ, Herrera-Rodríguez SE, Bagnato A, Guzmán LF, Milián-Suazo F, Román-Ponce SI. Genome-Wide Association Study in Mexican Holstein Cattle Reveals Novel Quantitative Trait Loci Regions and Confirms Mapped Loci for Resistance to Bovine Tuberculosis. Animals (Basel) 2019; 9:E636. [PMID: 31480266 PMCID: PMC6769677 DOI: 10.3390/ani9090636] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 12/26/2022] Open
Abstract
Bovine tuberculosis (bTB) is a disease of cattle that represents a risk to public health and causes severe economic losses to the livestock industry. Recently, genetic studies, like genome-wide association studies (GWAS) have greatly improved the investigation of complex diseases identifying thousands of disease-associated genomic variants. Here, we present evidence of genetic variants associated with resistance to TB in Mexican dairy cattle using a case-control approach with a selective DNA pooling experimental design. A total of 154 QTLRs (quantitative trait loci regions) at 10% PFP (proportion of false positives), 42 at 5% PFP and 5 at 1% PFP have been identified, which harbored 172 annotated genes. On BTA13, five new QTLRs were identified in the MACROD2 and KIF16B genes, supporting their involvement in resistance to bTB. Six QTLRs harbor seven annotated genes that have been previously reported as involved in immune response against Mycobacterium spp: BTA (Bos taurus autosome) 1 (CD80), BTA3 (CTSS), BTA 3 (FCGR1A), BTA 23 (HFE), BTA 25 (IL21R), and BTA 29 (ANO9 and SIGIRR). We identified novel QTLRs harboring genes involved in Mycobacterium spp. immune response. This is a first screening for resistance to TB infection on Mexican dairy cattle based on a dense SNP (Single Nucleotide Polymorphism) chip.
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Affiliation(s)
- Sara González-Ruiz
- Doctorado en Ciencias Biológicas, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro C.P. 76230, Mexico
| | - Maria G Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Via Trentacoste, 2, 20134 Milano, Italy.
| | - Marina Durán-Aguilar
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro C.P. 76230, Mexico
| | - Germinal J Cantó-Alarcón
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro C.P. 76230, Mexico
| | - Sara E Herrera-Rodríguez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Guadalajara C.P. 44270, Mexico
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Via Trentacoste, 2, 20134 Milano, Italy
| | - Luis F Guzmán
- Centro Nacional de Recursos Genéticos, INIFAP, Tepatitlán de Morelos 47600, Mexico
| | - Feliciano Milián-Suazo
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro C.P. 76230, Mexico
| | - Sergio I Román-Ponce
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento animal, INIFAP, SAGARPA, Km. 1 Carretera a Colón, Ajuchitlán, Colón, Querétaro C.P. 76280, Mexico.
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5
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Li J, Bed’hom B, Marthey S, Valade M, Dureux A, Moroldo M, Péchoux C, Coville J, Gourichon D, Vieaud A, Dorshorst B, Andersson L, Tixier‐Boichard M. A missense mutation in
TYRP1
causes the chocolate plumage color in chicken and alters melanosome structure. Pigment Cell Melanoma Res 2018; 32:381-390. [DOI: 10.1111/pcmr.12753] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 09/19/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Jingyi Li
- Department of Animal and Poultry Sciences Virginia Tech Blacksburg Virginia
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas
| | - Bertrand Bed’hom
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Sylvain Marthey
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Mathieu Valade
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Audrey Dureux
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Marco Moroldo
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Christine Péchoux
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Jean‐Luc Coville
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | | | - Agathe Vieaud
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Ben Dorshorst
- Department of Animal and Poultry Sciences Virginia Tech Blacksburg Virginia
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
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6
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Kawaguchi F, Kigoshi H, Nakajima A, Matsumoto Y, Uemoto Y, Fukushima M, Yoshida E, Iwamoto E, Akiyama T, Kohama N, Kobayashi E, Honda T, Oyama K, Mannen H, Sasazaki S. Pool-based genome-wide association study identified novel candidate regions on BTA9 and 14 for oleic acid percentage in Japanese Black cattle. Anim Sci J 2018; 89:1060-1066. [DOI: 10.1111/asj.13035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/22/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Hiroto Kigoshi
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Ayaka Nakajima
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Yuta Matsumoto
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Yoshinobu Uemoto
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Tohoku University; Sendai Japan
| | - Moriyuki Fukushima
- Northern Center of Agricultural Technology, General Technological Center of Hyogo Prefecture for Agriculture, Forestry and Fisheries; Asago Japan
| | - Emi Yoshida
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries; Kasai Japan
| | - Eiji Iwamoto
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries; Kasai Japan
| | - Takayuki Akiyama
- Northern Center of Agricultural Technology, General Technological Center of Hyogo Prefecture for Agriculture, Forestry and Fisheries; Asago Japan
| | - Namiko Kohama
- Northern Center of Agricultural Technology, General Technological Center of Hyogo Prefecture for Agriculture, Forestry and Fisheries; Asago Japan
| | - Eiji Kobayashi
- Division of Animal Breeding and Reproduction Research; Institute of Livestock and Grassland Science; National Agriculture and Food Research Organization; Tsukuba Japan
| | - Takeshi Honda
- Food Resources Education & Research Center; Kobe University; Kasai Japan
| | - Kenji Oyama
- Food Resources Education & Research Center; Kobe University; Kasai Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
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7
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Nakajima A, Kawaguchi F, Uemoto Y, Fukushima M, Yoshida E, Iwamoto E, Akiyama T, Kohama N, Kobayashi E, Honda T, Oyama K, Mannen H, Sasazaki S. A genome-wide association study for fat-related traits computed by image analysis in Japanese Black cattle. Anim Sci J 2018; 89:743-751. [DOI: 10.1111/asj.12987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/30/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Ayaka Nakajima
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Yoshinobu Uemoto
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Tohoku University; Sendai Japan
| | - Moriyuki Fukushima
- Northern Center of Agricultural Technology; General Technological Center of Hyogo Prefecture for Agriculture, Forest and Fishery; Asago Japan
| | - Emi Yoshida
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries; Kasai Japan
| | - Eiji Iwamoto
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries; Kasai Japan
| | - Takayuki Akiyama
- Northern Center of Agricultural Technology; General Technological Center of Hyogo Prefecture for Agriculture, Forest and Fishery; Asago Japan
| | - Namiko Kohama
- Northern Center of Agricultural Technology; General Technological Center of Hyogo Prefecture for Agriculture, Forest and Fishery; Asago Japan
| | - Eiji Kobayashi
- Division of Animal Breeding and Reproduction Research; Institute of Livestock and Grassland Science; National Agriculture and Food Research Organization; Tsukuba Japan
| | - Takeshi Honda
- Food Resources Education & Research Center; Kobe University; Kasai Japan
| | - Kenji Oyama
- Food Resources Education & Research Center; Kobe University; Kasai Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics; Graduate School of Agricultural Science; Kobe University; Kobe Japan
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8
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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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9
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Riaz M, Lorés-Motta L, Richardson AJ, Lu Y, Montgomery G, Omar A, Koenekoop RK, Chen J, Muether P, Altay L, Schick T, Fauser S, Smailhodzic D, van Asten F, de Jong EK, Hoyng CB, Burdon KP, MacGregor S, Guymer RH, den Hollander AI, Baird PN. GWAS study using DNA pooling strategy identifies association of variant rs4910623 in OR52B4 gene with anti-VEGF treatment response in age-related macular degeneration. Sci Rep 2016; 6:37924. [PMID: 27892514 PMCID: PMC5124940 DOI: 10.1038/srep37924] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 11/02/2016] [Indexed: 12/20/2022] Open
Abstract
Pooled DNA based GWAS to determine genetic association of SNPs with visual acuity (VA) outcome in anti-vascular endothelial growth factor (anti-VEGF) treated neovascular age-related macular degeneration (nAMD) patients. We performed pooled DNA based GWAS on 285 anti-VEGF treated nAMD patients using high density Illumina 4.3 M array. Primary outcome was change in VA in Early Treatment Diabetic Retinopathy Study (ETDRS) letters after 6 months of anti-VEGF treatment (patients who lost ≥5 ETDRS letters classified as non-responders and all remaining classified as responders). GWAS analysis identified 44 SNPs of interest: 37 with strong evidence of association (p < 9 × 10−8), 2 in drug resistance genes (p < 5 × 10−6) and 5 nonsynonymous changes (p < 1 × 10−4). In the validation phase, individual genotyping of 44 variants showed three SNPs (rs4910623 p = 5.6 × 10−5, rs323085 p = 6.5 × 10−4 and rs10198937 p = 1.30 × 10−3) remained associated with VA response at 6 months. SNP rs4910623 also associated with treatment response at 3 months (p = 1.5 × 10−3). Replication of these three SNPs in 376 patients revealed association of rs4910623 with poor VA response after 3 and 6 months of treatment (p = 2.4 × 10−3 and p = 3.5 × 10−2, respectively). Meta-analysis of both cohorts (673 samples) confirmed association of rs4910623 with poor VA response after 3 months (p = 1.2 × 10−5) and 6 months (p = 9.3 × 10−6) of treatment in nAMD patients.
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Affiliation(s)
- Moeen Riaz
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Australia
| | - Laura Lorés-Motta
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands
| | - Andrea J Richardson
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Australia
| | - Yi Lu
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Grant Montgomery
- Molecular Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Amer Omar
- Montreal Retina Institute, Westmount, Canada
| | - Robert K Koenekoop
- Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, Montreal, Quebec, Canada
| | - John Chen
- Department of Ophthalmology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Philipp Muether
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Lebriz Altay
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Tina Schick
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Sascha Fauser
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Dzenita Smailhodzic
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands
| | - Freekje van Asten
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS and Dept: Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Stuart MacGregor
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Robyn H Guymer
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Australia
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Paul N Baird
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Australia
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10
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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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11
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Khong JJ, Burdon KP, Lu Y, Laurie K, Leonardos L, Baird PN, Sahebjada S, Walsh JP, Gajdatsy A, Ebeling PR, Hamblin PS, Wong R, Forehan SP, Fourlanos S, Roberts AP, Doogue M, Selva D, Montgomery GW, Macgregor S, Craig JE. Pooled genome wide association detects association upstream of FCRL3 with Graves' disease. BMC Genomics 2016; 17:939. [PMID: 27863461 PMCID: PMC5116198 DOI: 10.1186/s12864-016-3276-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/09/2016] [Indexed: 12/29/2022] Open
Abstract
Background Graves’ disease is an autoimmune thyroid disease of complex inheritance. Multiple genetic susceptibility loci are thought to be involved in Graves’ disease and it is therefore likely that these can be identified by genome wide association studies. This study aimed to determine if a genome wide association study, using a pooling methodology, could detect genomic loci associated with Graves’ disease. Results Nineteen of the top ranking single nucleotide polymorphisms including HLA-DQA1 and C6orf10, were clustered within the Major Histo-compatibility Complex region on chromosome 6p21, with rs1613056 reaching genome wide significance (p = 5 × 10−8). Technical validation of top ranking non-Major Histo-compatablity complex single nucleotide polymorphisms with individual genotyping in the discovery cohort revealed four single nucleotide polymorphisms with p ≤ 10−4. Rs17676303 on chromosome 1q23.1, located upstream of FCRL3, showed evidence of association with Graves’ disease across the discovery, replication and combined cohorts. A second single nucleotide polymorphism rs9644119 downstream of DPYSL2 showed some evidence of association supported by finding in the replication cohort that warrants further study. Conclusions Pooled genome wide association study identified a genetic variant upstream of FCRL3 as a susceptibility locus for Graves’ disease in addition to those identified in the Major Histo-compatibility Complex. A second locus downstream of DPYSL2 is potentially a novel genetic variant in Graves’ disease that requires further confirmation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3276-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jwu Jin Khong
- Melbourne Medical School Western Campus, Department of Medicine, University of Melbourne, Sunshine Hospital, 176 Furlong Road, St Albans, VIC, 3021, Australia. .,Orbital, Plastics and Lacrimal Unit, The Royal Victorian Eye and Ear Hospital, Heidelberg, VIC, Australia. .,Department of Ophthalmology and Department of Surgery, University of Melbourne, Austin Health, Heidelberg, VIC, Australia.
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Yi Lu
- Statistical Genetics, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Kate Laurie
- Department of Ophthalmology, Flinders University of South Australia, Bedford Park, South Australia, Australia
| | - Lefta Leonardos
- Department of Ophthalmology, Flinders University of South Australia, Bedford Park, South Australia, Australia
| | - Paul N Baird
- Department of Surgery, Centre for Eye Research Australia and Ophthalmology, University of Melbourne, East Melbourne, VIC, Australia
| | - Srujana Sahebjada
- Department of Surgery, Centre for Eye Research Australia and Ophthalmology, University of Melbourne, East Melbourne, VIC, Australia
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia.,School of Medicine and Pharmacology, The University of Western Australia, Crawley, WA, Australia
| | - Adam Gajdatsy
- Centre for Ophthalmology and Visual Sciences, University of Western Australia, Western Australia, Australia
| | - Peter R Ebeling
- Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Peter Shane Hamblin
- Melbourne Medical School Western Campus, Department of Medicine, University of Melbourne, Sunshine Hospital, 176 Furlong Road, St Albans, VIC, 3021, Australia.,Department of Endocrinology and Diabetes, Western Health, St Albans, VIC, Australia
| | - Rosemary Wong
- Department of Endocrinology and Diabetes, Western Health, St Albans, VIC, Australia
| | - Simon P Forehan
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Spiros Fourlanos
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Anthony P Roberts
- Department of Endocrinology, The Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Matthew Doogue
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Dinesh Selva
- South Australian Institute of Ophthalmology, University of Adelaide, South Australia, Australia
| | - Grant W Montgomery
- Molecular Epidemiology, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Stuart Macgregor
- Statistical Genetics, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University of South Australia, Bedford Park, South Australia, Australia
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12
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Sousa I, Abrantes P, Francisco V, Teixeira G, Monteiro M, Neves J, Norte A, Robalo Cordeiro C, Moura e Sá J, Reis E, Santos P, Oliveira M, Sousa S, Fradinho M, Malheiro F, Negrão L, Feijó S, Oliveira SA. Multicentric Genome-Wide Association Study for Primary Spontaneous Pneumothorax. PLoS One 2016; 11:e0156103. [PMID: 27203581 PMCID: PMC4874577 DOI: 10.1371/journal.pone.0156103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/08/2016] [Indexed: 11/18/2022] Open
Abstract
Despite elevated incidence and recurrence rates for Primary Spontaneous Pneumothorax (PSP), little is known about its etiology, and the genetics of idiopathic PSP remains unexplored. To identify genetic variants contributing to sporadic PSP risk, we conducted the first PSP genome-wide association study. Two replicate pools of 92 Portuguese PSP cases and of 129 age- and sex-matched controls were allelotyped in triplicate on the Affymetrix Human SNP Array 6.0 arrays. Markers passing quality control were ranked by relative allele score difference between cases and controls (|RASdiff|), by a novel cluster method and by a combined Z-test. 101 single nucleotide polymorphisms (SNPs) were selected using these three approaches for technical validation by individual genotyping in the discovery dataset. 87 out of 94 successfully tested SNPs were nominally associated in the discovery dataset. Replication of the 87 technically validated SNPs was then carried out in an independent replication dataset of 100 Portuguese cases and 425 controls. The intergenic rs4733649 SNP in chromosome 8 (between LINC00824 and LINC00977) was associated with PSP in the discovery (P = 4.07E-03, ORC[95% CI] = 1.88[1.22–2.89]), replication (P = 1.50E-02, ORC[95% CI] = 1.50[1.08–2.09]) and combined datasets (P = 8.61E-05, ORC[95% CI] = 1.65[1.29–2.13]). This study identified for the first time one genetic risk factor for sporadic PSP, but future studies are warranted to further confirm this finding in other populations and uncover its functional role in PSP pathogenesis.
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Affiliation(s)
- Inês Sousa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Patrícia Abrantes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Vânia Francisco
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | | - João Neves
- Centro Hospitalar do Porto, Porto, Portugal
| | - Ana Norte
- Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | | | - João Moura e Sá
- Centro Hospitalar de Vila Nova de Gaia, Vila Nova de Gaia, Portugal
| | | | - Patrícia Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Susana Sousa
- Hospital de São Bernardo (Centro Hospitalar de Setúbal, E.P.E.), Setúbal, Portugal
| | - Marta Fradinho
- Hospital Egas Moniz (Centro Hospitalar de Lisboa Ocidental), Lisboa, Portugal
| | | | - Luís Negrão
- Instituto Português do Sangue e da Transplantacão, Centro Regional de Sangue de Lisboa, Lisboa, Portugal
| | | | - Sofia A. Oliveira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail:
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13
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Shivakumar BM, Chakrabarty S, Rotti H, Seenappa V, Rao L, Geetha V, Tantry BV, Kini H, Dharamsi R, Pai CG, Satyamoorthy K. Comparative analysis of copy number variations in ulcerative colitis associated and sporadic colorectal neoplasia. BMC Cancer 2016; 16:271. [PMID: 27080994 PMCID: PMC4831153 DOI: 10.1186/s12885-016-2303-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 04/07/2016] [Indexed: 12/12/2022] Open
Abstract
Background The incidence of and mortality from colorectal cancers (CRC) can be reduced by early detection. Currently there is a lack of established markers to detect early neoplastic changes. We aimed to identify the copy number variations (CNVs) and the associated genes which could be potential markers for the detection of neoplasia in both ulcerative colitis-associated neoplasia (UC-CRN) and sporadic colorectal neoplasia (S-CRN). Methods We employed array comparative genome hybridization (aCGH) to identify CNVs in tissue samples of UC nonprogressor, progressor and sporadic CRC. Select genes within these CNV regions as a panel of markers were validated using quantitative real time PCR (qRT-PCR) method along with the microsatellite instability (MSI) in an independent cohort of samples. Immunohistochemistry (IHC) analysis was also performed. Results Integrated analysis showed 10 overlapping CNV regions between UC-Progressor and S-CRN, with the 8q and 12p regions showing greater overlap. The qRT-PCR based panel of MYC, MYCN, CCND1, CCND2, EGFR and FNDC3A was successful in detecting neoplasia with an overall accuracy of 54 % in S-CRN compared to that of 29 % in UC neoplastic samples. IHC study showed that p53 and CCND1 were significantly overexpressed with an increasing frequency from pre-neoplastic to neoplastic stages. EGFR and AMACR were expressed only in the neoplastic conditions. Conclusion CNVs that are common and unique to both UC-associated and sporadic colorectal neoplasm could be the key players driving carcinogenesis. Comparative analysis of CNVs provides testable driver aberrations but needs further evaluation in larger cohorts of samples. These markers may help in developing more effective neoplasia-detection strategies during screening and surveillance programs. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2303-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B M Shivakumar
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal University, Manipal, India.,School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | | | - Harish Rotti
- School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Venu Seenappa
- School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Lakshmi Rao
- Department of Pathology, Kasturba Medical College, Manipal University, Manipal, India
| | - Vasudevan Geetha
- Department of Pathology, Kasturba Medical College, Manipal University, Manipal, India
| | - B V Tantry
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal University, Mangalore, India
| | - Hema Kini
- Department of Pathology, Kasturba Medical College, Manipal University, Mangalore, India
| | - Rajesh Dharamsi
- Dharamsi Hospital, Chandni Chowk, Sangli, Maharashtra, India
| | - C Ganesh Pai
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal University, Manipal, India
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14
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Abrantes P, Santos MM, Sousa I, Xavier JM, Francisco V, Krug T, Sobral J, Matos M, Martins M, Jacinto A, Coiteiro D, Oliveira SA. Genetic Variants Underlying Risk of Intracranial Aneurysms: Insights from a GWAS in Portugal. PLoS One 2015; 10:e0133422. [PMID: 26186006 PMCID: PMC4505843 DOI: 10.1371/journal.pone.0133422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/26/2015] [Indexed: 12/03/2022] Open
Abstract
Subarachnoid hemorrhage (SAH) is a life-threatening event that most frequently leads to severe disability and death. Its most frequent cause is the rupture of a saccular intracranial aneurysm (IA), which is a blood vessel dilation caused by disease or weakening of the vessel wall. Although the genetic contribution to IA is well established, to date no single gene has been unequivocally identified as responsible for IA formation or rupture. We aimed to identify IA susceptibility genes in the Portuguese population through a pool-based multistage genome-wide association study. Replicate pools were allelotyped in triplicate in a discovery dataset (100 IA cases and 92 gender-matched controls) using the Affymetrix Human SNP Array 6.0. Top SNPs (absolute value of the relative allele score difference between cases and controls |RASdiff|≥13.0%) were selected for technical validation by individual genotyping in the discovery dataset. From the 101 SNPs successfully genotyped, 99 SNPs were nominally associated with IA. Replication of technically validated SNPs was conducted in an independent replication dataset (100 Portuguese IA cases and 407 controls). rs4667622 (between UBR3 and MYO3B), rs6599001 (between SCN11A and WDR48), rs3932338 (214 kilobases downstream of PRDM9), and rs10943471 (96 kilobases upstream of HTR1B) were associated with IA (unadjusted allelic chi-square tests) in the datasets tested (discovery: 6.84E-04≤P≤1.92E-02, replication: 2.66E-04≤P≤2.28E-02, and combined datasets: 6.05E-05≤P≤5.50E-04). Additionally, we confirmed the known association with IA of rs1333040 at the 9p21.3 genomic region, thus validating our dataset. These novel findings in the Portuguese population warrant further replication in additional independent studies, and provide additional candidates to more comprehensively understand IA etiopathogenesis.
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Affiliation(s)
- Patrícia Abrantes
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Maria M. Santos
- Serviço de Neurocirurgia, Hospital de Santa Maria, Lisboa, Portugal
| | - Inês Sousa
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Joana M. Xavier
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Vânia Francisco
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Tiago Krug
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - João Sobral
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Mafalda Matos
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Madalena Martins
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - António Jacinto
- Centro de Estudos de Doenças Crónicas (CEDOC), Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | | | - Sofia A. Oliveira
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail:
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15
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Li HH, Doiron K, Patterson AD, Gonzalez FJ, Fornace AJ. Identification of serum insulin-like growth factor binding protein 1 as diagnostic biomarker for early-stage alcohol-induced liver disease. J Transl Med 2013; 11:266. [PMID: 24152801 PMCID: PMC4016206 DOI: 10.1186/1479-5876-11-266] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 10/18/2013] [Indexed: 12/12/2022] Open
Abstract
Background Alcohol consumption is a major cause of liver disease in humans. The use and monitoring of biomarkers associated with early, pre-clinical stages of alcohol-induced liver disease (pre-ALD) could facilitate diagnosis and treatment, leading to improved outcomes. Methods We investigated the pathological, transcriptomic and protein changes in early stages of pre-ALD in mice fed the Lieber-Decarli liquid diet with or without alcohol for four months to identify biomarkers for the early stage of alcohol induced liver injury. Mice were sampled after 1, 2 and 4 months treatment. Results Pathological examination revealed a modest increase in fatty liver changes in alcohol-treated mice. Transcriptomics revealed gene alterations at all time points. Most notably, the Igfbp1 (Insulin-Like Growth Factor Binding Protein 1) was selected as the best candidate gene for early detection of liver damage since it showed early and continuously enhanced induction during the treatment course. Consistent with the microarray data, both Igfbp1mRNA expression in the liver tissue and the IGFBP1 serum protein levels showed progressive and significant increases over the course of pre-ALD development. Conclusions The results suggest that in conjunction with other tests, serum IGFBPI protein could provide an easily measured biomarker for early detection of alcohol-induced liver injury in humans.
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Affiliation(s)
| | | | | | | | - Albert J Fornace
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, 3970 Reservoir Road, NW, New Research Building, Room E504, Washington, DC 20057, USA.
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16
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McRae AF, Richter MM, Lind PA. Case-control association testing of common variants from sequencing of DNA pools. PLoS One 2013; 8:e65410. [PMID: 23762362 PMCID: PMC3676437 DOI: 10.1371/journal.pone.0065410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/25/2013] [Indexed: 12/05/2022] Open
Abstract
While genome-wide association studies (GWAS) have been successful in identifying a large number of variants associated with disease, the challenge of locating the underlying causal loci remains. Sequencing of case and control DNA pools provides an inexpensive method for assessing all variation in a genomic region surrounding a significant GWAS result. However, individual variants need to be ranked in terms of the strength of their association to disease in order to prioritise follow-up by individual genotyping. A simple method for testing for case-control association in sequence data from DNA pools is presented that allows the partitioning of the variance in allele frequency estimates into components due to the sampling of chromosomes from the pool during sequencing, sampling individuals from the population and unequal contribution from individuals during pool construction. The utility of this method is demonstrated on a sequence from the alcohol dehydrogenase (ADH) gene cluster on a case-control sample for heavy alcohol consumption.
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Affiliation(s)
- Allan F McRae
- University of Queensland Diamantina Institute, Brisbane, Australia.
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17
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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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18
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Genome-wide association study for ovarian cancer susceptibility using pooled DNA. Twin Res Hum Genet 2012; 15:615-623. [PMID: 22794196 DOI: 10.1017/thg.2012.38] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Recent Genome-Wide Association Studies (GWAS) have identified four low-penetrance ovarian cancer susceptibility loci. We hypothesized that further moderate- or low-penetrance variants exist among the subset of single-nucleotide polymorphisms (SNPs) not well tagged by the genotyping arrays used in the previous studies, which would account for some of the remaining risk. We therefore conducted a time- and cost-effective stage 1 GWAS on 342 invasive serous cases and 643 controls genotyped on pooled DNA using the high-density Illumina 1M-Duo array. We followed up 20 of the most significantly associated SNPs, which are not well tagged by the lower density arrays used by the published GWAS, and genotyping them on individual DNA. Most of the top 20 SNPs were clearly validated by individually genotyping the samples used in the pools. However, none of the 20 SNPs replicated when tested for association in a much larger stage 2 set of 4,651 cases and 6,966 controls from the Ovarian Cancer Association Consortium. Given that most of the top 20 SNPs from pooling were validated in the same samples by individual genotyping, the lack of replication is likely to be due to the relatively small sample size in our stage 1 GWAS rather than due to problems with the pooling approach. We conclude that there are unlikely to be any moderate or large effects on ovarian cancer risk untagged by less dense arrays. However, our study lacked power to make clear statements on the existence of hitherto untagged small-effect variants.
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Uemoto Y, Sasago N, Abe T, Okada H, Maruoka H, Nakajima H, Shoji N, Maruyama S, Kobayashi N, Mannen H, Kobayashi E. Practical capability and cost effectiveness of a DNA pool-based genome-wide association study using BovineSNP50 array in a cattle population. Anim Sci J 2012; 83:719-26. [PMID: 23126324 DOI: 10.1111/j.1740-0929.2012.01022.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Genome-wide association mapping for complex traits in cattle populations is a powerful, but expensive, selection tool. The DNA pooling technique can potentially reduce the cost of genome-wide association studies. However, in DNA pooling design, the additional variance generated by pooling-specific errors must be taken into account. Therefore, this study aimed to investigate factors such as: (i) the accuracy of allele frequency estimation; (ii) the magnitude of errors in pooling construction and in the array; and (iii) the effect of the number of replicate arrays on P-values estimated by a genome-wide association study. Results showed that the Illumina correction method is the most effective method to correct the allele frequency estimation; pooling errors, especially array variance, should be taken into account in DNA pooling design; and the risk of a type I error can be reduced by using at least two replicate arrays. These results indicate the practical capability and cost-effectiveness of pool-based genome-wide association studies using the BovineSNP50 array in a cattle population.
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20
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Gaj P, Maryan N, Hennig EE, Ledwon JK, Paziewska A, Majewska A, Karczmarski J, Nesteruk M, Wolski J, Antoniewicz AA, Przytulski K, Rutkowski A, Teumer A, Homuth G, Starzyńska T, Regula J, Ostrowski J. Pooled sample-based GWAS: a cost-effective alternative for identifying colorectal and prostate cancer risk variants in the Polish population. PLoS One 2012; 7:e35307. [PMID: 22532847 PMCID: PMC3331859 DOI: 10.1371/journal.pone.0035307] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/13/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Prostate cancer (PCa) and colorectal cancer (CRC) are the most commonly diagnosed cancers and cancer-related causes of death in Poland. To date, numerous single nucleotide polymorphisms (SNPs) associated with susceptibility to both cancer types have been identified, but their effect on disease risk may differ among populations. METHODS To identify new SNPs associated with PCa and CRC in the Polish population, a genome-wide association study (GWAS) was performed using DNA sample pools on Affymetrix Genome-Wide Human SNP 6.0 arrays. A total of 135 PCa patients and 270 healthy men (PCa sub-study) and 525 patients with adenoma (AD), 630 patients with CRC and 690 controls (AD/CRC sub-study) were included in the analysis. Allele frequency distributions were compared with t-tests and χ(2)-tests. Only those significantly associated SNPs with a proxy SNP (p<0.001; distance of 100 kb; r(2)>0.7) were selected. GWAS marker selection was conducted using PLINK. The study was replicated using extended cohorts of patients and controls. The association with previously reported PCa and CRC susceptibility variants was also examined. Individual patients were genotyped using TaqMan SNP Genotyping Assays. RESULTS The GWAS selected six and 24 new candidate SNPs associated with PCa and CRC susceptibility, respectively. In the replication study, 17 of these associations were confirmed as significant in additive model of inheritance. Seven of them remained significant after correction for multiple hypothesis testing. Additionally, 17 previously reported risk variants have been identified, five of which remained significant after correction. CONCLUSION Pooled-DNA GWAS enabled the identification of new susceptibility loci for CRC in the Polish population. Previously reported CRC and PCa predisposition variants were also identified, validating the global nature of their associations. Further independent replication studies are required to confirm significance of the newly uncovered candidate susceptibility loci.
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Affiliation(s)
- Pawel Gaj
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Natalia Maryan
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Ewa E. Hennig
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
- Department of Oncological Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Joanna K. Ledwon
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Aneta Majewska
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Oncological Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Monika Nesteruk
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Jan Wolski
- Department of Urology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Artur A. Antoniewicz
- Department of Urology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Krzysztof Przytulski
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
- Department of Oncological Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Andrzej Rutkowski
- Department of Colorectal Cancer, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Teresa Starzyńska
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - Jaroslaw Regula
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
- Department of Oncological Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
- Department of Oncological Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
- * E-mail:
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Anantharaman R, Andiappan AK, Nilkanth PP, Suri BK, Wang DY, Chew FT. Genome-wide association study identifies PERLD1 as asthma candidate gene. BMC MEDICAL GENETICS 2011; 12:170. [PMID: 22188591 PMCID: PMC3268734 DOI: 10.1186/1471-2350-12-170] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 12/21/2011] [Indexed: 11/10/2022]
Abstract
Background Recent genome-wide association studies (GWAS) for asthma have been successful in identifying novel associations which have been well replicated. The aim of this study is to identify the genetic variants that influence predisposition towards asthma in an ethnic Chinese population in Singapore using a GWAS approach. Methods A two-stage GWAS was performed in case samples with allergic asthma, and in control samples without asthma and atopy. In the discovery stage, 490 case and 490 control samples were analysed by pooled genotyping. Significant associations from the first stage were evaluated in a replication cohort of 521 case and 524 control samples in the second stage. The same 980 samples used in the discovery phase were also individually genotyped for purposes of a combined analysis. An additional 1445 non-asthmatic atopic control samples were also genotyped. Results 19 promising SNPs which passed our genome-wide P value threshold of 5.52 × 10-8 were individually genotyped. In the combined analysis of 1011 case and 1014 control samples, SNP rs2941504 in PERLD1 on chromosome 17q12 was found to be significantly associated with asthma at the genotypic level (P = 1.48 × 10-6, ORAG = 0.526 (0.369-0.700), ORAA = 0.480 (0.361-0.639)) and at the allelic level (P = 9.56 × 10-6, OR = 0.745 (0.654-0.848)). These findings were found to be replicated in 3 other asthma GWAS studies, thus validating our own results. Analysis against the atopy control samples suggested that the SNP was associated with allergic asthma and not to either the asthma or allergy components. Genotyping of additional SNPs in 100 kb flanking rs2941504 further confirmed that the association was indeed to PERLD1. PERLD1 is involved in the modification of the glycosylphosphatidylinositol anchors for cell surface markers such as CD48 and CD59 which are known to play multiple roles in T-cell activation and proliferation. Conclusions These findings reveal the association of a PERLD1 as a novel asthma candidate gene and reinforce the involvement of genes on the 17q12-21 chromosomal region in the etiology of asthma.
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Affiliation(s)
- Ramani Anantharaman
- Department of Biological Sciences, National University of Singapore, Singapore
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22
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Earp MA, Rahmani M, Chew K, Brooks-Wilson A. Estimates of array and pool-construction variance for planning efficient DNA-pooling genome wide association studies. BMC Med Genomics 2011; 4:81. [PMID: 22122996 PMCID: PMC3247851 DOI: 10.1186/1755-8794-4-81] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 11/28/2011] [Indexed: 01/01/2023] Open
Abstract
Background Until recently, genome-wide association studies (GWAS) have been restricted to research groups with the budget necessary to genotype hundreds, if not thousands, of samples. Replacing individual genotyping with genotyping of DNA pools in Phase I of a GWAS has proven successful, and dramatically altered the financial feasibility of this approach. When conducting a pool-based GWAS, how well SNP allele frequency is estimated from a DNA pool will influence a study's power to detect associations. Here we address how to control the variance in allele frequency estimation when DNAs are pooled, and how to plan and conduct the most efficient well-powered pool-based GWAS. Methods By examining the variation in allele frequency estimation on SNP arrays between and within DNA pools we determine how array variance [var(earray)] and pool-construction variance [var(econstruction)] contribute to the total variance of allele frequency estimation. This information is useful in deciding whether replicate arrays or replicate pools are most useful in reducing variance. Our analysis is based on 27 DNA pools ranging in size from 74 to 446 individual samples, genotyped on a collective total of 128 Illumina beadarrays: 24 1M-Single, 32 1M-Duo, and 72 660-Quad. Results For all three Illumina SNP array types our estimates of var(earray) were similar, between 3-4 × 10-4 for normalized data. Var(econstruction) accounted for between 20-40% of pooling variance across 27 pools in normalized data. Conclusions We conclude that relative to var(earray), var(econstruction) is of less importance in reducing the variance in allele frequency estimation from DNA pools; however, our data suggests that on average it may be more important than previously thought. We have prepared a simple online tool, PoolingPlanner (available at http://www.kchew.ca/PoolingPlanner/), which calculates the effective sample size (ESS) of a DNA pool given a range of replicate array values. ESS can be used in a power calculator to perform pool-adjusted calculations. This allows one to quickly calculate the loss of power associated with a pooling experiment to make an informed decision on whether a pool-based GWAS is worth pursuing.
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Affiliation(s)
- Madalene A Earp
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
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23
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Lambertini L, Lee TL, Chan WY, Lee MJ, Diplas A, Wetmur J, Chen J. Differential methylation of imprinted genes in growth-restricted placentas. Reprod Sci 2011; 18:1111-7. [PMID: 21693779 DOI: 10.1177/1933719111404611] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A complex network of epigenetic factors participates in regulating the monoallelic expression of a small subset of genes (~1%) in the human genome. This phenomenon goes under the definition of genomic imprinting, a parent-of-origin effect that, when altered during early embryogenesis, may influence fetal development into adulthood. Pertubations in genomic imprinting have been associated with placental and fetal growth restrictions. We analyzed the differential DNA methylation of all known imprinted genes on 10 appropriate-for-gestational-age, clinically normal, placentas and 7 severe intrauterine growth-restricted placentas. Samples were pooled according to the diagnosis and analyzed by methylated DNA immunoprecipitation (MeDIP) on a tiling microarray platform. The distribution of the differentially methylated regions (DMRs) identified in growth-restricted placentas showed a slight tendency toward hypermethylation. Imprinted genes not expressed in placenta showed a unique DMR profile with the fewest hyper- and hypomethylated DMRs. Promoter and CpG island DMRs were sporadic and randomly distributed. The vast majority of DMR identified (~99%) were mapped in introns, showing no common sequence features. Also, by using the more advanced array data mining softwares, no significant patterns emerged. In contrast, differential methylation showed a highly significant correlation with gene length. Overall these data suggest that differential methylation changes in growth-restricted placentas occur throughout the genomic regions, encompassing genes actively expressed in the placenta. These findings warrant caution in interpreting the significance of genes carrying clustered DMRs because the distribution of DMRs in a gene may be attributed as a function of its length rather than as a specific biological role.
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Affiliation(s)
- Luca Lambertini
- Department of Preventive Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA.
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24
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Deng L, Tang X, Chen W, Lin J, Lai Z, Liu Z, Zhang D. Scanning for genomic regions subject to selective sweeps using SNP-MaP strategy. GENOMICS PROTEOMICS & BIOINFORMATICS 2011; 8:256-61. [PMID: 21382594 PMCID: PMC5054161 DOI: 10.1016/s1672-0229(10)60027-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Population genomic approaches, which take advantages of high-throughput genotyping, are powerful yet costly methods to scan for selective sweeps. DNA-pooling strategies have been widely used for association studies because it is a cost-effective alternative to large-scale individual genotyping. Here, we performed an SNP-MaP (single nucleotide polymorphism microarrays and pooling) analysis using samples from Eurasia to evaluate the efficiency of pooling strategy in genome-wide scans for selection. By conducting simulations of allelotype data, we first demonstrated that the boxplot with average heterozygosity (HET) is a promising method to detect strong selective sweeps with a moderate level of pooling error. Based on this, we used a sliding window analysis of HET to detect the large contiguous regions (LCRs) putatively under selective sweeps from Eurasia datasets. This survey identified 63 LCRs in a European population. These signals were further supported by the integrated haplotype score (iHS) test using HapMap II data. We also confirmed the European-specific signatures of positive selection from several previously identified genes(KEL, TRPV5, TRPV6, EPHB6). In summary, our results not only revealed the high credibility of SNP-MaP strategy in scanning for selective sweeps, but also provided an insight into the population differentiation.
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Affiliation(s)
- Libin Deng
- Facuity of Basic Medical Science, Nanchang University, Nanchang 330006, China
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25
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Huang Y, Hinds DA, Qi L, Prentice RL. Pooled versus individual genotyping in a breast cancer genome-wide association study. Genet Epidemiol 2011; 34:603-12. [PMID: 20718042 DOI: 10.1002/gepi.20517] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We examine the measurement properties of pooled DNA odds ratio estimates for 7,357 single nucleotide polymorphisms (SNPs) genotyped in a genome-wide association study of postmenopausal breast cancer. This study involved DNA pools formed from 125 cases or 125 matched controls. Individual genotyping for these SNPs subsequently came available for a substantial majority of women included in seven pool pairs, providing the opportunity for a comparison of pooled DNA and individual odds ratio estimates and their variances. We find that the "per minor allele" odds ratio estimates from the pooled DNA comparisons agree fairly well with those from individual genotyping. Furthermore, the log-odds ratio variance estimates support a pooled DNA measurement model that we previously described, although with somewhat greater extra-binomial variation than was hypothesized in project design. Implications for the role of pooled DNA comparisons in the future genetic epidemiology research agenda are discussed.
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Affiliation(s)
- Ying Huang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA
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26
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Vallania FLM, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD. High-throughput discovery of rare insertions and deletions in large cohorts. Genome Res 2010; 20:1711-8. [PMID: 21041413 DOI: 10.1101/gr.109157.110] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Pooled-DNA sequencing strategies enable fast, accurate, and cost-effect detection of rare variants, but current approaches are not able to accurately identify short insertions and deletions (indels), despite their pivotal role in genetic disease. Furthermore, the sensitivity and specificity of these methods depend on arbitrary, user-selected significance thresholds, whose optimal values change from experiment to experiment. Here, we present a combined experimental and computational strategy that combines a synthetically engineered DNA library inserted in each run and a new computational approach named SPLINTER that detects and quantifies short indels and substitutions in large pools. SPLINTER integrates information from the synthetic library to select the optimal significance thresholds for every experiment. We show that SPLINTER detects indels (up to 4 bp) and substitutions in large pools with high sensitivity and specificity, accurately quantifies variant frequency (r = 0.999), and compares favorably with existing algorithms for the analysis of pooled sequencing data. We applied our approach to analyze a cohort of 1152 individuals, identifying 48 variants and validating 14 of 14 (100%) predictions by individual genotyping. Thus, our strategy provides a novel and sensitive method that will speed the discovery of novel disease-causing rare variants.
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Affiliation(s)
- Francesco L M Vallania
- Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63108, USA
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27
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Shental N, Amir A, Zuk O. Identification of rare alleles and their carriers using compressed se(que)nsing. Nucleic Acids Res 2010; 38:e179. [PMID: 20699269 PMCID: PMC2965256 DOI: 10.1093/nar/gkq675] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Revised: 06/20/2010] [Accepted: 07/19/2010] [Indexed: 11/29/2022] Open
Abstract
Identification of rare variants by resequencing is important both for detecting novel variations and for screening individuals for known disease alleles. New technologies enable low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. We propose a novel pooling design that enables the recovery of novel or known rare alleles and their carriers in groups of individuals. The method is based on a Compressed Sensing (CS) approach, which is general, simple and efficient. CS allows the use of generic algorithmic tools for simultaneous identification of multiple variants and their carriers. We model the experimental procedure and show via computer simulations that it enables the recovery of rare alleles and their carriers in larger groups than were possible before. Our approach can also be combined with barcoding techniques to provide a feasible solution based on current resequencing costs. For example, when targeting a small enough genomic region (∼100 bp) and using only ∼10 sequencing lanes and ∼10 distinct barcodes per lane, one recovers the identity of 4 rare allele carriers out of a population of over 4000 individuals. We demonstrate the performance of our approach over several publicly available experimental data sets.
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Affiliation(s)
- Noam Shental
- Department of Computer Science, The Open University of Israel, Raanana 43107, Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel and Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amnon Amir
- Department of Computer Science, The Open University of Israel, Raanana 43107, Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel and Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Or Zuk
- Department of Computer Science, The Open University of Israel, Raanana 43107, Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel and Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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28
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Anantharaman R, Chew FT. Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction. BMC Genet 2009; 10:82. [PMID: 20003400 PMCID: PMC2806376 DOI: 10.1186/1471-2156-10-82] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 12/14/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The use of pooled DNA on SNP microarrays (SNP-MaP) has been shown to be a cost effective and rapid manner to perform whole-genome association evaluations. While the accuracy of SNP-MaP was extensively evaluated on the early Affymetrix 10 k and 100 k platforms, there have not been as many similarly comprehensive studies on more recent platforms. In the present study, we used the data generated from the full Affymetrix 500 k SNP set together with the polynomial-based probe-specific correction (PPC) to derive allele frequency estimates. These estimates were compared to genotyping results of the same individuals on the same platform, as the basis to evaluate the reliability and accuracy of pooled genotyping on these high-throughput platforms. We subsequently extended this comparison to the new SNP6.0 platform capable of genotyping 1.8 million genetic variants. RESULTS We showed that pooled genotyping on the 500 k platform performed as well as those previously shown on the relatively lower throughput 10 k and 100 k array sets, with high levels of accuracy (correlation coefficient: 0.988) and low median error (0.036) in allele frequency estimates. Similar results were also obtained from the SNP6.0 array set. A novel pooling strategy of overlapping sub-pools was attempted and comparison of estimated allele frequencies showed this strategy to be as reliable as replicate pools. The importance of an appropriate reference genotyping data set for the application of the PPC algorithm was also evaluated; reference samples with similar ethnic background to the pooled samples were found to improve estimation of allele frequencies. CONCLUSION We conclude that use of the PPC algorithm to estimate allele frequencies obtained from pooled genotyping on the high throughput 500 k and SNP6.0 platforms is highly accurate and reproducible especially when a suitable reference sample set is used to estimate the beta values for PPC.
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Affiliation(s)
- Ramani Anantharaman
- Department of Biological Sciences, National University of Singapore, Science Drive 4, Singapore 117543
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Science Drive 4, Singapore 117543
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29
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Thomas DC, Casey G, Conti DV, Haile RW, Lewinger JP, Stram DO. Methodological Issues in Multistage Genome-wide Association Studies. Stat Sci 2009; 24:414-429. [PMID: 20607129 DOI: 10.1214/09-sts288] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Because of the high cost of commercial genotyping chip technologies, many investigations have used a two-stage design for genome-wide association studies, using part of the sample for an initial discovery of "promising" SNPs at a less stringent significance level and the remainder in a joint analysis of just these SNPs using custom genotyping. Typical cost savings of about 50% are possible with this design to obtain comparable levels of overall type I error and power by using about half the sample for stage I and carrying about 0.1% of SNPs forward to the second stage, the optimal design depending primarily upon the ratio of costs per genotype for stages I and II. However, with the rapidly declining costs of the commercial panels, the generally low observed ORs of current studies, and many studies aiming to test multiple hypotheses and multiple endpoints, many investigators are abandoning the two-stage design in favor of simply genotyping all available subjects using a standard high-density panel. Concern is sometimes raised about the absence of a "replication" panel in this approach, as required by some high-profile journals, but it must be appreciated that the two-stage design is not a discovery/replication design but simply a more efficient design for discovery using a joint analysis of the data from both stages. Once a subset of highly-significant associations has been discovered, a truly independent "exact replication" study is needed in a similar population of the same promising SNPs using similar methods. This can then be followed by (1) "generalizability" studies to assess the full scope of replicated associations across different races, different endpoints, different interactions, etc.; (2) fine-mapping or re-sequencing to try to identify the causal variant; and (3) experimental studies of the biological function of these genes. Multistage sampling designs may be more useful at this stage, say for selecting subsets of subjects for deep re-sequencing of regions identified in the GWAS.
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Affiliation(s)
- Duncan C Thomas
- Department of Preventive Medicine, University of Southern California
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30
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Craig JE, Hewitt AW, McMellon AE, Henders AK, Ma L, Wallace L, Sharma S, Burdon KP, Visscher PM, Montgomery GW, MacGregor S. Rapid inexpensive genome-wide association using pooled whole blood. Genome Res 2009; 19:2075-80. [PMID: 19801603 DOI: 10.1101/gr.094680.109] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies (GWAS) have now successfully identified important genetic variants associated with many human traits and diseases. The high cost of genotyping arrays in large data sets remains the major barrier to wider utilization of GWAS. We have developed a novel method in which whole blood from cases and controls, respectively, is pooled prior to DNA extraction for genotyping. We demonstrate proof of principle by clearly identifying the associated variants for eye color, age-related macular degeneration, and pseudoexfoliation syndrome in cohorts not previously studied. Blood pooling has the potential to reduce GWAS cost by several orders of magnitude and dramatically shorten gene discovery time. This method has profound implications for translation of modern genetic approaches to a multitude of diseases and traits yet to be analyzed by GWAS, and will enable developing nations to participate in GWAS.
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Affiliation(s)
- Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide SA 5042, Australia.
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31
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Kirov G, Zaharieva I, Georgieva L, Moskvina V, Nikolov I, Cichon S, Hillmer A, Toncheva D, Owen MJ, O'Donovan MC. A genome-wide association study in 574 schizophrenia trios using DNA pooling. Mol Psychiatry 2009; 14:796-803. [PMID: 18332876 DOI: 10.1038/mp.2008.33] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cost of genome-wide association (GWA) studies can be prohibitively high when large samples are genotyped. We conducted a GWA study on schizophrenia (SZ) and to reduce the cost, we used DNA pooling. We used a parent-offspring trios design to avoid the potential problems of population stratification. We constructed pools from 605 unaffected controls, 574 SZ patients and a third pool from all the parents of the patients. We hybridized each pool eight times on Illumina HumanHap550 arrays. We estimated the allele frequencies of each pool from the averaged intensities of the arrays. The significance level of results in the trios sample was estimated on the basis of the allele frequencies in cases and non-transmitted pseudocontrols, taking into account the technical variability of the data. We selected the highest ranked SNPs for individual genotyping, after excluding poorly performing SNPs and those that showed a trend in the opposite direction in the control pool. We genotyped 63 SNPs in 574 trios and analysed the results with the transmission disequilibrium test. Forty of those were significant at P<0.05, with the best result at P=1.2 x 10(-6) for rs11064768. This SNP is within the gene CCDC60, a coiled-coil domain gene. The third best SNP (P=0.00016) is rs893703, within RBP1, a candidate gene for schizophrenia.
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Affiliation(s)
- G Kirov
- Department of Psychological Medicine, Cardiff University, Henry Wellcome Building, Cardiff, UK.
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32
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Knight J, Saccone SF, Zhang Z, Ballinger DG, Rice JP. A comparison of association statistics between pooled and individual genotypes. Hum Hered 2009; 67:219-25. [PMID: 19172081 DOI: 10.1159/000194975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 07/25/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Markers for individual genotyping can be selected using quantitative genotyping of pooled DNA. This strategy saves time and money. METHODS To determine the efficacy of this approach, we investigated the bivariate distribution of association test statistics from pooled and individual genotypes. We used a sample of approximately 1,000 samples with individual and pooled genotyping on 40,000 SNPs. RESULTS AND CONCLUSIONS We found that the distribution of the joint test statistics can be modelled as a mixture of two bivariate normal distributions. One distribution has a correlation of zero, and is probably due to SNPs whose pooled genotyping was unsuccessful. The other distribution has a correlation of approximately 0.65 in our data. This latter distribution is probably accounted for by SNPs whose pooled genotyping accurately predicts the underlying allele frequency. Approximately 87% of the data belongs to this distribution. We also derived a method to investigate the effect of both the correlation and selection cut-off on the relative power of pooling studies. We demonstrate that pooled genotyping has good power to detect SNPs that are truly associated with disease-causing variants for SNPs showing good correlation between pooled and individual genotyping. Therefore, this approach is a cost effective tool for association studies.
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Affiliation(s)
- Jo Knight
- Social Genetic & Developmental Psychiatry MRC Centre, Institute of Psychiatry, Kings College London, London, UK.
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Zhao Y, Wang S. Optimal DNA pooling-based two-stage designs in case-control association studies. Hum Hered 2008; 67:46-56. [PMID: 18931509 DOI: 10.1159/000164398] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 01/03/2007] [Indexed: 11/19/2022] Open
Abstract
Study cost remains the major limiting factor for genome-wide association studies due to the necessity of genotyping a large number of SNPs for a large number of subjects. Both DNA pooling strategies and two-stage designs have been proposed to reduce genotyping costs. In this study, we propose a cost-effective, two-stage approach with a DNA pooling strategy. During stage I, all markers are evaluated on a subset of individuals using DNA pooling. The most promising set of markers is then evaluated with individual genotyping for all individuals during stage II. The goal is to determine the optimal parameters (pi(p)(sample ), the proportion of samples used during stage I with DNA pooling; and pi(p)(marker ), the proportion of markers evaluated during stage II with individual genotyping) that minimize the cost of a two-stage DNA pooling design while maintaining a desired overall significance level and achieving a level of power similar to that of a one-stage individual genotyping design. We considered the effects of three factors on optimal two-stage DNA pooling designs. Our results suggest that, under most scenarios considered, the optimal two-stage DNA pooling design may be much more cost-effective than the optimal two-stage individual genotyping design, which use individual genotyping during both stages.
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Affiliation(s)
- Yihong Zhao
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, N.Y., USA
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Abstract
The analysis of genome wide variation offers the possibility of unravelling the genes involved in the pathogenesis of disease. Genome wide association studies are also particularly useful for identifying and validating targets for therapeutic intervention as well as for detecting markers for drug efficacy and side effects. The cost of such large-scale genetic association studies may be reduced substantially by the analysis of pooled DNA from multiple individuals. However, experimental errors inherent in pooling studies lead to a potential increase in the false positive rate and a loss in power compared to individual genotyping. Here we quantify various sources of experimental error using empirical data from typical pooling experiments and corresponding individual genotyping counts using two statistical methods. We provide analytical formulas for calculating these different errors in the absence of complete information, such as replicate pool formation, and for adjusting for the errors in the statistical analysis. We demonstrate that DNA pooling has the potential of estimating allele frequencies accurately, and adjusting the pooled allele frequency estimates for differential allelic amplification considerably improves accuracy. Estimates of the components of error show that differential allelic amplification is the most important contributor to the error variance in absolute allele frequency estimation, followed by allele frequency measurement and pool formation errors. Our results emphasise the importance of minimising experimental errors and obtaining correct error estimates in genetic association studies.
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Affiliation(s)
- A Jawaid
- Research & Development Genetics, AstraZeneca Pharmaceuticals, Macclesfield Cheshire SK104TG, UK.
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Abraham R, Moskvina V, Sims R, Hollingworth P, Morgan A, Georgieva L, Dowzell K, Cichon S, Hillmer AM, O'Donovan MC, Williams J, Owen MJ, Kirov G. A genome-wide association study for late-onset Alzheimer's disease using DNA pooling. BMC Med Genomics 2008; 1:44. [PMID: 18823527 PMCID: PMC2570675 DOI: 10.1186/1755-8794-1-44] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Accepted: 09/29/2008] [Indexed: 02/05/2023] Open
Abstract
Background Late-onset Alzheimer's disease (LOAD) is an age related neurodegenerative disease with a high prevalence that places major demands on healthcare resources in societies with increasingly aged populations. The only extensively replicable genetic risk factor for LOAD is the apolipoprotein E gene. In order to identify additional genetic risk loci we have conducted a genome-wide association (GWA) study in a large LOAD case – control sample, reducing costs through the use of DNA pooling. Methods DNA samples were collected from 1,082 individuals with LOAD and 1,239 control subjects. Age at onset ranged from 60 to 95 and Controls were matched for age (mean = 76.53 years, SD = 33), gender and ethnicity. Equimolar amounts of each DNA sample were added to either a case or control pool. The pools were genotyped using Illumina HumanHap300 and Illumina Sentrix HumanHap240S arrays testing 561,494 SNPs. 114 of our best hit SNPs from the pooling data were identified and then individually genotyped in the case – control sample used to construct the pools. Results Highly significant association with LOAD was observed at the APOE locus confirming the validity of the pooled genotyping approach. For 109 SNPs outside the APOE locus, we obtained uncorrected p-values ≤ 0.05 for 74 after individual genotyping. To further test these associations, we added control data from 1400 subjects from the 1958 Birth Cohort with the evidence for association increasing to 3.4 × 10-6 for our strongest finding, rs727153. rs727153 lies 13 kb from the start of transcription of lecithin retinol acyltransferase (phosphatidylcholine – retinol O-acyltransferase, LRAT). Five of seven tag SNPs chosen to cover LRAT showed significant association with LOAD with a SNP in intron 2 of LRAT, showing greatest evidence of association (rs201825, p-value = 6.1 × 10-7). Conclusion We have validated the pooling method for GWA studies by both identifying the APOE locus and by observing a strong enrichment for significantly associated SNPs. We provide evidence for LRAT as a novel candidate gene for LOAD. LRAT plays a prominent role in the Vitamin A cascade, a system that has been previously implicated in LOAD.
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Affiliation(s)
- Richard Abraham
- Department of Psychological Medicine, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
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Chen HH, Jou YS, Lee WJ, Pan WH. Applying polynomial standard curve method to correct bias encountered in estimating allele frequencies using DNA pooling strategy. Genomics 2008; 92:429-35. [PMID: 18793711 DOI: 10.1016/j.ygeno.2008.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 08/15/2008] [Accepted: 08/18/2008] [Indexed: 11/25/2022]
Abstract
DNA pooling approach is a cost-saving strategy which is crucial for multiple-SNP association study and particularly for laboratories with limited budget. However, the biased allele frequency estimates cannot be completely abolished by kappa correction. Using the SNaPshottrade mark, we systematically examined the relations between actual minor allele frequencies (AMiAFs) levels and estimates obtained from the pooling process for all six types of SNPs. We applied principle of polynomial standard curves method (PSCM) to produce allele frequency estimates in pooled DNA samples and compared it with the kappa method. The results showed that estimates derived from the PSCM were in general closer to AMiAFs than those from the kappa method, particularly for C/G and G/T polymorphisms at the range of AMiAF between 20-40%. We demonstrated that applying PSCM in the SNaPshottrade mark platform is suitable for multiple-SNP association study using pooling strategy, due to its cost effectiveness and estimation accuracy.
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Affiliation(s)
- Hsin-Hung Chen
- Institute of Biomedical Sciences, Academia Sinica, Taiwan, ROC
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Homer N, Tembe WD, Szelinger S, Redman M, Stephan DA, Pearson JV, Nelson SF, Craig D. Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies. Bioinformatics 2008; 24:1896-902. [PMID: 18617537 PMCID: PMC2732219 DOI: 10.1093/bioinformatics/btn333] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 06/26/2008] [Accepted: 06/27/2008] [Indexed: 12/26/2022] Open
Abstract
For many genome-wide association (GWA) studies individually genotyping one million or more SNPs provides a marginal increase in coverage at a substantial cost. Much of the information gained is redundant due to the correlation structure inherent in the human genome. Pooling-based GWA studies could benefit significantly by utilizing this redundancy to reduce noise, improve the accuracy of the observations and increase genomic coverage. We introduce a measure of correlation between individual genotyping and pooling, under the same framework that r(2) provides a measure of linkage disequilibrium (LD) between pairs of SNPs. We then report a new non-haplotype multimarker multi-loci method that leverages the correlation structure between SNPs in the human genome to increase the efficacy of pooling-based GWA studies. We first give a theoretical framework and derivation of our multimarker method. Next, we evaluate simulations using this multimarker approach in comparison to single marker analysis. Finally, we experimentally evaluate our method using different pools of HapMap individuals on the Illumina 450S Duo, Illumina 550K and Affymetrix 5.0 platforms for a combined total of 1 333 631 SNPs. Our results show that use of multimarker analysis reduces noise specific to pooling-based studies, allows for efficient integration of multiple microarray platforms and provides more accurate measures of significance than single marker analysis. Additionally, this approach can be extended to allow for imputing the association significance for SNPs not directly observed using neighboring SNPs in LD. This multimarker method can now be used to cost-effectively complete pooling-based GWA studies with multiple platforms across over one million SNPs and to impute neighboring SNPs weighted for the loss of information due to pooling.
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Affiliation(s)
- Nils Homer
- Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
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Macgregor S, Zhao ZZ, Henders A, Nicholas MG, Montgomery GW, Visscher PM. Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays. Nucleic Acids Res 2008; 36:e35. [PMID: 18276640 PMCID: PMC2346606 DOI: 10.1093/nar/gkm1060] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association (GWA) studies to map genes for complex traits are powerful yet costly. DNA-pooling strategies have the potential to dramatically reduce the cost of GWA studies. Pooling using Affymetrix arrays has been proposed and used but the efficiency of these arrays has not been quantified. We compared and contrasted Affymetrix Genechip HindIII and Illumina HumanHap300 arrays on the same DNA pools and showed that the HumanHap300 arrays are substantially more efficient. In terms of effective sample size, HumanHap300-based pooling extracts >80% of the information available with individual genotyping (IG). In contrast, Genechip HindIII-based pooling only extracts approximately 30% of the available information. With HumanHap300 arrays concordance with IG data is excellent. Guidance is given on best study design and it is shown that even after taking into account pooling error, one stage scans can be performed for >100-fold reduced cost compared with IG. With appropriately designed two stage studies, IG can provide confirmation of pooling results whilst still providing approximately 20-fold reduction in total cost compared with IG-based alternatives. The large cost savings with Illumina HumanHap300-based pooling imply that future studies need only be limited by the availability of samples and not cost.
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Affiliation(s)
- Stuart Macgregor
- Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia.
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Pettersson E, Zajac P, Ståhl PL, Jacobsson JA, Fredriksson R, Marcus C, Schiöth HB, Lundeberg J, Ahmadian A. Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads. Hum Mutat 2008; 29:323-9. [PMID: 17994569 DOI: 10.1002/humu.20655] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Here we present an approach for allelotyping combining the multiplexing features of the trinucleotide threading (TnT) method with pooling of genomic DNA and massively parallel pyrosequencing, enabling reliable allele frequency estimation in large cohorts. The approach offers several benefits as compared to array-based methods and allows undertaking highly complex studies without compromising accuracy, while keeping the workload to a minimum. This proof-of-concept study involves formation of trinucleotide threads, targeting a total of 147 single-nucleotide polymorphisms (SNPs) related to obesity and cancer, for multiplex amplification and allele extraction from a pool of 462 genomes, followed by massively parallel pyrosequencing. Approximately 177k reads were approved, identified, and assigned to SNP-carrying threads rendering representative allele frequencies in the cohort.
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Affiliation(s)
- Erik Pettersson
- Department of Gene Technology, Royal Institute of Technology (Kungliga Tekniska Högskolan, KTH), AlbaNova University Center, Stockholm, Sweden
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Butcher LM, Davis OSP, Craig IW, Plomin R. Genome-wide quantitative trait locus association scan of general cognitive ability using pooled DNA and 500K single nucleotide polymorphism microarrays. GENES BRAIN AND BEHAVIOR 2008; 7:435-46. [PMID: 18067574 PMCID: PMC2408663 DOI: 10.1111/j.1601-183x.2007.00368.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
General cognitive ability (g), which refers to what cognitive abilities have in common, is an important target for molecular genetic research because multivariate quantitative genetic analyses have shown that the same set of genes affects diverse cognitive abilities as well as learning disabilities. In this first autosomal genome-wide association scan of g, we used a two-stage quantitative trait locus (QTL) design with pooled DNA to screen more than 500 000 single nucleotide polymorphisms (SNPs) on microarrays, selecting from a sample of 7000 7-year-old children. In stage 1, we screened for allele frequency differences between groups pooled for low and high g. In stage 2, 47 SNPs nominated in stage 1 were tested by individually genotyping an independent sample of 3195 individuals, representative of the entire distribution of g scores in the full 7000 7-year-old children. Six SNPs yielded significant associations across the normal distribution of g, although only one SNP remained significant after a false discovery rate of 0.05 was imposed. However, none of these SNPs accounted for more than 0.4% of the variance of g, despite 95% power to detect associations of that size. It is likely that QTL effect sizes, even for highly heritable traits such as cognitive abilities and disabilities, are much smaller than previously assumed. Nonetheless, an aggregated ‘SNP set’ of the six SNPs correlated 0.11 (P < 0.00000003) with g. This shows that future SNP sets that will incorporate many more SNPs could be useful for predicting genetic risk and for investigating functional systems of effects from genes to brain to behavior.
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Affiliation(s)
- L M Butcher
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
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Docherty SJ, Butcher LM, Schalkwyk LC, Plomin R. Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies. BMC Genomics 2007; 8:214. [PMID: 17610740 PMCID: PMC1925094 DOI: 10.1186/1471-2164-8-214] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 07/04/2007] [Indexed: 01/02/2023] Open
Abstract
Background Genetic influences underpinning complex traits are thought to involve multiple quantitative trait loci (QTLs) of small effect size. Detection of such QTL associations requires systematic screening of large numbers of DNA markers within large sample populations. Using pooled DNA on SNP microarrays to screen for allelic frequency differences between groups such as cases and controls (called SNP Microarray and Pooling, or SNP-MaP) has been validated as an efficient solution on both 10 k and 100 k platforms. We demonstrate that this approach can be effectively applied to the truly genomewide Affymetrix GeneChip® Mapping 500 K Array. Results In comparisons between five independent DNA pools (N ~200 per pool) on separate Affymetrix GeneChip® Mapping 500 K Array sets, we show that, for SNPs with minor allele frequencies > 0.05, the reliability of the rank order of estimated allele frequencies, assessed as the average correlation between allele frequency estimates across the DNA pools, was 0.948 (average mean difference across the five pools = 0.069). Similarly, validity of the SNP-MaP approach was demonstrated by a rank-order correlation of 0.937 (average mean difference = 0.095) between the average DNA pool allele frequency estimates and the allele frequencies of an independent (CEPH) sample of 60 unrelated individually genotyped subjects. Conclusion We conclude that SNP-MaP can be extended for use on the Affymetrix GeneChip® Mapping 500 K Array, providing a cost-effective, reliable and valid initial screen of 500 K SNP microarrays in genomewide association scans.
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Affiliation(s)
- Sophia J Docherty
- Social, Genetic and Developmental Psychiatry Centre, Box Number P082, Institute of Psychiatry, DeCrispigny Park, London, SE5 8AF, UK
| | - Lee M Butcher
- Social, Genetic and Developmental Psychiatry Centre, Box Number P082, Institute of Psychiatry, DeCrispigny Park, London, SE5 8AF, UK
| | - Leonard C Schalkwyk
- Social, Genetic and Developmental Psychiatry Centre, Box Number P082, Institute of Psychiatry, DeCrispigny Park, London, SE5 8AF, UK
| | - Robert Plomin
- Social, Genetic and Developmental Psychiatry Centre, Box Number P082, Institute of Psychiatry, DeCrispigny Park, London, SE5 8AF, UK
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