1
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Statistically efficient association analysis of quantitative traits with haplotypes and untyped SNPs in family studies. BMC Genet 2020; 21:99. [PMID: 32894040 PMCID: PMC7487716 DOI: 10.1186/s12863-020-00902-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 08/17/2020] [Indexed: 11/23/2022] Open
Abstract
Background Associations between haplotypes and quantitative traits provide valuable information about the genetic basis of complex human diseases. Haplotypes also provide an effective way to deal with untyped SNPs. Two major challenges arise in haplotype-based association analysis of family data. First, haplotypes may not be inferred with certainty from genotype data. Second, the trait values within a family tend to be correlated because of common genetic and environmental factors. Results To address these challenges, we present an efficient likelihood-based approach to analyzing associations of quantitative traits with haplotypes or untyped SNPs. This approach properly accounts for within-family trait correlations and can handle general pedigrees with arbitrary patterns of missing genotypes. We characterize the genetic effects on the quantitative trait by a linear regression model with random effects and develop efficient likelihood-based inference procedures. Extensive simulation studies are conducted to examine the performance of the proposed methods. An application to family data from the Childhood Asthma Management Program Ancillary Genetic Study is provided. A computer program is freely available. Conclusions Results from extensive simulation studies show that the proposed methods for testing the haplotype effects on quantitative traits have correct type I error rates and are more powerful than some existing methods.
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Granot-Hershkovitz E, Wu P, Karasik D, Peter I, Peloso GM, Levy D, Vasan RS, Adrienne Cupples L, Liu CT, Meigs JB, Siscovick DS, Dupuis J, Friedlander Y, Hochner H. Searching for parent-of-origin effects on cardiometabolic traits in imprinted genomic regions. Eur J Hum Genet 2020; 28:646-655. [PMID: 31896779 PMCID: PMC7170899 DOI: 10.1038/s41431-019-0568-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 11/08/2022] Open
Abstract
Cardiometabolic traits pose a major global public health burden. Large-scale genome-wide association studies (GWAS) have identified multiple loci accounting for up to 30% of the genetic variance in complex traits such as cardiometabolic traits. However, the contribution of parent-of-origin effects (POEs) to complex traits has been largely ignored in GWAS. Family-based studies enable the assessment of POEs in genetic association analyses. We investigated POEs on a range of complex traits in 3 family-based studies. The discovery phase was carried out in large pedigrees from the Kibbutzim Family Study (n = 901 individuals) and in 872 parent-offspring trios from the Jerusalem Perinatal Study. Focusing on imprinted genomic regions, we examined parent-specific associations with 12 complex traits (i.e., body-size, blood pressure, lipids), mostly cardiometabolic risk traits. Forty five of the 11,967 SNPs initially found to have POE were evaluated for replication (p value < 1 × 10-4) in Framingham Heart Study families (max n = 8000 individuals). Three common variants yielded evidence of POE in the meta-analysis. Two variants, located on chr6 in the HLA region, showed a paternal effect on height (rs1042136: βpaternal = -0.023, p value = 1.5 × 10-8 and rs1431403: βpaternal = -0.011, p value = 5.4 × 10-6). The corresponding maternally-derived effects were statistically nonsignificant. The variant rs9332053, located on chr13 in RCBTB2 gene, demonstrated a maternal effect on hip circumference (βmaternal = -4.24, p value = 9.6 × 10-6; βpaternal = 1.29, p value = 0.23). These findings provide evidence for the utility of incorporating POEs into association studies of cardiometabolic traits, especially anthropometric traits. The study highlights the benefits of using family-based data for deciphering the genetic architecture of complex traits.
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Affiliation(s)
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Daniel Levy
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Ramachandran S Vasan
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- Sections of Preventive medicine and Epidemiology, and cardiovascular medicine, Departments of Medicine and Epidemiology, Boston University Schools of Medicine and Public health, Boston, MA, 02118, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - James B Meigs
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - David S Siscovick
- Institute for Urban Health, New York Academy of Medicine, New York, NY, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Yechiel Friedlander
- Braun School of Public Health, The Hebrew University of Jerusalem, 99112102, Jerusalem, Israel
| | - Hagit Hochner
- Braun School of Public Health, The Hebrew University of Jerusalem, 99112102, Jerusalem, Israel.
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3
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Amish SJ, Ali O, Peacock M, Miller M, Robinson M, Smith S, Luikart G, Neville H. Assessing thermal adaptation using family‐based association and
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outlier tests in a threatened trout species. Mol Ecol 2019; 28:2573-2593. [DOI: 10.1111/mec.15100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 03/15/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Stephen J. Amish
- Conservation Genomics Group, Division of Biological Sciences University of Montana Missoula Montana
- Flathead Biological Station University of Montana Polson Montana
| | - Omar Ali
- Department of Animal Science University of California Davis California
| | - Mary Peacock
- Department of Biology University of Nevada Reno Nevada
| | - Michael Miller
- Department of Animal Science University of California Davis California
| | | | - Seth Smith
- Flathead Biological Station University of Montana Polson Montana
| | - Gordon Luikart
- Conservation Genomics Group, Division of Biological Sciences University of Montana Missoula Montana
- Flathead Biological Station University of Montana Polson Montana
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4
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Ersig AL, Schutte DL, Standley J, Leslie EJ, Zimmerman B, Hanrahan K, Murray JC, McCarthy AM. Genetic Variants and the Cortisol Response in Children: An Exploratory Study. Biol Res Nurs 2019; 21:157-165. [PMID: 30700110 PMCID: PMC6700893 DOI: 10.1177/1099800419826315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OBJECTIVE We examined genomic variation potentially associated with the cortisol stress response in children having a painful medical procedure. DESIGN Children 4-10 years old having a peripheral intravenous line inserted provided saliva samples for evaluation of the cortisol response as a biological measure of distress: two on the day of the procedure and two at home on a nonstressful day for comparison values. Children and biological parents also provided samples for genotyping of variants with known or suspected association with the cortisol stress response. Analysis included child-only association and family-based transmission disequilibrium tests (TDTs). RESULTS Genotype and phenotype data on the cortisol stress response were available from 326 children for child-only association analyses and 376 complete family trios for TDTs. Children were 50% female, an average of 7.5 years old, and mostly (83%) White/non-Hispanic. We identified four single-nucleotide polymorphisms (SNPs) potentially associated with the cortisol stress response: rs1176744 ( HTR3B), rs10062367 ( CRHBP), rs634479 ( OPRM1), and rs8030107 ( NTRK3). Family-based analysis identified a two-SNP haplotype in HTR1B suggestive for association with the cortisol response (rs6296, rs11568817). Allelic TDTs identified rs7897947 ( NFKB2) as potentially related to cortisol response. CONCLUSIONS Findings provide preliminary evidence for genes potentially important in cortisol response to an acute stressor in children in the serotonin, dopamine, and brain-derived neurotrophic factor pathways, the hypothalamic-pituitary-adrenal axis, and the inflammatory response. Combined with analyses of related phenotypes and clinical data, these results could help identify patients at increased risk of adverse responses to painful medical procedures who might benefit from tailored interventions.
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Affiliation(s)
- Anne L. Ersig
- School of Nursing, University of Wisconsin–Madison, Madison, WI, USA
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5
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Robust Rare-Variant Association Tests for Quantitative Traits in General Pedigrees. STATISTICS IN BIOSCIENCES 2018; 10:491-505. [DOI: 10.1007/s12561-017-9197-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Ersig AL, Schutte DL, Standley J, Leslie E, Zimmerman B, Kleiber C, Hanrahan K, Murray JC, McCarthy AM. Relationship of Genetic Variants With Procedural Pain, Anxiety, and Distress in Children. Biol Res Nurs 2017; 19:339-349. [PMID: 28413930 DOI: 10.1177/1099800417692878] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE This study used a candidate gene approach to examine genomic variation associated with pain, anxiety, and distress in children undergoing a medical procedure. STUDY DESIGN Children aged 4-10 years having an IV catheter insertion were recruited from three Midwestern children's hospitals. Self-report measures of pain, anxiety, and distress were obtained as well as an observed measure of distress. Samples were collected from children and biological parents for analysis of genomic variation. Genotyped variants had known or suspected association with phenotypes of interest. Analyses included child-only association and family-based transmission disequilibrium tests. RESULTS Genotype and phenotype data were available from 828 children and 376 family trios. Children were 50% male, had a mean age of 7.2 years, and were 84% White/non-Hispanic. In family-based analysis, one single-nucleotide polymorphism (SNP; rs1143629, interleukin ( IL1B) 1β) was associated with observed child distress at Bonferroni-corrected levels of significance ( p = .00013), while two approached significance for association with high state anxiety (rs6330 Nerve Growth Factor, Beta Subunit, [ NGFB]) and high trait anxiety (rs6265 brain-derived neurotrophic factor [ BDNF]). In the child-only analysis, multiple SNPs showed nominal evidence of relationships with phenotypes of interest. rs6265 BDNF and rs2941026 cholecystokinin B receptor had possible relationships with trait anxiety in child-only and family-based analyses. CONCLUSIONS Exploring genomic variation furthers our understanding of pain, anxiety, and distress and facilitates genomic screening to identify children at high risk of procedural pain, anxiety, and distress. Combined with clinical observations and knowledge, such explorations could help guide tailoring of interventions to limit procedure-related distress and identify genes and pathways of interest for future genotype-phenotype studies.
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Affiliation(s)
- Anne L Ersig
- 1 College of Nursing, The University of Iowa, Iowa City, IA, USA
| | - Debra L Schutte
- 2 College of Nursing, Wayne State University, Detroit, MI, USA
| | | | - Elizabeth Leslie
- 4 School of Dental Medicine, The University of Pittsburgh, Pittsburgh, PA, USA
| | - Bridget Zimmerman
- 5 College of Public Health, The University of Iowa, Iowa City, IA, USA
| | | | - Kirsten Hanrahan
- 6 The University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Jeffrey C Murray
- 3 College of Medicine, The University of Iowa, Iowa City, IA, USA
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Prasad RB, Lessmark A, Almgren P, Kovacs G, Hansson O, Oskolkov N, Vitai M, Ladenvall C, Kovacs P, Fadista J, Lachmann M, Zhou Y, Sonestedt E, Poon W, Wollheim CB, Orho-Melander M, Stumvoll M, Tuomi T, Pääbo S, Koranyi L, Groop L. Excess maternal transmission of variants in the THADA gene to offspring with type 2 diabetes. Diabetologia 2016; 59:1702-13. [PMID: 27155871 DOI: 10.1007/s00125-016-3973-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 04/01/2016] [Indexed: 02/04/2023]
Abstract
AIMS/HYPOTHESIS Genome-wide association studies (GWAS) have identified more than 65 genetic loci associated with risk of type 2 diabetes. However, the contribution of distorted parental transmission of alleles to risk of type 2 diabetes has been mostly unexplored. Our goal was therefore to search for parent-of-origin effects (POE) among type 2 diabetes loci in families. METHODS Families from the Botnia study (n = 4,211, 1,083 families) were genotyped for 72 single-nucleotide polymorphisms (SNPs) associated with type 2 diabetes and assessed for POE on type 2 diabetes. The family-based Hungarian Transdanubian Biobank (HTB) (n = 1,463, >135 families) was used to replicate SNPs showing POE. Association of type 2 diabetes loci within families was also tested. RESULTS Three loci showed nominal POE, including the previously reported variants in KCNQ1, for type 2 diabetes in families from Botnia (rs2237895: p POE = 0.037), which can be considered positive controls. The strongest POE was seen for rs7578597 SNP in the THADA gene, showing excess transmission of the maternal risk allele T to diabetic offspring (Botnia: p POE = 0.01; HTB p POE = 0.045). These data are consistent with previous evidence of allelic imbalance for expression in islets, suggesting that the THADA gene can be imprinted in a POE-specific fashion. Five CpG sites, including those flanking rs7578597, showed differential methylation between diabetic and non-diabetic donor islets. CONCLUSIONS/INTERPRETATION Taken together, the data emphasise the need for genetic studies to consider from which parent an offspring has inherited a susceptibility allele.
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Affiliation(s)
- Rashmi B Prasad
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden.
| | - Anna Lessmark
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Peter Almgren
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | | | - Ola Hansson
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Nikolay Oskolkov
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Marta Vitai
- Heart Center Foundation, DRC, Balatonfured, Hungary
| | - Claes Ladenvall
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Peter Kovacs
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Joao Fadista
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | | | - Yuedan Zhou
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Emily Sonestedt
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Wenny Poon
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Claes B Wollheim
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
- Department of Cell Physiology and Metabolism, University Medical Center, Geneva, Switzerland
| | - Marju Orho-Melander
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Tiinamaija Tuomi
- Folkhälsan Research Centre, Helsinki, Finland
- Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Leif Groop
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University CRC, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden.
- Finnish Institute of Molecular Medicine (FIMM), Helsinki University, Helsinki, Finland.
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8
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Thameem F, Puppala S, Farook VS, Kasinath BS, Blangero J, Duggirala R, Abboud HE. Genetic Variants in Toll-Like Receptor 4 Gene and Their Association Analysis with Estimated Glomerular Filtration Rate in Mexican American Families. Cardiorenal Med 2016; 6:301-6. [PMID: 27648011 DOI: 10.1159/000445754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 03/08/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIM Toll-like receptor 4 (TLR4) is one of the regulators of the innate immune response. Genetic variations in TLR4 have been associated with inflammatory diseases, including type 2 diabetes. However, to our knowledge, there are no reports on the role of variations in TLR4 in chronic kidney disease susceptibility. The objective of this study is to determine whether the genetic variants in TLR4 are associated with the estimated glomerular filtration rate (eGFR), a measure of renal function. METHODS To evaluate the association between TLR4 variants and eGFR, we used data obtained from 434 Mexican American participants from the San Antonio Family Diabetes/Gallbladder Study. GFR was estimated using the Modification of Diet in Renal Disease formula. The Asp(299)Gly (rs4986790) and Thr(399)Ile (rs4986791) variants of TLR4 were genotyped using the TaqMan assay. Association analyses between genotypes and eGFR were performed using the measured genotype approach. RESULTS Of the two genetic markers examined for association, only the Asp(299)Gly variant of TLR4 exhibited a nominally significant association with eGFR (p = 0.025) after accounting for the covariate effects of age and sex terms, diabetes, duration of diabetes, systolic blood pressure, body mass index, and antihypertensive treatment. Carriers of Gly299 had significantly decreased eGFR values. Although, the Thr(399)Ile variant failed to exhibit a statistically significant association with eGFR, the carriers of Ile399, however, showed a trend towards decrease in eGFR. CONCLUSION We show for the first time that Asp(299)Gly variants of TLR4 are associated with decrease in renal function in Mexican Americans.
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Affiliation(s)
- Farook Thameem
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center, San Antonio, Tex, USA; Department of Biochemistry, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Sobha Puppala
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Tex, USA
| | - Vidya S Farook
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Tex., and Edinburg, Tex., USA
| | - Balakuntalam S Kasinath
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center, San Antonio, Tex, USA; South Texas Veterans Healthcare System, San Antonio, Tex, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Tex., and Edinburg, Tex., USA
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, Tex., and Edinburg, Tex., USA
| | - Hanna E Abboud
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center, San Antonio, Tex, USA; South Texas Veterans Healthcare System, San Antonio, Tex, USA
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Hochner H, Allard C, Granot-Hershkovitz E, Chen J, Sitlani CM, Sazdovska S, Lumley T, McKnight B, Rice K, Enquobahrie DA, Meigs JB, Kwok P, Hivert MF, Borecki IB, Gomez F, Wang T, van Duijn C, Amin N, Rotter JI, Stamatoyannopoulos J, Meiner V, Manor O, Dupuis J, Friedlander Y, Siscovick DS. Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults. PLoS Genet 2015; 11:e1005573. [PMID: 26451733 PMCID: PMC4599806 DOI: 10.1371/journal.pgen.1005573] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 09/15/2015] [Indexed: 01/23/2023] Open
Abstract
Loci identified in genome-wide association studies (GWAS) of cardio-metabolic traits account for a small proportion of the traits' heritability. To date, most association studies have not considered parent-of-origin effects (POEs). Here we report investigation of POEs on adiposity and glycemic traits in young adults. The Jerusalem Perinatal Family Follow-Up Study (JPS), comprising 1250 young adults and their mothers was used for discovery. Focusing on 18 genes identified by previous GWAS as associated with cardio-metabolic traits, we used linear regression to examine the associations of maternally- and paternally-derived offspring minor alleles with body mass index (BMI), waist circumference (WC), fasting glucose and insulin. We replicated and meta-analyzed JPS findings in individuals of European ancestry aged ≤50 belonging to pedigrees from the Framingham Heart Study, Family Heart Study and Erasmus Rucphen Family study (total N≅4800). We considered p<2.7x10-4 statistically significant to account for multiple testing. We identified a common coding variant in the 4th exon of APOB (rs1367117) with a significant maternally-derived effect on BMI (β = 0.8; 95%CI:0.4,1.1; p = 3.1x10-5) and WC (β = 2.7; 95%CI:1.7,3.7; p = 2.1x10-7). The corresponding paternally-derived effects were non-significant (p>0.6). Suggestive maternally-derived associations of rs1367117 were observed with fasting glucose (β = 0.9; 95%CI:0.3,1.5; p = 4.0x10-3) and insulin (ln-transformed, β = 0.06; 95%CI:0.03,0.1; p = 7.4x10-4). Bioinformatic annotation for rs1367117 revealed a variety of regulatory functions in this region in liver and adipose tissues and a 50% methylation pattern in liver only, consistent with allelic-specific methylation, which may indicate tissue-specific POE. Our findings demonstrate a maternal-specific association between a common APOB variant and adiposity, an association that was not previously detected in GWAS. These results provide evidence for the role of regulatory mechanisms, POEs specifically, in adiposity. In addition this study highlights the benefit of utilizing family studies for deciphering the genetic architecture of complex traits. To date, genetic variants identified in large-scale genetic studies using recent technical and methodological advances explain only a small proportion of the genetic basis of obesity, diabetes and other cardiovascular risk factors. These studies were typically conducted in samples of unrelated individuals. Here we utilize a family-based approach to identify genetic variants associated with obesity-related traits. Specifically, we examined the separate contribution of maternally- vs. paternally-inherited common genetic variants to these traits. By examining 1250 young adults and their mothers from Jerusalem, we show that a specific genetic variant, rs1367117, located in the APOB gene on chromosome 2 is related to body mass index and waist circumference when inherited from mother and not from father. This maternal effect is not restricted to Jerusalemites, but is also seen in a large sample of individuals of European descent from independent family studies worldwide. Our findings provide support of the role of complex genetic mechanisms in obesity, and highlight the benefit of utilizing family studies for uncovering genetic pathways underlying common risk factors and diseases.
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Affiliation(s)
- Hagit Hochner
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
- * E-mail:
| | - Catherine Allard
- Département de Mathématiques, Université de Sherbrooke and Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
| | | | - Jinbo Chen
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Colleen M. Sitlani
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
| | - Sandra Sazdovska
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Thomas Lumley
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Daniel A. Enquobahrie
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - James B. Meigs
- Harvard Medical School and General Medicine Division, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Pui Kwok
- Institute of Human Genetics, University of California, San Francisco, California, United States of America
- Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
- Department of Dermatology, University of California, San Francisco, California, United States of America
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States of America
| | - Ingrid B. Borecki
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Felicia Gomez
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Cornelia van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam, the Netherlands
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - John Stamatoyannopoulos
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Vardiella Meiner
- Department of Genetics and Metabolism, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Orly Manor
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Yechiel Friedlander
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - David S. Siscovick
- New York Academy of Medicine, New York, New York, United States of America
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10
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GRIN2B mediates susceptibility to intelligence quotient and cognitive impairments in developmental dyslexia. Psychiatr Genet 2015; 25:9-20. [DOI: 10.1097/ypg.0000000000000068] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Identification of genetic variants associated with capecitabine-induced hand-foot syndrome through integration of patient and cell line genomic analyses. Pharmacogenet Genomics 2014; 24:231-7. [PMID: 24595012 DOI: 10.1097/fpc.0000000000000037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVE A primary challenge in identifying replicable pharmacogenomic markers from clinical genomewide association study (GWAS) trials in oncology is the difficulty in performing a second large clinical trial with the same drugs and dosage regimen. We sought to overcome this challenge by incorporating GWAS results from cell-based studies using the same chemotherapy as a clinical cohort. METHODS In this study, we test whether the overlap between genetic variants identified in a preclinical study and a clinical study on capecitabine is more than expected by chance. A GWAS of capecitabine-induced cytotoxicity was performed in 164 lymphoblastoid cell lines derived from the CEU HapMap population and compared with a GWAS of hand-foot syndrome (HFS), the most frequent capecitabine-induced adverse drug reaction, in Spanish breast and colorectal cancer patients (n=160) treated with capecitabine. RESULTS We observed an overlap of 16 single nucleotide polymorphisms associated with capecitabine-induced cytotoxicity (P<0.001) in lymphoblastoid cell lines and HFS (P<0.05) in patients, which is a greater overlap than expected by chance (genotype-phenotype permutation empirical P=0.015). Ten tag single nucleotide polymorphisms, which cover the overlap loci, were genotyped in a second patient cohort (n=85) and one of them, rs9936750, was associated with capecitabine-induced HFS (P=0.0076). CONCLUSION The enrichment results imply that cellular models of capecitabine-induced cytotoxicity may capture components of the underlying polygenic architecture of related toxicities in patients.
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Modulation at age of onset in tunisian huntington disease patients: implication of new modifier genes. GENETICS RESEARCH INTERNATIONAL 2014; 2014:210418. [PMID: 25254119 PMCID: PMC4164136 DOI: 10.1155/2014/210418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/26/2014] [Accepted: 08/13/2014] [Indexed: 11/17/2022]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder. The causative mutation is an expansion of more than 36 CAG repeats in the first exon of IT15 gene. Many studies have shown that the IT15 interacts with several modifier genes to regulate the age at onset (AO) of HD. Our study aims to investigate the implication of CAG expansion and 9 modifiers in the age at onset variance of 15 HD Tunisian patients and to establish the correlation between these modifiers genes and the AO of this disease. Despite the small number of studied patients, this report consists of the first North African study in Huntington disease patients. Our results approve a specific effect of modifiers genes in each population.
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Jiang Y, Conneely KN, Epstein MP. Flexible and robust methods for rare-variant testing of quantitative traits in trios and nuclear families. Genet Epidemiol 2014; 38:542-51. [PMID: 25044337 DOI: 10.1002/gepi.21839] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/21/2014] [Accepted: 05/29/2014] [Indexed: 11/07/2022]
Abstract
Most rare-variant association tests for complex traits are applicable only to population-based or case-control resequencing studies. There are fewer rare-variant association tests for family-based resequencing studies, which is unfortunate because pedigrees possess many attractive characteristics for such analyses. Family-based studies can be more powerful than their population-based counterparts due to increased genetic load and further enable the implementation of rare-variant association tests that, by design, are robust to confounding due to population stratification. With this in mind, we propose a rare-variant association test for quantitative traits in families; this test integrates the QTDT approach of Abecasis et al. [Abecasis et al., ] into the kernel-based SNP association test KMFAM of Schifano et al. [Schifano et al., ]. The resulting within-family test enjoys the many benefits of the kernel framework for rare-variant association testing, including rapid evaluation of P-values and preservation of power when a region harbors rare causal variation that acts in different directions on phenotype. Additionally, by design, this within-family test is robust to confounding due to population stratification. Although within-family association tests are generally less powerful than their counterparts that use all genetic information, we show that we can recover much of this power (although still ensuring robustness to population stratification) using a straightforward screening procedure. Our method accommodates covariates and allows for missing parental genotype data, and we have written software implementing the approach in R for public use.
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Affiliation(s)
- Yunxuan Jiang
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, United States of America
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DeMenna J, Puppala S, Chittoor G, Schneider J, Kim JY, Shaibi GQ, Mandarino LJ, Duggirala R, Coletta DK. Association of common genetic variants with diabetes and metabolic syndrome related traits in the Arizona Insulin Resistance registry: a focus on Mexican American families in the Southwest. Hum Hered 2014; 78:47-58. [PMID: 25060389 DOI: 10.1159/000363411] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 05/06/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND/AIMS The increased occurrence of type 2 diabetes and its clinical correlates is a global public health issue, and there are continued efforts to find its genetic determinant across ethnically diverse populations. The aims of this study were to determine the heritability of diabetes and metabolic syndrome phenotypes in the Arizona Insulin Resistance (AIR) registry and to perform an association analysis of common single nucleotide polymorphisms (SNPs) identified by GWAS with these traits. All study participants were Mexican Americans from the AIR registry. METHODS Metabolic, anthropometric, demographic and medical history information was obtained on the 667 individuals enrolled in the registry. RESULTS The heritability estimates were moderate to high in magnitude and significant, indicating that the AIR registry is well suited for the identification of genetic factors contributing to diabetes and the metabolic syndrome. From the 30 GWAS genes selected (some genes were represented by multiple SNPs), 20 SNPs exhibited associations with one or more of the diabetes related traits with nominal significance (p ≤ 0.05). In addition, 25 SNPs were nominally significantly associated with one or more of the metabolic phenotypes tested (p ≤ 0.05). Most notably, 5 SNPs from 5 genes [body mass index (BMI), hip circumference: rs3751812/FTO; fasting plasma glucose, hemoglobin A1c: rs4607517/GCK; very-low-density lipoprotein: rs10830963/MTNR1B; BMI: rs13266634/SLC30A8, and total cholesterol, low-density lipoprotein: rs7578597/THADA] were significantly associated with obesity, glycemic, and lipid phenotypes when using the multiple testing significance threshold of 0.0015. CONCLUSION These findings extend previous work on Mexican Americans to suggest that metabolic disease is strongly influenced by genetic background in this high-risk population.
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Affiliation(s)
- Jacob DeMenna
- School of Life Sciences, Arizona State University, Tempe, Ariz., USA
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15
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Chen Z, Tan KR, Bull SB. Multiphase analysis by linkage, quantitative transmission disequilibrium, and measured genotype: systolic blood pressure in complex Mexican American pedigrees. BMC Proc 2014; 8:S108. [PMID: 25519311 PMCID: PMC4143726 DOI: 10.1186/1753-6561-8-s1-s108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We apply a multiphase strategy for pedigree-based genetic analysis of systolic blood pressure data collected in a longitudinal study of large Mexican American pedigrees. In the first phase, we conduct variance-components linkage analysis to identify regions that may harbor quantitative trait loci. In the second phase, we carry out pedigree-based association analysis in a selected region with common and low-frequency variants from genome-wide association studies and whole genome sequencing data. Using sequencing data, we compare approaches to pedigree analysis in a 10 megabase candidate region on chromosome 3 harboring a gene previously identified by a consortium for blood pressure genome-wide association studies. We observe that, as expected, the measured genotype analysis tends to provide larger signals than the quantitative transmission disequilibrium test. We also observe that while linkage signals are contributed by common variants, strong associations are found mainly at rare variants. Multiphase analysis can improve computational efficiency and reduce the multiple testing burden.
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Affiliation(s)
- Zhijian Chen
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, 60 Murray Street, Box 18, Toronto, Ontario M5T 3L9, Canada
| | - Kuan-Rui Tan
- Dalla Lana School of Public Health, Health Sciences Building, 155 College Street, University of Toronto, Toronto, Ontario M5T 3M7, Canada
| | - Shelley B Bull
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, 60 Murray Street, Box 18, Toronto, Ontario M5T 3L9, Canada ; Dalla Lana School of Public Health, Health Sciences Building, 155 College Street, University of Toronto, Toronto, Ontario M5T 3M7, Canada
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Hu Y, Hui Q, Sun YV. Association analysis of whole genome sequencing data accounting for longitudinal and family designs. BMC Proc 2014; 8:S89. [PMID: 25519416 PMCID: PMC4143808 DOI: 10.1186/1753-6561-8-s1-s89] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Using the whole genome sequencing data and the simulated longitudinal phenotypes for 849 pedigree-based individuals from Genetic Analysis Workshop 18, we investigated various approaches to detecting the association of rare and common variants with blood pressure traits. We compared three strategies for longitudinal data: (a) using the baseline measurement only, (b) using the average from multiple visits, and (c) using all individual measurements. We also compared the power of using all of the pedigree-based data and the unrelated subset. The analyses were performed without knowledge of the underlying simulating model.
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Affiliation(s)
- Yijuan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Qin Hui
- Department of Epidemiology, Emory University, Atlanta, GA, USA
| | - Yan V Sun
- Department of Epidemiology, Emory University, Atlanta, GA, USA ; Department of Biomedical Informatics, Emory University, Atlanta, GA, USA ; Center for Health Research, Kaiser Permanente Georgia, Atlanta, GA, USA
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17
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Bull SB, Chen Z, Tan KR, Poirier J. An exploration of heterogeneity in genetic analysis of complex pedigrees: linkage and association using whole genome sequencing data in the MAP4 region. BMC Proc 2014; 8:S107. [PMID: 25519361 PMCID: PMC4143705 DOI: 10.1186/1753-6561-8-s1-s107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We conduct pedigree-based linkage and association analyses of simulated systolic blood pressure data in the nonascertained large Mexican American pedigrees provided by Genetic Analysis Workshop 18, focusing on observed sequence variants in MAP4 on chromosome 3. Because pedigrees are large and sequence data have been completed by imputation, it is feasible to conduct analysis for each pedigree separately as well as for all pedigrees combined. We are interested in quantifying and explaining between-pedigree heterogeneity in linkage and association signals. To this end, we first examine minor allele frequency differences between pedigrees. In some of the pedigrees, rare and low-frequency variants occur at a higher prevalence than in all pedigrees combined. In simulation replicate 1, we conduct variance-components linkage and association analysis of all 894 MAP4 variants to compare analytic approaches in single pedigree and combined analysis. In all 200 replicates, we similarly examine the 15 causal variants in MAP4 known under the generating model. We illustrate how random allele frequency variation among pedigrees leads to heterogeneity in pedigree-specific linkage and association signals.
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Affiliation(s)
- Shelley B Bull
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, 60 Murray Street, Box 18, Toronto, Ontario M5T 3L9, Canada ; Dalla Lana School of Public Health, Health Sciences Building, 155 College Street, University of Toronto, Toronto, Ontario M5T 3M7, Canada
| | - Zhijian Chen
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, 60 Murray Street, Box 18, Toronto, Ontario M5T 3L9, Canada
| | - Kuan-Rui Tan
- Dalla Lana School of Public Health, Health Sciences Building, 155 College Street, University of Toronto, Toronto, Ontario M5T 3M7, Canada
| | - Julia Poirier
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, 60 Murray Street, Box 18, Toronto, Ontario M5T 3L9, Canada
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18
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Voruganti VS, Franceschini N, Haack K, Laston S, MacCluer JW, Umans JG, Comuzzie AG, North KE, Cole SA. Replication of the effect of SLC2A9 genetic variation on serum uric acid levels in American Indians. Eur J Hum Genet 2013; 22:938-43. [PMID: 24301058 DOI: 10.1038/ejhg.2013.264] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/08/2013] [Accepted: 10/18/2013] [Indexed: 12/21/2022] Open
Abstract
Increased serum uric acid (SUA) or hyperuricemia, a risk factor for gout, renal and cardiovascular diseases, is caused by either increased production or decreased excretion of uric acid or a mix of both. The solute carrier protein 2 family, member 9 (SLC2A9) gene encodes a transporter that mediates urate flux across the renal proximal tubule. Genome-wide association studies have consistently shown the association of single-nucleotide polymorphisms in this gene with SUA in majority populations. American Indian participants of the Strong Heart Family Study, belonging to multigenerational families, have high prevalence of hyperuricemia. We conducted measured genotype analyses, based on variance components decomposition method and accounting for family relationships, to assess whether the association between SUA and SLC2A9 gene polymorphisms generalized to American Indians (n=3604) of this study. Seven polymorphisms were selected for genotyping based on their association with SUA levels in other populations. A strong association was found between SLC2A9 gene polymorphisms and SUA in all centers combined (P-values: 1.3 × 10(-31)-5.1 × 10(-23)) and also when stratified by recruitment center; P-values: 1.2 × 10(-14)-1.0 × 10(-5). These polymorphisms were also associated with the estimated glomerular filtration rate and serum creatinine but not albumin-creatinine ratio. In summary, the association of polymorphisms in the uric acid transporter gene with SUA levels extends to a new population of American Indians.
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Affiliation(s)
- V Saroja Voruganti
- 1] Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA [2] Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karin Haack
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sandra Laston
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Jean W MacCluer
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Jason G Umans
- 1] Medstar Health Research Institute, Hyattsville, MD, USA [2] Georgetown-Howard Universities Center for Clinical and Translational Science, Washington, DC, USA
| | - Anthony G Comuzzie
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Kari E North
- 1] Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA [2] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shelley A Cole
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
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Pikkuhookana P, Sillanpää MJ. Combined linkage disequilibrium and linkage mapping: Bayesian multilocus approach. Heredity (Edinb) 2013; 112:351-60. [PMID: 24253936 DOI: 10.1038/hdy.2013.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 09/02/2013] [Accepted: 09/27/2013] [Indexed: 01/24/2023] Open
Abstract
Quantitative trait loci (QTL) affecting the phenotype of interest can be detected using linkage analysis (LA), linkage disequilibrium (LD) mapping or a combination of both (LDLA). The LA approach uses information from recombination events within the observed pedigree and LD mapping from the historical recombinations within the unobserved pedigree. We propose the Bayesian variable selection approach for combined LDLA analysis for single-nucleotide polymorphism (SNP) data. The novel approach uses both sources of information simultaneously as is commonly done in plant and animal genetics, but it makes fewer assumptions about population demography than previous LDLA methods. This differs from approaches in human genetics, where LDLA methods use LA information conditional on LD information or the other way round. We argue that the multilocus LDLA model is more powerful for the detection of phenotype-genotype associations than single-locus LDLA analysis. To illustrate the performance of the Bayesian multilocus LDLA method, we analyzed simulation replicates based on real SNP genotype data from small three-generational CEPH families and compared the results with commonly used quantitative transmission disequilibrium test (QTDT). This paper is intended to be conceptual in the sense that it is not meant to be a practical method for analyzing high-density SNP data, which is more common. Our aim was to test whether this approach can function in principle.
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Affiliation(s)
- P Pikkuhookana
- 1] Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland [2] Department of Biology, University of Oulu, Oulu, Finland [3] Department of Mathematical Sciences, University of Oulu, Oulu, Finland [4] Biocenter Oulu, University of Oulu, Oulu, Finland
| | - M J Sillanpää
- 1] Department of Biology, University of Oulu, Oulu, Finland [2] Department of Mathematical Sciences, University of Oulu, Oulu, Finland [3] Biocenter Oulu, University of Oulu, Oulu, Finland
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20
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Kaskow BJ, Diepeveen LA, Proffitt JM, Rea AJ, Ulgiati D, Blangero J, Moses EK, Abraham LJ. Molecular prioritization strategies to identify functional genetic variants in the cardiovascular disease-associated expression QTL Vanin-1. Eur J Hum Genet 2013; 22:688-95. [PMID: 24045843 DOI: 10.1038/ejhg.2013.208] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/31/2013] [Accepted: 08/16/2013] [Indexed: 11/09/2022] Open
Abstract
There is now good evidence that non-coding sequence variants are involved in the heritability of many common complex traits. The current 'gold standard' approach for assessing functionality is the in vitro reporter gene assay to assess allelic differences in transcriptional activity, usually followed by electrophoretic mobility shift assays to assess allelic differences in transcription factor binding. Although widely used, these assays have inherent limitations, including the lack of endogenous chromatin context. Here we present a more contemporary approach to assessing functionality of non-coding sequence variation within the Vanin-1 (VNN1) promoter. By combining 'gold standard' assays with in vivo assessments of chromatin accessibility, we greatly increase our confidence in the statistically assigned functional relevance. The standard assays revealed the -137 single nucleotide variant to be functional but the -587 variant to have no functional relevance. However, our in vivo tests show an allelic difference in chromatin accessibility surrounding the -587 variant supporting strong functional potential at both sites. Our approach advances the identification of functional variants by providing strong in vivo biological evidence for function.
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Affiliation(s)
- Belinda J Kaskow
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, Australia
| | - Luke A Diepeveen
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, Australia
| | - J Michael Proffitt
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Alexander J Rea
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, Australia
| | - Daniela Ulgiati
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, Australia
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Eric K Moses
- Centre for Genetic Origins of Health and Disease (GOHaD), University of Western Australia, Crawley, WA, Australia
| | - Lawrence J Abraham
- 1] School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA, Australia [2] Centre for Genetic Origins of Health and Disease (GOHaD), University of Western Australia, Crawley, WA, Australia
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21
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Gribble MO, Voruganti VS, Cropp CD, Francesconi KA, Goessler W, Umans JG, Silbergeld EK, Laston SL, Haack K, Kao WHL, Fallin MD, Maccluer JW, Cole SA, Navas-Acien A. SLCO1B1 variants and urine arsenic metabolites in the Strong Heart Family Study. Toxicol Sci 2013; 136:19-25. [PMID: 23970802 DOI: 10.1093/toxsci/kft181] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Arsenic species patterns in urine are associated with risk for cancer and cardiovascular diseases. The organic anion transporter coded by the gene SLCO1B1 may transport arsenic species, but its association with arsenic metabolites in human urine has not yet been studied. The objective of this study is to evaluate associations of urine arsenic metabolites with variants in the candidate gene SLCO1B1 in adults from the Strong Heart Family Study. We estimated associations between % arsenic species biomarker traits and 5 single-nucleotide polymorphisms (SNPs) in the SLCO1B1 gene in 157 participants, assuming additive genetics. Linear regression models for each SNP accounted for kinships and were adjusted for sex, body mass index, and study center. The minor allele of rs1564370 was associated with lower %MMA (p = .0003) and higher %DMA (p = .0002), accounting for 8% of the variance for %MMA and 9% for %DMA. The rs1564370 minor allele homozygote frequency was 17% and the heterozygote frequency was 43%. The minor allele of rs2291075 was associated with lower %MMA (p = .0006) and higher %DMA (p = .0014), accounting for 7% of the variance for %MMA and 5% for %DMA. The frequency of rs2291075 minor allele homozygotes was 1% and of heterozygotes was 15%. Common variants in SLCO1B1 were associated with differences in arsenic metabolites in a preliminary candidate gene study. Replication of this finding in other populations and analyses with respect to disease outcomes are needed to determine whether this novel candidate gene is important for arsenic-associated disease risks.
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Affiliation(s)
- Matthew O Gribble
- * Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205
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Mu W, Zhang W. Molecular Approaches, Models, and Techniques in Pharmacogenomic Research and Development. Pharmacogenomics 2013. [DOI: 10.1016/b978-0-12-391918-2.00008-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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23
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Wheeler HE, Gamazon ER, Wing C, Njiaju UO, Njoku C, Baldwin RM, Owzar K, Jiang C, Watson D, Shterev I, Kubo M, Zembutsu H, Winer EP, Hudis CA, Shulman LN, Nakamura Y, Ratain MJ, Kroetz DL, Cox NJ, Dolan ME. Integration of cell line and clinical trial genome-wide analyses supports a polygenic architecture of Paclitaxel-induced sensory peripheral neuropathy. Clin Cancer Res 2012. [PMID: 23204130 DOI: 10.1158/1078-0432.ccr-12-2618] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PURPOSE We sought to show the relevance of a lymphoblastoid cell line (LCL) model in the discovery of clinically relevant genetic variants affecting chemotherapeutic response by comparing LCL genome-wide association study (GWAS) results to clinical GWAS results. EXPERIMENTAL DESIGN A GWAS of paclitaxel-induced cytotoxicity was conducted in 247 LCLs from the HapMap Project and compared with a GWAS of sensory peripheral neuropathy in patients with breast cancer (n = 855) treated with paclitaxel in the Cancer and Leukemia Group B (CALGB) 40101 trial. Significant enrichment was assessed by permutation resampling analysis. RESULTS We observed an enrichment of LCL cytotoxicity-associated single-nucleotide polymorphisms (SNP) in the sensory peripheral neuropathy-associated SNPs from the clinical trial with concordant allelic directions of effect (empirical P = 0.007). Of the 24 SNPs that overlap between the clinical trial (P < 0.05) and the preclinical cytotoxicity study (P < 0.001), 19 of them are expression quantitative trait loci (eQTL), which is a significant enrichment of this functional class (empirical P = 0.0447). One of these eQTLs is located in RFX2, which encodes a member of the DNA-binding regulatory factor X family. Decreased expression of this gene by siRNA resulted in increased sensitivity of Neuroscreen-1(NS-1; rat pheochromocytoma) cells to paclitaxel as measured by reduced neurite outgrowth and increased cytotoxicity, functionally validating the involvement of RFX2 in nerve cell response to paclitaxel. CONCLUSIONS The enrichment results and functional example imply that cellular models of chemotherapeutic toxicity may capture components of the underlying polygenic architecture of related traits in patients.
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Affiliation(s)
- Heather E Wheeler
- Sections of Hematology/Oncology and Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
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Mascheretti S, Bureau A, Battaglia M, Simone D, Quadrelli E, Croteau J, Cellino MR, Giorda R, Beri S, Maziade M, Marino C. An assessment of gene-by-environment interactions in developmental dyslexia-related phenotypes. GENES BRAIN AND BEHAVIOR 2012; 12:47-55. [DOI: 10.1111/gbb.12000] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 09/26/2012] [Accepted: 10/24/2012] [Indexed: 01/02/2023]
Affiliation(s)
- S. Mascheretti
- The Academic Centre for the study of Behavioural Plasticity; Vita-Salute San Raffaele University; Milan; 20132; Italy
| | | | | | - D. Simone
- Department of Child Psychiatry; Scientific Institute Eugenio Medea; Bosisio Parini; Lecco; 23842; Italy
| | - E. Quadrelli
- Department of Child Psychiatry; Scientific Institute Eugenio Medea; Bosisio Parini; Lecco; 23842; Italy
| | - J. Croteau
- Centre de Recherche de l'Institut universitaire en santé mentale de Québec; Québec; G1J 2 G3; Canada
| | - M. R. Cellino
- Centro Regionale di Riferimento per i Disturbi dell'Apprendimento - CRRDA, ULSS 20; Verona; 37122; Italy
| | - R. Giorda
- Molecular Biology Laboratory; Scientific Institute Eugenio Medea; Bosisio Parini; Lecco; 23842; Italy
| | - S. Beri
- Molecular Biology Laboratory; Scientific Institute Eugenio Medea; Bosisio Parini; Lecco; 23842; Italy
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Pehlić M, Vrkić D, Skrabić V, Jerončić A, Stipančić G, Urojić AŠ, Marjanac I, Jakšić J, Kačić Z, Boraska V, Zemunik T. IL12RB2 gene is associated with the age of type 1 diabetes onset in Croatian family Trios. PLoS One 2012; 7:e49133. [PMID: 23152861 PMCID: PMC3496735 DOI: 10.1371/journal.pone.0049133] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 10/04/2012] [Indexed: 11/30/2022] Open
Abstract
Background Common complex diseases are influenced by both genetic and environmental factors. Many genetic factors overlap between various autoimmune diseases. The aim of the present study is to determine whether four genetic variants known to be risk variants for several autoimmune diseases could be associated with an increased susceptibility to type 1 diabetes mellitus. Methods and Findings We genotyped four genetic variants (rs2358817, rs1049550, rs6679356, rs9865818) within VTCN1, ANXA11, IL12RB2 and LPP genes respectively, in 265 T1DM family trios in Croatian population. We did not detect association of these polymorphisms with T1DM. However, quantitative transmission disequilibrium test (QTDT, orthogonal model) revealed a significant association between the age of onset of T1DM and IL12RB2 rs6679356 variant. An earlier onset of T1DM was associated with the rs6679356 minor dominant allele C (p = 0.005). The association remained significant even after the Bonferroni correction for multiple testing and permutation. Conclusions Variants originally associated with juvenile idiopathic arthritis (VTCN1 gene), sarcoidosis (ANXA11 gene), primary biliary cirrhosis (IL12RB2 gene) and celiac disease (LPP gene) were not associated with type 1 diabetes in our dataset. Nevertheless, association of IL12RB2 rs6679356 polymorphism with the age of T1DM onset suggests that this gene plays a role in defining the time of disease onset.
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Affiliation(s)
- Marina Pehlić
- Department of Medical Biology, University of Split, School of Medicine, Split, Croatia.
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Teyssèdre S, Elsen JM, Ricard A. Statistical distributions of test statistics used for quantitative trait association mapping in structured populations. Genet Sel Evol 2012; 44:32. [PMID: 23146127 PMCID: PMC3817592 DOI: 10.1186/1297-9686-44-32] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 10/31/2012] [Indexed: 11/25/2022] Open
Abstract
Background Spurious associations between single nucleotide polymorphisms and phenotypes are a major issue in genome-wide association studies and have led to underestimation of type 1 error rate and overestimation of the number of quantitative trait loci found. Many authors have investigated the influence of population structure on the robustness of methods by simulation. This paper is aimed at developing further the algebraic formalization of power and type 1 error rate for some of the classical statistical methods used: simple regression, two approximate methods of mixed models involving the effect of a single nucleotide polymorphism (SNP) and a random polygenic effect (GRAMMAR and FASTA) and the transmission/disequilibrium test for quantitative traits and nuclear families. Analytical formulae were derived using matrix algebra for the first and second moments of the statistical tests, assuming a true mixed model with a polygenic effect and SNP effects. Results The expectation and variance of the test statistics and their marginal expectations and variances according to the distribution of genotypes and estimators of variance components are given as a function of the relationship matrix and of the heritability of the polygenic effect. These formulae were used to compute type 1 error rate and power for any kind of relationship matrix between phenotyped and genotyped individuals for any level of heritability. For the regression method, type 1 error rate increased with the variability of relationships and with heritability, but decreased with the GRAMMAR method and was not affected with the FASTA and quantitative transmission/disequilibrium test methods. Conclusions The formulae can be easily used to provide the correct threshold of type 1 error rate and to calculate the power when designing experiments or data collection protocols. The results concerning the efficacy of each method agree with simulation results in the literature but were generalized in this work. The power of the GRAMMAR method was equal to the power of the FASTA method at the same type 1 error rate. The power of the quantitative transmission/disequilibrium test was low. In conclusion, the FASTA method, which is very close to the full mixed model, is recommended in association mapping studies.
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Affiliation(s)
- Simon Teyssèdre
- INRA, UR 631 Station d’Amélioration Génétique des Animaux, Castanet-Tolosan F-31326, France
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Bourget G. Handling missing data in transmission disequilibrium test in nuclear families with one affected offspring. PLoS One 2012; 7:e46100. [PMID: 23056239 PMCID: PMC3466247 DOI: 10.1371/journal.pone.0046100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 08/28/2012] [Indexed: 11/29/2022] Open
Abstract
The Transmission Disequilibrium Test (TDT) compares frequencies of transmission of two alleles from heterozygote parents to an affected offspring. This test requires all genotypes to be known from all members of the nuclear families. However, obtaining all genotypes in a study might not be possible for some families, in which case, a data set results in missing genotypes. There are many techniques of handling missing genotypes in parents but only a few in offspring. The robust TDT (rTDT) is one of the methods that handles missing genotypes for all members of nuclear families [with one affected offspring]. Even though all family members can be imputed, the rTDT is a conservative test with low power. We propose a new method, Mendelian Inheritance TDT (MITDT-ONE), that controls type I error and has high power. The MITDT-ONE uses Mendelian Inheritance properties, and takes population frequencies of the disease allele and marker allele into account in the rTDT method. One of the advantages of using the MITDT-ONE is that the MITDT-ONE can identify additional significant genes that are not found by the rTDT. We demonstrate the performances of both tests along with Sib-TDT (S-TDT) in Monte Carlo simulation studies. Moreover, we apply our method to the type 1 diabetes data from the Warren families in the United Kingdom to identify significant genes that are related to type 1 diabetes.
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Affiliation(s)
- Gulhan Bourget
- Department of Mathematics, California State University, Fullerton, California, United States of America.
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Thameem F, Puppala S, Schneider J, Bhandari B, Arya R, Arar NH, Vasylyeva TL, Farook VS, Fowler S, Almasy L, Blangero J, Duggirala R, Abboud HE. The Gly(972)Arg variant of human IRS1 gene is associated with variation in glomerular filtration rate likely through impaired insulin receptor signaling. Diabetes 2012; 61:2385-93. [PMID: 22617042 PMCID: PMC3425400 DOI: 10.2337/db11-1078] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The objective of this study is to identify and characterize the genetic variants related to the glomerular filtration rate (GFR) linkage on 2q37. Of the positional candidate genes, we selected IRS1 and resequenced its 2-kb promoter region and exons for sequence variants in 32 subjects. A total of 11 single nucleotide polymorphisms (SNPs) were identified. To comprehensively cover the 59-kb-long intron-1, eight additional tagging SNPs were selected from the HapMap. All the 19 SNPs were genotyped by TaqMan Assay in the entire data set (N = 670; 39 families). Association analyses between the SNPs and GFR and type 2 diabetes-related traits were performed using the measured genotype approach. Of the SNPs examined for association, only the Gly(972)Arg variant of IRS1 exhibited a significant association with GFR (P = 0.0006) and serum triglycerides levels (P = 0.003), after accounting for trait-specific covariate effects. Carriers of Arg972 had significantly decreased GFR values. Gly(972)Arg contributed to 26% of the linkage signal on 2q. Expression of IRS1 mutant Arg972 in human mesangial cells significantly reduced the insulin-stimulated phosphorylation of IRS1 and Akt kinase. Taken together, the data provide the first evidence that genetic variation in IRS1 may influence variation in GFR probably through impaired insulin receptor signaling.
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Affiliation(s)
- Farook Thameem
- Division of Nephrology, The University of Texas Health Science Center, San Antonio, Texas, USA.
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Abstract
OBJECTIVE(S) Developmental dyslexia is a heritable condition, with genetic factors accounting for 44-75% of the variance in performance tests of reading component subphenotypes. Compelling genetic linkage and association evidence supports a quantitative trait locus in the 6p21.3 region that encodes a gene called DCDC2. In this study, we explored the contribution of two DCDC2 markers to dyslexia, related reading and memory phenotypes in nuclear families of Italian origin. METHODS The 303 nuclear families recruited on the basis of having a proband with developmental dyslexia have been studied with 6p21.3 markers, BV677278 and rs793862. Marker-trait association was investigated by the quantitative transmission disequilibrium test (version 2.5.1) that allows for the analyses of quantitative traits. Seven phenotypes were used in association analyses, that is, word and nonword reading, word and nonword spelling, orthographic choice, memory, and the affected status based on inclusion criteria. RESULTS Quantitative transmission disequilibrium test analyses yielded evidence for association between reading skills and the BV677278 deletion (empirical P-values=0.025-0.029) and between memory and BV677278 allele 10 (empirical P-value=0.0001). CONCLUSION Our result adds further evidence in support of DCDC2 contributing to the deficits in developmental dyslexia. More specifically, our data support the view that DCDC2 influences both reading and memory impairments thus shedding further light into the etiologic basis and the phenotypic complexity of developmental dyslexia.
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Ding X, Wang C, Zhang Q. Pedigree transmission disequilibrium test for quantitative traits in farm animals. CHINESE SCIENCE BULLETIN-CHINESE 2012. [DOI: 10.1007/s11434-012-5218-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Xiao WJ, Ke YH, He JW, Zhang H, Yu JB, Hu WW, Gu JM, Gao G, Yue H, Wang C, Hu YQ, Li M, Liu YJ, Fu WZ, Zhang ZL. Polymorphisms in the human ALOX12 and ALOX15 genes are associated with peak bone mineral density in Chinese nuclear families. Osteoporos Int 2012; 23:1889-97. [PMID: 22089472 DOI: 10.1007/s00198-011-1835-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 09/06/2011] [Indexed: 10/15/2022]
Abstract
SUMMARY Association between ten single-nucleotide polymorphisms (SNPs) in the human ALOX12 and ALOX15 genes and variations in peak bone mineral density (BMD) in a large sample of Chinese nuclear families with female offspring using the quantitative transmission disequilibrium test (QTDT). Our results suggest that the genetic polymorphisms in both human ALOX12 and ALOX15 may contribute to variations in the peak BMD of Chinese women. INTRODUCTION The aim of this study was to investigate whether polymorphisms in the human ALOX12 and ALOX15 genes are associated with variations in peak BMD in Chinese nuclear families with female offspring. METHODS Each five SNPs in the ALOX12 and ALOX15 genes were genotyped in a total of 1,260 individuals from 401 Chinese nuclear families. The BMD of the lumbar spine, femoral neck and total hip was measured by dual-energy X-ray absorptiometry. We tested whether a single SNP or a haplotype was associated with peak BMD variations using the QTDT. RESULTS Using QTDT to measure within-family associations in ALOX15, we observed a significant association between rs916055 and BMD in the lumbar spine (p = 0.027 in the permutation 1,000 test). However, in ALOX12, rs312470 was significantly associated with BMD in the femoral neck (p = 0.029 and p = 0.036 in the permutation 1,000 test). The results of a haplotype analysis supported the findings of the single locus test for ALOX15. CONCLUSIONS Our results suggest that the genetic polymorphisms in both human ALOX12 and ALOX15 may contribute to variations in the peak BMD of Chinese women.
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Affiliation(s)
- W-J Xiao
- Metabolic Bone Disease and Genetics Research Unit, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital, Shanghai Jiaotong University, Shanghai, 200233, China
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Association between the 2-bp deletion polymorphism in the duplicated version of the alpha7 nicotinic receptor gene and P50 sensory gating. Eur J Hum Genet 2012; 21:76-81. [PMID: 22588665 DOI: 10.1038/ejhg.2012.81] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
There is considerable evidence implicating the 15q13.3 region in neuropsychiatric disorders, with the α7 nicotinic receptor gene CHRNA7 the most plausible candidate. This region has multiple duplications and many copy number variants (CNVs). A common CNV involves a partial duplication of CHRNA7 (CHRFAM7A), which occurs in either orientation. We examined the distribution of these alternative genomic arrangements in a large cohort of psychiatric patients, their relatives and controls using the 2-bp deletion polymorphism as a marker for the orientation of CHRFAM7A. We investigated three common alleles for association with psychosis and with the P50 sensory gating deficit, which is strongly associated with psychosis and strongly linked to 15q13.3. We found significant within-family association with P50 (empirical P=0.004), which is robust to population stratification. Most of the effect came from the 2-bp deletion allele, which tags the variant of CHRFAM7A in the same orientation as CHRNA7. This allele is associated with the presence of the P50 sensory gating deficit (empirical P=0.0006). Tests comparing within-family and between-family components of association suggest considerable population stratification in the sample. We found no evidence for association with psychosis, but this may reflect lower power using this phenotype. Four out of six previous association studies found association of different psychiatric phenotypes with the same 2-bp deletion allele.
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Functional polymorphisms in IL13 are protective against high Schistosoma mansoni infection intensity in a Brazilian population. PLoS One 2012; 7:e35863. [PMID: 22574126 PMCID: PMC3345031 DOI: 10.1371/journal.pone.0035863] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 03/27/2012] [Indexed: 11/30/2022] Open
Abstract
Background IL-13 is a signature cytokine of the helper T cell type 2 (TH2) pathway which underlies host defense to helminthic infection and activates production of IgE in both parasitized populations and in urban settings after allergen exposure. Methodology/Principal Findings Two functional polymorphisms in IL13, rs1800925 (or c.1-1111C>T) and rs20541 (or R130Q) were previously found to be associated with Schistosoma hematobium infection intensity. They have not been thoroughly explored in S. mansoni-endemic populations, however, and were selected along with 5 tagging SNPs for genotyping in 812 individuals in 318 nuclear families from a schistosomiasis-endemic area of Conde, Bahia, in Brazil. Regression models using GEE to account for family membership and family-based quantitative transmission disequilibrium tests (QTDT) were used to evaluate associations with total serum IgE (tIgE) levels and S. mansoni fecal egg counts adjusted for non-genetic covariates. We identified a protective effect for the T allele at rs20541 (P = 0.005) against high S. mansoni egg counts, corroborated by QTDT (P = 0.014). Our findings also suggested evidence for protective effects for the T allele at rs1800925 and A allele at rs2066960 after GEE analysis only (P = 0.050, 0.0002). Conclusions/Significance The two functional variants in IL13 are protective against high S. mansoni egg counts. These markers showed no evidence of association with tIgE levels, unlike tIgE levels previously studied in non-parasitized or atopic study populations.
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De Lobel L, Thijs L, Kouznetsova T, Staessen JA, Van Steen K. A family-based association test to detect gene-gene interactions in the presence of linkage. Eur J Hum Genet 2012; 20:973-80. [PMID: 22419171 DOI: 10.1038/ejhg.2012.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
For many complex diseases, quantitative traits contain more information than dichotomous traits. One of the approaches used to analyse these traits in family-based association studies is the quantitative transmission disequilibrium test (QTDT). The QTDT is a regression-based approach that models simultaneously linkage and association. It splits up the association effect in a between- and a within-family genetic component to adjust and test for population stratification and includes a variance components method to model linkage. We extend this approach to detect gene-gene interactions between two unlinked QTLs by adjusting the definition of the between- and within-family component and the variance components included in the model. We simulate data to investigate the influence of the epistasis model, linkage disequilibrium patterns between the markers and the QTLs, and allele frequencies on the power and type I error rates of the approach. Results show that for some of the investigated settings, power gains are obtained in comparison with FAM-MDR. We conclude that our approach shows promising results for candidate-gene studies where too few markers are available to correct for population stratification using standard methods (for example EIGENSTRAT). The proposed method is applied to real-life data on hypertension from the FLEMENGHO study.
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Affiliation(s)
- Lizzy De Lobel
- Department of Applied Mathematics and Computer Science, Ghent University, Ghent, Belgium.
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O'Donnell PH, Stark AL, Gamazon ER, Wheeler HE, McIlwee BE, Gorsic L, Im HK, Huang RS, Cox NJ, Dolan ME. Identification of novel germline polymorphisms governing capecitabine sensitivity. Cancer 2012; 118:4063-73. [PMID: 22864933 DOI: 10.1002/cncr.26737] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 11/11/2022]
Abstract
BACKGROUND Capecitabine, an oral 5-fluorouracil (5-FU) prodrug, is widely used in the treatment of breast, colorectal, and gastric cancers. To guide the selection of patients with potentially the greatest benefit of experiencing antitumor efficacy, or, alternatively, of developing toxicities, identifying genomic predictors of capecitabine sensitivity could permit its more informed use. METHODS The objective of this study was to perform capecitabine sensitivity genome-wide association studies (GWAS) using 503 well genotyped human cell lines from individuals representing multiple different world populations. A meta-analysis that included all ethnic populations then enabled the identification of novel germline determinants (single nucleotide polymorphisms [SNPs]) of capecitabine susceptibility. RESULTS First, an intrapopulation GWAS of Caucasian individuals identified reference SNP 4702484 (rs4702484) (within adenylate cyclase 2 [ADCY2]) at a level reaching genome-wide significance (P = 5.2 × 10(-8) ). This SNP is located upstream of the 5 methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR) gene, and it is known that the enzyme for MTRR is involved in the methionine-folate biosynthesis and metabolism pathway, which is the primary target of 5-FU-related compounds, although the authors were unable to identify a direct relation between rs4702484 and MTRR expression in a tested subset of cells. In the meta-analysis, 4 SNPs comprised the top hits, which, again, included rs4702484 and 3 additional SNPs (rs8101143, rs576523, and rs361433) that approached genome-wide significance (P values from 1.9 × 10(-7) to 8.8 × 10(-7) ). The meta-analysis also identified 1 missense variant (rs11722476; serine to asparagine) within switch/sucrose nonfermentable-related, matrix-associated, actin-dependent regulator of chromatin (SMARCAD1), a novel gene for association with capecitabine/5-FU susceptibility. CONCLUSIONS Toward the goal of individualizing cancer chemotherapy, the current study identified novel SNPs and genes associated with capecitabine sensitivity that are potentially informative and testable in any patient regardless of ethnicity.
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Affiliation(s)
- Peter H O'Donnell
- Section of Hematology-Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois, USA
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Igo RP, Schnell AH. Comparison of requirements and capabilities of major multipurpose software packages. Methods Mol Biol 2012; 850:539-58. [PMID: 22307719 DOI: 10.1007/978-1-61779-555-8_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The aim of this chapter is to introduce the reader to commonly used software packages and illustrate their input requirements, analysis options, strengths, and limitations. We focus on packages that perform more than one function and include a program for quality control, linkage, and association analyses. Additional inclusion criteria were (1) programs that are free to academic users and (2) currently supported, maintained, and developed. Using those criteria, we chose to review three programs: Statistical Analysis for Genetic Epidemiology (S.A.G.E.), PLINK, and Merlin. We will describe the required input format and analysis options. We will not go into detail about every possible program in the packages, but we will give an overview of the packages requirements and capabilities.
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Affiliation(s)
- Robert P Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA.
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Hiekkalinna T, Göring HHH, Lambert B, Weiss KM, Norrgrann P, Schäffer AA, Terwilliger JD. On the statistical properties of family-based association tests in datasets containing both pedigrees and unrelated case-control samples. Eur J Hum Genet 2011; 20:217-23. [PMID: 21934707 DOI: 10.1038/ejhg.2011.173] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A common approach to genetic mapping of loci for complex diseases is to perform a genome-wide association study (GWAS) by analyzing a vast number of SNP markers in cohorts of unrelated cases and controls. A direct motivation for the case-control design is that unrelated, affected individuals can be easier to collect than large families with multiple affected persons in the Western world. Despite its higher potential power, investigators have not actively pursued family ascertainment in part because of a dearth of methods for analyzing such correlated data on a large scale. We examine the statistical properties of several commonly used family-based association tests, as to their performance using real-life mixtures of families and singletons taken from our own migraine and schizophrenia studies, as well as population-based data for a complex trait simulated with the evolutionary phenogenetic simulator, ForSim. In virtually every situation, the full likelihood-based methods in the PSEUDOMARKER program outperformed those implemented in FBAT, GENEHUNTER TDT, PLINK (family-based options), HRR/HHRR, QTDT, TRANSMIT, UNPHASED, MENDEL, and LAMP. We further show that GWAS is much more powerful when family samples are used rather than unrelateds, on a genotype-by-genotype basis.
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Affiliation(s)
- Tero Hiekkalinna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
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Choh AC, Curran JE, Odegaard AO, Nahhas RW, Czerwinski SA, Blangero J, Towne B, Demerath EW. Differences in the heritability of growth and growth velocity during infancy and associations with FTO variants. Obesity (Silver Spring) 2011; 19:1847-54. [PMID: 21720422 PMCID: PMC4013792 DOI: 10.1038/oby.2011.175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
While the associations of common variants in the FTO gene with obesity have been widely replicated in adults, there is conflicting evidence regarding their effects in infancy. We hypothesize that the genetic influences on growth traits vary during infancy, and that conflicting results may stem from variation in the ages at which FTO associations have been examined. Using longitudinal weight and length data at 0, 1, 3, 6, 9, 12, 18, 24, 30, and 36 months in 917 (444 females, 473 males) family members from the Fels Longitudinal Study, we used a variance components-based approach (SOLAR) to: (i) examine differences in heritability (gene-by-age interaction) in weight, length, relative weight (BMI and ponderal index (PI)) and instantaneous weight and length velocities over the course of infancy, and (ii) test whether a common FTO variant (rs9939609) was associated with infant growth at three ages (maximum trait heritability, birth and 36 months). All heritabilities at birth (of 39-74%) were significant (P < 3.9 × 10(-10)), but changed with age (gene-by-age interaction, P < 0.05). Weight, relative weight, and weight velocity reached maximum heritabilities (of 76-89%) at 6-9 months, while length and length velocity reached maximum heritabilities (of 96-99%) at 18-30 months. We found no association of rs9939609 with growth status or velocity measured at any age (P > 0.11). This study for the first time demonstrates the fluctuation of genetic influences on infant growth, but further work is required to determine which gene variants explain the strong additive genetic effects observed.
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Affiliation(s)
- Audrey C Choh
- Lifespan Health Research Center, Department of Community Health, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA.
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Wheeler HE, Gamazon ER, Stark AL, O'Donnell PH, Gorsic LK, Huang RS, Cox NJ, Dolan ME. Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations. THE PHARMACOGENOMICS JOURNAL 2011; 13:35-43. [PMID: 21844884 PMCID: PMC3370147 DOI: 10.1038/tpj.2011.38] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Platinating agents are used in the treatment of many cancers, yet they can induce toxicities and resistance that limit their utility. Using previously published and additional world population panels of diverse ancestry totaling 608 lymphoblastoid cell lines (LCLs), we performed meta-analyses of over 3 million SNPs for both carboplatin- and cisplatin-induced cytotoxicity. The most significant SNP in the carboplatin meta-analysis is located in an intron of NBAS (p = 5.1 × 10−7). The most significant SNP in the cisplatin meta-analysis is upstream of KRT16P2 (p = 5.8 × 10−7). We also show that cisplatin-susceptibility SNPs are enriched for carboplatin-susceptibility SNPs. Most of the variants that associate with platinum-induced cytotoxicity are polymorphic across multiple world populations; therefore, they could be tested in follow-up studies in diverse clinical populations. Seven genes previously implicated in platinating agent response, including BCL2, GSTM1, GSTT1, ERCC2, and ERCC6 were also implicated in our meta-analyses.
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Affiliation(s)
- H E Wheeler
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
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Abstract
Radiation exposure through environmental, medical, and occupational settings is increasingly common. While radiation has harmful effects, it has utility in many applications such as radiotherapy for cancer. To increase the efficacy of radiation treatment and minimize its risks, a better understanding of the individual differences in radiosensitivity and the molecular basis of radiation response is needed. Here, we integrated human genetic and functional genomic approaches to study the response of human cells to radiation. We measured radiation-induced changes in gene expression and cell death in B cells from normal individuals. We found extensive individual variation in gene expression and cellular responses. To understand the genetic basis of this variation, we mapped the DNA sequence variants that influence expression response to radiation. We also identified radiation-responsive genes that regulate cell death; silencing of these genes by small interfering RNA led to an increase in radiation-induced cell death in human B cells, colorectal and prostate cancer cells. Together these results uncovered DNA variants that contribute to radiosensitivity and identified genes that can be targeted to increase the sensitivity of tumors to radiation.
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Hiekkalinna T, Schäffer AA, Lambert B, Norrgrann P, Göring HH, Terwilliger JD. PSEUDOMARKER: a powerful program for joint linkage and/or linkage disequilibrium analysis on mixtures of singletons and related individuals. Hum Hered 2011; 71:256-66. [PMID: 21811076 PMCID: PMC3190175 DOI: 10.1159/000329467] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 05/17/2011] [Indexed: 11/19/2022] Open
Abstract
A decade ago, there was widespread enthusiasm for the prospects of genome-wide association studies to identify common variants related to common chronic diseases using samples of unrelated individuals from populations. Although technological advancements allow us to query more than a million SNPs across the genome at low cost, a disappointingly small fraction of the genetic portion of common disease etiology has been uncovered. This has led to the hypothesis that less frequent variants might be involved, stimulating a renaissance of the traditional approach of seeking genes using multiplex families from less diverse populations. However, by using the modern genotyping and sequencing technology, we can now look not just at linkage, but jointly at linkage and linkage disequilibrium (LD) in such samples. Software methods that can look simultaneously at linkage and LD in a powerful and robust manner have been lacking. Most algorithms cannot jointly analyze datasets involving families of varying structures in a statistically or computationally efficient manner. We have implemented previously proposed statistical algorithms in a user-friendly software package, PSEUDOMARKER. This paper is an announcement of this software package. We describe the motivation behind the approach, the statistical methods, and software, and we briefly demonstrate PSEUDOMARKER's advantages over other packages by example.
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Affiliation(s)
- Tero Hiekkalinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Unit of Public Health Genomics, Helsinki, Finland
| | - Alejandro A. Schäffer
- Computational Biology Branch, National Center for Biotechnology Information, NIH, DHHS, Bethesda, Md
| | - Brian Lambert
- Department of Anthropology, Pennsylvania State University, State College, Pa
| | - Petri Norrgrann
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Unit of Public Health Genomics, Helsinki, Finland
| | - Harald H.H. Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Tex
| | - Joseph D. Terwilliger
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Psychiatry, Columbia University, New York, N.Y., USA
- Department of Genetics and Development, Columbia University, New York, N.Y., USA
- Department of Columbia Genome Center, Columbia University, New York, N.Y., USA
- Division of Medical Genetics, New York State Psychiatric Institute, New York, N.Y., USA
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Wheeler HE, Gorsic LK, Welsh M, Stark AL, Gamazon ER, Cox NJ, Dolan ME. Genome-wide local ancestry approach identifies genes and variants associated with chemotherapeutic susceptibility in African Americans. PLoS One 2011; 6:e21920. [PMID: 21755009 PMCID: PMC3130766 DOI: 10.1371/journal.pone.0021920] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/08/2011] [Indexed: 12/31/2022] Open
Abstract
Chemotherapeutic agents are used in the treatment of many cancers, yet variable resistance and toxicities among individuals limit successful outcomes. Several studies have indicated outcome differences associated with ancestry among patients with various cancer types. Using both traditional SNP-based and newly developed gene-based genome-wide approaches, we investigated the genetics of chemotherapeutic susceptibility in lymphoblastoid cell lines derived from 83 African Americans, a population for which there is a disparity in the number of genome-wide studies performed. To account for population structure in this admixed population, we incorporated local ancestry information into our association model. We tested over 2 million SNPs and identified 325, 176, 240, and 190 SNPs that were suggestively associated with cytarabine-, 5'-deoxyfluorouridine (5'-DFUR)-, carboplatin-, and cisplatin-induced cytotoxicity, respectively (p≤10(-4)). Importantly, some of these variants are found only in populations of African descent. We also show that cisplatin-susceptibility SNPs are enriched for carboplatin-susceptibility SNPs. Using a gene-based genome-wide association approach, we identified 26, 11, 20, and 41 suggestive candidate genes for association with cytarabine-, 5'-DFUR-, carboplatin-, and cisplatin-induced cytotoxicity, respectively (p≤10(-3)). Fourteen of these genes showed evidence of association with their respective chemotherapeutic phenotypes in the Yoruba from Ibadan, Nigeria (p<0.05), including TP53I11, COPS5 and GAS8, which are known to be involved in tumorigenesis. Although our results require further study, we have identified variants and genes associated with chemotherapeutic susceptibility in African Americans by using an approach that incorporates local ancestry information.
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Affiliation(s)
- Heather E. Wheeler
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Lidija K. Gorsic
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Marleen Welsh
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Amy L. Stark
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Eric R. Gamazon
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Nancy J. Cox
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - M. Eileen Dolan
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
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Van Steen K. Perspectives on genome-wide multi-stage family-based association studies. Stat Med 2011; 30:2201-21. [DOI: 10.1002/sim.4259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 03/07/2011] [Indexed: 01/03/2023]
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Thameem F, Puppala S, Arar NH, Blangero J, Duggirala R, Abboud HE. Genetic variants in transient receptor potential cation channel, subfamily M 1 (TRPM1) and their risk of albuminuria-related traits in Mexican Americans. Clin Chim Acta 2011; 412:2058-62. [PMID: 21439949 DOI: 10.1016/j.cca.2011.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/18/2011] [Accepted: 03/18/2011] [Indexed: 01/06/2023]
Abstract
BACKGROUND Evidence for linkage of albuminuria to GABRB3 marker region on chromosome 15q12 was previously reported in Mexican Americans. The objective of this study is to scan a positional candidate gene, Transient Receptor Potential cation channel, subfamily M 1 (TRPM1), for genetic variants that may contribute to the variation in albumin-to-creatinine ratio (ACR). METHODS To identify the sequence variants, the exons and 2 kb putative promoter region of TRPM1 were PCR amplified and sequenced in 32 selected individuals. Identified variants were genotyped in the entire data set (N=670; 39 large families) by TaqMan assays. Association analyses between the sequence variants and ACR, type 2 diabetes (T2DM) and related phenotypes were carried out using a measured genotype approach as implemented in the program SOLAR. RESULTS Sequencing analysis identified 18 single nucleotide polymorphisms (SNPs) including 8 SNPs in the coding regions, 7 SNPs in the promoter region and 3 SNPs in introns. Of the 8 SNPs identified in the coding regions, 3 were non synonymous [Met(1)Thr, Ser(32)Asn, Val(1395)Ile] and one SNP caused stop codon (Glu1375/*). Of the SNPs examined, none of them exhibited statistically significant association with ACR after accounting for the effect of age, sex, diabetes, duration of diabetes, systolic blood pressure and anti-hypertensive medications. However, a SNP (rs11070811) located in the putative promoter region showed a modest association with triglycerides levels (P=0.039). CONCLUSION The present investigation found no evidence for an association between sequence variation at the TRPM1 gene and ACR in Mexican Americans, although it appears to have modest influence on T2DM risk factors.
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Affiliation(s)
- Farook Thameem
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA.
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Cummings N, Shields KA, Curran JE, Bozaoglu K, Trevaskis J, Gluschenko K, Cai G, Comuzzie AG, Dyer TD, Walder KR, Zimmet P, Collier GR, Blangero J, Jowett JBM. Genetic variation in SH3-domain GRB2-like (endophilin)-interacting protein 1 has a major impact on fat mass. Int J Obes (Lond) 2011; 36:201-6. [PMID: 21407171 DOI: 10.1038/ijo.2011.67] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE The SH3-domain GRB2-like (endophilin)-interacting protein 1 (SGIP1) gene has been shown to be differentially expressed in the hypothalamus of lean versus obese Israeli sand rats (Psammomys obesus), and is suspected of having a role in regulating food intake. The purpose of this study was to assess the role of genetic variation in SGIP1 in human disease. SUBJECTS We performed single-nucleotide polymorphism (SNP) genotyping in a large family pedigree cohort from the island of Mauritius. The Mauritius Family Study (MFS) consists of 400 individuals from 24 Indo-Mauritian families recruited from the genetically homogeneous population of Mauritius. We measured markers of the metabolic syndrome, including diabetes and obesity-related phenotypes such as fasting plasma glucose, waist:hip ratio, body mass index and fat mass. RESULTS Statistical genetic analysis revealed associations between SGIP1 polymorphisms and fat mass (in kilograms) as measured by bioimpedance. SNP genotyping identified associations between several genetic variants and fat mass, with the strongest association for rs2146905 (P=4.7 × 10(-5)). A strong allelic effect was noted for several SNPs where fat mass was reduced by up to 9.4% for individuals homozygous for the minor allele. CONCLUSIONS Our results show association between genetic variants in SGIP1 and fat mass. We provide evidence that variation in SGIP1 is a potentially important determinant of obesity-related traits in humans.
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Affiliation(s)
- N Cummings
- Genomics and Systems Biology, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
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Alpargu G. Allowing for missing genotypes in any members of the nuclear families in transmission disequilibrium test. Comput Stat Data Anal 2011. [DOI: 10.1016/j.csda.2010.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Peter B, Raskind WH, Matsushita M, Lisowski M, Vu T, Berninger VW, Wijsman EM, Brkanac Z. Replication of CNTNAP2 association with nonword repetition and support for FOXP2 association with timed reading and motor activities in a dyslexia family sample. J Neurodev Disord 2011; 3:39-49. [PMID: 21484596 PMCID: PMC3163991 DOI: 10.1007/s11689-010-9065-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 10/21/2010] [Indexed: 12/01/2022] Open
Abstract
Two functionally related genes, FOXP2 and CNTNAP2, influence language abilities in families with rare syndromic and common nonsyndromic forms of impaired language, respectively. We investigated whether these genes are associated with component phenotypes of dyslexia and measures of sequential motor ability. Quantitative transmission disequilibrium testing (QTDT) and linear association modeling were used to evaluate associations with measures of phonological memory (nonword repetition, NWR), expressive language (sentence repetition), reading (real word reading efficiency, RWRE; word attack, WATT), and timed sequential motor activities (rapid alternating place of articulation, RAPA; finger succession in the dominant hand, FS-D) in 188 family trios with a child with dyslexia. Consistent with a prior study of language impairment, QTDT in dyslexia showed evidence of CNTNAP2 single nucleotide polymorphism (SNP) association with NWR. For FOXP2, we provide the first evidence for SNP association with component phenotypes of dyslexia, specifically NWR and RWRE but not WATT. In addition, FOXP2 SNP associations with both RAPA and FS-D were observed. Our results confirm the role of CNTNAP2 in NWR in a dyslexia sample and motivate new questions about the effects of FOXP2 in neurodevelopmental disorders.
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Affiliation(s)
- Beate Peter
- Department of Speech and Hearing Sciences, University of Washington, P.O. Box 354875, Seattle, WA, 98195, USA,
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Martin ER, Rampersaud E. Family-based genetic association tests. Cold Spring Harb Protoc 2011; 2011:pdb.top96. [PMID: 21285276 DOI: 10.1101/pdb.top96] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hatemi PK, Dawes CT, Frost-Keller A, Settle JE, Verhulst B. Integrating social science and genetics: news from the political front. BIODEMOGRAPHY AND SOCIAL BIOLOGY 2011; 57:67-87. [PMID: 21845928 DOI: 10.1080/19485565.2011.568276] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
There has been growing interest in the use of genetic models to expand the understanding of political preferences, attitudes, and behaviors. Researchers in the social sciences have begun incorporating these models and have revealed that genetic differences account for individual differences in political beliefs, behaviors, and responses to the political environment. The first Integrating Genetics and the Social Sciences Conference, held at Boulder, Colorado in May of 2010, brought together these researchers. As a result, we jointly review the last 5 years of research in this area. In doing so, we explicate the methods, findings, and limitations of behavior genetic approaches, including twin designs, association studies, and genome-wide analyses, in their application toward exploring political preferences.
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Affiliation(s)
- Peter K Hatemi
- United States Studies Centre, University of Sydney, New South Wales, Australia.
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