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Incorporating information from markers in LD with test locus for detecting imprinting and maternal effects. Eur J Hum Genet 2020; 28:1087-1097. [PMID: 32080366 DOI: 10.1038/s41431-020-0590-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/26/2019] [Accepted: 02/04/2020] [Indexed: 11/08/2022] Open
Abstract
Numerous statistical methods have been developed to explore genomic imprinting and maternal effects by identifying parent-of-origin patterns in complex human diseases. However, because most of these methods only use available locus-specific genotype data, it is sometimes impossible for them to infer the distribution of parental origin of a variant allele, especially when some genotypes are missing. In this article, we propose a two-step approach, LIMEhap, to improve upon a recent partial likelihood inference method. In the first step, the distribution of the missing genotypes is inferred through the construction of haplotypes by using information from nearby loci. In the second step, a partial likelihood method is applied to the inferred data. To substantiate the validity of the proposed procedures, we simulated data in a genomic region of gene GPX1. The results show that, by borrowing genetic information from nearby loci, the power of the proposed method can be close to that with complete genotype data at the locus of interest. Since the inference on the genotype distribution is made under the assumption of Hardy-Weinberg Equilibrium (HWE), we further studied the robustness of LIMEhap to violation of HWE. Finally, we demonstrate the utility of LIMEhap by applying it to an autism dataset.
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Lu J, Zhang Y, Wang S, Bi Y, Huang T, Luo X, Cai YD. Analysis of Four Types of Leukemia Using Gene Ontology Term and Kyoto Encyclopedia of Genes and Genomes Pathway Enrichment Scores. Comb Chem High Throughput Screen 2019; 23:295-303. [PMID: 30599106 DOI: 10.2174/1386207322666181231151900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/24/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022]
Abstract
AIM AND OBJECTIVE Leukemia is the second common blood cancer after lymphoma, and its incidence rate has an increasing trend in recent years. Leukemia can be classified into four types: acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), and chronic myelogenous leukemia (CML). More than forty drugs are applicable to different types of leukemia based on the discrepant pathogenesis. Therefore, the identification of specific drug-targeted biological processes and pathways is helpful to determinate the underlying pathogenesis among such four types of leukemia. METHODS In this study, the gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were highly related to drugs for leukemia were investigated for the first time. The enrichment scores for associated GO terms and KEGG pathways were calculated to evaluate the drugs and leukemia. The feature selection method, minimum redundancy maximum relevance (mRMR), was used to analyze and identify important GO terms and KEGG pathways. RESULTS Twenty Go terms and two KEGG pathways with high scores have all been confirmed to effectively distinguish four types of leukemia. CONCLUSION This analysis may provide a useful tool for the discrepant pathogenesis and drug design of different types of leukemia.
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Affiliation(s)
- Jing Lu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 32 Qingquan Road, Yantai 264005, China
| | - YuHang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - ShaoPeng Wang
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Yi Bi
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 32 Qingquan Road, Yantai 264005, China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of MateriaMedica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai 200444, China
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Kreile M, Rots D, Zarina A, Rautiainen L, Visnevska-Preciniece Z, Kovalova Z, Gailite L. Association of ARID5B Genetic Variants with Risk of Childhood B Cell Precursor Acute Lymphoblastic Leukaemia in Latvia. Asian Pac J Cancer Prev 2018; 19:91-95. [PMID: 29373897 PMCID: PMC5844642 DOI: 10.22034/apjcp.2018.19.1.91] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Background: Acute lymphoblastic leukaemia (ALL) is the most common malignancy in childhood. Despite
numerous investigations very little is still known about its aetiology. However, in one genome wide association study
conducted to identify the possible genetic risk factors, two allelic variations rs10821936 and rs10994982 in the 3rd
intron of the ARID5B gene were identified as possible ALL risk alleles. Association between ARID5B gene variants and
ALL risk was also been confirmed for different ethnic groups. Materials and Methods: Eight genetic variants in the
gene ARID5B were genotyped - rs10994982, rs7908445, rs7923074, rs10821936, rs10821937, rs7896246, rs10821938
and rs7089424 in 77 ALL patients in remission and in 122 age and gender matched controls; parental samples were
also genotyped in 50 cases. Results: Six out of the eight (rs7908445, rs7923074, rs10821936, rs10821937, rs7896246
and rs7089424) analysed allelic variations were identified in the case-control analysis as statistically significant risk
alleles for ALL development. In the family study and using hybrid analysis, all allelic variations were significantly
associated with ALL. During the study, risk haplotype was identified rs10994982/rs7908445/rs7923074/ rs10821936/
rs10821937/rs7896246/rs10821938/rs7089424 – ATACCAAG – with a frequency in cases of 0.17 and in the control
group at 0.29 (chi square = 6.69, p value = 0.009). In the family association study the same haplotype showed statistical
significance (chi squared = 10.3, p value = 0.001). Conclusions: Results of the study replicate and extend previously
published findings for ARID5B localized allelic variants, but do not explain the mechanism of action related to the
pathogenesis of ALL.
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Affiliation(s)
- Madara Kreile
- Riga Stradiņš University, University Scientific Laboratory of Molecular Genetics, Riga Stradiņš University, Institute of Oncology, Children’s Clinical University Hospital, Latvia.
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Fucic A, Guszak V, Mantovani A. Transplacental exposure to environmental carcinogens: Association with childhood cancer risks and the role of modulating factors. Reprod Toxicol 2017. [PMID: 28624605 DOI: 10.1016/j.reprotox.2017.06.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biological responses to carcinogens from environmental exposure during adulthood are modulated over years or decades. Conversely, during transplacental exposure, the effects on the human foetus change within weeks, intertwining with developmental mechanisms: even short periods of transplacental exposure may be imprinted in the organism for a lifetime. The pathways leading to childhood and juvenile cancers, such as leukaemias, neuroblastoma/brain tumours, hepatoblastoma, and Willm's tumour involve prenatally-induced genomic, epigenomic and/or non-genomic effects caused by xenobiotics. Pregnant women most often live in complex environmental settings that cause transplacental exposure of the foetus to xenobiotic mixtures. Mother-child biomonitoring should integrate the analysis of chemicals/radiation present in the living and workplace environment with relevant risk modulators related to life style. The interdisciplinary approach for transplacental cancer risk assessment in high-pressure areas should be based on an integrated model for mother-child exposure estimation via profiling the exposure level by water quality analysis, usage of emission grids, and land use maps.
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Affiliation(s)
- A Fucic
- Institute for Medical Research and Occupational Health, Zagreb, Croatia.
| | - V Guszak
- University Clinical Centre "Zagreb", Zagreb, Croatia
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Archer NP, Perez-Andreu V, Scheurer ME, Rabin KR, Peckham-Gregory EC, Plon SE, Zabriskie RC, De Alarcon PA, Fernandez KS, Najera CR, Yang JJ, Antillon-Klussmann F, Lupo PJ. Family-based exome-wide assessment of maternal genetic effects on susceptibility to childhood B-cell acute lymphoblastic leukemia in hispanics. Cancer 2016; 122:3697-3704. [PMID: 27529658 DOI: 10.1002/cncr.30241] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/31/2016] [Accepted: 07/06/2016] [Indexed: 11/11/2022]
Abstract
BACKGROUND Children of Hispanic ancestry have a higher incidence of acute lymphoblastic leukemia (ALL) compared with other ethnic groups, but to the authors' knowledge, the genetic basis for these racial disparities remain incompletely understood. Genome-wide association studies of childhood ALL to date have focused on inherited genetic effects; however, maternal genetic effects (the role of the maternal genotype on phenotype development in the offspring) also may play a role in ALL susceptibility. METHODS The authors conducted a family-based exome-wide association study of maternal genetic effects among Hispanics with childhood B-cell ALL using the Illumina Infinium HumanExome BeadChip. A discovery cohort of 312 Guatemalan and Hispanic American families and an independent replication cohort of 152 Hispanic American families were used. RESULTS Three maternal single-nucleotide polymorphisms (SNPs) approached the study threshold for significance after correction for multiple testing (P<1.0 × 10-6 ): MTL5 rs12365708 (testis expressed metallothionein-like protein [tesmin]) (relative risk [RR], 2.62; 95% confidence interval [95% CI], 1.61-4.27 [P = 1.8 × 10-5 ]); ALKBH1 rs6494 (AlkB homolog 1, histone H2A dioxygenase) (RR, 3.77; 95% CI, 1.84-7.74 [P = 3.7 × 10-5 ]); and NEUROG3 rs4536103 (neurogenin 3) (RR, 1.75; 95% CI, 1.30-2.37 [P = 1.2 × 10-4 ]). Although effect sizes were similar, these SNPs were not nominally significant in the replication cohort in the current study. In a meta-analysis comprised of the discovery cohort and the replication cohort, these SNPs were still not found to be statistically significant after correction for multiple comparisons (rs12365708: pooled RR, 2.27 [95% CI, 1.48-3.50], P = 1.99 × 10-4 ; rs6494: pooled RR, 2.31 [95% CI, 1.38-3.85], P = .001; and rs4536103: pooled RR, 1.67 [95% CI, 1.29-2.16] P = 9.23 × 10-5 ). CONCLUSIONS In what to the authors' knowledge is the first family-based based exome-wide association study to investigate maternal genotype effects associated with childhood ALL, the results did not implicate a strong role of maternal genotype on disease risk among Hispanics; however, 3 maternal SNPs were identified that may play a modest role in susceptibility. Cancer 2016;122:3697-704. © 2016 American Cancer Society.
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Affiliation(s)
- Natalie P Archer
- Austin Regional Campus, University of Texas School of Public Health, Austin, Texas
| | - Virginia Perez-Andreu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee.,Hematologic Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael E Scheurer
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Karen R Rabin
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Erin C Peckham-Gregory
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Sharon E Plon
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ryan C Zabriskie
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Pedro A De Alarcon
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, Illinois
| | - Karen S Fernandez
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, Illinois
| | - Cesar R Najera
- National Pediatric Oncology Unit, Guatemala City, Guatemala
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee.,Hematologic Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Federico Antillon-Klussmann
- National Pediatric Oncology Unit, Guatemala City, Guatemala.,School of Medicine, Francisco Marroquin University, Guatemala City, Guatemala
| | - Philip J Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
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Kreile M, Piekuse L, Rots D, Dobele Z, Kovalova Z, Lace B. Analysis of possible genetic risk factors contributing to development of childhood acute lymphoblastic leukaemia in the Latvian population. Arch Med Sci 2016; 12:479-85. [PMID: 27279837 PMCID: PMC4889682 DOI: 10.5114/aoms.2016.59920] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/10/2014] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION Childhood acute lymphoblastic leukaemia (ALL) is a complex disease caused by a combination of genetic susceptibility and environmental exposure. Previous genome-wide association studies have reported several single nucleotide polymorphisms (SNPs) associated with the incidence of ALL. Several variations in genes encoding enzymes involved in carcinogenesis are suggested as being associated with an increased risk of ALL development. MATERIAL AND METHODS We enrolled 77 paediatric ALL patients and 122 healthy controls, and in addition parental DNA was also available for 45 probands. SNPs rs10821936 (ARID5B), rs4132601 (IKZF1), rs2239633 (CEBPE), rs3731217 (CDKN2A) and rs1800566 (NQO1) and the presence of GSTT1 and GSTM1 null variants were detected. For statistical analysis the hybrid method of two designs 'Haplin' was used as well as linkage disequilibrium for family-based association studies. RESULTS We identified the SNP rs10821936 in the ARID5B gene as being statistically significantly associated with childhood ALL, especially if the C allele is in a homozygous state, relative risk (RR) 4.65, 95% CI: 2.03-10.6, p = 0.0006. Statistically significant differences were not found in other SNPs. We found risk combinations including all five variations, the strongest association being found in a combination where all five genetic variants are in a homozygous state, CCTTTTTTCC, p = 0.032. CONCLUSIONS The identified SNP rs10821936 could serve as a potential risk marker for childhood ALL development. Further studies in an independent population are needed for verification.
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Affiliation(s)
- Madara Kreile
- Scientific Laboratory of Molecular Genetics, Riga Stradiņš University, Riga, Latvia
- Institute of Oncology, Riga Stradiņš University, Riga, Latvia
| | - Linda Piekuse
- Scientific Laboratory of Molecular Genetics, Riga Stradiņš University, Riga, Latvia
| | - Dmitrijs Rots
- Scientific Laboratory of Molecular Genetics, Riga Stradiņš University, Riga, Latvia
| | - Zane Dobele
- Scientific Laboratory of Molecular Genetics, Riga Stradiņš University, Riga, Latvia
| | - Zhanna Kovalova
- Department of Hematology and Oncology, Children's Clinical University Hospital, Riga, Latvia
| | - Baiba Lace
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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Zhang F, Khalili A, Lin S. Optimum study design for detecting imprinting and maternal effects based on partial likelihood. Biometrics 2015; 72:95-105. [PMID: 26288102 DOI: 10.1111/biom.12380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 06/01/2015] [Accepted: 07/01/2015] [Indexed: 11/28/2022]
Abstract
Despite spectacular advances in molecular genomic technologies in the past two decades, resources available for genomic studies are still finite and limited, especially for family-based studies. Hence, it is important to consider an optimum study design to maximally utilize limited resources to increase statistical power in family-based studies. A particular question of interest is whether it is more profitable to genotype siblings of probands or to recruit more independent families. Numerous studies have attempted to address this study design issue for simultaneous detection of imprinting and maternal effects, two important epigenetic factors for studying complex diseases. The question is far from settled, however, mainly due to the fact that results and recommendations in the literature are based on anecdotal evidence from limited simulation studies rather than based on rigorous statistical analysis. In this article, we propose a systematic approach to study various designs based on a partial likelihood formulation. We derive the asymptotic properties and obtain formulas for computing the information contents of study designs being considered. Our results show that, for a common disease, recruiting additional siblings is beneficial because both affected and unaffected individuals will be included. However, if a disease is rare, then any additional siblings recruited are most likely to be unaffected, thus contributing little additional information; in such cases, additional families will be a better choice with a fixed amount of resources. Our work thus offers a practical strategy for investigators to select the optimum study design within a case-control family scheme before data collection.
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Affiliation(s)
- Fangyuan Zhang
- Department of Statistics, The Ohio State University, 1958 Neil Avenue, Columbus, Ohio 43210, U.S.A
| | - Abbas Khalili
- Department of Mathematics and Statistics, McGill University, 805 Sherbrooke Street West, Montreal, Quebec H3A 0B9, Canada
| | - Shili Lin
- Department of Statistics, The Ohio State University, 1958 Neil Avenue, Columbus, Ohio 43210, U.S.A
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Lopes BA, Emerenciano M, Gonçalves BAA, Vieira TM, Rossini A, Pombo-de-Oliveira MS. Polymorphisms in CYP1B1, CYP3A5, GSTT1, and SULT1A1 Are Associated with Early Age Acute Leukemia. PLoS One 2015; 10:e0127308. [PMID: 25992585 PMCID: PMC4436276 DOI: 10.1371/journal.pone.0127308] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/14/2015] [Indexed: 01/01/2023] Open
Abstract
Based on observational studies, early age leukemia (EAL) was associated with maternal hormone exposure during pregnancy. We studied the association between genetic polymorphisms of estrogen metabolism and EAL. Using data from the Brazilian Collaborative Study Group of Infant Acute Leukemia (2000–2012), 350 cases and 404 age-matched controls and 134 mothers of cases and controls were genotyped to explore polymorphisms in genes of the estrogen metabolism pathway: CYP1B1 (c.1294C>G, rs1056836), CYP3A4 (c.-392A>G, rs2740574), CYP3A5 (c.219-237G>A, rs776746), GSTM1/GSTT1 deletions, and SULT1A1 (c.638G>A, rs9282861; and c.667A>G, rs1801030). Logistic regression was used to calculate the odds ratios (OR) with 95% confidence intervals (CIs), and unconditional logistic regression was used to estimate adjusted odds ratios (aORs) by ethnicity. Because of multiple testing, p values < 0.01 were significant after Bonferroni correction. SULT1A1 (c.638G>A) was associated to infant acute lymphoblastic leukemia and acute myeloid leukemia (AML) risk in males (additive model: aOR = 0.52; 95% CI: 0.29–0.95, p = 0.03; dominant model: aOR = 2.18; 95% CI: 1.17–4.05, p = 0.01, respectively). CYP1B1 polymorphism was associated with a decreased risk of AML either for non-white or female children (additive model: OR = 0.24; 95% CI: 0.08–0.76, p < 0.01; additive model: aOR = 0.27; 95% CI: 0.08–0.89, p = 0.03, respectively). Since polymorphisms of Cytochrome P450 genes presented gender-specific risk associations, we also investigated their expression. CYP1B1 was not expressed in 57.1% of EAL cases, and its expression varied by genotype, gender, and leukemia subtype. Maternal-fetal GSTT1 null genotype was associated with risk of EAL. This study shows that polymorphisms in genes of estrogen metabolism confer genetic susceptibility to EAL, mainly in males, and maternal susceptibility genes modify the risk for developing EAL in newborns.
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Affiliation(s)
- Bruno Almeida Lopes
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Mariana Emerenciano
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Bruno Alves Aguiar Gonçalves
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Tállita Meciany Vieira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Ana Rossini
- Department of Biochemistry, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Maria S. Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
- * E-mail:
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Abstract
The causes of childhood cancer have been systematically studied for decades, but apart from high-dose radiation and prior chemotherapy there are few strong external risk factors. However, inherent risk factors including birth weight, parental age, and congenital anomalies are consistently associated with most types of pediatric cancer. Recently the contribution of common genetic variation to etiology has come into focus through genome-wide association studies. These have highlighted genes not previously implicated in childhood cancers and have suggested that common variation explains a larger proportion of childhood cancers than adult. Rare variation and nonmendelian inheritance may also contribute to childhood cancer risk but have not been widely examined.
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Affiliation(s)
- Logan G. Spector
- Division of Epidemiology/Clinical Research Department of Pediatrics University of Minnesota 420 Delaware Street, SE, MMC 715 Minneapolis, MN 55455
| | - Nathan Pankratz
- Department of Lab Medicine and Pathology University of Minnesota
| | - Erin L. Marcotte
- Division of Epidemiology/Clinical Research Department of Pediatrics University of Minnesota
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Kreile M, Rots D, Piekuse L, Cebura E, Grutupa M, Kovalova Z, Lace B. Lack of Association between Polymorphisms in Genes MTHFR and MDR1 with Risk of Childhood Acute Lymphoblastic Leukemia. Asian Pac J Cancer Prev 2014; 15:9707-11. [DOI: 10.7314/apjcp.2014.15.22.9707] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Cao Y, Lupo PJ, Swartz MD, Nousome D, Scheurer ME. Using a Bayesian hierarchical model for identifying single nucleotide polymorphisms associated with childhood acute lymphoblastic leukemia risk in case-parent triads. PLoS One 2013; 8:e84658. [PMID: 24367687 PMCID: PMC3868670 DOI: 10.1371/journal.pone.0084658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 11/18/2013] [Indexed: 11/28/2022] Open
Abstract
Childhood acute lymphoblastic leukemia (ALL) is a condition that arises from complex etiologies. The absence of consistent environmental risk factors and the presence of modest familial associations suggest ALL is a complex trait with an underlying genetic component. The identification of genetic factors associated with disease is complicated by complex genetic covariance structures and multiple testing issues. Both issues can be resolved with appropriate Bayesian variable selection methods. The present study was undertaken to extend our hierarchical Bayesian model for case-parent triads to incorporate single nucleotide polymorphisms (SNPs) and incorporate the biological grouping of SNPs within genes. Based on previous evidence that genetic variation in the folate metabolic pathway influences ALL risk, we evaluated 128 tagging SNPs in 16 folate metabolic genes among 118 ALL case-parent triads recruited from the Texas Children’s Cancer Center (Houston, TX) between 2003 and 2010. We used stochastic search gene suggestion (SSGS) in hierarchical Bayesian models to evaluate the association between folate metabolic SNPs and ALL. Using Bayes factors among these variants in childhood ALL case-parent triads, two SNPs were identified with a Bayes factor greater than 1. There was evidence that the minor alleles of NOS3 rs3918186 (OR = 2.16; 95% CI: 1.51-3.15) and SLC19A1 rs1051266 (OR = 2.07; 95% CI: 1.25-3.46) were positively associated with childhood ALL. Our findings are suggestive of the role of inherited genetic variation in the folate metabolic pathway on childhood ALL risk, and they also suggest the utility of Bayesian variable selection methods in the context of case-parent triads for evaluating the role of SNPs on disease risk.
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Affiliation(s)
- Ying Cao
- Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, United States of America
| | - Philip J. Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael D. Swartz
- Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, United States of America
| | - Darryl Nousome
- Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas School of Public Health, Houston, Texas, United States of America
| | - Michael E. Scheurer
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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