scholarly journals Detecting epistasis via Markov bases

2011 ◽  
Vol 2 (1) ◽  
Author(s):  
Anna-Sapfo Malaspinas ◽  
Caroline Uhler
Keyword(s):  
Simulated Data ◽  
Research Progress ◽  
Nucleotide Polymorphisms ◽  
Two Stage ◽  
Data Set ◽  
Exact Test ◽  
Multiple Loci ◽  
Genome Wide ◽  
A Genome ◽  
Logistic Regression Method

Rapid research progress in genotyping techniques have allowed large genome-wide associationstudies. Existing methods often focus on determining associations between single loci anda specic phenotype. However, a particular phenotype is usually the result of complex relationshipsbetween multiple loci and the environment. In this paper, we describe a two-stage methodfor detecting epistasis by combining the traditionally used single-locus search with a search formultiway interactions. Our method is based on an extended version of Fisher's exact test. Toperform this test, a Markov chain is constructed on the space of multidimensional contingencytables using the elements of a Markov basis as moves. We test our method on simulated data andcompare it to a two-stage logistic regression method and to a fully Bayesian method, showing thatwe are able to detect the interacting loci when other methods fail to do so. Finally, we apply ourmethod to a genome-wide data set consisting of 685 dogs and identify epistasis associated withcanine hair length for four pairs of single nucleotide polymorphisms (SNPs).

scholarly journals A genome-wide scan for a simulated data set using two newly developed methods

1999 ◽  
Vol 17 (S1) ◽  
pp. S621-S626
Author(s):  
Li Hsu ◽  
Corinne Aragaki ◽  
Filemon Quiaoit ◽  
Xiangjing Wang ◽  
Xiubin Xu ◽  
...  
Keyword(s):  
Simulated Data ◽  
Data Set ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Scan

scholarly journals A Clustering Approach for Motif Discovery in ChIP-Seq Dataset

Entropy ◽  
2019 ◽  
Vol 21 (8) ◽  
pp. 802
Author(s):  
Chun-xiao Sun ◽  
Yu Yang ◽  
Hua Wang ◽  
Wen-hu Wang
Keyword(s):  
Dna Sequences ◽  
Motif Discovery ◽  
Simulated Data ◽  
Data Set ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Clustering Approach ◽  
Ap Clustering ◽  
Generation Sequencing

Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-Seq) technology has enabled the identification of transcription factor binding sites (TFBSs) on a genome-wide scale. To effectively and efficiently discover TFBSs in the thousand or more DNA sequences generated by a ChIP-Seq data set, we propose a new algorithm named AP-ChIP. First, we set two thresholds based on probabilistic analysis to construct and further filter the cluster subsets. Then, we use Affinity Propagation (AP) clustering on the candidate cluster subsets to find the potential motifs. Experimental results on simulated data show that the AP-ChIP algorithm is able to make an almost accurate prediction of TFBSs in a reasonable time. Also, the validity of the AP-ChIP algorithm is tested on a real ChIP-Seq data set.

scholarly journals Genome-Wide Single-Nucleotide Polymorphism Map for Candida albicans

2004 ◽  
Vol 3 (3) ◽  
pp. 705-714 ◽  
Author(s):  
Anja Forche ◽  
P. T. Magee ◽  
B. B. Magee ◽  
Georgiana May
Keyword(s):  
Candida Albicans ◽  
Genome Rearrangement ◽  
Snp Markers ◽  
Chromosome Loss ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Snp Map

ABSTRACT Single-nucleotide polymorphisms (SNPs) are essential tools for studying a variety of organismal properties and processes, such as recombination, chromosomal dynamics, and genome rearrangement. This paper describes the development of a genome-wide SNP map for Candida albicans to study mitotic recombination and chromosome loss. C. albicans is a diploid yeast which propagates primarily by clonal mitotic division. It is the leading fungal pathogen that causes infections in humans, ranging from mild superficial lesions in healthy individuals to severe, life-threatening diseases in patients with suppressed immune systems. The SNP map contains 150 marker sequences comprising 561 SNPs and 9 insertions-deletions. Of the 561 SNPs, 437 were transition events while 126 were transversion events, yielding a transition-to-transversion ratio of 3:1, as expected for a neutral accumulation of mutations. The average SNP frequency for our data set was 1 SNP per 83 bp. The map has one marker placed every 111 kb, on average, across the 16-Mb genome. For marker sequences located partially or completely within coding regions, most contained one or more nonsynonymous substitutions. Using the SNP markers, we identified a loss of heterozygosity over large chromosomal fragments in strains of C. albicans that are frequently used for gene manipulation experiments. The SNP map will be useful for understanding the role of heterozygosity and genome rearrangement in the response of C. albicans to host environments.

scholarly journals Nonparametric Disequilibrium Mapping of Functional Sites Using Haplotypes of Multiple Tightly Linked Single-Nucleotide Polymorphism Markers

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1175-1187
Author(s):  
Rong Cheng ◽  
Jennie Z Ma ◽  
Fred A Wright ◽  
Shili Lin ◽  
Xin Gao ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Simulated Data ◽  
Haplotype Frequency ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Functional Sites ◽  
Genome Wide ◽  
Snp Map ◽  
Risk Of Disease

Abstract As the speed and efficiency of genotyping single-nucleotide polymorphisms (SNPs) increase, using the SNP map, it becomes possible to evaluate the extent to which a common haplotype contributes to the risk of disease. In this study we propose a new procedure for mapping functional sites or regions of a candidate gene of interest using multiple linked SNPs. Based on a case-parent trio family design, we use expectation-maximization (EM) algorithm-derived haplotype frequency estimates of multiple tightly linked SNPs from both unambiguous and ambiguous families to construct a contingency statistic S for linkage disequilibrium (LD) analysis. In the procedure, a moving-window scan for functional SNP sites or regions can cover an unlimited number of loci except for the limitation of computer storage. Within a window, all possible widths of haplotypes are utilized to find the maximum statistic S* for each site (or locus). Furthermore, this method can be applied to regional or genome-wide scanning for determining linkage disequilibrium using SNPs. The sensitivity of the proposed procedure was examined on the simulated data set from the Genetic Analysis Workshop (GAW) 12. Compared with the conventional and generalized TDT methods, our procedure is more flexible and powerful.

scholarly journals Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genomic Region ◽  
Rubus Idaeus ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Red Raspberry ◽  
Genome Wide ◽  
A Genome ◽  
Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

scholarly journals Eyes of Africa: The Genetics of Blindness: Study Design and Methodology

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Olusola Olawoye ◽  
Chimdi Chuka-Okosa ◽  
Onoja Akpa ◽  
Tony Realini ◽  
Michael Hauser ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Case Control Study ◽  
African Ancestry ◽  
Collaborative Study ◽  
Data Set ◽  
Human Heredity ◽  
Genome Wide ◽  
A Genome ◽  
Multiplex Families ◽  
Control Study

Abstract Background This report describes the design and methodology of the “Eyes of Africa: The Genetics of Blindness,” a collaborative study funded through the Human Heredity and Health in Africa (H3Africa) program of the National Institute of Health. Methods This is a case control study that is collecting a large well phenotyped data set among glaucoma patients and controls for a genome wide association study. (GWAS). Multiplex families segregating Mendelian forms of early-onset glaucoma will also be collected for exome sequencing. Discussion A total of 4500 cases/controls have been recruited into the study at the end of the 3rd funded year of the study. All these participants have been appropriately phenotyped and blood samples have been received from these participants. Recent GWAS of POAG in African individuals demonstrated genome-wide significant association with the APBB2 locus which is an association that is unique to individuals of African ancestry. This study will add to the existing knowledge and understanding of POAG in the African population.

Bisphosphonate-related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in multiple myeloma: a genome-wide single nucleotide polymorphism analysis

Blood ◽  
2008 ◽  
Vol 112 (7) ◽  
pp. 2709-2712 ◽  
Author(s):  
Maria E. Sarasquete ◽  
Ramon García-Sanz ◽  
Luis Marín ◽  
Miguel Alcoceba ◽  
Maria C. Chillón ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Cytochrome P450 ◽  
Genome Wide Association Study ◽  
Osteonecrosis Of The Jaw ◽  
Bisphosphonate Therapy ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome

Abstract We have explored the potential role of genetics in the development of osteonecrosis of the jaw (ONJ) in multiple myeloma (MM) patients under bisphosphonate therapy. A genome-wide association study was performed using 500 568 single nucleotide polymorphisms (SNPs) in 2 series of homogeneously treated MM patients, one with ONJ (22 MM cases) and another without ONJ (65 matched MM controls). Four SNPs (rs1934951, rs1934980, rs1341162, and rs17110453) mapped within the cytochrome P450-2C gene (CYP2C8) showed a different distribution between cases and controls with statistically significant differences (P = 1.07 × 10−6, P = 4.231 × 10−6, P = 6.22 × 10−6, and P = 2.15 × 10−6, respectively). SNP rs1934951 was significantly associated with a higher risk of ONJ development even after Bonferroni correction (P corrected value = .02). Genotyping results displayed an overrepresentation of the T allele in cases compared with controls (48% vs 12%). Thus, individuals homozygous for the T allele had an increased likelihood of developing ONJ (odds ratio 12.75, 95% confidence interval 3.7-43.5).

scholarly journals Genome-wide analyses reveal clustering in Cannabis cultivars: the ancient domestication trilogy of a panacea

2015 ◽  
Author(s):  
Philippe Henry
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Open Access ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Access Data ◽  
Diagnostic Snps ◽  
Shed Light

In the present research, I used an open access data set (Medicinal Genomics) consisting of nearly 200'000 genome-wide single nucleotide polymorphisms (SNPs) typed in 28 cannabis accessions to shed light on the plant's underlying genetic structure. Genome-wide loadings were used to sequentially cull less informative markers. The process involved reducing the number of SNPs to 100K, 10K, 1K, 100 until I identified a set of 42 highly informative SNPs that I present here. The two first principal components, encompass over 3/4 of the genetic variation present in the dataset (PCA1 = 48.6%, PCA2= 26.3%). This set of diagnostic SNPs is then used to identify clusters into which cannabis accession segregate. I identified three clear and consistent clusters; reflective of the ancient domestication trilogy of the genus Cannabis.

scholarly journals Genome-Wide Association Mapping for Heat and Drought Adaptive Traits in Pea

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1897
Author(s):  
Endale G. Tafesse ◽  
Krishna K. Gali ◽  
V. B. Reddy Lachagari ◽  
Rosalind Bueckert ◽  
Thomas D. Warkentin
Keyword(s):  
Association Mapping ◽  
Candidate Genes ◽  
Vegetation Index ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Adaptive Traits ◽  
Flowering Duration ◽  
Genome Wide ◽  
A Genome

Heat and drought, individually or in combination, limit pea productivity. Fortunately, substantial genetic diversity exists in pea germplasm for traits related to abiotic stress resistance. Understanding the genetic basis of resistance could accelerate the development of stress-adaptive cultivars. We conducted a genome-wide association study (GWAS) in pea on six stress-adaptive traits with the aim to detect the genetic regions controlling these traits. One hundred and thirty-five genetically diverse pea accessions were phenotyped in field studies across three or five environments under stress and control conditions. To determine marker trait associations (MTAs), a total of 16,877 valuable single nucleotide polymorphisms (SNPs) were used in association analysis. Association mapping detected 15 MTAs that were significantly (p ≤ 0.0005) associated with the six stress-adaptive traits averaged across all environments and consistent in multiple individual environments. The identified MTAs were four for lamina wax, three for petiole wax, three for stem thickness, two for the flowering duration, one for the normalized difference vegetation index (NDVI), and two for the normalized pigment and chlorophyll index (NPCI). Sixteen candidate genes were identified within a 15 kb distance from either side of the markers. The detected MTAs and candidate genes have prospective use towards selecting stress-hardy pea cultivars in marker-assisted selection.

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