Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses

Wongseree, Waranyu; Assawamakin, Anunchai; Piroonratana, Theera; Sinsomros, Saravudh; Limwongse, Chanin; Chaiyaratana, Nachol

doi:10.1186/1471-2105-10-294

Cited by 32 publications

(38 citation statements)

References 78 publications

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“…A second area where we can expect continued development is the exploration of additional analytic approaches. Novel methods continue to emerge (Greene et al , 2010;Steffens et al , 2010;Wongseree et al , 2009). Finally, as gene sequencing continues to become cost effective, for gene-region, whole exome, and eventually whole genome sequencing, methods for looking for epistasis in these data will become critical.…”

Section: Future Workmentioning

confidence: 99%

Using Biological Knowledge to Uncover the Mystery in the Search for Epistasis in Genome-Wide Association Studies

Ritchie

2010

Annals of Human Genetics

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The search for the missing heritability in genome-wide association studies (GWAS) has become an important focus for the human genetics community. One suspected location of these genetic effects is in gene-gene interactions, or epistasis. The computational burden of exploring gene-gene interactions in the wealth of data generated in GWAS, along with small to moderate sample sizes, have led to epistasis being an afterthought, rather than a primary focus of GWAS analyses. In this review, we discuss some potential approaches to filter a GWAS dataset to a smaller, more manageable dataset where searching for epistasis is considerably more feasible. We describe a number of alternative approaches, but primarily focus on the use of prior biological knowledge from databases in the public domain to guide the search for epistasis. The manner in which prior knowledge is incorporated into a GWA study can be many and these data can be extracted from a variety of database sources. We discuss a number of these approaches and propose that a comprehensive approach will likely be most fruitful for searching for epistasis in large-scale genomic studies of the current state-of-the-art and into the future.

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Section: Future Workmentioning

confidence: 99%

Using Biological Knowledge to Uncover the Mystery in the Search for Epistasis in Genome-Wide Association Studies

Ritchie

2010

Annals of Human Genetics

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“…Thameem et al (2002) concluded that polymorphism of this gene did not contribute significantly to T2D etiology in Pima Indians (Thameem et al, 2002). On the other hand, an evidence of association between two intronic SNPs of the LMX1A and T2D in the British population has been reported by Wongseree et al (2009).…”

Section: Discussionmentioning

confidence: 98%

Polymorphism of the pig LMX1A gene, localized within the FAT1 region, is not associated with growth and fatness

Chmurzyńska¹,

Grzes²,

Kregielska³

et al. 2010

J. Anim. Feed Sci.

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The LMX1A gene, located within the 3.3 cM FAT1 QTL on porcine chromosome 4, was tested as a positional and functional candidate for fatness traits. A gene fragment consisting of the partial promoter, 5'UTR, exon 1, and partial intron 1, was sequenced in a panel of 79 pigs of Polish Large White (PLW), Polish Landrace (PL), Duroc and Pietrain breeds. Only a G to A substitution in intron 1 (182 bp upstream of the translation start site) was found. In total, 738 gilts were genotyped: 191 PLWs, 249 PLs, 239 of synthetic line 990 (L990), 21 Pietrain and 38 Duroc. The genotype distributions appeared to be breed-specific. Association studies were performed for 12 growth and fatness traits in the PLW, PL and L990 pigs and no association was found. The only result which approached the significance level (P=0.047) concerned the lean meat content. Our results indicate that the LMX1A gene should not be considered as a candidate gene for QTL in the FAT1 region in the studied Polish pig breeds.

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“…Mutations in PARK2 have been associated with juvenile autosomal recessive Parkinsonism [13], leprosy [14], diabetes mellitus type 2 [15], Alzheimer’s dementia [16], multiple sclerosis [17], Attention Deficit Hyperactivity Disorder (ADHD) [18], autism [19], typhoid and paratyphoid fever [20, 21], and more recently to cancer [22]. Among the cancers already presenting PARK2 alterations are: ovarian, breast, kidney, lung, liver, colorectal, melanoma, acute lymphoblastic leukemia, Burkitt’s lymphoma, and B-cell non-Hodgkin’s lymphoma [23].…”

Section: Introductionmentioning

confidence: 99%

Association of a PARK2 Germline Variant and Epithelial Ovarian Cancer in a Southern Brazilian Population

Klimczak

Ventury²,

Faucz³

et al. 2016

Oncology

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Ovarian cancer (OC) is the eighth most common cancer among women in Brazil and seventh in the world population. OC has a high mortality rate and is difficult to diagnose. Currently, OC detection most often occurs at an advanced stage of the disease due to its silent progression, which contributes to the high mortality rate. Available genetic markers are not considered specifically enough for an initial and definite diagnosis. The association with new genes involved with OC can provide a better understanding of this pathology as well as contribute to the development of a marker scenario, providing an improvement in the treatment and survival of patients. The aim of this study was to examine the potential association between the PARK2 gene and epithelial ovarian cancer (EOC). Accordingly, we conducted a study for which 25 patients and 87 controls were recruited. Linkage disequilibrium analysis showed that the four studied tag SNPs (rs2803073, rs6930532, rs1040079, and rs2276201) were independent. Our results using the multivariate analysis between the additive and dominant model demonstrated that tag SNP rs2803073 of PARK2 is associated with susceptibility to EOC (p = 0.018, OR = 0.42). These findings suggest that hereditary variation in the PARK2 gene could influence EOC development mechanisms.

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Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses

Cited by 32 publications

References 78 publications

Using Biological Knowledge to Uncover the Mystery in the Search for Epistasis in Genome-Wide Association Studies

Using Biological Knowledge to Uncover the Mystery in the Search for Epistasis in Genome-Wide Association Studies

Polymorphism of the pig <i>LMX1A</i> gene, localized within the FAT1 region, is not associated with growth and fatness

Association of a <b><i>PARK2</i></b> Germline Variant and Epithelial Ovarian Cancer in a Southern Brazilian Population

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