Expression Quantitative Trait Loci Analysis of 13 Genes in the Rat Prostate

Yamashita, Satoshi; Wakazono, Kuniko; Nomoto, Tomoko; Tsujino, Yoshimi; Kuramoto, Takashi

doi:10.1534/genetics.104.038174

Cited by 34 publications

(25 citation statements)

References 27 publications

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“…It also appears that the number of trans-acting genes identified reduced as our detection stringency increased. Such an effect was recently reported in two tissues in rats, where generally the cis eQTL detected had much greater LOD scores than the trans-acting eQTL (Yamashita et al 2005).…”

Section: Discussionsupporting

confidence: 64%

SFP Genotyping From Affymetrix Arrays Is Robust But Largely Detects Cis-acting Expression Regulators

Luo

Potokina

Druka³

et al. 2007

Genetics

106

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The recent development of Affymetrix chips designed from assembled EST sequences has spawned considerable interest in identifying single-feature polymorphisms (SFPs) from transcriptome data. SFPs are valuable genetic markers that potentially offer a physical link to the structural genes themselves. However, most current SFP prediction methodologies were developed for sequenced species although SFPs are particularly valuable for species with complex and unsequenced genomes. To establish the sensitivity and specificity of prediction, we explored four methods for identifying SFPs from experiments involving two tissues in two commercial barleys and their doubled-haploid progeny. The methods were compared in terms of numbers of SFPs predicted and their ability to identify known sequence polymorphisms in the features, to confirm existing SNP genotypes and to match existing maps and individual haplotypes. We identified .4000 separate SFPs that accurately predicted the SNP genotype of .98% of the doubled-haploid (DH) lines. They were highly enriched for features containing sequence polymorphisms but all methods uniformly identified a majority of SFPs ($64%) in features for which there was no sequence polymorphism while 5% mapped to different locations, indicating that ''SFPs'' mainly represent polymorphism in cis-acting regulators. All methods are efficient and robust at predicting markers for gene mapping.

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Section: Discussionsupporting

confidence: 64%

SFP Genotyping From Affymetrix Arrays Is Robust But Largely Detects Cis-acting Expression Regulators

Luo

Potokina

Druka³

et al. 2007

Genetics

106

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“…62 CNTN6 was also identified as a top candidate for a human prostate cancer susceptibility gene through a genome-wide association analysis, although no mutations were found in a screen of this gene. 62,63 CHL1 is similar to the L1 gene family of neural adhesion molecules, 64 and recent studies suggest its role in neurite regeneration. 65 Mice deficient in the orthologous gene Chl1 exhibit neurologically related problems 54,66,67 but no cancer susceptibility.…”

Section: Discussionmentioning

confidence: 98%

Molecular Genetic Analysis of a Cell Adhesion Molecule With Homology to L1CAM, Contactin 6, and Contactin 4 Candidate Chromosome 3p26pter Tumor Suppressor Genes in Ovarian Cancer

Manderson¹,

Birch²,

Shen

et al. 2009

International Journal of Gynecological Cancer

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Loss of heterozygosity (LOH) analyses of epithelial ovarian cancers (EOCs) previously identified a candidate tumor suppressor gene (TSG) locus within the chromosomal region 3p25.3-pter. Loss of heterozygosity analysis was performed to define the locus and identify candidates for further study. Loss of heterozygosity analysis of 124 malignant EOC samples of different histopathologic subtypes using 12 polymorphic microsatellite repeat markers identified a 330-kilobase minimal region of overlapping deletions at 3p26.3 that contained contactin 4 (CNTN4) as the only known TSG candidate. However, evaluation of the LOH patterns in the serous EOC samples, the most common subtype, enabled the identification of a second, broader region of LOH also included the cell adhesion molecule with homology to L1CAM (CHL1) and CNTN6 as candidates. Gene expression by reverse transcription polymerase chain reaction was not detectable in primary cultures of normal ovarian surface epithelial cells for any of these candidates. CNTN6 expression was also not detectable in serous EOC samples. In contrast, gene expression of CNTN4 and CHL1, particularly overexpression of CHL1, was observed in serous EOC samples. Mutation and gene expression analyses of well-defined EOC cell lines (OV-90, TOV-112D, TOV-21G, and TOV-81D) that differ in their tumorigenic potential and chromosome 3p26-pter genomic content revealed CNTN4 expression and a novel mutation only in the tumorigenic EOC cell line TOV-21G. This mutation was neither observed in controls (n = 105) nor detected by sequencing analysis of complementary DNA. Taken together, these results do not support the candidacy of CHL1, CNTN6, and CNTN4 as TSGs in the 3p26-pter region. However, the overexpression of CHL1, a member of the L1 cell adhesion molecule (L1CAM) family, warrants further investigation.

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“…Cyclin-dependent kinase inhibitor 1a (Cdkn1a), also called p21, is a tumor suppressor gene and considered a good candidate for one of the prostate cancer susceptibility genes. The 119-bp insertion was associated with high Cdkn1a expression in the rat prostate, which might imply resistance to prostate cancer in the BUF/NacJcl rat (24,25). The insertion was shared in 49 strains including the prostate cancer-resistant BUF/NacJcl, but not in 92 strains including the prostate cancer-susceptible ACI/NJcl.…”

Section: Rat Functional Polymorphismsmentioning

confidence: 96%

Functional polymorphisms in inbred rat strains and their allele frequencies in commercially available outbred stocks

Kuramoto

Nakanishi

Serikawa

2008

Physiological Genomics

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Polymorphisms that have been proven to influence gene functions are called functional polymorphisms. It is significant to know the distribution of functional polymorphisms in the rat, widely used in animal models for human diseases. In this study, we assessed 16 functional polymorphisms consisting of 3 coat color and 13 disease-associated genes in 136 rat strains, as a part of the genetic profiling program of the National Bio Resource Project for the Rat (NBRP-Rat). Polymorphisms of Cdkn1a, Fcgr3, Grp10, Lss, and Fdft1, which were proven to function in prostate tumorigenesis, glomerulonephritis, hyperphagia, and cholesterol biosynthesis, were shared among various inbred strains. These findings indicated that most rat strains harbored the disease-associated alleles and suggested that many unidentified functional polymorphisms might exist in inbred rat strains. The functional polymorphisms shared in inbred strains were also observed within outbred stocks available commercially. Therefore, this implies that experimental plans based on either rat inbred strains or outbred stocks need to be carefully designed with a full understanding of the genetic characteristics of the animals. To select the most suitable strains for experiments, the NBRP-Rat will periodically improve and update the genetic profiles of rat strains.

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Expression Quantitative Trait Loci Analysis of 13 Genes in the Rat Prostate

Cited by 34 publications

References 27 publications

SFP Genotyping From Affymetrix Arrays Is Robust But Largely Detects Cis-acting Expression Regulators

SFP Genotyping From Affymetrix Arrays Is Robust But Largely Detects Cis-acting Expression Regulators

Molecular Genetic Analysis of a Cell Adhesion Molecule With Homology to L1CAM, Contactin 6, and Contactin 4 Candidate Chromosome 3p26pter Tumor Suppressor Genes in Ovarian Cancer

Functional polymorphisms in inbred rat strains and their allele frequencies in commercially available outbred stocks

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