A protocol comparison for the analysis of heat shock protein A1B +A1538G SNP

Contreras-Sesvold, Carmen; Sambuughin, Nyamkhishig; Blokhin, Andrei V.; Deuster, Patricia A.

doi:10.1007/s12192-009-0134-9

Cited by 7 publications

(4 citation statements)

References 17 publications

(30 reference statements)

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“…To our knowledge, variations in HSP70 by ethnicity have not been previously been reported. Further, the genetic distribution for HSPA1B is in agreement with previous work [ 31 ], but AA had a significantly greater percentage who were homozygous for the minor allele. Interestingly, a significant difference for reduced HSP70 concentrations was associated with caffeine use.…”

Section: Discussionsupporting

confidence: 90%

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Association of Plasma Heat Shock Protein 70, Interleukin 6, and Creatine Kinase Concentrations in a Healthy, Young Adult Population

Contreras-Sesvold

Revenis

O’Connor

et al. 2015

Journal of Biomarkers

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Variations of baseline plasma concentrations of creatine kinase (CK), heat shock protein 70 (HSP70), and interleukin 6 (IL-6) have been reported. We report categorical associations which may influence these protein levels. Methods. Blood was harvested for DNA and plasma protein analysis from 567 adults. Mean protein levels of CK, HSP70, and IL-6 were compared by sex, ethnicity, genetic variants—CKMM Nco1 (rs1803285), HSPA1B +A1538G (rs1061581), and IL6 G-174C (rs1800795)—self-reported history of exercise, oral contraceptive use, and dietary supplement use. Results. SNP major allele frequencies for CKMM, HSPA1B, and IL6 were 70% A, 57% A, and 60%. Mean CK statistically differed by sex, ethnicity, oral contraceptives, and caffeine. Plasma HSP70 differed by caffeine and protein. Mean IL-6 concentration differed by sex, ethnicity, and genotype. Plasma IL-6 was significantly lower (29%) in males (1.92 ± 0.08 pg/mL) and higher (29%) among African Americans (2.85 ± 0.50 pg/mL) relative to the others. IL6 G-174C GG genotype (2.23 ± 0.14 pg/mL) was 19% greater than CG or CC genotypes. Conclusion. Differences in baseline CK and IL-6 plasma protein concentrations are associated with genetics, sex, ethnicity, and the use of oral contraceptives, caffeine, and protein supplements in this young and athletic population.

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Section: Discussionsupporting

confidence: 90%

“…Analysis of single nucleotide polymorphisms (SNP) for CKMM Nco1 A ∗ to G (rs1803285) [ 5 ] n = 453, HSPA1B +A ∗ 1538G (MP1 assay) [ 31 ] (rs1061581) n = 455, and IL6 G ∗ -174C (rs1800795) [ 30 ] n = 454 was accomplished as previously described [ 5 , 30 , 31 ]. Asterisks denote the major alleles.…”

Section: Methodsmentioning

confidence: 99%

Association of Plasma Heat Shock Protein 70, Interleukin 6, and Creatine Kinase Concentrations in a Healthy, Young Adult Population

Contreras-Sesvold

Revenis

O’Connor

et al. 2015

Journal of Biomarkers

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“…These three genes are extremely similar in their sequences, and part of a large HSP superfamily (Calderwood & Ciocca, ). As a result, their genotyping is extremely difficult (Contreras‐Sesvold, Sambuughin, Blokhin, & Deuster, ) and almost impossible with high‐throughput methods. This must be why the HSPA1B SNP has never been examined in GWAS despite its replicated associations with susceptibility to cancer in candidate gene studies (Guo et al., ; Ucisik‐Akkaya, Davis, Gorodezky, Alaez, & Dorak, ).…”

Section: Unique Features Of the Extended Mhc Regionmentioning

confidence: 99%

What hasGWASdone forHLAand disease associations?

Kennedy

Özbek

Dorak

2017

Int J Immunogenetics

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The major histocompatibility complex (MHC) is located in chromosome 6p21 and contains crucial regulators of immune response, including human leucocyte antigen (HLA) genes, alongside other genes with nonimmunological roles. More recently, a repertoire of noncoding RNA genes, including expressed pseudogenes, has also been identified. The MHC is the most gene dense and most polymorphic part of the human genome. The region exhibits haplotype-specific linkage disequilibrium patterns, contains the strongest cis- and trans-eQTLs/meQTLs in the genome and is known as a hot spot for disease associations. Another layer of complexity is provided to the region by the extreme structural variation and copy number variations. While the HLA-B gene has the highest number of alleles, the HLA-DR/DQ subregion is structurally most variable and shows the highest number of disease associations. Reliance on a single reference sequence has complicated the design, execution and analysis of GWAS for the MHC region and not infrequently, the MHC region has even been excluded from the analysis of GWAS data. Here, we contrast features of the MHC region with the rest of the genome and highlight its complexities, including its functional polymorphisms beyond those determined by single nucleotide polymorphisms or single amino acid residues. One of the several issues with customary GWAS analysis is that it does not address this additional layer of polymorphisms unique to the MHC region. We highlight alternative approaches that may assist with the analysis of GWAS data from the MHC region and unravel associations with all functional polymorphisms beyond single SNPs. We suggest that despite already showing the highest number of disease associations, the true extent of the involvement of the MHC region in disease genetics may not have been uncovered.

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“…Genomic DNA was successfully extracted from 254 participants as previously described [26]. Portions of DNA stock solutions were subsequently diluted to 25 ng/ L to create standardized working solutions.…”

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

The Association of 5-HTTLPR XLL Genotype with Higher Cortisol Levels in African Americans

Contreras-Sesvold

Abraham

Devaney

et al. 2015

International Journal of Medical Genetics

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Genetic variants of the human serotonin transporter (SERT) may contribute to HPA axis dysregulation. SERT has two promoter region polymorphisms (5-HTTLPR: VNTR and SNP: rs25531), which may alter levels of SERT protein and its function. Combining these polymorphisms creates a functional polymorphism (FN) which may modulate mRNA expression. This study examines the relationship between these genetic variants and morning and evening salivary samples of both cortisol and dehydroepiandrosterone sulfate (DHEAS) concentrations in 269 African American (AA) adults. Resultant allele frequencies for the VNTR, SNP, and FN genotypes were 70% L (2% XLL), 84% A, and 54% LA (2% XLLA), respectively. The XLL genotype was associated with significantly higher concentrations of cortisol (∼3X) and DHEAS (∼2X) for both VNTR and FN polymorphisms. No significant differences were found for SNP genotypes. Conclusions were that persons with VNTR and FN XLL polymorphisms had significantly higher cortisol and DHEAS concentrations than other genotypes. AAs also appear to have a higher frequency of the rare XL allele than Caucasians. Whether the XLL genotype predisposes AAs to greater health challenges will require further research to determine the implications of these findings.

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A protocol comparison for the analysis of heat shock protein A1B +A1538G SNP

Cited by 7 publications

References 17 publications

Association of Plasma Heat Shock Protein 70, Interleukin 6, and Creatine Kinase Concentrations in a Healthy, Young Adult Population

Association of Plasma Heat Shock Protein 70, Interleukin 6, and Creatine Kinase Concentrations in a Healthy, Young Adult Population

What hasGWASdone forHLAand disease associations?

The Association of 5-HTTLPR XLL Genotype with Higher Cortisol Levels in African Americans

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