Sequence Diversity in Genes of Lipid Metabolism

Garcia, Christine Kim; Mues, Gabriele; Liao, Yuanlan; Hyatt, Tommy; Patil, Nila; Cohen, Jonathan C.; Hobbs, Helen H.

doi:10.1101/gr.172301

Cited by 20 publications

(13 citation statements)

References 59 publications

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“…Furthermore, over 74% of the SNP (210 of 283) were transitions, similar to the ratio (75%) obtained from 10 human genes [14]. Although most SNP were bi-allele polymorphisms, two tri-allelic variations were observed in the insulin gene (T/C/A, nt 1295 of AY 438372) and the LEPR gene (T/G/A, nt 885 of AF 222783), respectively.…”

Section: Discussionsupporting

confidence: 78%

Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography

Nie¹,

Lei²,

Ouyang³

et al. 2005

Genet. Sel. Evol.

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-The genes that are part of the somatotropic axis play a crucial role in the regulation of growth and development of chickens. The identification of genetic polymorphisms in these genes will enable the scientist to evaluate the biological relevance of such polymorphisms and to gain a better understanding of quantitative traits like growth. In the present study, 75 pairs of primers were designed and four chicken breeds, significantly differing in growth and reproduction characteristics, were used to identify single nucleotide polymorphisms (SNP) using the denaturing high performance liquid chromatography (DHPLC) technology. A total of 283 SNP were discovered in 31 897 base pairs (bp) from 12 genes of the growth hormone (GH), growth hormone receptor (GHR), ghrelin, growth hormone secretagogue receptor (GHSR), insulin-like growth factor I and II (IGF-I and -II), insulin-like growth factor binding protein 2 (IGFBP-2), insulin, leptin receptor (LEPR), pituitary-specific transcription factor-1 (PIT-1), somatostatin (SS), thyroid-stimulating hormone beta subunit (TSH-β). The observed average distances in bp between the SNP in the 5'UTR, coding regions (non-and synonymous), introns and 3'UTR were 172, 151 (473 and 222), 89 and 141 respectively. Fifteen non-synonymous SNP altered the translated precursors or mature proteins of GH, GHR, ghrelin, IGFBP-2, PIT-1 and SS. Fifteen indels of no less than 2 bps and 2 poly (A) polymorphisms were also observed in 9 genes. Fifty-nine PCR-RFLP markers were found in 11 genes. The SNP discovered in this study provided suitable markers for association studies of candidate genes for growth related traits in chickens.chickens / genes / SNP / DHPLC * Corresponding author: xqzhang@scau.edu.cn 340 Q. Nie et al.

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Section: Discussionsupporting

confidence: 78%

Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography

Nie¹,

Lei²,

Ouyang³

et al. 2005

Genet. Sel. Evol.

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“…28 In addition, a Portuguese ADH study found only 48% of its total received cases with clinical diagnosis of ADH had genetic defects on LDLR, APOB or PCSK9, leaving the other 52% of ADH cases with possible undiscovered gene mutations. 29 In a study by Garcia et al, 30 the researchers used gene chip (robo arrays) to resequence the coding regions of 10 key genes of lipid metabolism in 80 dyslipidemic cases. In all, 14 non-synonymous and 22 synonymous SNPs were identified, which were confirmed by conventional sequencing.…”

Section: Resultsmentioning

confidence: 99%

Differences in allele frequencies of autosomal dominant hypercholesterolemia SNPs in the Malaysian population

Alex¹,

Chahil²,

Lye³

et al. 2012

J Hum Genet

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Hypercholesterolemia is caused by different interactions of lifestyle and genetic determinants. At the genetic level, it can be attributed to the interactions of multiple polymorphisms, or as in the example of familial hypercholesterolemia (FH), it can be the result of a single mutation. A large number of genetic markers, mostly single nucleotide polymorphisms (SNP) or mutations in three genes, implicated in autosomal dominant hypercholesterolemia (ADH), viz APOB (apolipoprotein B), LDLR (low density lipoprotein receptor) and PCSK9 (proprotein convertase subtilisin/kexin type-9), have been identified and characterized. However, such studies have been insufficiently undertaken specifically in Malaysia and Southeast Asia in general. The main objective of this study was to identify ADH variants, specifically ADH-causing mutations and hypercholesterolemia-associated polymorphisms in multiethnic Malaysian population. We aimed to evaluate published SNPs in ADH causing genes, in this population and to report any unusual trends. We examined a large number of selected SNPs from previous studies of APOB, LDLR, PCSK9 and other genes, in clinically diagnosed ADH patients (n ¼ 141) and healthy control subjects (n ¼ 111). Selection of SNPs was initiated by searching within genes reported to be associated with ADH from known databases. The important finding was 137 mono-allelic markers (44.1%) and 173 polymorphic markers (55.8%) in both subject groups.

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“…In addition to measuring the mRNA expression levels, DNA microarrays are also used to characterize spliced genes [16], resequence whole stretches of DNA [17], and identify single nucleotide polymorphisms (SNPs) [18].…”

Section: Data Collectionmentioning

confidence: 99%

Improved understanding of gene expression regulation using systems biology

Kuczenski

Aggarwal

Lee

2005

Expert Review of Proteomics

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This article reviews the current state of systems biology approaches, including the experimental tools used to generate 'omic' data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. Some of the challenges facing this field and the future opportunities in the systems biology era are highlighted.

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Sequence Diversity in Genes of Lipid Metabolism

Cited by 20 publications

References 59 publications

Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography

Identification and characterization of single nucleotide polymorphisms in 12 chicken growth-correlated genes by denaturing high performance liquid chromatography

Differences in allele frequencies of autosomal dominant hypercholesterolemia SNPs in the Malaysian population

Improved understanding of gene expression regulation using systems biology

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