Limits...
Gene expression profiling as a tool for positional cloning of genes-shortcut or the longest way round.

Rosenlöf LW - Curr. Genomics (2008)

Bottom Line: This has resulted in a number of publications where carefully performed genomic analyses present likely candidate genes for their respective QTL s.However, seldom the findings are reconnected to the QTL controlled phenotypes.In this review, we use our own data as an illustrative example that "very likely candidate genes" identified by genomic/proteomics is not necessarily the same as true QTL underlying genes.

View Article: PubMed Central - PubMed

Affiliation: Section for Immunogenetics, University of Rostock, Germany.

ABSTRACT
The identification of quantitative trait loci, QTL, in arthritis animal models is a straight forward process. However, to identify the underlying genes is a great challenge. One strategy frequently used, is to combine QTL analysis with genomic/proteomic screens. This has resulted in a number of publications where carefully performed genomic analyses present likely candidate genes for their respective QTL s. However, seldom the findings are reconnected to the QTL controlled phenotypes. In this review, we use our own data as an illustrative example that "very likely candidate genes" identified by genomic/proteomics is not necessarily the same as true QTL underlying genes.

No MeSH data available.


Related in: MedlinePlus

Plasma from healthy and chronically ill DA and DA.Pia6 rats were separated by charge on pH4-7 Immobiline dry strips and separated for size on 12% SDS-PAGE. All samples were repeated three times. According to analysis there was one major difference between the DA and DA.Pia6, the single (DA) and duplicated spot (DA.Pia6+/-) (marked with a ring). According to mass-spectrometry these dots were identified as two isoforms of the vitamin D binding protein encoded from the Gc locus.
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Figure 1: Plasma from healthy and chronically ill DA and DA.Pia6 rats were separated by charge on pH4-7 Immobiline dry strips and separated for size on 12% SDS-PAGE. All samples were repeated three times. According to analysis there was one major difference between the DA and DA.Pia6, the single (DA) and duplicated spot (DA.Pia6+/-) (marked with a ring). According to mass-spectrometry these dots were identified as two isoforms of the vitamin D binding protein encoded from the Gc locus.

Mentions: QTL underlying genes do not necessarily have to show differential expression, but can show qualitative differences in the protein product. Such differences might be detectable on a 2D gel. Therefore, in parallel with the Affymetrix experiment, we did 2D gel screens of the DA and DA.pia6 rats. As we had a robust, reproducible phenotype in the differential concentration of plasma lipocalin proteins, we decided to analyze plasma from healthy and chronically ill DA and DA.Pia6 rats. After repeating each gel run at least three times per animal and time point, we could observe on major spot difference between DA and heterozygous DA.Pia6 rats both in healthy and chronically ill animals (Fig. 1). The DA rat had one spot in this position whereas the DA.Pia6 rat had two. After extraction, digestion and mass-spectrometry analysis of the resulting peptides we could identify the spots as isoforms of vitamin D binding protein most likely representing different glycoforms. The vitamin D binding protein is encoded from the Gc locus positioned at 20.2 MBp, very close to the top marker in the linkage analysis (Csna, 21.9). Interestingly, vitamin D binding protein plays an important role in regulation of neutrophils and activation of macrophages [31-33]. Accordingly, both regarding its mapping position and its known function it was a very likely candidate for the gene underlying the Pia6 QTL.


Gene expression profiling as a tool for positional cloning of genes-shortcut or the longest way round.

Rosenlöf LW - Curr. Genomics (2008)

Plasma from healthy and chronically ill DA and DA.Pia6 rats were separated by charge on pH4-7 Immobiline dry strips and separated for size on 12% SDS-PAGE. All samples were repeated three times. According to analysis there was one major difference between the DA and DA.Pia6, the single (DA) and duplicated spot (DA.Pia6+/-) (marked with a ring). According to mass-spectrometry these dots were identified as two isoforms of the vitamin D binding protein encoded from the Gc locus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2691671&req=5

Figure 1: Plasma from healthy and chronically ill DA and DA.Pia6 rats were separated by charge on pH4-7 Immobiline dry strips and separated for size on 12% SDS-PAGE. All samples were repeated three times. According to analysis there was one major difference between the DA and DA.Pia6, the single (DA) and duplicated spot (DA.Pia6+/-) (marked with a ring). According to mass-spectrometry these dots were identified as two isoforms of the vitamin D binding protein encoded from the Gc locus.
Mentions: QTL underlying genes do not necessarily have to show differential expression, but can show qualitative differences in the protein product. Such differences might be detectable on a 2D gel. Therefore, in parallel with the Affymetrix experiment, we did 2D gel screens of the DA and DA.pia6 rats. As we had a robust, reproducible phenotype in the differential concentration of plasma lipocalin proteins, we decided to analyze plasma from healthy and chronically ill DA and DA.Pia6 rats. After repeating each gel run at least three times per animal and time point, we could observe on major spot difference between DA and heterozygous DA.Pia6 rats both in healthy and chronically ill animals (Fig. 1). The DA rat had one spot in this position whereas the DA.Pia6 rat had two. After extraction, digestion and mass-spectrometry analysis of the resulting peptides we could identify the spots as isoforms of vitamin D binding protein most likely representing different glycoforms. The vitamin D binding protein is encoded from the Gc locus positioned at 20.2 MBp, very close to the top marker in the linkage analysis (Csna, 21.9). Interestingly, vitamin D binding protein plays an important role in regulation of neutrophils and activation of macrophages [31-33]. Accordingly, both regarding its mapping position and its known function it was a very likely candidate for the gene underlying the Pia6 QTL.

Bottom Line: This has resulted in a number of publications where carefully performed genomic analyses present likely candidate genes for their respective QTL s.However, seldom the findings are reconnected to the QTL controlled phenotypes.In this review, we use our own data as an illustrative example that "very likely candidate genes" identified by genomic/proteomics is not necessarily the same as true QTL underlying genes.

View Article: PubMed Central - PubMed

Affiliation: Section for Immunogenetics, University of Rostock, Germany.

ABSTRACT
The identification of quantitative trait loci, QTL, in arthritis animal models is a straight forward process. However, to identify the underlying genes is a great challenge. One strategy frequently used, is to combine QTL analysis with genomic/proteomic screens. This has resulted in a number of publications where carefully performed genomic analyses present likely candidate genes for their respective QTL s. However, seldom the findings are reconnected to the QTL controlled phenotypes. In this review, we use our own data as an illustrative example that "very likely candidate genes" identified by genomic/proteomics is not necessarily the same as true QTL underlying genes.

No MeSH data available.


Related in: MedlinePlus