Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

T (Brachyury) gene duplication confers major susceptibility to familial chordoma

ABSTRACT: Using high-resolution array-CGH, we identified unique duplications of a region on 6q27 in four multiplex (≥ with ≥ 3 cases) families of chordoma, a cancer of presumed notochordal origin. comparison of test samples from chordoma families to a reference DNA sample

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Kelley

PROVIDER: E-GEOD-17668 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

T (brachyury) gene duplication confers major susceptibility to familial chordoma.

Yang Xiaohong R XR Ng David D Alcorta David A DA Liebsch Norbert J NJ Sheridan Eamonn E Li Sufeng S Goldstein Alisa M AM Parry Dilys M DM Kelley Michael J MJ

Nature genetics 20091004 11

Using high-resolution array-CGH, we identified unique duplications of a region on 6q27 in four multiplex families with at least three cases of chordoma, a cancer of presumed notochordal origin. The duplicated region contains only the T (brachyury) gene, which is important in notochord development and is expressed in most sporadic chordomas. Our findings highlight the value of screening for complex genomic rearrangements in searches for cancer-susceptibility genes. ...[more]

PMID: 19801981

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Project description:MarekM-bM-^@M-^Ys disease virus (MDV) is an oncovirus causing tumor disease known as MarekM-bM-^@M-^Ys disease (MD) in chicken. Breeding of chickens genetically resistant to MD is considered a vital augment to better control MD. To find the mechanism underlying the genetic resistance to MD, a genomic structural variation, copy number variation (CNV), was examined in inbred MD-resistant and -susceptible chicken lines by using the comparative genomic hybridization (CGH) technique. A total of 45 copy number variation regions (CNVRs) were found spanning across 3,297,038 bp in length of the chicken genome in 4 lines of chickens. Ten CNVRs were selectively confirmed with quantitative real-time PCR. The comparison between the resistant and susceptible chicken lines revealed 28 differentially presented CNVRs, which are functionally involved in immune response, cell proliferation in midbrain, G-protein coupled receptor signaling pathway, and protein-glutamine gamma-glutamyltransferase activity. Two CNVRs that are related with MD-resistance and M-bM-^@M-^Ssusceptibility were also found transmitted to descendent recombinant congenic lines that differ in susceptibility to MD. A positive correlation was identified between the CNVRs and gene expression, indicating the importance of gene expression dosage in disease resistance. We also found the overlapping between the CNVR region and the MarekM-bM-^@M-^Ys disease trait related quantitative trait loci (QTLs). In conclusion, our data provided additional information elucidating one of possible mechanisms underlying of genetic resistance to MD. The findings may eventually lead to better strategies for genetic improvement of resistance to MD in poultry. L63: highly resistant to MD; L72: highly susceptible to MD; RCS-L: moderate resistant to MD; RCS-M: moderate susceptible to MD Red blood cell DNAs were isolated from L63, L72, RCS-L and RCS-M and then labeled with Cy3. DNA from Red Junglefowl was labeled with Cy5 as reference and mixed with Cy3 labeled DNA, then hybridized to the 385K chicken tiling array. The hybridization, normalization and segmentation analysis were performed by NimbleGen Systems Inc. (Madison, USA). A detailed description of their technical specifics can be found on http://www.nimblegen.com/products/lit/lit.html. Briefly, the segments with five or more probes having a mean log2 ratio greater than M-BM-10.5 (0.5_5) were chosen as candidate CNVs.

Dataset Information

T (Brachyury) gene duplication confers major susceptibility to familial chordoma

Publications

T (brachyury) gene duplication confers major susceptibility to familial chordoma.

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