Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human peripheral blood from healthy and predisposed individuals reveals a homozygouse germline mutation in the DDB2 gene in a patient with severe facial tumors

ABSTRACT: Characterization of the underlying genetic defects in patients with a rare and peculiar phenotype is challenging. Here we have utilized whole genome expression profiling, and identified a homozygous germline mutation in the DDB2 gene in a patient with several facial tumors. The feasibility of using blood derived RNA, diminishing costs of the technology, and the limited number of samples needed provide this approach a powerful new tool that may substantially aid in such gene identification efforts. Experiment Overall Design: RNA from patientâs and his parentsâ blood samples, as well as from twelve individuals available from other projects, were subjected to Human GeneChip U133 Plus 2.0 whole genome expression arrays (Affymetrix).

ORGANISM(S): Homo sapiens

SUBMITTER: Antti Kokko

PROVIDER: E-GEOD-6351 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Blood-derived gene-expression profiling in unravelling susceptibility to recessive disease.

Vahteristo P P Kokko A A Saksela O O Aittomäki K K Aaltonen L A LA

Journal of medical genetics 20070727 11

Identification of new disease predisposition genes with chip-based technologies typically requires extensive financial and sample resources. We have recently shown that combining peripheral blood genome and transcriptome (BGT) information in highly selected materials can be a successful low-cost approach to unravelling dominant tumour susceptibility. In this study, we extended our investigations to recessively inherited tumour predisposition, and identified a homozygous germline mutation in the ...[more]

PMID: 17660462

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Project description:Non-syndromic facial asymmetry is commonly found in dentofacial deformity populations with skeletal malocclusions. Asymmetry of this type may result from imbalanced growth and function of both the jaw and associated muscles. Among the multiple genes that interact to affect the craniofacial musculoskeletal complex during pre and postnatal growth and development, NODAL signaling pathwy (NSP) genes are active in adult skeletal muscle and may be key factors in development, growth and maintenance of facial asymmetry. It is of interest to determine whether expression of NODAL pathway genes might differ in masseter muscles between individuals with malocclusion that have facial asymmetry and normal symmetry. Human Transcriptome 2.0 GeneChips (HTA2.0) were used to examine global gene expression in masster muscles between malocclusion subjects with posterior facial asymmetry and with normal facial symmetry. Eleven patients undergoing orthoganthic surgery were selected for comparison of masseter muscle gene expression on microarrays. Two subjects had posterior facial asymmetry (one with class II open bite and one with class III open bite malocclusion) and nine subjects had normal facial symmetry (three with class II open bite, two with class III open bite and four with class II deep bite malocclusion). RNA representative of total gene expression in masseter muscles of the malocclusion subjects with and without posterior facial asymmetry was prepared for labeling and hybridization on HTA2.0 chips. The two subjects with facial asymmetry clustered separately from eight other malocclusion subjects by a principle component analysis (PCA), even though one had a class II and the other a class III malocclusion. Sample 4L_Open_II is from a subject who has sleep apnea. Data from 4L_Open_II clustered independent of the asymmetry group and the eight other subjects of the symmetry group by PCA and was not included in analysis of differential expression with facial symmetry. Masseter muscles are paired jaw muscles (i.e. right and left masseter). In some cases, there was not sufficient quantity/quality of RNA from one side, thus the other side was used. Please note that the following information is provided in the 'source name' field of each sample record; subject ID number; either left or right masseter; J CRANIOFAC SURG_ID# corresponding to the data presented in the manuscript

Dataset Information

Transcription profiling of human peripheral blood from healthy and predisposed individuals reveals a homozygouse germline mutation in the DDB2 gene in a patient with severe facial tumors

Publications

Blood-derived gene-expression profiling in unravelling susceptibility to recessive disease.

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