Genetic Disease Gene Identification

This study is enrolling participants by invitation only.
Sponsor:
Information provided by:
State University of New York - Upstate Medical University
ClinicalTrials.gov Identifier:
NCT00916903
First received: June 8, 2009
Last updated: June 9, 2009
Last verified: June 2009

June 8, 2009
June 9, 2009
October 2005
October 2010   (final data collection date for primary outcome measure)
Identification of gene/mutation responsible for disorder. [ Designated as safety issue: No ]
Same as current
Complete list of historical versions of study NCT00916903 on ClinicalTrials.gov Archive Site
Not Provided
Not Provided
Not Provided
Not Provided
 
Genetic Disease Gene Identification
Genetic Disease Gene Identification

This is a a study to identify inherited disease genes. The study will use molecular techniques to map genetic diseases using techniques such as Affymetrix SNP chips. The powerful combination of the information generated by the Human Genome Project and technical advances such as microarrays enables attempts to identify genes responsible for inherited disorders more possible than ever before. Starting with even modest pedigrees of only a few individuals, or even single individuals, it is possible to identify the gene(s) involved. It is proposed to collect up to 20 ml of peripheral blood and/or buccal cell samples from subjects and relevant family members. Currently the following disorders are approved for investigation.

The current list of disorders:

Aarskog-Scott syndrome, Café-au-Lait spots, Cerebral cavernous malformation, delXp, del2q, del10p, del11q, del12p, del13q, del14q, del16q, del17q, del18q, del Xp21, Choreoathetosis, Congenital Vertical Talus (CVT), Clubfoot, Tarsal coalition and other congenital limb deformities, Cystic Fibrosis (CF)-like disease, Desbuquois syndrome, Droopy Eyelid syndrome (Ptosis), Fanconi-Bickel syndrome (FBS), FENIB (familial encephalopathy with neuroserpin inclusion bodies), FG syndrome, Idiopathic generalised epilepsy (IGE), Renpenning syndrome, transient neonatal diabetes with 6q UPD, translocation (13;14), translocation (3;8), translocation (2;18), Uncharacterized familial dementia and X-linked mental retardation (XLMR).

It is proposed to identify and recruit individuals and/or families with specified the disorders listed above. 10-20 ml (2-4 teaspoons) of peripheral blood will be collect¬ed from all adult subjects. Smaller volumes of blood would be collected from children based on their age/size. In some cases, as an adequate alternative to collecting peripheral blood, buccal cells will be collected using cheek swabs (Epicentre Biotechnologies). All relevant living members of each pedigree will be asked to partici¬pate, free of charge, on a research basis only. Genomic DNA will be extracted by standard methods and used as template for Polymerase Chain Reac¬tion (PCR) amplification reactions. Individuals will be genotyped at markers and candidate gene sequenced.

Essentially two approaches will be used:

  1. Circumstances that may provide knowledge of candidate genes include reviews of the literature, biology of the disease, understanding of biological pathways, chromosomal rearrangements, mutants in model organisms etc. When candidate genes exist, it is proposed to use linked microsatellite and/or single nucleotide polymorphism (SNP) PCR primer pairs on the DNA from families to determine if there is co-segregation of the disease and markers and thus linkage between the disease gene and previously mapped markers.

    If the disease appears to be linked to the candidate gene, PCR primers flanking all coding exons will be used to amplify the exons and intron/exon boundaries followed by sequencing to detect disease-causing mutations. A web site that enables the design of primers to amplify candidate gene exons is available (http://genome.ucsc.edu/cgi-bin/hgGateway ). If a very strong candidate gene exists, candidate gene sequencing will be performed on affected individual samples without first performing a linkage study.

  2. When no obvious candidate genes exist, and a family of sufficient size has been collected, it is proposed to use Affymetrix SNP microarrays to perform a human genome-wide search for linkage. We have used this approach successfully before (Shrimpton et al 2004), utilizing the whole genome linkage analysis with the Human Mapping 10K Array (Affymetrix Inc., Santa Clara, CA). The 10K Array permits the simultaneous genotyping of more than 11,200 mapped SNPs spaced throughout the human genome at 210 KB intervals. Affymetrix 100K and 500K arrays are also available. SNP genotype information will be analyzed using Varia (Silicon Genetics) and/or Merlin software. The data will be used to define a critical region. If statistically significant segregation is detected, candidate genes within the critical region will be evaluated and ranked in order of their likelihood of being the disease gene. Candidate genes will then be sequenced as detailed above.

Summary.

  1. Identify candidate disease genes from linkage studies, strong circumstantial evidence or clues from the phenotype.
  2. Sequence candidate genes to detect disease-causing mutations.
  3. Evaluation of detected variation.
Observational
Observational Model: Family-Based
Time Perspective: Retrospective
Not Provided
Retention:   Samples With DNA
Description:

DNA will be isolated from peripheral blood or cheek scraoes.

Non-Probability Sample

Patients and their families identified by physicians.

  • Congenital Vertical Talus
  • Familial Encephalopathy With Neuroserpin Inclusion Bodies
  • Idiopathic Generalised Epilepsy
  • Familial Dementia
  • X-Linked Mental Retardation
Not Provided
  • 1
    Patients with genetic condition being studied.
  • 2
    Matched controls

*   Includes publications given by the data provider as well as publications identified by ClinicalTrials.gov Identifier (NCT Number) in Medline.
 
Enrolling by invitation
200
October 2010
October 2010   (final data collection date for primary outcome measure)

Inclusion Criteria:

  • Patients and their families identified by physicians.

Exclusion Criteria:

  • Patients with unrelated disorders.
Both
6 Months and older
Yes
Contact information is only displayed when the study is recruiting subjects
United States
 
NCT00916903
IRBPHS#4280F
No
Antony E Shrimpton PhD, Assoc Prof, SUNY Upstate Medical University
State University of New York - Upstate Medical University
Not Provided
Principal Investigator: Antony E Shrimpton, PhD State University of New York - Upstate Medical University
State University of New York - Upstate Medical University
June 2009

ICMJE     Data element required by the International Committee of Medical Journal Editors and the World Health Organization ICTRP