Breakpoint Analysis of de Novo Apparently Balanced Chromosomal Translocations

Development of a Technique to Identify New Genes by Studying and Cloning the Breakpoints of de Novo Apparently Balanced Chromosomal Translocations in Patients Presenting With Syndromic Psychomotor Retardation

For every child with developmental delay, the investigators do a constitutional karyotype. This karyotype can reveal an apparently balanced chromosomal rearrangement (no visible loss or gain of genetic material), such as a translocation between two or more chromosomes of accidental occurrence (not transmitted by parents). However, an apparently balanced translocation does not explain the phenotype of the child. Among the hypotheses that could explain the child's symptoms, there is the possibility of another chromosomal abnormality at the translocation breakpoints, another defect elsewhere on the chromosomes or gene disruption at or near the breakpoints. Because the resolution of a constitutional karyotype is limited, these microanomalies can go undiagnosed. The goal of this study is to look for a microanomaly on a chromosome using a technology of higher resolution than that of the conventional karyotype. The proposed study uses DNA microarray technology on DNA extracted from blood lymphocytes to perform high-resolution analysis of all chromosomes to search for an unbalanced microrearrangement (such as loss or gain of chromosomal material). If no microrearrangement is found, the investigators will pursue by looking for a gene disruption defect at or near the breakpoints involved in the translocation. This will be done by first isolating the chromosomes involved in the translocation by flow cytometry and then hybridizing each of the isolated chromosomes on a new microarray. The purpose of this study is to find a possible cause to explain the phenotype (microrearrangement or gene disruption).

Study Overview

• Status: Unknown
• Conditions: Balanced Chromosomal Translocation
• Intervention / Treatment: Biological: Identification of breakpoints

Detailed Description

Psychomotor delay is observed in approximately 3% of the general population and has various causes: environmental, genetic (gene or chromosome) or unknown. Chromosomal abnormalities have been identified in 15% of syndromic psychomotor delay (ie. associated with another symptom). Balanced chromosomal translocations are observed in one out of every 1000 individuals and only 6% of patients with de novo apparently balanced translocations have an abnormal phenotype (Warburton, 1991). Review of the literature, concerning the microarray analysis of de novo apparently balanced translocations in patients with psychomotor delay, reveals:* in 40% of cases: an abnormality not identified on the karyotype, either at the translocation breakpoints or at a different location on the genome,* in 60% of cases: no abnormalities are found with a resolution of up to 25kb (Schluth-Bolard et al., 2009). The technique generally used to clone a breakpoint and identify a disrupted gene is a "walk" on the chromosome. This technique uses fluorescent probes, such as BACs or PACs, located on the derivative chromosomes on both sides of the breakpoints. This technique is labor-intensive, time-consuming and expensive because one must probe along the derivative chromosomes, closer and closer to the breakpoint, in order to find the probe overlapping the breakpoint. The investigators propose an original, innovative and quick technique to map chromosome translocation breakpoints in patients with psychomotor delay and no abnormalities on microarray analysis. The main aim is to develop a technique to identify new genes by cloning and mapping chromosome translocation breakpoints. These genes would then be candidate to explain the phenotype of the patient.The study covers a 24 month period and includes 10 patients. The feasibility of the technique, as well as its application to routine laboratory diagnosis, will be evaluated. The study was approved by our local Bioethics Committee and respects french law of bioethics.Methodology:Patients well be selected during staff meetings including clinicians and biologists. An initial microarray analysis well be performed to identify a gain or loss of genetic material. Samples for which no gain or loss is identified well then undergo flow cytometry to isolate the derivative chromosomes. Each derivative chromosome well then be hybridised to a new microarray, thus revealing the breakpoint. The breakpoints will be confirmed by FISH technique and molecular biology techniques well be applied to clone and sequence the breakpoints. Databases well be used to check for genes located in or around the breakpoints. Required information: Administrative data (3 first letters of the last name and 2 first letters of the first name, date of birth, identification of parents, informed consent). Clinical and biological data (phenotype, karyotype, other genetic studies). Expected results: Development of rapid and less expensive technique to clone translocation breakpoints, Identification of genes potentially involved in mental delay and anomalies of embryo development, Evaluation of the distribution of various causes of syndromic mental delay (unbalanced translocation on microarray, additional rearrangement on microarray, gene disruption, or unidentified cause).

• Study Type: Interventional
• Enrollment (Anticipated): 10
• Phase: Early Phase 1

Contacts and Locations

Study Locations

• France
  • Montpellier, France, 34295
    • Laboratory of Chromosomal Genetics - Universitary Hospital

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Child; Adult; Older Adult
• Accepts Healthy Volunteers: No
• Genders Eligible for Study: All

Description

Inclusion Criteria:

• patient with syndromic psychomotor delay
• patient with a apparently balanced de novo chromosomal translocation
• patient with health insurance
• informed consent signed by patient or by parents or by the legal representative for children

Exclusion Criteria:

• patient with an inherited translocation

Study Plan

How is the study designed?

Design Details

• Allocation: N/A
• Interventional Model: Single Group Assignment
• Masking: None (Open Label)

Number of Arms

1

Arms and Interventions

Participant Group / Arm	Intervention / Treatment
No Intervention: Psychomotor retardation syndromic; Psychomotor retardation syndromic by Identification of breakpoints	Biological: Identification of breakpoints; Identification of breakpoints in Molecular Biology : demonstration of a chimeric sequence corresponding to a junction region between the two chromosomes

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Evaluation of the proportion of cases for which a cause explaining the phenotype is found for patients with a apparently balance de novo translocation	Evaluation of the proportion of cases for which a cause explaining the phenotype is found for patients with a apparently balance de novo translocation	6 months and 2 years

Collaborators and Investigators

• Sponsor: University Hospital, Montpellier
• Investigators: Principal Investigator: Jacques MD Puechberty, PHD, Laboratory of Chromosomal Genetics - Universitary Hospital

Publications and helpful links

General Publications

• Gribble SM, Prigmore E, Burford DC, Porter KM, Ng BL, Douglas EJ, Fiegler H, Carr P, Kalaitzopoulos D, Clegg S, Sandstrom R, Temple IK, Youings SA, Thomas NS, Dennis NR, Jacobs PA, Crolla JA, Carter NP. The complex nature of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes. J Med Genet. 2005 Jan;42(1):8-16. doi: 10.1136/jmg.2004.024141.

Study record dates

Study Major Dates

• Study Start: October 1, 2011
• Primary Completion (Actual): January 1, 2013
• Study Completion (Anticipated): April 1, 2015

Study Registration Dates

• First Submitted: March 29, 2012
• First Submitted That Met QC Criteria: April 3, 2013
• First Posted (Estimate): April 8, 2013

Study Record Updates

• Last Update Posted (Estimate): December 31, 2014
• Last Update Submitted That Met QC Criteria: December 30, 2014
• Last Verified: April 1, 2013

More Information

Terms related to this study

• Keywords: Chromosomal translocations; psychomotor delay
• Additional Relevant MeSH Terms: Pathologic Processes; Chromosome Aberrations; Translocation, Genetic
• Other Study ID Numbers: UF 8688