Identification of subtelomeric genomic imbalances and breakpoint mapping with quantitative PCR in 296 individuals with congenital defects and/or mental retardation

Institute of Human Genetics, Georg August University, Göttingen, Germany. .
Molecular Cytogenetics (Impact Factor: 2.14). 02/2009; 2(1):10. DOI: 10.1186/1755-8166-2-10
Source: PubMed


Submicroscopic imbalances in the subtelomeric regions of the chromosomes are considered to play an important role in the aetiology of mental retardation (MR). The aim of the study was to evaluate a quantitative PCR (qPCR) protocol established by Boehm et al. (2004) in the clinical routine of subtelomeric testing.
296 patients with MR and a normal karyotype (500-550 bands) were screened for subtelomeric imbalances by using qPCR combined with SYBR green detection. In total, 17 patients (5.8%) with 20 subtelomeric imbalances were identified. Six of the aberrations (2%) were classified as causative for the symptoms, because they occurred either de novo in the patients (5 cases) or the aberration were be detected in the patient and an equally affected parent (1 case). The extent of the deletions ranged from 1.8 to approximately 10 Mb, duplications were 1.8 to approximately 5 Mb in size. In 6 patients, the copy number variations (CNVs) were rated as benign polymorphisms, and the clinical relevance of these CNVs remains unclear in 5 patients (1.7%). Therefore, the overall frequency of clinically relevant imbalances ranges between 2% and 3.7% in our cohort.
This study illustrates that the qPCR/SYBR green technique represents a rapid and versatile method for the detection of subtelomeric imbalances and the option to map the breakpoint. Thus, this technique is highly suitable for genotype/phenotype studies in patients with MR/developmental delay and/or congenital defects.

Download full-text


Available from: Thomas Liehr,
  • Source
    • "Most deletions are located near telomeric regions, a common feature in MR patients [2]. Unfortunately, in most patients (60%) the etiology of MR remains unclear [3], despite the use of good quality metaphase preparations in high resolution assays [4]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background Mental retardation (MR) is a heterogeneous condition that affects 2-3% of the general population and is a public health problem in developing countries. Chromosomal abnormalities are an important cause of MR and subtelomeric rearrangements (STR) have been reported in 4-35% of individuals with idiopathic MR or an unexplained developmental delay, depending on the screening tests and patient selection criteria used. Clinical checklists such as that suggested by de Vries et al. have been used to improve the predictive value of subtelomeric screening. Findings Fifteen patients (1–20 years old; five females and ten males) with moderate to severe MR from a genetics outpatient clinic of the Gaffrée and Guinle Teaching Hospital (HUGG) of the Federal University of Rio de Janeiro State (UNIRIO) were screened with Multiprobe T FISH after normal high resolution karyotyping. No subtelomeric rearrangements were detected even though the clinical score of the patients ranged from four to seven. Conclusion In developing countries, FISH-based techniques such as Multiprobe T FISH are still expensive. Although Multiprobe T FISH is a good tool for detecting STR, in this study it did not detect STR in patients with unexplained MR/developmental delay even though these patients had a marked chromosomal imbalance. Our findings also show that clinical scores are not reliable predictors of STR.
    Journal of Negative Results in BioMedicine 12/2012; 11(1):16. DOI:10.1186/1477-5751-11-16 · 1.47 Impact Factor
  • Source
    • "The fluorescent in situ hybridization (FISH) technique has been frequently used for subtelomere investigation; however, it is not suitable either for the detection of sequential submicroscopic duplications or of small exon deletions (De Vries et al. 2003; Hoebeeck et al. 2005). For these purposes, quantitative and highly sensitive methodologies such as the multiplex ligation-dependent probe amplification (MLPA) technique, quantitative PCR (qPCR) and chip arrays have been shown to be more appropriate (Boehm et al. 2004; Madrigal et al. 2007; Auber et al. 2009; Hochstenbach et al. 2009; Okizuka et al. 2009). The use of these methodologies for subtelomere investigation is providing new data about the incidence of this type of genomic variation in the general population. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The most prevalent type of structural variation in the human genome is represented by copy number variations that can affect transcription levels, sequence, structure and function of genes. In the present study, we used the multiplex ligation-dependent probe amplification (MLPA) technique and quantitative PCR for the detection of copy number variation in 132 intellectually disabled male patients with normal karyotypes and negative fragile-X-testing. Ten of these patients (7.6%) showed copy number variation in the subtelomeric regions, including deletions and duplications. Duplications of the SECTM1 gene, located at 17q25.3, and of the FLJ22115 gene, located at 20p13, could be associated with phenotype alterations. This study highlights the relevance in the aetiology of intellectual disability of subtelomeric rearrangements that can be screened by MLPA and other molecular techniques.
    Journal of Intellectual Disability Research 10/2010; 54(10):938-42. DOI:10.1111/j.1365-2788.2010.01325.x · 2.41 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Congenital malformations are a major cause of morbidity and mortality in newborn infants, and genomic imbalances are a significant component of their etiology. The aim of this study was to evaluate the ability of prenatal multiplex ligation probe amplification screening to detect cryptic chromosomal imbalances in fetuses with ultrasound abnormalities of unknown etiology. Multiplex ligation probe amplification was performed with three separate sets of probes: two for subtelomeric regions and one for mental retardation syndrome loci. Sixty-one fetuses with significant ultrasound anomalies and normal karyotype at a minimum of 400-band resolution were tested between January 2007 and January 2009. We identified four unbalanced rearrangements: one del 18pter/amp 5pter, one del 9pter, one 15q11q13 microdeletion, and one 22q11 microdeletion with atypical presentation. After genetic counseling, two of the pregnancies were terminated. Multiplex ligation probe amplification analysis was able to identify clinically significant rearrangements in 6.5% of fetuses with prenatally identified sonographic abnormalities. This prospective study highlights that multiplex ligation probe amplification screening of fetuses with ultrasound abnormalities in the prenatal period is technically feasible and relevant for diagnosis and prognosis.
    Genetics in medicine: official journal of the American College of Medical Genetics 06/2010; 12(6):376-80. DOI:10.1097/GIM.0b013e3181e074c6 · 7.33 Impact Factor
Show more