Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions

Uddin, Raihan; Zhang, Yang; Siu, Victoria Mok; Fan, Yao Shan; O’Reilly, Richard; Rao, Jay; Singh, Shiva M.

doi:10.1186/1471-2350-7-18

Cited by 21 publications

(18 citation statements)

References 38 publications

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“…Indeed, there are numerous reports of disease-causing deletions resulting from recombination between Alu elements (Batzer and Deininger, 2002;Nishimura et al, 2005;Casarin et al, 2006;Has et al, 2006;Kozak et al, 2006;Li et al, 2006;Matejas et al, 2006;Nissen et al, 2006;Sen et al, 2006;Shabbeer et al, 2006;Uddin et al, 2006;Xie et al, 2006;Zhang et al, 2006). If a large proportion of Alu elements indeed fosters euchromatic domains as suggested by the aforementioned study (Willoughby et al, 2000), then flanking sequences may also be destabilized.…”

Section: Non-random Repeat Distributions Via Natural Selectionmentioning

confidence: 94%

Repetitive sequence environment distinguishes housekeeping genes

Eller¹,

Regelson²,

Merriman³

et al. 2007

Gene

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Housekeeping genes are expressed across a wide variety of tissues. Since repetitive sequences have been reported to influence the expression of individual genes, we employed a novel approach to determine whether housekeeping genes can be distinguished from tissue-specific genes their repetitive sequence context. We show that Alu elements are more highly concentrated around housekeeping genes while various longer (>400-bp) repetitive sequences ("repeats"), including Long Interspersed Nuclear Element 1 (LINE-1) elements, are excluded from these regions. We further show that isochore membership does not distinguish housekeeping genes from tissue-specific genes and that repetitive sequence environment distinguishes housekeeping genes from tissue-specific genes in every isochore. The distinct repetitive sequence environment, in combination with other previously published sequence properties of housekeeping genes, were used to develop a method of predicting housekeeping genes on the basis of DNA sequence alone. Using expression across tissue types as a measure of success, we demonstrate that repetitive sequence environment is by far the most important sequence feature identified to date for distinguishing housekeeping genes.

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Section: Non-random Repeat Distributions Via Natural Selectionmentioning

confidence: 94%

Repetitive sequence environment distinguishes housekeeping genes

Eller¹,

Regelson²,

Merriman³

et al. 2007

Gene

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“…in 2006. [23] Eight sets of primers representing the established STS markers spanning the 3 Mb TDR were used for this purpose. PCR was carried out in a volume of 25 μl using a thermal DNA cycler (Eppendorf, Germany).…”

Section: Methodsmentioning

confidence: 99%

Evaluation of 22q11.2 deletion in Cleft Palate patients

Prabodha

Dias

Nanayakkara

et al. 2012

Ann Maxillofac Surg

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Background:Cleft palate is the commonest multifactorial epigenetic disorder with a prevalence of 0.43-2.45 per 1000. The objectives of this study were to evaluate the clinical features and identify the 22q11.2 deletion in patients with cleft palate in Sri Lanka.Materials and Methods:Cleft patients attending a Teaching Hospital in Sri Lanka were recruited for this study. The relevant data were obtained from review of case notes, interviews, and examination of patients according to a standard evaluation sheet. Quantitative multiplex polymerase chain reaction (PCR) was performed to identify the 22q11.2 deletion. A gel documentation system (Bio-Doc) was used to quantify the PCR product following electrophoresis on 0.8% agarose gel.Results and Conclusion:There were 162 cleft palate patients of whom 59% were females. A total of 92 cleft palate subjects (56.2%) had other associated clinical features. Dysmorphic features (25.27%) and developmental delays (25.27%) were the commonest medical problems encountered. The cleft was limited to the soft palate in 125 patients, while in 25 patients it involved both the hard and the soft palate. There were seven subjects with bifid uvula and five subjects with submucous cleft palate. None of the patients had 22q11.2 deletion in this study population. A multicentered large population-based study is needed to confirm the results of this study and to develop guidelines on the appropriate use of 22q11.2 deletion testing, which are valid for cleft palate patients in Sri Lanka.

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“…The clinical features of patients with schizophrenia are for all practical purposes indistinguishable whether they do or do not carry del22q11. This observation has led to a special focus on genes localized to the common deletion representing the 3.0 Mb region covering del22q11 (Uddin et al, 2006). This region contains more than 45 genes and a hemizygous loss of ∼ 30 genes has been observed in most individuals with del22q11, both with and without schizophrenia (Meechan et al, 2007).…”

Section: Introductionmentioning

confidence: 97%