Subtelomere specific microarray based comparative genomic hybridisation: a rapid detection system for cryptic rearrangements in idiopathic mental retardation

Harada, Naoki; Hatchwell, Eli; Okamoto, Nobuhiko; Tsukahara, Masato; Kurosawa, Kenji; Kawame, Hiroshi; Kondoh, Tatsuro; Ohashi, Hirofumi; Tsukino, Ryuichi; Kondoh, Yuki; Shimokawa, Osamu; Ida, Tomoko; Nagai, Toshiro; Fukushima, Yoshimitsu; Yoshiura, Ko Ichiro; Niikawa, Norio; Matsumoto, Naomichi

doi:10.1136/jmg.2003.014639

Cited by 50 publications

(41 citation statements)

References 26 publications

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“…ish del(9)(q34.3)de novo (Case B: described as Patient 1 in Iwakoshi et al 2004), 46,XY. ish del(9)(q34.3)de novo (Case C: described as N03R003 and Patient 2 in Harada et al 2004 andIwakoshi et al 2004, respectively), 46,XX. ish der(9)t(5;9)(q35.3;q34.3)pat (Case D: described as Patient 1 in Dawson et al 2002), 46,XX.…”

Section: Subjectsmentioning

confidence: 99%

A 1-Mb critical region in six patients with 9q34.3 terminal deletion syndrome

et al. 2004

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Patients with 9q34.3 terminal deletion usually show a clinically recognizable phenotype characterized by specific facial features (microcephaly, flat face, arched eyebrows, hypertelorism, short nose, anteverted nostrils, carp mouth and protruding tongue) in combination with severe mental retardation, hypotonia, and other anomalies. We analyzed six unrelated patients with a various 9q34.3 terminal deletion. While having different-sized 9q34.3 deletions, all of these patients shared several distinctive anomalies. These anomalies are likely to arise from a commonly deleted region at distal 9q34.3. Fluorescence in situ hybridization (FISH) analysis using a dozen BAC clones mapped at the 9q34.13-q34.3 region defined the shortest region of deletion overlap (SRO) as a 1-Mb segment proximal to 9qter containing eight known genes. Possible candidate genes delineating specific phenotypes of the 9q34.3 terminal deletion syndrome are discussed.

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Section: Subjectsmentioning

confidence: 99%

A 1-Mb critical region in six patients with 9q34.3 terminal deletion syndrome

et al. 2004

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“…13 Veltman et al 14 first applied aCGH for a telomere integrity screen in 20 patients. More recently, Harada et al 15 used a similar telomere clone array to screen for subtelomeric rearrangements in 69 patients. Although these studies successfully demonstrated that aCGH can detect copy number gains or losses for 41 telomere regions, a survey of the copy number of only one clone for each telomere region may not provide enough information to accurately interpret the clinical meaning of the imbalance.…”

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confidence: 99%

Detection and calibration of microdeletions and microduplications by array-based comparative genomic hybridization and its applicability to clinical genetic testing

Wong¹,

Martin²,

Heretis³

et al. 2005

Genetics in Medicine

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Purpose: Genome-wide telomere screening by fluorescence in situ hybridization (FISH) has revealed that Ϸ 6% of unexplained mental retardation is due to submicroscopic telomere imbalances. However, the use of FISH for telomere screening is labor intensive and time consuming, given that 41 telomeres are interrogated. We have evaluated the use of array-based Comparative Genomic Hybridization (aCGH) as a more efficient tool for identifying telomere rearrangements. Methods: In this study, 102 individuals with unexplained mental retardation, with either normal or abnormal FISH results, were selected for a blinded retrospective study using aCGH. Results between the two methodologies were compared to ascertain the ability of aCGH to be used in a clinical diagnostics setting. Results:We detected 100% of all imbalances previously identified by FISH (n ϭ 17) and identified two additional abnormalities, a 10q telomere duplication and an interstitial duplication of 22q11. Interphase FISH analysis verified all abnormal array results. We also demonstrated that aCGH can accurately calibrate the size of telomere imbalances by using an array with "molecular rulers" for the telomeric regions of 1p, 16p, 17p, and 22q.Conclusion: This study demonstrates that aCGH is an equivalent methodology to telomere FISH for detecting submicroscopic deletions. In addition, small duplications that are not easily visible by FISH can be accurately detected using aCGH. Because aCGH allows simultaneous interrogation of hundreds to thousands of DNA probes and is more amenable to automation, it offers an efficient and high-throughput alternative for detecting and calibrating unbalanced rearrangements, both of the telomere region, as well as other genomic locations. Genet Med 2005:7(4):264 -271.

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“…Average normalized inter-locus fluorescence ratio (ANILFR) was calculated for each CGH (Mantripragada et al 2003). On the basis of results from a previous study, the normal ANILFR range was defined as average within ±2SD (Harada et al 2004).…”

Section: Microarray Cghmentioning

confidence: 99%

“…The procedure used for microarray-CGH analysis has been described elsewhere (Harada et al 2004;Miyake et al 2006). Briefly, the 800 ng digested subject DNA was labeled with Cy3, and control DNA with Cy5 (CGH 1).…”

Section: Microarray Cghmentioning

confidence: 99%

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Microarray comparative genomic hybridization (CGH)-based prenatal diagnosis for chromosome abnormalities using cell-free fetal DNA in amniotic fluid

Miura

Masuzaki

et al. 2006

J Hum Genet

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Microarray comparative genomic hybridization (CGH)-based prenatal diagnosis for chromosome abnormalities using cell-free fetal DNA in amniotic fluid Abstract Cell-free fetal DNA (cffDNA) in the supernatant of amniotic fluid, which is usually discarded, can be used as a sample for prenatal diagnosis. For rapid prenatal diagnosis of frequent chromosome abnormalities, for example trisomies 13, 18, and 21, and monosomy X, using cffDNA, we have developed a targeted microarray-based comparative genomic hybridization (CGH) panel on which BAC clones from chromosomes 13, 18, 21, X, and Y were spotted. Microarray-CGH analysis was performed for a total of 13 fetuses with congenital anomalies using cffDNA from their uncultured amniotic fluid. Microarray CGH with cffDNA led to successful molecular karyotyping for 12 of 13 fetuses within 5 days. Karyotypes of the 12 fetuses (one case of trisomy 13, two of trisomy 18, two of trisomy 21, one of monosomy X, and six of normal karyotype) were later confirmed by conventional chromosome analysis using cultured amniocytes. The one fetus whose molecularkaryotype was indicated as normal by microarray CGH actually had a balanced translocation, 45,XY,-der(14;21)(q10;q10). The results indicated that microarray CGH with cffDNA is a useful rapid prenatal diagnostic method at late gestation for chromosome abnormalities with copy-number changes, especially when combined with conventional karyotyping of cultured amniocytes.

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Subtelomere specific microarray based comparative genomic hybridisation: a rapid detection system for cryptic rearrangements in idiopathic mental retardation

Cited by 50 publications

References 26 publications

A 1-Mb critical region in six patients with 9q34.3 terminal deletion syndrome

A 1-Mb critical region in six patients with 9q34.3 terminal deletion syndrome

Detection and calibration of microdeletions and microduplications by array-based comparative genomic hybridization and its applicability to clinical genetic testing

Microarray comparative genomic hybridization (CGH)-based prenatal diagnosis for chromosome abnormalities using cell-free fetal DNA in amniotic fluid

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