Identification of origin of unknown derivative chromosomes by array-based comparative genomic hybridization using pre- and postnatal clinical samples

Choe, Jun-Ho; Kang, Jaeku; Bae, Chang-Jun; Lee, Dong-Suk; Hwang, Dae Hyun; Kim, Ki-Chul; Woong-Yang, Park; Lee, Jong-Ho; Seo, Jong-Soo

doi:10.1007/s10038-007-0199-1

Cited by 13 publications

(14 citation statements)

References 35 publications

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“…Therefore, sex chromosome aneuploidies such as 47,XXX or 47,XYY can be missed. 11,22 Furthermore, the correct interpretation of results in female patients with X chromosome duplications and males with deletions is challenging when using sex-mismatched reference DNA, and are greatly dependent on the number of probes interrogating the region of genomic imbalance in the patient.…”

Section: Discussionmentioning

confidence: 99%

Microarray-Based Comparative Genomic Hybridization Using Sex-Matched Reference DNA Provides Greater Sensitivity for Detection of Sex Chromosome Imbalances than Array-Comparative Genomic Hybridization with Sex-Mismatched Reference DNA

Yatsenko

Shaw

et al. 2009

The Journal of Molecular Diagnostics

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In array-comparative genomic hybridization (array-CGH) experiments, the measurement of DNA copy number of sex chromosomal regions depends on the sex of the patient and the reference DNAs used. We evaluated the ability of bacterial artificial chromosomes/P1-derived artificial and oligonucleotide array-CGH analyses to detect constitutional sex chromosome imbalances using sex-mismatched reference DNAs. Twenty-two samples with imbalances involving either the X or Y chromosome, including deletions, duplications, triplications, derivative or isodicentric chromosomes, and aneuploidy, were analyzed. Although concordant results were obtained for approximately onehalf of the samples when using sex-mismatched and sex-matched reference DNAs, array-CGH analyses with sex-mismatched reference DNAs did not detect genomic imbalances that were detected using sex-matched reference DNAs in 6 of 22 patients. Small duplications and deletions of the X chromosome were most difficult to detect in female and male patients, respectively, when sex-mismatched reference DNAs were used. Sexmatched reference DNAs in array-CGH analyses provides optimal sensitivity and enables an automated statistical evaluation for the detection of sex chromosome imbalances when compared with an experimental design using sex-mismatched reference DNAs. Using sexmismatched reference DNAs in array-CGH analyses may generate false-negative, false-positive, and ambiguous results for sex chromosome-specific probes, thus masking potential pathogenic genomic imbalances. Therefore, to optimize both detection of clinically relevant sex chromosome imbalances and ensure proper experimental performance, we suggest that alternative internal controls be developed and used instead of using sex-mismatched reference DNAs.

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Section: Discussionmentioning

confidence: 99%

Microarray-Based Comparative Genomic Hybridization Using Sex-Matched Reference DNA Provides Greater Sensitivity for Detection of Sex Chromosome Imbalances than Array-Comparative Genomic Hybridization with Sex-Mismatched Reference DNA

Yatsenko

Shaw

et al. 2009

The Journal of Molecular Diagnostics

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“…No patients had received pre-operative chemotherapy or radiation. This study was reviewed and approved by the Institutional Characterization of amplification patterns and target genes on the short arm of chromosome 7 in early-stage lung adenocarcinoma Preparation of DNA targets, labeling, hybridization, washing, staining and scanning was conducted according to the manufacturer's instructions (Macrogen, Seoul, Korea) (8)(9)(10)(11)(12)(13). Briefly, arrays were pre-hybridized with salmon sperm DNA to block repetitive sequences in the BACs.…”

Section: Methodsmentioning

confidence: 99%

Characterization of amplification patterns and target genes on the short arm of chromosome 7 in early-stage lung adenocarcinoma

Kang

2013

Molecular Medicine Reports

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Abstract. Chromosomal alterations are a predominant genomic force contributing to the development of lung adenocarcinoma (ADC). High density genomic arrays were conducted to identify critical genetic landmarks that may be important mediators in the formation or progression of early-stage ADC. In this study, the most noteworthy and consistent observation was a copy number gain on the short arm of chromosome 7, which was detected in 85.7% (12/14) of cases. Notably, three distinct regions of amplification were identified between the 7p22.3 and q11.2 regions in 28.6% (4/14) of cases; at a size of 4.1 Mbp (7p22.3-p21.1), 2.6 Mbp (7p15.2-p14.1) and 1.5 Mbp (7p12.3-p11.2). Variations of the 7p11.2 locus that encodes EGFR are known to be oncogenic. Furthermore, potential target genes were identified that were previously not assumed to be involved in the pathogenesis of ADC, including CALM1P2 (7p11.2), HOXA4, HOXA5, HOXA6, HOXA7, HOXA9, HOXA10, HOXA11 and HOXA13 (7p15.2) and LOC442586, LOC442589, LOC442282, FAM20C and LOC442651 (7p22.3). The present study determined critical regions on the 7p arm of chromosome 7, which were implicated in ADC. The pattern of rearrangements on the 7p arm may be a consequence of the high density of potential targets and the identified genes at the 7p regions may aid in the development of therapeutic targets for ADC.

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“…Array-CGH was run on the MacArray™ Karyo 4000 K BAC-chip (Macrogen, Seoul, Korea; http:// www.macrogen.co.kr) (3,(14)(15)(16)(17)(18), consisting of 4,046 human BACs applied in duplicate and a resolution of 1 Mbp. All clones were two-end sequenced using an ABI PRISM 3700 DNA Analyzer (Applied Biosystems, Foster City, CA), and their sequences were blasted (using BLAST; http://blast.ncbi.…”

Section: Methodsmentioning

confidence: 99%

Frequent silence of chromosome 9p, homozygous DOCK8, DMRT1 and DMRT3 deletion at 9p24.3 in squamous cell carcinoma of the lung

Kang

Koo²,

Kwon³

et al. 2010

Int J Oncol

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Abstract. Chromosomal alterations are a major genomic force contributing to the development of lung cancer. We subjected 22 cases of squamous cell carcinoma of the lung (SCC) to whole-genome microarray-CGH (resolution, 1 Mb) to identify critical genetic landmarks that might be important mediators in the formation or progression of SCC. On a genome-wide profile, copy number losses (log 2 ratio <-0.25) on chromosome 9p occurred in 72.7% (16/22) of the SCC cases, and the delineated minimal common region was 9p24.3-p21.1. The progression of SCC to advanced stages or poorly differentiated malignancy was significantly associated with an increase in the copy number losses on 9p (P=0.033). More specifically, 2 distinct homozygous deletion (HD) loci (log 2 ratio <-1) were identified as novel loci for candidate tumor suppressor genes (TSGs) in SCC: one, spanning 128 kbp on 9p21.1 [4.5% (1/22)] and the other, spanning approximately 200 kbp on 9p24.3 [13.6% (3/22)]. The HDs at 9p24.3 was found to contain the putative TSG, DOCK8 and 2 possible candidate TSGs, DMRT1 and DMRT3. Quantitative real-time PCR (qRT-PCR) analysis demonstrated the array-CGHdetected potential candidate genes DMRT1, DMRT3 and DOCK8, at 9p24.3 were under-expressed in SCCs. Our study indicated that chromosome 9p loss is the hallmark of SCC, and DMRT1, DMRT3 and DOCK8 genes at 9p24.3 might be of interest for the study of the pathophysiology of SCC as potential targets for therapeutic measures.

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Identification of origin of unknown derivative chromosomes by array-based comparative genomic hybridization using pre- and postnatal clinical samples

Cited by 13 publications

References 35 publications

Microarray-Based Comparative Genomic Hybridization Using Sex-Matched Reference DNA Provides Greater Sensitivity for Detection of Sex Chromosome Imbalances than Array-Comparative Genomic Hybridization with Sex-Mismatched Reference DNA

Microarray-Based Comparative Genomic Hybridization Using Sex-Matched Reference DNA Provides Greater Sensitivity for Detection of Sex Chromosome Imbalances than Array-Comparative Genomic Hybridization with Sex-Mismatched Reference DNA

Characterization of amplification patterns and target genes on the short arm of chromosome 7 in early-stage lung adenocarcinoma

Frequent silence of chromosome 9p, homozygous DOCK8, DMRT1 and DMRT3 deletion at 9p24.3 in squamous cell carcinoma of the lung

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