scholarly journals An Xq22.3 duplication detected by comparative genomic hybridization microarray (Array-CGH) defines a new locus (FGS5) for FG syndrome

2005 ◽  
Vol 139A (3) ◽  
pp. 221-226 ◽  
Author(s):  
Fernanda Sarquis Jehee ◽  
Carla Rosenberg ◽  
Ana Cristina Krepischi-Santos ◽  
Fernando Kok ◽  
Jeroen Knijnenburg ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Array Cgh ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Comparative Genomic Hybridization Microarray

Clinical Utility of Array Comparative Genomic Hybridization for Detection of Chromosomal Abnormalities in Pediatric Acute Lymphoblastic Leukemia.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2275-2275
Author(s):  
Karen Rabin ◽  
Chris Man ◽  
Sharon Plon ◽  
Pulivarthi Rao ◽  
Rizwan Naeem
Keyword(s):  
Comparative Genomic Hybridization ◽  
Clinical Utility ◽  
Array Comparative Genomic Hybridization ◽  
Array Cgh ◽  
Lymphoblastic Leukemia ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Structural Abnormalities ◽  
Pediatric All ◽  
Balanced Translocations

Abstract Chromosomal structural abnormalities in ALL are powerful independent predictors of prognosis, and directly impact choice of therapy. Currently, clinical detection of these abnormalities is based on karyotype and fluorescent in-situ hybridization (FISH), but these methods have limitations. Under optimal circumstances, structural abnormalities are detectable in well over 90% of ALL cases, but in actuality, typical cytogenetic laboratories demonstrate only a 50–60% abnormality detection rate. Karyotype may fail due to unsuccessful cell growth in culture and/or relative overgrowth of normal lymphocytes. FISH is limited by the expense and labor intensity of performing a separate assay for each probe used. Array comparative genomic hybridization (CGH) may have clinical utility as a complementary diagnostic tool in pediatric ALL. Its advantages include the ability to detect copy number changes in regions too small to be identifiable by karyotype; to identify novel abnormalities for which specific FISH probes do not exist in current diagnostic laboratories; and to provide information in as many as 50% of cases which show a failed or normal karyotype. In addition to its clinical utility, array CGH provides a wealth of information which may be mined for discovery of new pathways in leukemogenesis and additional prognostic factors within existing disease subgroups. The main limitation of array CGH is its inability to detected balanced translocations. We evaluated the diagnostic utility of a bacterial artificial chromosome (BAC) array CGH platform, the SpectralChip 2600, with an average resolution of 1.0 MB across the genome. We analyzed 50 pediatric ALL bone marrow specimens obtained at diagnosis, and compared the findings to the clinical results based on karyotype and standard 5-probe FISH panel. The cases ranged from 1–15 years (mean 5 years), with marrow containing between 33–94% leukemic blasts (mean 77%). Each sample was hybridized to the chip with a healthy control of the opposite gender. The sensitivity of array CGH in detecting abnormalities identified by karyotype and FISH was approximately 88%. Several of the abnormalities “missed” by CGH, which lowered the sensitivity score, were subsequently found to be erroneous karyotype calls when followed up with specific FISH probes. In addition, array CGH detected numerous additional areas of amplification and deletion which were subsequently validated by FISH, including in 10 cases for which cytogenetics was either normal or unsuccessful. Loss of 1p31, loss of 7p21, and gain of 16p13 were aberrations that were each noted to occur in three or more different cases, and hence may be worthy of further study. In the future, development of a customized ALL chip which is enriched for probes at sites of known amplification and deletion could further heighten diagnostic sensitivity, obviate the need for performance of multiple FISH tests, and provide valuable information in the substantial number of cases with a normal or failed karyotype analysis. Balanced translocations would still require testing via a multiplex PCR assay or a combination of available FISH probes.

scholarly journals Development of a Focused Oligonucleotide-Array Comparative Genomic Hybridization Chip for Clinical Diagnosis of Genomic Imbalance

2007 ◽  
Vol 53 (12) ◽  
pp. 2051-2059 ◽  
Author(s):  
Yiping Shen ◽  
David T Miller ◽  
Sau Wai Cheung ◽  
Va Lip ◽  
Xiaoming Sheng ◽  
...  
Keyword(s):  
Mental Retardation ◽  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Developmental Disorders ◽  
Array Cgh ◽  
Clinical Laboratory ◽  
Oligonucleotide Array ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Genomic Imbalance

Abstract Background: Submicroscopic genomic imbalance underlies well-defined microdeletion and microduplication syndromes and contributes to general developmental disorders such as mental retardation and autism. Array comparative genomic hybridization (CGH) complements routine cytogenetic methods such as karyotyping and fluorescence in situ hybridization (FISH) for the detection of genomic imbalance. Oligonucleotide arrays in particular offer advantages in ease of manufacturing, but standard arrays for single-nucleotide polymorphism genotyping or linkage analysis offer variable coverage in clinically relevant regions. We report the design and validation of a focused oligonucleotide-array CGH assay for clinical laboratory diagnosis of genomic imbalance. Methods: We selected >10 000 60-mer oligonucleotide features from Agilent’s eArray probe library to interrogate all subtelomeric and pericentromeric regions and 95 additional clinically relevant regions for a total of 179 loci. Sensitivity and specificity were measured for 105 patient samples, including 51 with known genomic-imbalance events, as detected by bacterial artificial chromosome–based array CGH, FISH, or multiplex ligation-dependent probe amplification. Results: Focused array CGH detected all known regions of genomic imbalance in 51 validation samples with 100% concordance and an excellent signal-to-noise ratio. The mean SD among log2 ratios of all noncontrol features without copy number alteration was 0.062 (median, 0.055). Clinical testing of another 211 samples from individuals with developmental delay, unexplained mental retardation, dysmorphic features, or multiple congenital anomalies revealed genomic imbalance in 25 samples (11.9%). Conclusions: This focused oligonucleotide-array CGH assay, a flexible, robust method for clinically diagnosing genetic disorders associated with genomic imbalance, offers appreciable advantages over currently available platforms.

scholarly journals Comparative Genomic Hybridization Selection of Blastocysts for Repeated Implantation Failure Treatment: A Pilot Study

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Ermanno Greco ◽  
Sara Bono ◽  
Alessandra Ruberti ◽  
Anna Maria Lobascio ◽  
Pierfrancesco Greco ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Array Cgh ◽  
Preimplantation Genetic Screening ◽  
Clinical Results ◽  
Good Prognosis ◽  
Comparative Genomic ◽  
Implantation Failure ◽  
Genomic Hybridization ◽  
Repeated Implantation Failure ◽  
Patient Groups

The aim of this study is to determine if the use of preimplantation genetic screening (PGS) by array comparative genomic hybridization (array CGH) and transfer of a single euploid blastocyst in patients with repeated implantation failure (RIF) can improve clinical results. Three patient groups are compared: 43 couples with RIF for whom embryos were selected by array CGH (group RIF-PGS), 33 couples with the same history for whom array CGH was not performed (group RIF NO PGS), and 45 good prognosis infertile couples with array CGH selected embryos (group NO RIF PGS). A single euploid blastocyst was transferred in groups RIF-PGS and NO RIF PGS. Array CGH was not performed in group RIF NO PGS in which 1-2 blastocysts were transferred. One monoembryonic sac with heartbeat was found in 28 patients of group RIF PGS and 31 patients of group NO RIF PGS showing similar clinical pregnancy and implantation rates (68.3% and 70.5%, resp.). In contrast, an embryonic sac with heartbeat was only detected in 7 (21.2%) patients of group RIF NO PGS. In conclusion, PGS by array CGH with single euploid blastocyst transfer appears to be a successful strategy for patients with multiple failed IVF attempts.

scholarly journals Prenatal Diagnosis by Array Comparative Genomic Hybridization in Fetuses with Cardiac Abnormalities

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 2021
Author(s):  
Katarzyna Kowalczyk ◽  
Magdalena Bartnik-Głaska ◽  
Marta Smyk ◽  
Izabela Plaskota ◽  
Joanna Bernaciak ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Comparative Genomic Hybridization ◽  
Congenital Heart Defects ◽  
Congenital Heart ◽  
Array Cgh ◽  
Heart Diseases ◽  
Heart Defects ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Fetal Ultrasound

Congenital heart defects (CHDs) appear in 8–10 out of 1000 live born newborns and are one of the most common causes of deaths. In fetuses, the congenital heart defects are found even 3–5 times more often. Currently, microarray comparative genomic hybridization (array CGH) is recommended by worldwide scientific organizations as a first-line test in the prenatal diagnosis of fetuses with sonographic abnormalities, especially cardiac defects. We present the results of the application of array CGH in 484 cases with prenatally diagnosed congenital heart diseases by fetal ultrasound scanning (256 isolated CHD and 228 CHD coexisting with other malformations). We identified pathogenic aberrations and likely pathogenic genetic loci for CHD in 165 fetuses and 9 copy number variants (CNVs) of unknown clinical significance. Prenatal array-CGH is a useful method allowing the identification of all unbalanced aberrations (number and structure) with a much higher resolution than the currently applied traditional assessment techniques karyotype. Due to this ability, we identified the etiology of heart defects in 37% of cases.

Array CGH Analysis for PTCL-U Revealed Two Genetically Distinct Subgroups.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2054-2054
Author(s):  
Masao Nakagawa ◽  
Aya Oshiro ◽  
Hiroyuki Tagawa ◽  
Sivasundaram Karnan ◽  
Shinobu Tsuzuki ◽  
...  
Keyword(s):  
T Cell ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Array Cgh ◽  
Comparative Genomic ◽  
Simple Type ◽  
Genomic Hybridization ◽  
Complex Type ◽  
Average Copy Number ◽  
Average Copy

Abstract Peripheral T-cell lymphoma, unspecified (PTCL-U) is the most common group among Peripheral T-cell lymphomas (PTCLs). This category consists of the cases which do not belong to any of the recognizable subtypes of PTCLs in WHO classification. PTCL-U comprises heterogeneous groups in morphology and phenotype. Molecular basis of clinical heterogeneity is needed to identify distinct subgroups with clnical relevance. Several reports of conventional cytogenetic studies including comparative genomic hybridization (CGH) showed some recurrent aberrations, but failed to identify the genetic hallmarks to categorize distinct subgroups. So far, no array-based comparative genomic hybridization (array CGH) study for PTCL-U has been reported. Here we analyzed 29 cases of PTCL-U by means of array CGH consisting of 2265 artificial chromosome clones that cover the whole genome at a 1.3 mega base resolution. The analysis clearly divided these cases into two distinct subgroups on the basis of frequency of genomic alterations. One group consists of 17 cases which showed significant lower copy number changes (average copy number gains: 0.5 regions, average copy number losses: 0.1 regions). The other group had average copy number gains of 15.7 regions and losses of 15.0 regions in 12 cases. We designate the former as “simple type” and the latter as “complex type”. In the complex type, regions of recurrent (>20%) gain are detected on chromosome 1q23.3-24.2, 3q25.31-tel, 4p15.1-16.1, 4q28.3-31.23, 5q34, 6p24.1-25.1, 7p21.3-tel, 7p21.1, 7q, 8q24.23, 11q13.4-tel, 12p11.21-11.22, 16p12.3-13.3, 17q11.2-22. Regions of recurrent (>20%) losses are detected on chromosome 1p13.1-13.3, 2q37.3, 4q21.21-21.23, 4q34.3-35.1, 5q21.2-23.1, 6p12.1-q14.3, 6q23.2-24.1, 6q25.1-26, 7p14.3-22.1, 9p21.3, 10p14-qtel, 12p13.1-13.2, 13, 14q12, 16q, 17p, 18p, 20q13-2, 22q11.21-12.2. Median age is 62 years in the simple type and 73 years in the complex type, respectively. Median survival is 27 months in the simple type and 11 months in the complex type. Log-rank test for overall survival between the simple type and the complex type showed inferior survival for the complex type but significance was marginal (p=0.21). Our findings showed that PTCL-U comprised two genetically distinct subgroups, implying that distinct mechanisms underlay in molecular pathogenesis of PTCL-U. Furthermore cilinicopathological features of each group are also being studied.

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