Detection Of Imbalances Research Articles

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

BackgroundSubmicroscopic 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.Results296 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.ConclusionThis 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.

Cell-free Tumor DNA in Blood Plasma As a Marker for Circulating Tumor Cells in Prostate Cancer

Circulating cell-free DNA in the blood of cancer patients harbors tumor-specific aberrations. Here, we investigated whether this DNA might also reflect the presence of circulating tumor cells (CTC). To identify the source of cell-free DNA in blood, plasma derived from 81 patients with prostate cancer was examined for CTCs and cell-free DNA. An epithelial immunospot assay was applied for detection of CTCs, and a PCR-based fluorescence microsatellite analysis with a panel of 14 polymorphic markers was used for detection of allelic imbalances (AI). The plasma DNA levels significantly correlated with the diagnosis subgroups of localized (stage M0, n = 69) and metastasized prostate cancer (stage M1, n = 12; P = 0.03) and with the tumor stage of these patients (P < 0.005). AI was found on cell-free DNA in plasma from 45.0% and 58.5% of M0 and M1 patients, respectively. Detection of CTCs showed that 71.0% or 92.0% of the M0 and M1 patients harbored 1 to 40 CTCs in their blood, respectively. The occurrence of CTCs correlated with tumor stage (P < 0.03) and increasing Gleason scores (P = 0.04). Notably, significant associations of the number of CTCs with the AI frequencies at the markers D8S137 (P = 0.03), D9S171 (P = 0.04), and D17S855 (P = 0.02) encoding the cytoskeletal protein dematin, the inhibitor of the cyclin-dependent kinase CDKN2/p16 and BRCA1, respectively, were observed. These findings show, for the first time, a relationship between the occurrence of CTCs and circulating tumor-associated DNA in blood, which, therefore, might become a valuable new source for monitoring metastatic progression in cancer patients.

Imbalance Estimation Without Test Masses for Wind Turbines

Rotor imbalances of a wind turbine can cause severe damage of the turbine or its components and thus reduce the lifespan and security of the turbine significantly. At present, balancing of the rotor is a time consuming and expensive process due to the necessity of mounting test weights to measure a reference imbalance state. We describe a new method for the detection and reconstruction of imbalances in the rotor of a wind turbine avoiding test weight measurements. The method is based on a wind turbine model, which is derived by the finite element method. In some respect, the model information replaces the information of a reference imbalance state. A mathematical equation linking imbalances and the resulting vibrations is derived using the model. Thus the inverse problem of computing an imbalance from vibration measured at the nacelle is solvable with the usual techniques for ill-posed problems. We show that our model for a wind turbine can be used to predict the vibrations for a given imbalance distribution. In particular, it can be used to reconstruct the imbalance distribution of a wind turbine from noisy measurements in real time, which is verified both for artificial and real data. Also, an optimization strategy is presented in order to adapt the model to the wind turbine at hand. The new method requires a simple model of a wind turbine under consideration but reduces the measuring effort for the computation of balancing weights. It can be implemented into a condition monitoring system (CMS). For the first time, there can be not only an alarm generation but also the actual imbalance and balancing weights and positions can be computed directly from the observed CMS data.

Clinical Utility of Array CGH for the Detection of Chromosomal Imbalances Associated with Mental Retardation and Multiple Congenital Anomalies

Microarray-based comparative genomic hybridization (array CGH) has revolutionized clinical cytogenetics, as it provides a relatively quick method to scan the genome for gains and losses of chromosomal material with significantly higher resolution and greater clinical yield than was previously possible. A number of different array CGH platforms have emerged and are being used successfully in the diagnostic setting. In the past few years, these new methodologies have led to the identification of novel genomic disorders in patients with developmental delay/mental retardation and/or multiple congenital anomalies (DD/MR/MCA) as well as the discovery that each individual carries inherited copy number variations (CNV) whose contributions to genetic variation and complex disease are not yet well understood. Although array CGH is currently being used as an adjunct test to standard karyotype analysis, it is likely to become the genetic test of choice, especially in cases of idiopathic MR/MCA.

Allelic Imbalance Analysis Using a Single-Nucleotide Polymorphism Microarray for the Detection of Bladder Cancer Recurrence

Non-muscle-invasive bladder cancer is a frequently occurring cancer, with an extremely high recurrence risk. Recurrence detection is based on cytology and urethrocystoscopy. A previous study suggested that a single-nucleotide polymorphism (SNP) array may be effective for noninvasive detection of allelic imbalances in urine. We investigated whether this method is suitable to detect allelic imbalance as an indicator of recurrences in non-muscle-invasive bladder cancer follow-up. DNA from blood and urine from 158 patients (113 with and 45 without recurrence) was hybridized to the Affymetrix GeneChip Mapping 10K 2.0. Allelic imbalance detection was based on SNPs showing changes from heterozygosity in blood to homozygosity in urine and on automatic analysis of copy number changes using Copy Number Analyser for GeneChip. Urine samples with tumor showed allelic imbalance at 0.4% of all informative SNPs. In samples without tumors, 0.04% of these SNPs were affected (P = 0.07). In addition, Copy Number Analyser for GeneChip analysis showed more copy number changes in samples with a tumor (P = 0.001). Losses and gains of chromosomal regions showed clustering, overlapping with known bladder cancer loci. However, 25 (22%) patients with a tumor recurrence did not display any regions with copy number changes, whereas 24 (53%) individuals without a recurrence did. Receiver operating characteristic curve analysis using the number of SNPs displaying copy number changes from the Copy Number Analyser for GeneChip analysis resulted in an area under the curve of only 0.67 (95% confidence interval, 0.58-0.76). Single-nucleotide polymorphism microarray analysis of allelic imbalance in urine cannot replace urethrocystoscopy and cytology for the detection of recurrences in non-muscle-invasive bladder cancer follow-up.

559: Prenatal array comparative genomic hybridization analysis amongst women choosing invasive prenatal diagnosis: A decision analysis

To examine the decision of whether to undergo prenatal array comparative genomic hybridization (aCGH) analysis for the detection of chromosomal imbalances amongst women already electing to undergo invasive prenatal diagnosis (PNDx). A decision-analytic model was designed for women who have already elected to undergo PNDx. The model compared: (1) undergoing aCGH to determine if the fetus is affected by a microdeletion/duplication syndrome, a finding of unknown clinical significance (FUS), or a normal outcome to (2) not undergoing aCGH. Baseline assumptions included a live-birth incidence of known genetic syndromes and subtelomeric rearrangements of 1:1000 and a 1% rate (range: 0.66 - 2%) of detecting a FUS after parental specimens have been analyzed. Outcomes were assigned utilities and quality adjusted life years (QALYs) were calculated. Inputs were varied over a wide theoretical range in sensitivity analyses. In the baseline analysis, obtaining an aCGH analysis is the preferred option leading to greater diagnoses of affected fetuses with an improvement of 0.00132 QALYs. However, this decision was extremely sensitive to both the risk of genetic syndromes and the risk of FUS (figure). With a rate of FUS of 2% or above at a rate of genetic syndromes and subtelomeric rearrangements of 1/1000, individuals would do better not to obtain this information. While aCGH can provide valuable prenatal diagnostic information, the decision whether to provide it to all women is dependent upon both the risk of genetic syndromes that would be potentially diagnosed or missed and the rate of FUS. Further research in this area would be well-served to characterize these FUS and to delineate the rate of microdeletion/duplication syndromes.

685: Prenatal detection of genomic imbalances in six days from uncultured amniocytes by targeted oligonucleotide array CGH

685: Prenatal detection of genomic imbalances in six days from uncultured amniocytes by targeted oligonucleotide array CGH

Identification of chromosome abnormalities in subtelomeric regions by microarray analysis: A study of 5,380 cases

Subtelomeric imbalances are a significant cause of congenital disorders. Screening for these abnormalities has traditionally utilized GTG-banding analysis, fluorescence in situ hybridization (FISH) assays, and multiplex ligation-dependent probe amplification. Microarray-based comparative genomic hybridization (array-CGH) is a relatively new technology that can identify microscopic and submicroscopic chromosomal imbalances. It has been proposed that an array with extended coverage at subtelomeric regions could characterize subtelomeric aberrations more efficiently in a single experiment. The targeted arrays for chromosome microarray analysis (CMA), developed by Baylor College of Medicine, have on average 12 BAC/PAC clones covering 10 Mb of each of the 41 subtelomeric regions. We screened 5,380 consecutive clinical patients using CMA. The most common reasons for referral included developmental delay (DD), and/or mental retardation (MR), dysmorphic features (DF), multiple congenital anomalies (MCA), seizure disorders (SD), and autistic, or other behavioral abnormalities. We found pathogenic rearrangements at subtelomeric regions in 236 patients (4.4%). Among these patients, 103 had a deletion, 58 had a duplication, 44 had an unbalanced translocation, and 31 had a complex rearrangement. The detection rates varied among patients with a normal karyotype analysis (2.98%), with an abnormal karyotype analysis (43.4%), and with an unavailable or no karyotype analysis (3.16%). Six patients out of 278 with a prior normal subtelomere-FISH analysis showed an abnormality including an interstitial deletion, two terminal deletions, two interstitial duplications, and a terminal duplication. In conclusion, genomic imbalances at subtelomeric regions contribute significantly to congenital disorders. Targeted array-CGH with extended coverage (up to 10 Mb) of subtelomeric regions will enhance the detection of subtelomeric imbalances, especially for submicroscopic imbalances.

Detection of cryptic subtelomeric imbalances in fetuses with ultrasound abnormalities

It is known from postnatal diagnosis that imbalances of the subtelomeric regions contribute significantly to idiopathic mental retardation. Consequently, subtelomere screening has been incorporated into the recommendations for the evaluation of individuals with unexplained mental retardation and a normal karyotype. Previous studies suggested that for fetuses with ultrasound abnormalities and a normal karyotype, additional screening for submicroscopic imbalances can be relevant for diagnosis and prognosis. In the present paper, we report the detection of such (subtelomeric) imbalances in three fetuses. Prenatally, the three fetuses presented with ultrasound abnormalities highly suspected of a chromosomal aberration. In two of the fetuses, routine karyotyping showed no aberrations but with MLPA or FISH a small subtelomeric imbalance, that could explain the anomalies, was detected. In the third fetus, a chromosomal abnormality was detected with routine cytogenetic analysis (del(X)(p22.1)), but this abnormality could not explain the ultrasound observations and only with subtelomere screening by MLPA a causative chromosomal aberration was detected. As the three fetuses were already prenatally suspected of a chromosomal aberration, this underlines the potential relevance of subtelomere screening in such fetuses, leading to better clinical diagnosis, prognosis and care. Furthermore, when using MLPA, the analysis can be extended to other regions of known clinical importance.

Detection of genomic imbalances in microdissected Hodgkin and Reed-Sternberg cells of classical Hodgkin's lymphoma by array-based comparative genomic hybridization

Cytogenetic analysis of classical Hodgkin's lymphoma is limited by the low content of the neoplastic Hodgkin-Reed-Sternberg cells in the affected tissues. However, available cytogenetic data point to an extreme karyotype complexity. To obtain insights into chromosomal imbalances in classical Hodgkin's lymphoma, we applied array-based comparative genomic hybridization (array comparative genomic hybridization) using DNA from microdissected Hodgkin-Reed-Sternberg cells. To avoid biases introduced by DNA amplification for array comparative genomic hybridization, cHL cases rich in Hodgkin-Reed-Sternberg cells were selected. DNA obtained from approximately 100,000 microdissected Hodgkin-Reed-Sternberg cells of each of ten classical Hodgkin's lymphoma cases was hybridized onto commercial 105 K oligonucleotide comparative genomic hybridization microarrays. Selected imbalances were confirmed by interphase cytogenetics and quantitative polymerase chain reaction analysis and further studied in an independent series of classical Hodgkin's lymphoma. Gains identified in at least five cHL affected 2p12-16, 5q15-23, 6p22, 8q13, 8q24, 9p21-24, 9q34, 12q13-14, 17q12, 19p13, 19q13 and 20q11 whereas losses recurrent in at least five cases involved Xp21, 6q23-24 and 13q22. Copy number changes of selected genes and a small deletion (156 kb) of the CDKN2B (p15) gene were confirmed by interphase cytogenetics and polymerase chain reaction analysis, respectively. Several gained regions included genes constitutively expressed in cHL. Among these, gains of STAT6 (12q13), NOTCH1 (9q34) and JUNB (19p13) were present in additional cHL with the usual low Hodgkin-Reed-Sternberg cell content. The present study demonstrates that array comparative genomic hybridization of microdissected Hodgkin-Reed-Sternberg cells is suitable for identifying and characterizing chromosomal imbalances. Regions affected by genomic changes in Hodgkin-Reed-Sternberg cells recurrently include genes constitutively expressed in cHL.

Integration of conventional cytogenetics, comparative genomic hybridisation and interphase fluorescence in situ hybridisation for the detection of genomic rearrangements in acute leukaemia

Aims:To screen for genomic imbalances in patients with acute leukaemia using conventional (G-banding) and molecular (comparative genomic hybridisation (CGH) and fluorescence in situ hybridisation (FISH)) methods to determine whether an...

Strength Imbalances and Prevention of Hamstring Injury in Professional Soccer Players

Background The relationship between muscle injury and strength disorders remains a matter of controversy. Purpose Professional soccer players performed a preseason isokinetic testing aimed at determining whether (1) strength variables could be predictors of subsequent hamstring strain and (2) normalization of strength imbalances could reduce the incidence of hamstring injury. Study Design Cohort study (prognosis); Level of evidence, 1. Methods A standardized concentric and eccentric isokinetic assessment was used to identify soccer players with strength imbalances. Subjects were classified among 4 subsets according to the imbalance management content. Recording subsequent hamstring injuries allowed us to define injury frequencies and relative risks between groups. Results Of 687 players isokinetically tested in preseason, a complete follow-up was obtained in 462 players, for whom 35 hamstring injuries were recorded. The rate of muscle injury was significantly increased in subjects with untreated strength imbalances in comparison with players showing no imbalance in preseason (relative risk = 4.66; 95% confidence interval: 2.01-10.8). The risk of injury remained significantly higher in players with strength imbalances who had subsequent compensating training but no final isokinetic control test than in players without imbalances (relative risk = 2.89; 95% confidence interval: 1.00-8.32). Conversely, normalizing the isokinetic parameters reduced the risk factor for injury to that observed in players without imbalances (relative risk = 1.43; 95% confidence interval: 0.44-4.71). Conclusion The outcomes showed that isokinetic intervention gives rise to the preseason detection of strength imbalances, a factor that increases the risk of hamstring injury. Restoring a normal strength profile decreases the muscle injury incidence.

Chromosomal Genotype in Breast Cancer Progression: Comparison of Primary and Secondary Manifestations

The purpose of this study was to compare the chromosomal genotype between breast cancers with and without secondary manifestations and between primary tumors and their secondary manifestations. Eighty six breast cancers, twenty lymph node metastases, ten distant metastases and ten local recurrences were analyzed by comparative genomic hybridization. Tumors with local recurrences showed significant more frequent losses at 2q32 than the tumors without recurrences. Lymph node positive cases showed significant more frequent losses at 9p21 than node negative cases. Lymph node metastases exhibited significant more frequent losses at 7q11, 14q24.3–q31 and 17q22–q24 than their primary tumors. In cases with distant metastases, losses at 5q23 were more frequent than in those without, but not reaching the significance level. The distant metastases showed significant more frequent losses at 5p15, 12q24 and 17q22–q24 than the primary tumors. These results reveal strong evidence that the potential for progression is determined in the primary tumor and that different ways of the development of local recurrences, lymph node and distant metastases exist. After confirmation of the results by interphase FISH on tissue micro arrays, the detection of these specific chromosomal imbalances may contribute to a more individual prediction of prognosis in breast cancer.

22q11.2 Distal Deletion: A Recurrent Genomic Disorder Distinct from DiGeorge Syndrome and Velocardiofacial Syndrome

Microdeletions within chromosome 22q11.2 cause a variable phenotype, including DiGeorge syndrome (DGS) and velocardiofacial syndrome (VCFS). About 97% of patients with DGS/VCFS have either a common recurrent approximately 3 Mb deletion or a smaller, less common, approximately 1.5 Mb nested deletion. Both deletions apparently occur as a result of homologous recombination between nonallelic flanking low-copy repeat (LCR) sequences located in 22q11.2. Interestingly, although eight different LCRs are located in proximal 22q, only a few cases of atypical deletions utilizing alternative LCRs have been described. Using array-based comparative genomic hybridization (CGH) analysis, we have detected six unrelated cases of deletions that are within 22q11.2 and are located distal to the approximately 3 Mb common deletion region. Further analyses revealed that the rearrangements had clustered breakpoints and either a approximately 1.4 Mb or approximately 2.1 Mb recurrent deletion flanked proximally by LCR22-4 and distally by either LCR22-5 or LCR22-6, respectively. Parental fluorescence in situ hybridization (FISH) analyses revealed that none of the available parents (11 out of 12 were available) had the deletion, indicating de novo events. All patients presented with characteristic facial dysmorphic features. A history of prematurity, prenatal and postnatal growth delay, developmental delay, and mild skeletal abnormalities was prevalent among the patients. Two patients were found to have a cardiovascular malformation, one had truncus arteriosus, and another had a bicuspid aortic valve. A single patient had a cleft palate. We conclude that distal deletions of chromosome 22q11.2 between LCR22-4 and LCR22-6, although they share some characteristic features with DGS/VCFS, represent a novel genomic disorder distinct genomically and clinically from the well-known DGS/VCF deletion syndromes.

Validation of a targeted DNA microarray for the clinical evaluation of recurrent abnormalities in chronic lymphocytic leukemia

Recurrent genomic alterations, mainly losses and gains of specific chromosomes and/or regions, in chronic lymphocytic leukemia (CLL) are recognized as important independent predictors of prognosis and disease progression. The current standard clinical practice for identifying these alterations is chromosome analysis and in situ hybridization with probes targeting 4-5 chromosome regions. We sought to apply array comparative genomic hybridization (array-CGH) technology for the simultaneous detection of genomic imbalances of all loci implicated in CLL. DNA from enriched B-cells from CLL patients were analyzed by array-CGH on a customized CLL BAC array. Copy number changes were detected in 87% of samples with a sensitivity of 100% in samples with clonal abnormalities present in at least 23% of the cells. Furthermore, in nine cases genomic alterations were observed that were undetectable by standard cytogenetic and/or FISH analyses. One of these patients had a 13q14 deletion that was missed by the clinical CLL FISH panel probe set. Our results suggest that a subset of potentially significant genomic alterations in CLL is being missed by the current available techniques. Furthermore, this pilot study clearly shows the robustness, high sensitivity, and high specificity for the targeted CLL microarray analysis as well as the potential for use in routine screening in CLL.

Genomic Profiling of Different Subtypes of B-Cell Non-Hodgkin's Lymphoma Using High-Density Single Nucleotide Polymorphism (SNP) Microarrays.

B-cell non-Hodgkin's lymphoma (B-NHL) is a constellation of mature B-cell neoplasms characterized by distinct pathological and molecular genetic features, including diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), MATL-type lymphoma (MALT-L). These B-NHLs undergo a wide variety of genetic alterations, including gains and losses of genetic materials, as well as abnormalities in allelic composition, and these alterations may collectively comprise unique genomic profiles specific to different subtypes of B-NHL, which are tightly linked to the pathogenesis of each B-NHL subtype. Recently, we have developed a robust method (CNAG/AsCNAR) to detect allelic imbalances and other copy number changes in cancer genomes using SNP-genotyping microarrays (Nannya et al. Cancer Res, 2005 and Yamamoto et al. Am J Hum Genet, 2007). Without depending on the availability of constitutive genomic DNA, it enables sensitive detection of allelic imbalances including loss of heterozygosity (LOH) as well as copy number (CN) alterations in the face of 70–80% of normal cell components. In the current study, we performed SNP-chip/CNAG/AsCNAR analysis of 171 B-NHL specimens, including 65 cases of DLBCL, 61 cases of FL, and 45 cases of MALT-L in order to comparatively investigate the unique genomic profiles of different B-NHL subtypes. A large number of gains and losses of chromosomal/genomic segments as well as allelic imbalances were identified. While individual genomic profiles are substantially variable among different cases, they collectively showed a characteristic genomic profile in each B-NHL subtypes; +1q, +2p and +18 are common to DLBCL and FL, while +3 and +11q were more frequently found in DLBCL and +11p was more characteristic to FL. MALT-L also showed +3 and +18, but rarely had +1q and +2p. CN neutral LOH due to mitotic recombination (uniparental disomy; UPD) events are frequently found in DLBCL (70%) and FL (54%), but less common in MALT-L. UPD most commonly involves 1p, 1q, 6p, 9p and 12q. In total, 29 loci of high-grade amplification were identified. Among these recurring amplifications were observed at 1q and 2p, which involves FCGR2B, and cRel genes, respectively. These amplifications were detected in both DLBCL and FL, but rare in MALT-L. Total 14 loci of homozygous deletion were also detected and differentially distributed among different B-NHL subtypes. In conclusion, SNP-chip with CNAG/AsCNAR analysis revealed characteristic genomic signatures of distinctive B-NHL subtypes, implicating their unique pathogenesis.

Submicroscopic chromosomal imbalances detected by array-CGH are a frequent cause of congenital heart defects in selected patients

Congenital heart defects (CHDs) are frequently caused by chromosomal imbalances, especially when associated with additional malformations, dysmorphism, or developmental delay. Only in a subset of such patients, a chromosomal aberration can be identified with current cytogenetic tests. Array Comparative Genomic Hybridization (Array-CGH) now enables the detection of submicroscopic chromosomal imbalances at high resolution. In this report, we evaluate for the first time the use of array-CGH as a diagnostic tool in a selected group of patients with a CHD. Sixty patients with a CHD of unknown cause but with features suggestive of a chromosomal aberration were selected. Array-CGH was performed using an in-house made 1 Mb micro-array. Chromosomal imbalances not previously described as polymorphisms were detected in 18/60 patients (30%). Ten of these (17%) are considered to be causal. In three deletions, genes known to cause CHDs were implicated (NKX2.5, NOTCH1, NSD1, EHMT). One patient carried a duplication of chromosome 22q11.2, previously associated with CHD. In the other six patients, both the de novo occurrence as well as the size of the imbalance indicated causality. In addition, seven inherited aberrations unreported thus far were detected. Their causal relationship with CHDs remains to be established. Finally, a mosaic monosomy 7 was not considered as causal but did enable to make a diagnosis of Fanconi anaemia. This study shows that array-CGH is able to provide an etiological diagnosis in a large proportion of patients with a CHD, selected for a 'chromosomal phenotype'. Besides their usefulness in genetic counselling, identified chromosomal aberrations may aid in the medical follow-up of these individuals.

Diagnostic utility of array‐based comparative genomic hybridization in a clinical setting

Array-based comparative genomic hybridization is a recently introduced technique for the detection of submicroscopic genomic imbalances (deletions or duplications) across the entire genome. To assess the potential utility of a widely available array-based comparative genomic hybridization platform that targets specific, clinically relevant, loci across the genome for cytogenetic diagnosis in a clinical setting, we reviewed the medical records of all 373 patients at Children's Hospital Boston who had normal chromosomal analysis and were tested with this targeted array-based comparative genomic hybridization over a 1-year period from November 1, 2004 to October 31, 2005. These patients were tested because of a suspicion of chromosomal abnormalities based on their clinical presentation. Thirty-six patients (9.7%) had abnormal array-based comparative genomic hybridization results. Twenty patients (5.4%) had potentially pathogenetic genomic imbalances and 16 patients (4.3%) had copy number variations that are not believed to be pathogenetic. Thirteen of 234 patients (5.6%) with mental retardation/global developmental delay, 10/114 patients (8.8%) with facial dysmorphism, 5/58 patients (8.6%) with multiple congenital anomalies, and 4/35 patients (11.4%) with both facial dysmorphism and multiple congenital anomalies had potentially pathogenetic genomic imbalances. Targeted array-based comparative genomic hybridization is a clinically available test that is useful in the evaluation of patients suspected of having chromosomal disorders. However, it is best used as an adjunct to chromosomal analysis when a clear genetic diagnosis is unavailable.

Combining array‐based approaches for the identification of candidate tumor suppressor loci in mature lymphoid neoplasms

Tumor suppressor gene (TSG) inactivation by chromosomal deletions and/or mutations is a well-characterized genetic alteration in lymphomas. Array-based technologies have greatly increased the detection and characterization of chromosomal imbalances and regions with loss of heterozygosity (LOH), leading to the identification of a number of novel candidate TSG loci. In addition, microarray platforms for studying DNA methylation and histone modifications enable identifying epigenetic changes affecting gene expression of TSG. Combining these microarray technologies with gene expression profiling is a promising strategy to discover novel TSG in regions targeted by genetic or epigenetic alterations. In this review we present an outline of methodological aspects of the various microarray technologies, and discuss their potentials and restrictions. Furthermore, we survey research findings derived from these high-throughput techniques, which are allowing a deeper insight into the mechanisms of lymphomagenesis.

Screening of 20 patients with X-linked mental retardation using chromosome X-specific array-MAPH

The rapid advancement of high-resolution DNA copy number assessment methods revealed the significant contribution of submicroscopic genetic imbalances to abnormal phenotypes, including mental retardation. In order to detect submicroscopic genetic imbalances, we have screened 20 families with X-linked mental retardation (XLMR) using a chromosome X-specific array-MAPH platform with median resolution of 238 kb. Among the 20 families, 18 were experimental, as they were not previously screened with any microarray method, and two were blind controls with known aberrations, as they were previously screened by array-CGH. This study presents the first clinical application of chromosome X-specific array-MAPH methodology. The screening of 20 affected males from 20 unrelated XLMR families resulted in the detection of an unknown deletion, spanning a region of 7–23 kb. Family studies and population screening demonstrated that the detected deletion is an unknown rare copy number variant. One of the control samples, carrying approximately 6-Mb duplication was correctly identified, moreover it was found to be interrupted by a previously unknown 19 kb region of normal copy number. The second control 50 kb deletion was not identified, as this particular region was not covered by array-MAPH probes. This study demonstrates that the chromosome X-specific array-MAPH platform is a valuable tool for screening patients with XLMR, or other X-linked disorders, and emerges the need for introducing new high-resolution screening methods for the detection of genetic imbalances.