Oligonucleotide arrays for high-resolution analysis of copy number alteration in mental retardation/multiple congenital anomalies

Whole genome analysis identifies the association of TP53 genomic deletions with lower survival in Stage III colorectal cancer

DNA copy number aberrations (CNA) are frequently observed in colorectal cancers (CRC). There is an urgent need for CNA-based biomarkers in clinics,. n For Stage III CRC, if combined with imaging or pathologic evidence, these markers promise more precise care. We conducted this Stage III specific biomarker discovery with a cohort of 134 CRCs, and with a newly developed high-efficiency CNA profiling protocol. Specifically, we developed the profiling protocol for tumor-normal matched tissue samples based on low-coverage clinical whole-genome sequencing (WGS). We demonstrated the protocol’s accuracy and robustness by a systematic benchmark with microarray, high-coverage whole-exome and -genome approaches, where the low-coverage WGS-derived CNA segments were highly accordant (PCC >0.95) with those derived from microarray, and they were substantially less variable if compared to exome-derived segments. A lasso-based model and multivariate cox regression analysis identified a chromosome 17p loss, containing the TP53 tumor suppressor gene, that was significantly associated with reduced survival (P = 0.0139, HR = 1.688, 95% CI = [1.112–2.562]), which was validated by an independent cohort of 187 Stage III CRCs. In summary, this low-coverage WGS protocol has high sensitivity, high resolution and low cost and the identified 17p-loss is an effective poor prognosis marker for Stage III patients.

Single nucleotide polymorphism array analysis uncovers a large, novel duplication in Xq13.1 in a floppy infant syndrome patient

OBJECTIVE

To identify candidate genes for the clinical diagnosis of floppy infant syndrome (FIS) using single nucleotide polymorphism (SNP) array in a specific FIS family.

METHODS

SNP array analysis of the whole chromosome copy number was performed in the proband (III₁). Multiple polymerase chain reaction (PCR) combined with denaturing high-performance liquid chromatography (DHPLC) was used to validate the array data.

RESULTS

A large 5.818182 Mb duplication (Xq13.1: 67987646-73805828), which encompasses 66 known genes, was found in III₁. The start and end points of the duplication were confirmed with an SNP array. Duplicated genes with potential roles in central and/or peripheral nervous system development (HDAC8, PHKA1, TAF1, DLG3, KIF4A, IGBP1, PJA1, and SLC16A2) were confirmed by multiple PCR-DHPLC in III₁. The patient's mother and grandmother carry duplications in these eight genes, but only on one X chromosome, while the patient's aunt does not carry any of the duplications.

CONCLUSION

Based on the location of the eight candidate genes in Xq13.1, the large duplication found by SNP array does indeed exist and is predicted to be both novel and pathogenic. Moreover, we recommend SNP array as the first option for genetic diagnosis of both large-scale and rare/complicated diseases, such as FIS.

Examining genotypic variation in autism spectrum disorder and its relationship to parental age and phenotype

Background

Previous studies on genetic testing of chromosomal abnormalities in individuals diagnosed with autism spectrum disorder (ASD) found that ~80% have negative genetic test results (NGTRs) and ~20% have positive genetic test results (PGTRs), of which ~7% were probable de novo mutations (PDNMs). Research suggests that parental age is a risk factor for an ASD diagnosis. This study examined genotypic variation in ASD and its relationship to parental age and phenotype.

Methods

Phenotype was derived from detailed clinical information, and genotype was derived from high-resolution blood chromosome and blood whole-genome copy number variant genetic testing on a consecutive cohort (born: 1983–2009) of subjects diagnosed with ASD (N=218).

Results

Among the subjects examined, 80.3% had NGTRs and 19.7% had PGTRs, of which 6.9% had PDNMs. NGTR subjects were born more recently (the risk of PDNMs decreasing by 12% per more recent birth year) and tended to have an increased male–female ratio compared to PDNM subjects. PDNM subjects had significantly increased mean parental age and paternal age at subject’s birth (the risk of a PDNM increasing by 7%–8% per year of parental or paternal age) compared to NGTR subjects. PGTR and NGTR subjects showed significant improvements in speech/language/communication with increasing age. PGTR subjects showed significant improvements in sociability, a core feature of an ASD diagnosis, with increasing age, whereas NGTR subjects showed significant worsening in sociability with increasing age.

Conclusion

This study helps to elucidate different phenotypic ASD subtypes and may even indicate the need for differential diagnostic classifications.

Cri-Du-Chat Syndrome: Clinical Profile and Chromosomal Microarray Analysis in Six Patients

Cri-du-chat syndrome is a chromosomal disorder caused by a deletion of the short arm of chromosome 5. The disease severity, levels of intellectual and developmental delay, and patient prognosis have been related to the size and position of the deletion. Aiming to establish genotype-phenotype correlations, we applied array-CGH to evaluate six patients carrying cytogenetically detected deletions of the short arm of chromosome 5 who were followed at a genetics community service. The patients' cytogenetic and clinical profiles were reevaluated. A database review was performed to predict additional genes and regulatory elements responsible for the characteristic phenotypic and behavioral traits of this disorder. Array-CGH analysis allowed for delineation of the terminal deletions, which ranged in size from approximately 11.2 Mb to 28.6 Mb, with breakpoints from 5p15.2 to 5p13. An additional dup(8)(p23) (3.5 Mb), considered to be a benign copy number variation, was also observed in one patient. The correlation coefficient value (ρ = 0.13) calculated indicated the presence of a weak relationship between developmental delay and deletion size. Genetic background, family history, epigenetic factors, quantitative trait locus polymorphisms, and environmental factors may also affect patient phenotype and must be taken into account in genotype-phenotype correlations.

Genetics of allergic diseases

Genome-wide association studies (GWAS) have been employed in the field of allergic disease, and significant associations have been published for nearly 100 asthma genes/loci. An outcome of GWAS in allergic disease has been the formation of national and international collaborations leading to consortia meta-analyses, and an appreciation for the specificity of genetic associations to sub-phenotypes of allergic disease. Molecular genetics has undergone a technological revolution, leading to next-generation sequencing strategies that are increasingly employed to hone in on the causal variants associated with allergic diseases. Unmet needs include the inclusion of diverse cohorts and strategies for managing big data.

Alterations of LKB1 and KRAS and risk of brain metastasis: comprehensive characterization by mutation analysis, copy number, and gene expression in non-small-cell lung carcinoma

BACKGROUND

Brain metastases are one of the most malignant complications of lung cancer and constitute a significant cause of cancer related morbidity and mortality worldwide. Recent years of investigation suggested a role of LKB1 in NSCLC development and progression, in synergy with KRAS alteration. In this study, we systematically analyzed how LKB1 and KRAS alteration, measured by mutation, gene expression (GE) and copy number (CN), are associated with brain metastasis in NSCLC.

MATERIALS AND METHODS

Patients treated at University of North Carolina Hospital from 1990 to 2009 with NSCLC provided frozen, surgically extracted tumors for analysis. GE was measured using Agilent 44,000 custom-designed arrays, CN was assessed by Affymetrix GeneChip Human Mapping 250K Sty Array or the Genome-Wide Human SNP Array 6.0 and gene mutation was detected using ABI sequencing. Integrated analysis was conducted to assess the relationship between these genetic markers and brain metastasis. A model was proposed for brain metastasis prediction using these genetic measurements.

RESULTS

17 of the 174 patients developed brain metastasis. LKB1 wild type tumors had significantly higher LKB1 CN (p<0.001) and GE (p=0.002) than the LKB1 mutant group. KRAS wild type tumors had significantly lower KRAS GE (p<0.001) and lower CN, although the latter failed to be significant (p=0.295). Lower LKB1 CN (p=0.039) and KRAS mutation (p=0.007) were significantly associated with more brain metastasis. The predictive model based on nodal (N) stage, patient age, LKB1 CN and KRAS mutation had a good prediction accuracy, with area under the ROC curve of 0.832 (p<0.001).

CONCLUSION

LKB1 CN in combination with KRAS mutation predicted brain metastasis in NSCLC.

An Evaluation of the Effect of Increasing Parental Age on the Phenotypic Severity of Autism Spectrum Disorder

It was recently postulated that because increased genetic load and increased parental age are both purportedly associated with the risk to develop an autism spectrum disorder, there must be a linkage between increasing genetic load and increasing parental age in autism spectrum disorder pathogenesis. The present study examined the hypothesis that if increased genetic load from increasing paternal age is important to autism spectrum disorder pathogenesis, then there should be a significant relationship between increasing parental age and increasing autism spectrum disorder phenotypic severity. Outpatient clinical records were retrospectively examined to identify a consecutive cohort of subjects diagnosed with an autism spectrum disorder (n = 351). Increasing autism spectrum disorder phenotypic severity was found not to be associated with increasing maternal/paternal age. The present study failed to support the hypothesis that increasing parental age was associated with increasing autism spectrum disorder phenotypic severity, but future studies should examine the relationship between genetic mutations in subjects diagnosed with an autism spectrum disorder and increasing parental age.

Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns

Copy number variation (CNV) analysis has had a major impact on the field of medical genetics, providing a mechanism to identify disease-causing genomic alterations in an unprecedented number of diseases and phenotypes. CNV analysis is now routinely used in the clinical diagnostic laboratory, and has led to a significant increase in the detection of chromosomal abnormalities. These findings are used for prenatal decision making, clinical management and genetic counseling. Although a powerful tool to identify genomic alterations, CNV analysis may also result in the detection of genomic alterations that have unknown clinical significance or reveal unintended information. This highlights the importance of informed consent and genetic counseling for clinical CNV analysis. This review examines the advantages and limitations of CNV discovery in the clinical diagnostic laboratory, as well as the impact on the clinician and family.

Oligonucleotide microarrays for clinical diagnosis of copy number variation and zygosity status

Detection of submicroscopic genomic copy number variation is now considered the first-tier clinical test-in place of standard G-banded karyotyping-in the evaluation of children with unexplained developmental delay, intellectual disability, autism spectrum disorders, or congenital anomalies. Fluorescence in situ hybridization (FISH) was the first molecular method for detection of submicroscopic genomic copy number variants (CNVs), but microarray-based comparative genomic hybridization (array CGH) has a much higher diagnostic yield for these patients when compared to traditional cytogenetic methods such as karyotype and FISH. This unit focuses on oligonucleotide arrays, including updated information about detection of long contiguous stretches of homozygosity (LCSH) through inclusion of single-nucleotide polymorphism (SNP) probes. Most clinical laboratories now offer arrays with some level of probe coverage throughout the genome, and many are offering detection of LCSH. Updated guidelines for array design and result interpretation are reviewed.

Context-based FISH localization of genomic rearrangements within chromosome 15q11.2q13 duplicons

BACKGROUND

Segmental duplicons (SDs) predispose to an increased frequency of chromosomal rearrangements. These rearrangements can cause a diverse range of phenotypes due to haploinsufficiency, in cis positional effects or gene interruption. Genomic microarray analysis has revealed gene dosage changes adjacent to duplicons, but the high degree of similarity between duplicon sequences has confounded unequivocal assignment of chromosome breakpoints within these intervals. In this study, we localize rearrangements within duplicon-enriched regions of Angelman/Prader-Willi (AS/PWS) syndrome chromosomal deletions with fluorescence in situ hybridization (FISH).

RESULTS

Breakage intervals in AS deletions were localized recursively with short, coordinate-defined, single copy (SC) and low copy (LC) genomic FISH probes. These probes were initially coincident with duplicons and regions of previously reported breakage in AS/PWS. Subsequently, probes developed from adjacent genomic intervals more precisely delineated deletion breakage intervals involving genes, pseudogenes and duplicons in 15q11.2q13. The observed variability in the deletion boundaries within previously described Class I and Class II deletion AS samples is related to the local genomic architecture in this chromosomal region.

CONCLUSIONS

Chromosome 15 abnormalities associated with SDs were precisely delineated at a resolution equivalent to genomic Southern analysis. This context-dependent approach can define the boundaries of chromosome rearrangements for other genomic disorders associated with SDs.

Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation

BACKGROUND

Clinical laboratories are adopting array genomic hybridization as a standard clinical test. A number of whole genome array genomic hybridization platforms are available, but little is known about their comparative performance in a clinical context.

METHODS

We studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500 K GeneChip SNP arrays, Agilent Human Genome 244 K oligonucleotide arrays and NimbleGen 385 K Whole-Genome oligonucleotide arrays. We also determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32 K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP arrays.

RESULTS

The Affymetrix 500 K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosomal CNVs in the 30 trios. 147 of these CNVs appeared to be de novo, but only 34 (22%) were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 most likely pathogenic and 2 possibly pathogenic CNVs for MR. All 9 of these putatively pathogenic CNVs were detected by the Affymetrix 500 K, Agilent, NimbleGen and the Illumina arrays, and 5 were found by the SMRT BAC array. Both putatively pathogenic CNVs identified in the 15 trios tested with the Affymetrix 6.0 were identified by this platform.

CONCLUSIONS

Our findings demonstrate that different results are obtained with different platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls on each of the platforms supports the need for validating clinically important findings with a different technology.

Identification of genome-wide copy number variations and a family-based association study of Avellino corneal dystrophy

OBJECTIVE

To determine the association of identified copy number variations (CNVs) in whole genome with the risk of Avellino corneal dystrophy (ACD) in a Korean population.

DESIGN

Case-control study.

PARTICIPANTS

A total of 146 patients with ACD and 226 control subjects.

METHODS

A total of 193 trios were genotyped by the Illumina HumanHapCNV370-Duo BeadChip (370,404 markers) (Illumina, Inc., San Diego, CA). The intensity signal (log R ratio) and allelic intensity ratio (B allele frequency) of each marker in all individuals were obtained by Illumina BeadStudio software (Illumina, Inc.). To obtain authentic CNVs in this study, we performed a family-based CNV validation and family-based boundary mapping using the PennCNV algorithm, which incorporates multiple factors, including total log R ratio, B allele frequency, and family information, based on an integrated hidden Markov model.

MAIN OUTCOME MEASURES

Statistical comparison and identification of CNVs between case and control using family information.

RESULTS

We identified 27,267 individual trio CNVs with a median size of 16.2 kb, aggregated in 2245 CNV regions. Most of the identified trio CNVs in this study showed well-defined CNV boundaries and overlapped with those in the Database of Genomic Variants (DGV) (83.4% in number and 79.2% in length). With the common CNV regions (264 CNV regions >5%), we performed a family-based association test with the risk of ACD.

CONCLUSIONS

Two CNV regions (chr6:29978470-29987783 and chr14:59896944-59916129) were significantly associated with the risk of ACD (P=0.05-0.003 and P=0.008, respectively). This study describes the first results of a genome-wide association analysis of individual CNVs with the risk of ACD and shows that 2 novel CNV loci may be involved in the risk of ACD.

FINANCIAL DISCLOSURE(S)

The author(s) have no proprietary or commercial interest in any materials discussed in this article.

A functional analysis of GABARAP on 17p13.1 by knockdown zebrafish

Array-based comparative genomic hybridization identified a 2.3-Mb microdeletion of 17p13.2p13.1 in a boy presenting with moderate mental retardation, intractable epilepsy and dysmorphic features. This deletion region was overlapped with the previously proposed shortest region overlapped for microdeletion of 17p13.1 in patients with mental retardation, microcephaly, microretrognathia and abnormal magnetic resonance imaging (MRI) findings of cerebral white matter, in which at least 17 known genes are included. Among them, DLG4/PSD95, GPS2, GABARAP and KCTD11 have a function in neuronal development. Because of the functional importance, we paid attention to DLG4/PSD95 and GABARAP, and analyzed zebrafish in which the zebrafish homolog of human DLG4/PSD95 and GABARAP was knocked down and found that gabarap knockdown resulted in small head and hypoplastic mandible. This finding would be similar to the common findings of the patients with 17p13.1 deletions. Although there were no pathogenic mutations in DLG4/PSD95 or GABARAP in a cohort study with 142 patients with idiopathic developmental delay with/without epilepsy, further studies would be required for genes included in this region.

Chromosomal microarray interpretation: what is a child neurologist to do?

The chromosomal microarray now plays a central role in the evaluation of children with neurologic developmental disorders, including global developmental delay, mental retardation, and increasingly also autistic spectrum disorders. As arrays become more sophisticated and their use more widespread, the child neurologist is likely to encounter abnormal chromosomal microarray results. The interpretation of such data is not always straightforward. This review article discusses in a practical manner the nature of chromosomal microarray results, describes an algorithm to help the child neurologist navigate a variety of testing scenarios, and proposes a standardized system for ranking array data based on levels of evidence of genotype-phenotype correlation.

High-resolution SNP arrays in mental retardation diagnostics: how much do we gain?

We used Affymetrix 6.0 GeneChip SNP arrays to characterize copy number variations (CNVs) in a cohort of 70 patients previously characterized on lower-density oligonucleotide arrays affected by idiopathic mental retardation and dysmorphic features. The SNP array platform includes approximately 900,000 SNP probes and 900,000 non-SNP oligonucleotide probes at an average distance of 0.7 Kb, which facilitates coverage of the whole genome, including coding and noncoding regions. The high density of probes is critical for detecting small CNVs, but it can lead to data interpretation problems. To reduce the number of false positives, parameters were set to consider only imbalances >75 Kb encompassing at least 80 probe sets. The higher resolution of the SNP array platform confirmed the increased ability to detect small CNVs, although more than 80% of these CNVs overlapped to copy number 'neutral' polymorphism regions and 4.4% of them did not contain known genes. In our cohort of 70 patients, of the 51 previously evaluated as 'normal' on the Agilent 44K array, the SNP array platform disclosed six additional CNV changes, including three in three patients, which may be pathogenic. This suggests that about 6% of individuals classified as 'normal' using the lower-density oligonucleotide array could be found to be affected by a genomic disorder when evaluated with the higher-density microarray platforms.

Parents' reports predict abnormal investigations in global developmental delay

AIMS

To identify symptoms reported by parents that predict abnormal laboratory investigations in preschoolers with global developmental delay (GDD).

METHODS

A cross-sectional descriptive study of 81 boys and 38 girls, with a mean age of 43.5 months (SD = 13.4), with global developmental delay. All parents/guardians completed the following: (1) a semistructured interview about their child and family; (2) the Child Development Inventory (CDI); (3) the Possible Problems Checklist (PPC); and (4) the Child Behavior Checklist 1(1/2)-5 (CBCL).

RESULTS

There were 61 abnormal results: MRI 37 (31%); high-resolution chromosomes 8 (7%); fragile X molecular testing 4 (3%); and microarray comparative genomic hybridization 12 (10%). A total of 47 children had abnormal tests (40%): none, 72 (60%); one, 36 (30%); two, 8 (7%); three, (3%). Younger children with more developmental delays are more likely to have abnormal tests. They are clumsy, more passive, and less disobedience. They had lower total, externalizing, and internalizing problems scores. The odds of finding an abnormal investigation are increasingly greater as parent's report of language comprehension and social development ratios increase, and decrease in likelihood for every increase in the expressive language and fine motor ratios.

INTERPRETATION

Parent's reports predict abnormal tests and indicate quantifiable differences requiring investigation.

Application of array-based comparative genome hybridization in children with developmental delay or mental retardation

Children with developmental delay or mental retardation (DD/MR) are commonly encountered in child neurology clinics, and establishing an etiologic diagnosis is a challenge for child neurologists. Among the etiologies, chromosomal imbalance is one of the most important causes. However, many of these chromosomal imbalances are submicroscopic and cannot be detected by conventional cytogenetic methods. Microarray-based comparative genomic hybridization (array CGH) is considered to be superior in the investigation of chromosomal deletions or duplications in children with DD/MR, and has been demonstrated to improve the diagnostic detection rate for these small chromosomal abnormalities. Here, we review the recent studies of array CGH in the evaluation of patients with idiopathic DD/MR.

Considerations regarding the genetics of obesity

The genetics of human body fat content (obesity) are clearly complex. Genetic and physiological analysis of rodents have helped enormously in pointing to critical molecules and cells in central nervous system and "peripheral" pathways mediating the requisite fine control over the defense of body fat. Human and animal studies are consistent with inferences from evolutionary considerations that the strengths of defenses against fat loss are greater than those against gain. Many of the genes participating in these pathways have reciprocal effects on both energy intake and expenditure, though different genes may have primary roles in respective responses to weight gain or loss. Such distinctions have important consequences for both research and treatment strategies. The body mass index (BMI) is a useful gross indicator of adiposity, but more refined measurements of body composition and energy homeostasis will be required to understand the functional consequences of allelic variation in genes of interest. Phenotypes related to energy intake and expenditure-which clearly are the major determinants of net adipose tissue storage-are not salient when individuals are in energy balance (weight stable); measurements obtained during weight perturbation studies are likely to provide more revealing phenotypes for genetic analysis. The advent of high-density genome-wide scans in large numbers of human subjects for association analysis will revolutionize the study of the genetics of complex traits such as obesity by generating substantial numbers of powerful linkage signals from smaller genetic intervals. Many of the genes implicated will not have been previously related to energy homeostasis (e.g., recent experience with FTO/FTM as described below), and will have relatively small effects on the associated phenotype(s). The mouse will again prove useful in determining the relevant physiology of these new genes. New analytic tools will have to be developed to permit the necessary analysis of the gene x gene interactions that must ultimately convey aggregate genetic effects on adiposity.

Oligonucleotide microarrays for clinical diagnosis of copy number variation

Detection of genomic copy number variation is now considered the standard of care in the evaluation of children with developmental delay, and is used for other clinical indications such as multiple congenital anomalies and autism spectrum disorders. Fluorescence in situ hybridization (FISH) was the first molecular method for detection of submicroscopic genomic copy number variation, but microarray based comparative genomic hybridization (array CGH) offers several advantages as an adjunct to traditional cytogenetic methods such as karyotype and FISH. This unit focuses on oligonucleotide arrays, but includes background information on basic differences between oligonucleotide arrays and bacterial artificial chromosome (BAC) arrays. Array sensitivity is influenced by probe coverage or density, probe location, and choice of oligo array formats (i.e., targeted versus whole genome). Array platform influences the likelihood of detecting variants of unknown significance. Clinical interpretation of such variants is discussed.

The array CGH and its clinical applications

Array comparative genomic hybridization (aCGH) is a technique enabling high-resolution, genome-wide screening of segmental genomic copy number variations (CNVs). It is becoming an essential and a routine clinical diagnostic tool and is gradually replacing cytogenetic methods. Most of the clinically available aCGH platforms are designed to detect aneuploidies, well-characterized microdeletion/microduplication syndromes and subtelomeric or other unbalanced chromosomal rearrangements. In addition, aCGH can uncover numerous CNVs of unclear significance scattered throughout the human genome. But this technology is not able to identify balanced chromosomal imbalances such as translocations and inversions and some ploidies. aCGH increased the ability to detect segmental genomic CNVs in patients with global developmental delay, mental retardation, autism, multiple congenital anomalies and dysmorphism, and is becoming a powerful tool in disease gene discovery and prenatal diagnostics. This tool is also showing promising data in cancer research and in the diagnosis, classification and prognostication of different malignancies.

Bacterial artificial chromosome-emulation oligonucleotide arrays for targeted clinical array-comparative genomic hybridization analyses

PURPOSE

The goal of this work was to test the ability of oligonucleotide-based arrays to reproduce the results of focused bacterial artificial chromosome (BAC)-based arrays used clinically in comparative genomic hybridization experiments to detect constitutional copy number changes in genomic DNA.

METHODS

Custom oligonucleotide (oligo) arrays were designed using the Agilent Technologies platform to give high-resolution coverage of regions within the genome sequence coordinates of BAC/P1 artificial chromosome (PAC) clones that had already been validated for use in previous versions of clone arrays used in clinical practice. Standard array-comparative genomic hybridization experiments, including a simultaneous blind analysis of a set of clinical samples, were conducted on both array platforms to identify copy number differences between patient samples and normal reference controls.

RESULTS

Initial experiments successfully demonstrated the capacity of oligo arrays to emulate BAC data without the need for dye-reversal comparisons. Empirical data and computational analyses of oligo response and distribution from a pilot array were used to design an optimized array of 44,000 oligos (44K). This custom 44K oligo array consists of probes localized to the genomic positions of >1400 fluorescence in situ hybridization-verified BAC/PAC clones covering more than 140 regions implicated in genetic diseases, as well as all clinically relevant subtelomeric and pericentromeric regions.

CONCLUSIONS

Our data demonstrate that oligo-based arrays offer a valid alternative for focused BAC arrays. Furthermore, they have significant advantages, including better design flexibility, avoidance of repetitive sequences, manufacturing processes amenable to good manufacturing practice standards in the future, increased robustness because of an enhanced dynamic range (signal to background), and increased resolution that allows for detection of smaller regions of change.

From microscopes to microarrays: dissecting recurrent chromosomal rearrangements

Submicroscopic chromosomal rearrangements that lead to copy-number changes have been shown to underlie distinctive and recognizable clinical phenotypes. The sensitivity to detect copy-number variation has escalated with the advent of array comparative genomic hybridization (CGH), including BAC and oligonucleotide-based platforms. Coupled with improved assemblies and annotation of genome sequence data, these technologies are facilitating the identification of new syndromes that are associated with submicroscopic genomic changes. Their characterization reveals the role of genome architecture in the aetiology of many clinical disorders. We review a group of genomic disorders that are mediated by segmental duplications, emphasizing the impact that high-throughput detection methods and the availability of the human genome sequence have had on their dissection and diagnosis.