New molecular biology methods have specified the evidence of chromosomal changes in the tumor tissue. These alterations can be proven to exist in the majority of malignant tumors. The fast progress of whole genome molecular biological methods has helped to improve the knowledge of tumor genetics. The evidence of genetic changes is a component of currently used diagnostic and prognostic schemes in particular cancer diseases. Karyotyping was the first method used in the clinical practice but its importance has decreased with the arrival of new molecular biological methods. The most common methods used for the detection of chromosomal deletions or amplifications are CGH, array-CGH and SNP array. The first two methods are based on the principle of comparison between tumor DNA and control DNA. The principle of SNP array uses the presence of single nucleotide polymorphisms that are located in the whole genome in each individual. SNP array can prove not only deletions or amplifications of the chromosomes but unlike CGH techniques it can also detect a loss of heterozygosity or uniparental disomy. The screening of chromosomal changes has nowadays become routine. These techniques are used for diagnosis, prognosis and treatment of cancer disease in certain cases.
- MeSH
- Chromosome Aberrations MeSH
- DNA, Neoplasm analysis genetics MeSH
- Polymorphism, Single Nucleotide genetics MeSH
- Humans MeSH
- Neoplasms diagnosis genetics MeSH
- Oligonucleotide Array Sequence Analysis methods MeSH
- Comparative Genomic Hybridization methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
- Names of Substances
- DNA, Neoplasm MeSH
MOTIVATION: Genome analysis has become one of the most important tools for understanding the complex process of cancerogenesis. With increasing resolution of CGH arrays, the demand for computationally efficient algorithms arises, which are effective in the detection of aberrations even in very noisy data. RESULTS: We developed a rather simple, non-parametric technique of high computational efficiency for CGH array analysis that adopts a median absolute deviation concept for breakpoint detection, comprising median smoothing for pre-processing. The resulting algorithm has the potential to outperform any single smoothing approach as well as several recently proposed segmentation techniques. We show its performance through the application of simulated and real datasets in comparison to three other methods for array CGH analysis. IMPLEMENTATION: Our approach is implemented in the R-language and environment for statistical computing (version 2.6.1 for Windows, R-project, 2007). The code is available at: http://www.iba.muni.cz/~budinska/msmad.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Multiple myeloma (MM) is a hematological disease caused by malignant proliferation of clonal plasma cells (PCs) known for its clinical and biological heterogeneity. Identification of chromosomal changes in genome of PCs plays a key role in MM pathogenesis and is supposed to have important prognostic significance for MM patients. There are two major genetic entities in MM. Hyperdiploid tumors (H-MM), which include about 50% of MM tumors, often have multiple trisomies involving chromosomes 3, 5, 7, 9, 11, 15, 19, and 21 and a substantially lower prevalence of IgH translocations. Nearly half of tumors are non-hyperdiploid (NH-MM), and mostly have one of five recurrent IgH translocations: 11ql13 (CCND1), 6p21 (CCND3), 16q23 (MAF), 20q12 (MAFB), and 4p16 (FGFR3 and MMSET). The development and expanded use of new technologies, such as genome-wide array-based comparative genomic hybridization (aCGH) has accelerated genomic research in MM. This technique is a powerful tool to globally analyze recurrent copy number changes in tumor genome in a single reaction and to study cancer biology and clinical behaviors. It widely overcame routinely used cytogenetic techniques (G-banding, FISH) both in minimal resolution of chromosomal changes and amount of obtained genomic data important for further analyses and clinical applications. Array CGH technique is now used to better understanding of molecular phenotypes, sensitivity to particular chemotherapeutic agents, and prognosis of these diseases. This paper brings brief literature and methodic overview of oligonucleotide-based array-CGH technique in MM diagnosis.
We report an infant with a unique combination of 22q11 deletion syndrome and 14q terminal deletion syndrome. The proband had clinical symptoms compatible with diagnosis of 22q11 deletion syndrome: microcephaly, micrognathia, high-arched palate, hypertelorism, short palpebral fissures, square nasal root, prominent tubular nose, hypoplastic nasal alae, bulbous nasal tip, dysplastic low-set ears, short philtrum, and heart defect, but no cell-mediated immunodeficiency typical for the syndrome. G-banding and fluorescence in situ hybridization analyses revealed a karyotype 45,XY,der(14)t(14;22)(q32.3;q11.2),-22.ish del(14)(q32.33)(D14S1420-),del(22)(q11.2q11.2)(N25-). Subsequent analyses disclosed a translocation between chromosomes 14 and 22 in the proband's mother with a deleted 14q telomere. Using comparative genome hybridization on oligonucleotide-based microarray (array-CGH), the deletion at 22q11.21 in the size of ∼4.25 Mb was revealed in the proband as well as the deletion of the telomeric area at 14q32.33qter (∼3.24 Mb) in the proband and his mother. However, both the proband and his mother showed mild symptoms (microcephaly, thin lips, carp-shaped mouth) typical for patients with the described terminal 14q deletion syndrome.
- Publication type
- Journal Article MeSH
Submicroscopic structural chromosomal aberrations (microduplications and microdeletions) are believed to be common causes of mental retardation. These so-called copy number variations can now be routinely detected using various platforms for array-based comparative genomic hybridization (array-CGH), which allow genome-wide identification of pathogenic genomic imbalances. In this study, oligonucleotide-based array-CGH was used to investigate a panel of 23 patients with mental retardation and developmental delay, dysmorphic features or congenital anomalies. Array-CGH confirmed or revealed 16 chromosomal aberrations in a total of 12 patients. Analysis of parental samples showed that five aberrations had occurred de novo: del(1)(p36.33p36.23), del(4)(p16.3p16.2) joined with dup(8)(p23.3p23.1), del(6)(q14.1q15), del(11)(q13.1q13.4). Three aberrations appeared to be inherited from an unaffected parent: dup(3)(q29), del(6)(q12), dup(16)(p13.11). Six aberrations appeared to be inherited from a parental carrier: del(1)(p36.33) joined with dup(12)(q24.32), del(21)(q22.2q22.3) joined with dup(11)(q24.2q25), del(X)(q22.3) and del(1)(q21.1). In two cases, parents were not available for testing: del(17)(q11.2q12) and del(2)(q24.3q31.1). Our results show that the use of oligonucleotide-based array- CGH in a clinical diagnostic laboratory increases the detection rate of pathogenic submicroscopic chromosomal aberrations in patients with mental retardation and congenital abnormalities, but it also presents challenges for clinical interpretation of the results (i.e., distinguishing between pathogenic and benign variants). Difficulties with analysis notwithstanding, the array-CGH is shown to be a sensitive, fast and reliable method for genome-wide screening of chromosomal aberrations in patients with mental retardation and congenital abnormalities.
- MeSH
- Chromosome Aberrations * MeSH
- Chromosome Deletion MeSH
- Child MeSH
- Gene Dosage MeSH
- Humans MeSH
- Intellectual Disability genetics MeSH
- Adolescent MeSH
- Comparative Genomic Hybridization MeSH
- Check Tag
- Child MeSH
- Humans MeSH
- Adolescent MeSH
- Male MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
Proximal 6q deletions have a milder phenotype than middle and distal 6q deletions. We describe 2 patients with non-overlapping deletions of about 15 and 19 Mb, respectively, which subdivide the proximal 6q region into 2 parts. The aberrations were identified using karyotyping and analysed using mBAND and array CGH. The unaffected mother of the first patient carried a mosaic karyotype with the deletion in all metaphases analysed and a small supernumerary marker formed by the deleted material in about 77% of cells. Her chromosome 6 centromeric signal was split between the deleted chromosome and the marker, suggesting that this deletion arose through the centromere fission mechanism. In this family the location of the proximal breakpoint in the centromere prevented cloning of the deletion junction, but the junction of the more distal deletion in the second patient was cloned and sequenced. This analysis showed that the latter aberration was most likely caused by non-homologous end joining. The second patient also had a remarkably more severe phenotype which could indicate a partial overlap of his deletion with the middle 6q interval. The phenotypes of both patients could be partly correlated with the gene content of their deletions and with phenotypes of other published patients.
- MeSH
- Chromosome Deletion MeSH
- Phenotype MeSH
- Genetic Association Studies * MeSH
- In Situ Hybridization, Fluorescence MeSH
- Karyotype MeSH
- Infant MeSH
- Humans MeSH
- Chromosomes, Human, Pair 6 genetics MeSH
- Child, Preschool MeSH
- Chromosome Banding MeSH
- Comparative Genomic Hybridization MeSH
- Check Tag
- Infant MeSH
- Humans MeSH
- Male MeSH
- Child, Preschool MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Case Reports MeSH
- Research Support, Non-U.S. Gov't MeSH
This report describes the usefulness of the BAC genome array-CGH platform in the detection of cryptic rearrangements. We examined ten patients with normal and/or abnormal karyotypes and dysmorphic features, associated with mental retardation, autism and/or epilepsy. This approach led us to discover further cryptic chromosomal rearrangements, not previously detected by conventional cytogenetic procedures, and allowed us to better delineate genotype/phenotype correlation. Our experience shows the validity of the BAC platform as a reliable method for genome-wide screening of chromosomal aberrations in patient with idiopathic mental retardation and/or in association with autism and epilepsy.
- MeSH
- Autistic Disorder complications genetics MeSH
- Chromosome Aberrations * MeSH
- Child MeSH
- Epilepsy complications genetics MeSH
- Humans MeSH
- Intellectual Disability complications genetics MeSH
- Adolescent MeSH
- Child, Preschool MeSH
- Comparative Genomic Hybridization * MeSH
- Chromosomes, Artificial, Bacterial * MeSH
- Check Tag
- Child MeSH
- Humans MeSH
- Adolescent MeSH
- Male MeSH
- Child, Preschool MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Case Reports MeSH
Characteristic recurrent copy number aberrations (CNAs) play a key role in multiple myeloma (MM) pathogenesis and have important prognostic significance for MM patients. Array-based comparative genomic hybridization (aCGH) provides a powerful tool for genome-wide classification of CNAs and thus should be implemented into MM routine diagnostics. We demonstrate the possibility of effective utilization of oligonucleotide-based aCGH in 91 MM patients. Chromosomal aberrations associated with effect on the prognosis of MM were initially evaluated by I-FISH and were found in 93.4% (85/91). Incidence of hyperdiploidy was 49.5% (45/91); del(13)(q14) was detected in 57.1% (52/91); gain(1)(q21) occurred in 58.2% (53/91); del(17)(p13) was observed in 15.4% (14/91); and t(4;14)(p16;q32) was found in 18.6% (16/86). Genome-wide screening using Agilent 44K aCGH microarrays revealed copy number alterations in 100% (91/91). Most common deletions were found at 13q (58.9%), 1p (39.6%), and 8p (31.1%), whereas gain of whole 1q was the most often duplicated region (50.6%). Furthermore, frequent homozygous deletions of genes playing important role in myeloma biology such as TRAF3, BIRC1/BIRC2, RB1, or CDKN2C were observed. Taken together, we demonstrated the utilization of aCGH technique in clinical diagnostics as powerful tool for identification of unbalanced genomic abnormalities with prognostic significance for MM patients.
- MeSH
- Genome-Wide Association Study * MeSH
- Chromosome Aberrations * MeSH
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Multiple Myeloma diagnosis genetics MeSH
- Neoplasm Proteins genetics MeSH
- Prognosis MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Comparative Genomic Hybridization methods MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Clinical Trial MeSH
- Multicenter Study MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
- Names of Substances
- Neoplasm Proteins MeSH
BACKGROUND: Catastrophic chromosomal event known as chromothripsis was proven to be a significant hallmark of poor prognosis in several cancer diseases. While this phenomenon is very rare in among multiple myeloma (MM) patients, its presence in karyotype is associated with very poor prognosis. CASE PRESENTATION: In our case, we report a 62 year female patient with rapid progression of multiple myeloma (MM) into extramedullary disease and short overall survival (OS = 23 months). I-FISH investigation revealed presence of gain 1q21 and hyperdiploidy (+ 5,+ 9,+ 15) in 82% and 86%, respectively, while IgH rearrangements, del(17)(p13) and del(13)(q14) were evaluated as negative.Whole-genome profiling using array-CGH showed complex genomic changes including hyperdiploidy (+ 3,+ 5,+ 9,+ 11, + 15,+ 19), monosomy X, structural gains (1q21-1q23.1, 1q32-1q44, 16p13.13-16p11.2) and losses (1q23.1-1q32.1; 8p23.3-8p11.21) of genetic material and chromothripsis in chromosome 18 with 6 breakpoint areas. Next-generation sequencing showed a total of 338 variants with 1.8% (6/338) of pathological mutations in NRAS (c.181C > A; p.Gln61Lys) or variants of unknown significance in TP53, CUX1 and POU4F1. CONCLUSIONS: Our findings suggest that presence of chromothripsis should be considered as another important genetic hallmark of poor prognosis in MM patients and utilization of genome-wide screening techniques such as array-CGH and NGS improves the clinical diagnostics of the disease.
- Keywords
- Array-CGH, Chromothripsis, Multiple myeloma, Mutation screening, NGS,
- Publication type
- Journal Article MeSH
- Case Reports MeSH
Identification of chromosomal changes and variation in DNA copy number allows us to understand pathogenesis of tumors. To the frequently diagnosed chromosomal changes belong acquired gains and losses of chromosomal regions carring genes involved in cellular proliferation and differentiation as well as oncogenes and tumor suppressor genes. The determination of gene changes is limited by techniques used for their identification. The introduction of genom-wide microarray technology, resolution has rapidly increased. Array comparative genomic hybridization (arrayCGH) offers higher resolution for genome-wide detection of chromosomal alteration and it is able to analyze hundreds to thousands of genes presented on microarray in one experiment. The aim of this study was to perform arrayCGH technology and to stress its value for the identification of chromosomal imbalances in hematological malignancies.
- MeSH
- Hematologic Neoplasms genetics MeSH
- Nucleic Acid Hybridization * MeSH
- Humans MeSH
- Oligonucleotide Array Sequence Analysis * MeSH
- Check Tag
- Humans MeSH
- Publication type
- English Abstract MeSH
- Journal Article MeSH
- Review MeSH
