Trisomy 12 in Epstein-Barr virus-transformed lymphoblastoid cell lines of normal individuals and patients with nonhematologic malignancies

Long-term Culture of EBV-induced Human Lymphoblastoid Cell Lines Reveals Chromosomal Instability

To preserve material for future genetic studies, human B-lymphocytes from whole blood samples are routinely transformed into lymphoblastoid cell lines (LCLs) by in vitro infection with Epstein-Barr virus. To determine the rate and frequency of chromosomal changes during long-term culture, we established 10 LCLs (from eight individuals). Before transformation, these cases showed a normal karyotype (three cases), a small supernumerary marker chromosome (three cases), or an aberrant karyotype (four cases). Chromosome analyses were performed at 8-week intervals over a period of at least 1 year, up to 3 years. Surprisingly, we demonstrate that chromosomal instability is the rule, rather than the exception, during long-term culture of LCLs. The most commonly observed acquired clonal aberration was trisomy 12, which emerged in all cell lines within 21 to 49 weeks after infection. Telomeric fusions indicating telomere shortening were found after ~21 weeks. After 1 year of cultivation, the proportion of cells with the original karyotype decreased to ≤10% in 7 of the 10 cell lines. To preserve cells with aberrant genomes, we conclude the cultivation time of LCLs must be restricted to the absolute minimum time required.

[Management of the CNVs in constitutional human genetics using array CGH]

In term of resolution, array-CGH technologies have shown a major progression these last years. This technological advance has generated an explosion of data describing newly recognized structural variants in the human genome that could be involved in genetic disorders. This review aims: (i) to clear up the terminology related to the field of these structural variations (CNVs); (ii) to determine the application fields of the array-CGH assays; and (iii) to help deciphering genotype-phenotype associations with CNVs which exist and which remain to be realized in the future.

PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data

Comprehensive identification and cataloging of copy number variations (CNVs) is required to provide a complete view of human genetic variation. The resolution of CNV detection in previous experimental designs has been limited to tens or hundreds of kilobases. Here we present PennCNV, a hidden Markov model (HMM) based approach, for kilobase-resolution detection of CNVs from Illumina high-density SNP genotyping data. This algorithm incorporates multiple sources of information, including total signal intensity and allelic intensity ratio at each SNP marker, the distance between neighboring SNPs, the allele frequency of SNPs, and the pedigree information where available. We applied PennCNV to genotyping data generated for 112 HapMap individuals; on average, we detected approximately 27 CNVs for each individual with a median size of approximately 12 kb. Excluding common rearrangements in lymphoblastoid cell lines, the fraction of CNVs in offspring not detected in parents (CNV-NDPs) was 3.3%. Our results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density SNP genotyping.

Challenges and standards in integrating surveys of structural variation

There has been an explosion of data describing newly recognized structural variants in the human genome. In the flurry of reporting, there has been no standard approach to collecting the data, assessing its quality or describing identified features. This risks becoming a rampant problem, in particular with respect to surveys of copy number variation and their application to disease studies. Here, we consider the challenges in characterizing and documenting genomic structural variants. From this, we derive recommendations for standards to be adopted, with the aim of ensuring the accurate presentation of this form of genetic variation to facilitate ongoing research.

Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases

The discovery of copy number variation in healthy individuals is far from complete, and owing to the resolution of detection systems used, the majority of loci reported so far are relatively large ( approximately 65%>10 kb). Applying a two-stage high-resolution array comparative genomic hybridization approach to analyse 50 healthy Caucasian males from northern France, we discovered 2208 copy number variants (CNVs) detected by more than one consecutive probe. These clustered into 1469 CNV regions (CNVRs), of which 721 are thought to be novel. The majority of these are small (median size 4.4 kb) and most have common boundaries, with a coefficient of variation less than 0.1 for 83% of endpoints in those observed in multiple samples. Only 6% of the CNVRs analysed showed evidence of both copy number losses and gains at the same site. A further 6089 variants were detected by single probes: 48% of these were observed in more than one individual. In total, 2570 genes were seen to intersect variants: 1284 in novel loci. Genes involved in differentiation and development were significantly over-represented and approximately half of the genes identified feature in the Online Mendelian Inheritance in Man database. The biological importance of many genes affected, along with the well-conserved nature of the majority of the CNVs, suggests that they could have important implications for phenotype and, thus, be useful for association studies of complex diseases.

Interphase cytogenetics in chronic lymphocytic leukemia

The incidence of trisomy 12 and 13q12-q14 abnormalities in patients with chronic lymphocytic leukemia (CLL) was determined by conventional cytogenetics and interphase fluorescence in situ hybridization (FISH). In the analysis of 580 consecutive patients, trisomy 12 was detected by conventional cytogenetics in 39 cases (9%) and 117 cases (20%) by FISH. Trisomy 12 was shown to be associated with advanced clinical stage, atypical morphology, and higher proliferative activity. Combined immunophenotyping and FISH showed that trisomy 12 was present only in a proportion of the clonal B-cells. These data suggest that trisomy 12 is a secondary event associated with features of disease progression. Sequential FISH showed clonal progression of the trisomic clone over time. Three hundred patients also were investigated for 13q deletions using FISH analysis of the RB1 locus (13q14). Monoallelic RB1 deletion was seen in 104 (34%) of cases. One case had a homozygous deletion in 90% of the cells. Dual-color FISH detected the presence of trisomy 12 and RB1 in 17 (5%) cases. DNA probes for 13q12.3 (BRCA2) and 13q14 (RB1 and DBM locus) were used in 35 cases. Twenty-eight (80%) cases showed deletion of a 1Mb 13q12.3 encompassing the BRCA2 locus, whereas 22/35 (63%) were deleted at 13q14. Our data suggest that abnormalities of 13q are more frequent than trisomy 12 in CLL and provide evidence for the presence of a new candidate gene at 13q12.3 that may be involved in the pathogenesis of CLL.