Intra-sample Heterogeneity Research Articles

Interlaboratory variability in fluorescence in situ hybridization analysis. The NCI Bladder Tumor Marker Network.

Reliable interpretation of fluorescence in situ hybridization (FISH) data, especially data that have been generated in more than one laboratory, requires knowledge of the sources of variability inherent in FISH analysis. Possible sources of variation may derive from differences in sample preparation, probes used, intrasample heterogeneity, hybridization protocols, counting criteria within and between scorers, fluorescence microscopes, and filters. This study characterized the relative weight of some of these factors in order to determine the degree to which FISH results are comparable between laboratories. We used a hierarchical partitioned chi 2 analysis to measure sources of variation. We found that replicate counts varied no more than expected based on counting statistics (i.e., multinomial variation). However, with replicate hybridizations done in two separate laboratories, the variability increased significantly. Thus, care must be taken when interpreting FISH data that are derived from more than one institution. Previously agreed upon counting criteria as well as standardized FISH hybridization protocols may decrease this variability.

Cytogenetic intratumor heterogeneity in soft tissue tumors

Multiple (two to seven) samples, obtained from the same surgical specimen or at different occasions, were analyzed in 54 benign and malignant soft tissue tumors, to investigate cytogenetic clonal evolution. In 28 tumors only normal karyotypes were found. Ten tumors had abnormal karyotypes, but were noninformative, most often due to a high level of karyotypic complexity or great cell-to-cell variation. Sixteen tumors were informative: four (leiomyosarcoma, liposarcoma, malignant Schwannoma, and a benign mesenchymal tumor, probably leiomyoma) had identical karyotypes in different samples, whereas the remaining 12 tumors (seven malignant fibrous histiocytomas [MFH], two leiomyosarcomas, two liposarcomas, and one synovial sarcoma) displayed intersample heterogeneity. Also, intrasample heterogeneity was detected; more than one clone was found in 21 of 73 samples with aberrations from 26 tumors. The different clones were related in all cases except two. In seven cases, samples from different occasions were studied, and clonal evolution could be evidenced in five of them, whereas in two cases the karyotypes remained unchanged. The results indicate that the acquisition of ring chromosomes is an early event in the development of MFH and possibly also pleomorphic liposarcoma. The findings, together with previous data, also indicate that rearrangements of 19p13 are late events in the progression of pleomorphic sarcomas. The overall conclusion from this study is that cytogenetic heterogeneity is common in soft tissue tumors, and that this might influence the evaluation of cytogenetic and molecular genetic findings.

Chromosome aberrations and cytogenetic intratumor heterogeneity in chondrosarcomas

Clonal chromosome aberrations identified after short-term culture are presented for 13 chondrosarcomas; in 5 cases both the primary tumors and local recurrences were studied. The stemline chromosome number was hypodiploid or hyperhaploid in 9 tumors. The most frequent numerical anomalies were, in falling order of frequency, loss of chromosomes Y, 10, 13, and 6, and gain of chromosomes 7 and 20. No recurrent structural rearrangement was found, but chromosome bands 5q13, 1q21, 7p11, and 20q11 were each involved in three different rearrangements. Karyotypic heterogeneity was assessed in two different ways: as the presence of more than one clone in one sample and as the presence of different clones in different samples from the same surgical specimen. Clonal karyotypic evolution was demonstrated in 6 of the 7 cases in which two or more samples could be investigated. All 6 showed intersample heterogeneity. Intrasample heterogeneity was found in only 5 of the 28 samples with aberrations. By comparing the incidences of the nonrandomly occurring aberrations in stemlines and sidelines in the heterogeneous tumors, it was possible to conclude that loss of chromosome 13 and rearrangement of band 5q13 were early events in the clonal evolution.