Cytogenetic studies using frozen blood samples

Cytogenetic analysis of cryopreserved bone marrow cells

We studied the results of culturing and karyotyping of fresh BM and defrosted BM cells from 11 patients with cytogenetic abnormalities with the diagnosis of acute myeloid leukemia (AML). In 8 of 11 patients the cytogenetic results from the fresh and defrosted BM were comparable with respect to the amount and quality of abnormal metaphases. In only one patient one abnormal cell-line (out of two) re-appeared in the frozen BM, probably due to selection, and in three patients we found a distinct decrease of amount and quality. In conclusion, cytogenetic analysis of cryopreserved BM cells can be a reliable alternative to analysis of fresh cells.

Estimation of distances and map construction using radiation hybrids

A method of estimating distances between pairs of genetic markers is described that directly uses their observed joint frequency distribution in a panel of radiation hybrids (RHs). The distance measure is based on the strength of association between marker pairs, which is high for close markers and decays with distance. These distances are then submitted to a previous method that generates linear coordinates for the markers directly from the intermarker distance matrix. This method of map building from RH data is simpler than others, because it uses only the observed joint frequency distributions of markers in the panel, and does not attempt to model unobserved quantities such as the retention of different sized fragments that contain the markers. It also incorporates directly the observed variation in retention of different markers, without needing a model for differential fragment retention dependent on chromosomal location, which is generally not known. Only small, precise distances are used in map construction, thereby reducing any effects of different fragment retention frequencies and local variations in X-ray sensitivity. The method is tested by simulation, and known marker distances and locations are successfully recovered from RH raw data. The method is also applied to publicly available data sets related to the recent transcript map of the human genome.

Hybrid selection as a method of increasing mapping power for radiation hybrids

Radiation hybrids have become a widely used tool for physical mapping. A drawback of the technique is that large numbers of hybrids are required to construct robust, high-resolution maps. The information contained within a panel of radiation hybrids is limited by the frequency of retention of chromosomal fragments from the donor cell line. In almost all experiments to date, the retention frequency has been below the optimal level; therefore, many hybrids are needed to produce high-quality maps. Because of the labor-intensive nature of large-scale mapping projects, it is important to make panels as small as possible. One method that has been adopted is to produce initially a large number of hybrids that are all typed with a few loci. Those hybrids showing satisfactorily high retention are admitted to the final panel and the rest are discarded. In this way, a panel of radiation hybrids with higher than expected retention can be created. Methods for conducting such a selection regime are discussed. To investigate the potential advantages of selecting hybrids based on their retention frequency, simulations were run under a variety of conditions. As expected panels with high retention (40%) provided better mapping resources than panels with lower (20%) retention. Beginning with an initial panel of 200 hybrids, comparisons of a random sample of 100 hybrids and the set of those 100 hybrids showing the highest marker retention demonstrated that selection may not be always the best strategy despite the increase in mean retention it yields. The selection of hybrids containing large numbers of fragments leads to an overestimation of the frequency of radiation-induced breaks. When breaks occur with high frequency (for example, when high radiation doses are used), the selection of hybrids leads to a loss of linkage and hence an inability to order the markers. As such, the merits of screening hybrids depends on both the radiation dose and the desired map resolution.

Cytogenetic analysis of thyroid tumors after cryopreservation

Current cytogenetic evaluation of solid tumors is performed on fresh tissue specimens requiring on-call tissue culture facilities. The application of cryopreservation to tumor samples prior to cytogenetic analysis allows collection of tumors to a desired sample size. We evaluated methods of cryopreservation for their effects on growth potential from 11 benign thyroids and one papillary thyroid cancer. Mitotic indices and thyroglobulin expression applying imunocytology were analyzed. Compared to fresh tumors, the revived tumor samples showed unaltered thyroglobulin expression. A statistically significant (p < 0.004) prolongation to develop mitotic activity occurred in samples received after the freezing of dispase digested tissues, but not in samples frozen as thinly cut pieces. In addition, the data show that cytogenetic analysis at the 400-band level can be achieved in cryopreserved thyroid tissues.

Experimental design and error detection for polyploid radiation hybrid mapping

In this paper we consider issues of experimental design and error detection and correction for polyploid radiation hybrid mapping. Using analytic methods and computer simulation, we first consider the combinations of fragment retention rate, ploidy, and marker spacing that provide the best chance to order markers. We find that in general, combinations of ploidy and chromosome-specific retention rates that lead to a per-hybrid retention rate of approximately 50% result in the greatest power to order markers. We also find that analyzing polyploid radiation hybrids as if they were haploid does not compromise the ability to order markers but does result in less accurate intermarker distance estimates. Second, we examine the effect of typing errors on two-locus information, ability to order multiple loci, and estimation of intermarker distances and total map length. Even low levels of error result in large losses of information about breakage probabilities, markedly reduce ability to order loci, and inflate estimates of intermarker distances and total map length. We compare the ordering accuracy that results from duplicate typing of hybrids to that of single typing twice as many hybrids and find that duplicate typing results in a higher probability of identifying the true order as one of the best orders, but that single typing of twice as many hybrids results in stronger support for the true order. For low error rates, framework maps constructed from the larger single-typed panels are only slightly less likely to be correct and include substantially more markers than the smaller double-typed panels. Third, we develop a method to calculate the distribution of the number of obligate chromosome breaks for a polyploid radiation hybrid under a given locus order and discuss how this method may be used to identify hybrids with suspiciously large numbers of chromosome breaks.