PCR amplification of specific DNA sequences from routinely fixed chromosomal spreads

Standardization of DNA extraction from methanol acetic acid fixed cytogenetic cells of cattle and buffalo

The aim of the study is to standardize the simple method for extracting DNA from cells fixed in fixative (3:1 ratio of methanol and acetic acid glacial) mostly used for chromosomal studies in cattle and buffaloes. These fixed cells were stored for more than 6 months at refrigerated temperature. The fixed cells were washed 2-3 times by the ice cold 1x Phosphate Buffer Saline (PBS) with pH 7.4, so that effect of fixative may be eliminated. The genomic DNA was extracted by adding cell lysis and nucleus lysis buffers. The quality and quantity of DNA were estimated. The readings of nano drop and agarose gel electrophoresis indicate good quality DNA isolated with a rapid and simple protocol routinely using in our laboratory. The method enables us to study the DNA of a cattle and buffaloes after completing cytogenetic investigation or in cases where DNA samples are otherwise not available. This protocol may be useful for molecular analysis of DNA from fixed cells palettes.

CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens

Background

The analysis of nucleic acids is limited by the availability of archival specimens and the quality and amount of the extracted material. Archived cytogenetic preparations are stored in many laboratories and are a potential source of total genomic DNA for array karyotyping and other applications. Array CGH using DNA from fixed cytogenetic preparations has been described, but it is not known whether it can be used for SNP arrays. Diagnostic bone marrow specimens taken during the assessment of hematological malignancies are also a potential source of DNA, but it is generally assumed that DNA must be extracted, or the specimen frozen, within a day or two of collection, to obtain DNA suitable for further analysis. We have assessed DNA extracted from these materials for both SNP array and array CGH.

Results

We show that both SNP array and array CGH can be performed on genomic DNA extracted from cytogenetic specimens stored in Carnoy's fixative, and from bone marrow which has been stored unfrozen, at 4°C, for at least 36 days. We describe a procedure for extracting a usable concentration of total genomic DNA from cytogenetic suspensions of low cellularity.

Conclusions

The ability to use these archival specimens for DNA-based analysis increases the potential for retrospective genetic analysis of clinical specimens. Fixed cytogenetic preparations and long-term refrigerated bone marrow both provide DNA suitable for array karyotyping, and may be suitable for a wider range of analytical procedures.

Trisomy of human chromosome 18: molecular studies on parental origin and cell stage of nondisjunction

We investigated the parent and cell division of origin of the extra chromosome 18 in 62 aneuploids with a free trisomy 18 by using chromosome-18-specific pericentromeric short-sequence repeats. In 46 cases, DNA of patients was recovered from archival specimens, such as paraffin-embedded tissues and fixed chromosomal spreads. In 56 families, the supernumerary chromosome was maternal in origin; in six families, it was paternal. Among the 56 maternally derived aneuploids, we could exclude a postzygotic mitotic error in 52 cases. Among those in which the nondisjunction was attributable to an error at meiosis, 11 were the result of a meiosis I nondisjunction and 17 were caused by a meiosis II error. This result differs markedly from findings in acrocentric chromosomes where nondisjunction at maternal meiosis I predominates. Among the six paternally derived cases, two originated from a meiotic error, indicating that a nondisjunction in paternal meiosis is not as rare as previously suggested.

Retrospective study of the parental origin of the extra chromosome in trisomy 18 (Edwards syndrome)

The parental origin of the extra chromosome in trisomy 18 was traced in 30 informative families using highly polymorphic (CA) repeats mapped on the long arm of chromosome 18. Proband DNA was recovered from slides of chromosome preparations in 28 cases and from paraffin-embedded tissues in two cases. The extra chromosome was found to be of maternal origin in 26 cases (86.7%), and paternal origin in 4 cases (13.3%).