Semiquantitative reverse transcription polymerase chain reaction analysis for detection of bcr/abl rearrangement using RNA extracts from bone marrow aspirates compared with glass slide smears after 0, 2 and 4 d of storage

Biobanking in genomic medicine

CONTEXT

Genomic medicine requires the identification of biomarkers and therapeutic targets, which in turn, requires high-quality biospecimens. Achieving high-quality biospecimens requires implementing standard operating procedures to control the variations of preanalytic variables in biobanking. Currently, most biobanks do not control the variations of preanalytic variables when collecting, processing, and storing their biospecimens. However, those variations have been shown to affect the quality of biospecimens and gene expression profiling.

OBJECTIVE

To identify evidence-based preanalytic parameters that can be applied and those parameters that need further study.

DATA SOURCES

We searched the Biospecimen Research and PubMed databases using defined key words. We retrieved and reviewed 212 articles obtained through those searches. We included 58 articles (27%) according to our inclusion and exclusion criteria for this review.

CONCLUSION

-Preanalytic variables in biobanking can degrade the quality of biospecimens and alter gene expression profiling. Variables that require further study include the effect of surgical manipulation; the effect of warm ischemia; the allowable duration of delayed specimen processing; the optimal type, duration, and temperature of preservation and fixation; and the optimal storage duration of formalin-fixed, paraffin embedded specimens in a fit-for-purpose approach.

Identification of the genomic BCR-ABL1 fusion sequence from blood specimen stored on filter paper

Chronic myeloid leukaemia (CML) is characterized by the Philadelphia chromosome resulting in the BCR-ABL1 gene whose mRNA transcript detection is commonly used for diagnosis and monitoring of therapeutic response. However, in collected blood specimen degradation of mRNA has to be considered during storage and transport thus jeopardizing the analysis. We here describe an alternative DNA-based technique applied after long-term blood storage. DNA was isolated from dried blood stains from CML patients stored on filter paper (Guthrie cards) after a median period from diagnosis of 11 years (range: 5-12 years) and analyzed with a two round long-range multiplex PCR (MLR-PCR) to identify the genomic BCR-ABL1 breakpoint. Patient-specific individual BCR-ABL1 fusion sites were successfully detected in 10 out of 13 patients. Dried blood stains represent a valuable resource for genomic DNA analyses. Long term preservation is easily manageable in paper envelopes with the patient's medical files with a minimum of financial costs and efforts. Such the cooperation between laboratories and hospitals separated by long distances is facilitated rendering possible offering specialized genomic analyses to patients with CML virtually everywhere around the world. This technique may also be a valuable approach for diagnostic procedures on a high molecular level in related haematological malignancies.

Quantification of RNA degradation by semi-quantitative duplex and competitive RT-PCR: a possible indicator of the age of bloodstains?

In vitro RNA degradation is a complex and non-linear process which can serve as indicator for the quality and age of stains. We have developed a semi-quantitative duplex reverse transcription-polymerase chain reaction (RT-PCR) assay which, in combination with competitive RT-PCR using an external standard, allows quantification of RNA degradation levels. Using this method, we have investigated 106 bloodstains stored up to 15 years. The distribution of the peak area quotients of standard and target messenger-RNA (mRNA) as measured by laser-induced fluorescence capillary electrophoresis was closely correlated with the age of the samples. Further statistical analysis showed that bloodstains with age differences of 5 years and more exhibit statistical significant variances in peak area quotients of both housekeeping genes included in this study, beta-actin and cyclophilin. This can be of value when evidence from old cases is re-investigated. Our data show, that, although RNA continues to be degraded in dried bloodstains, mRNA suitable for RT-PCR can be isolated from samples stored for at least 15 years.