AFCG Clinical Standards: DNA







Diana Benn, Jeanette Drew, Karen Holdaway, Peter Hobson, Christine Smyth


Mr Peter Dynes, Mr Peter Hobson, Dr Ian Taylor




Laboratory Safety

Specimens for DNA Analysis

Specimen Collection, Storage, and Transport

Specimen Integrity

Specimen Processing

Controls for DNA Investigations

Flow Cytometer Quality Control

Quality Assurance

Sample Analysis

Data Storage

DNA Histogram Interpretation

Data Reporting


Appendix: Examples of DNA histograms from frozen malignant solid tumours


At the 16th Annual Meeting of the Australasian Flow Cytometry Group in Melbourne in July 1993, it was requested that a DNA Subcommittee of the Flow Cytometry Standards Committee be established to produce recommendations which would serve as minimum performance criteria for clinical DNA investigations by flow cytometry.

The following document has been developed through the consensus process and describes minimum performance criteria for performing clinical DNA investigations by flow cytometry. The recommendations are written with a view to being a minimum standard and should not restrict an individual's ability to exceed these standards.

General laboratory operating practices such as confidentiality, laboratory safety, and standard report documentation should be performed in accordance with current prescribed state and national regulations/ recommendations. Therefore the finer details of these issues have not been addressed in this document.


DNA analysis by flow cytometry is a rapidly expanding technology that is moving from the research laboratory into the clinical laboratory. Recent advances in the promotion, availability, and increased usage of this technology have clearly created a need for procedural guidelines and proficiency testing programs.

International attempts have been made to identify the problems associated with quality assurance for DNA analysis by flow cytometry. These resulted in the production of DNA Consensus Documents1­7 which serve as guidelines for laboratories wishing to implement flow cytometric DNA ploidy and cell cycle analysis studies.

This document has been designed to aid scientists in the implementation of comparable practices between laboratories5,8, thereby leading to the establishment of national quality assurance procedures. The DNA Subcommittee recognises that as there are many types of flow cytometers. This document addresses only those issues common to all. Therefore, at this stage, all-encompassing guidelines are beyond the scope of this document.


Universal Precautions

All specimens are to be handled in accordance with the understanding that they may transmit hepatitis virus, human immunodeficiency virus, or other infectious agents. Detailed guidelines for specimen handling (Universal Precautions) are outlined in the Australian Standard Document AS 2243.39.

Many of the DNA staining dyes are known or suspected carcinogens and require appropriate precautions to be taken. Care should be taken against the production of hazardous aerosols by flow cytometers when potentially infectious material is being analysed.

Disinfection of Flow Cytometers

It is suggested that laboratories should disinfect cytometers according to the instrument manufacturer's recommendations. For example, daily or weekly (depending on work volume), flush a 20% solution of sodium hypochlorite (bleach) or ethanol through the fluidics system in place of sheath fluid for approximately 30 minutes. Then, rinse the system in a similar manner with distilled water for an additional 30 minutes. As a further biohazard precaution, add a small amount of sodium hypochlorite into the waste tank to neutralise biohazard particles.


All specimens for DNA content analysis by flow cytometry need to be prepared either as single cell suspensions or as isolated nuclei before running on a flow cytometer. DNA analysis may be performed on peripheral blood, bone marrow aspirates, tissues (fresh or frozen), archival biopsies (formalin­fixed/paraffin­embedded), and cytological specimens (e.g. urine, aspirates, cervical smears)10-12 .

Fresh and unfixed material for cellular DNA analysis is preferable to formalin­fixed/paraffin­embedded material. In most cases high quality single-cell suspensions can be obtained from fresh tissues (solid or fluid), which are considered the optimal tissue sample13.

Fresh/frozen tissue often proves to be more practical for routine clinical flow cytometric DNA analysis because of the difficulty of ensuring adequate handling and storage of fresh specimens from the time of surgical excision or collection. Consideration should be given in deciding whether to freeze all biopsies before analysis as a matter of course because fresh tissue is often required for multi-parametric analysis. Multi­parametric DNA analysis has not been addressed in this document.

Paraffin­embedded biopsies yield only bare nuclei from the disaggregation treatment to produce single nuclear suspensions for flow cytometric DNA analysis14,15. The histograms produced tend to have broader peaks (higher coefficients of variation ­ CVs), and increased cell debris when compared to fresh tissue preparations16. Using paraffin­embedded tissue has some advantages over the analysis of fresh tissues. Obtaining a separate piece of fresh tissue for analysis by flow cytometry is often difficult and may be impossible when:

Whole blood or bone marrow. As phenotyping may be performed in conjunction with DNA analysis in these samples, they require extra care in processing. If cell surface markers are required, refer to the appropriate AFCG document.


The nature of the collection and transport of the specimen will vary depending on the type of specimen. Recommendations for the major specimen types are listed below.

Sample Collection Conditions

Blood and bone marrow aspirates: Samples should not be haemolysed or clotted. ACD, EDTA, or heparin anti­coagulated specimens may be used and kept at room temperature for up to 24 hours and thereafter at 4°C. Analysis of specimens at greater than 3 days from time of collection is not recommended. If the samples are to be frozen for delayed analysis, it is necessary to remove erythrocytes before freezing (e.g. by gradient centrifugation or hypotonic lysis).

Cervical smears: Disperse the specimens into cold, physiological medium for subsequent investigation.

Fine needle aspirates: Collect into cold physiological medium on ice to reduce deterioration of the specimen.

Fresh tissues: Collect into clean container with abundant cold physiological medium kept on ice. Fresh tissue may be frozen in native state immediately after excision, or in tissue culture medium depending on tissue type and size.

Paraffin­embedded (archival) tissues: The effects of many different fixatives and preparation protocols have been widely examined and must be recognised when analysing and interpreting results from such samples. Neutral buffered 10% formalin is the fixative of choice for flow cytometric (FCM) DNA content on paraffin­embedded tissues. Fixation with Bouin's or Zenker fixatives results in poor to uninterpretable DNA histograms.

Pleural aspirates/Lavage fluids: Some samples may require anticoagulation. Store on ice.

Urine/Bladder washes: Store on ice prior to analysis, and process within 24 hours.

Sample Storage Conditions

If fresh specimens cannot be analysed within 24 hours of disruption from the host, process the specimens for freezing.

The recommended freezing options for fresh tissue and cell suspensions are:

Freezing medium (e.g. DMSO) is excellent for preserving cell suspensions17.

Sample Transport Conditions

Blood and bone marrow aspirates: Transport at room temperature.

Other fresh specimens: Transport chilled on ice.

Frozen specimens: Transport on dry ice or in liquid nitrogen.

Paraffin­embedded (archival) tissues: Transport at room temperature.


Blood / Bone marrow: Samples should not be haemolysed or clotted. Analysis of specimens greater than 3 days from time of collection is not recommended.

Cervical smears: Examine specimens for clumping, degeneration, or autolysis by microscopy. Analysis of specimens greater than 24 hours from time of collection is not recommended.

Fine needle aspirates: Examine specimens for clumping, degeneration, or autolysis by microscopy. Analysis of specimens greater than 24 hours from time of collection is not recommended. Fresh cells from needle aspiration biopsies have to be rapidly processed to minimise cell clumping and cell deterioration, and to maximise tumour cell yields.

Fresh/Frozen tissues: Examine specimens macroscopically for suitability for DNA analysis by ascertaining the presence of sufficient representative areas of the tissue/tumour. Avoid necrotic, fibrotic, or fatty tissue components. If no other more suitable area for sampling exists, care should be taken in interpreting histograms derived from such specimens.

Paraffin­embedded tissues: Examine an H&E section of the biopsy microscopically for its suitability for analysis. Avoid areas of necrosis, fibrosis, or inflammation. Focal areas of interest (tumour) may be selectively removed for analysis by scoring with a scalpel, taking punch biopsies of the blocks, or by careful separation of these areas after the sections have been cut.

Pleural aspirates/Lavage fluids: Examine specimens for clumping, degeneration, or autolysis by microscopy. Analysis of specimens greater than 24 hours from time of collection is not recommended due to the high protein content of these fluids.

Urine/Bladder washings: Examine specimens for degeneration or autolysis by microscopy. Analysis of specimens greater than 24 hours from time of collection is not recommended.


For body fluid samples and washings, less than 20% tumour cells may be present and still be adequate for DNA ploidy analysis.

Specific methods for sample handling and preparation for analysis and storage will vary depending on the specimen type, tumour system, and methodology. It would be presumptive for these guidelines to suggest procedures which would encompass all specimens. It is the view of the DNA subcommittee that laboratories performing these analyses communicate with others performing similar studies and keep abreast of literature in their areas of interest18-21.


Fresh/Frozen tissue

DNA diploid reference cells should always be used to identify the position of the DNA diploid G0/G1 peak on the DNA histogram. "The ideal reference cells are diploid cells from the same tissue and the same individual"1, in that both the chromatin structure and the DNA stainability most closely parallel the cells of interest. This is not always practical and the following suggestion provides an alternative.

Purified preparations of normal peripheral blood mononuclear cells (PBMCs), frozen in small aliquots, are an acceptable and practical standard for DNA investigations.

For reliable quantitation of DNA, identical processing is essential for the tumour and the tissue control. The reference cells should be mixed with the sample before staining when used as an internal standard. The sample should also be run without reference cells.

Chicken red blood cells or trout red blood cells may be used for instrument calibration but are not appropriate for calculating the DNA index.

Paraffin­embedded tissue

Paraffin­embedded, normal human tissue (e.g. lymph node, spleen) should be used for inter­run performance assessment of staining.

For each specimen, adjacent non­malignant tissue within the paraffin block is the most suitable DNA diploid reference standard. Where this is not available, non­malignant tissue from another patient may be used. It must have been fixed and paraffin­embedded in an identical manner at the same time as the tumour specimen of interest. Mixing of the DNA diploid standard and the tumour sample should not be performed5.

Freshly prepared PBMCs or non­mammalian nucleated erythrocytes are not suitable as diploid reference standards.


Each laboratory should possess documentation of all its internal quality control procedures.


Following the instrument manufacturer's instructions is highly recommended.

There are a number of commercially available fluorescent microspheres for instrument calibration. The coefficient of variation on such standards should be less than 3.0% or as documented by their manufacturer20.


It is important to establish linearity (or lack of linearity) of the instrument. Departure from linearity can give non­standard G2/G1 ratios, altered DNA indices, and possible difficulty in modelling aggregation. If lack of linearity is established, it can be corrected or at least understood and not misinterpreted. It should be noted that the G2/G1 ratio of normal diploid cells is slightly less than 2.0 due to S phase cells contaminating the G0/G1 and the G2/M peaks.

The instrument manufacturers have guidelines for calibrating linearity of the flow cytometer and methods of calibration have been suggested in the literature22.




Instrument settings during the sample data acquisition (e.g. sample flow rate, voltage, etc.) should not be changed.

It is recommended that the data acquisition rate be less than 200 events per second.


To date, there has been no agreed upon criterion for the number of cells required for generating an adequate DNA histogram. As a rule, 20,000 cells represent the desired quantity; however, ploidy information and in some cases, accurate cell cycle data may be obtained with fewer cells. 5,000 cells are considered the absolute minimum for any interpretation. The object of acquiring larger numbers of cells is to reduce statistical fluctuations in the histogram.


As much information as possible should be gathered on the sample whilst data is being acquired by the cytometer. This may include time as a parameter. Time versus fluorescence gives valuable information about sample flow rates and instrument performance. Exclusion of data seemingly erroneous at the time may be required at a later date. Data above the G2 of the population with highest ploidy may contain valuable information relating to the degree of aggregation and DNA aneuploid hyperdiploid peaks may not be detected if these 'high' channels are discarded or are accumulated in the last 'overflow' channel. As a general rule, observe channels at least 50 percent above the highest G2 peak .


Debris should be included in the events for analysis not ignored. Do not set a higher discriminator or gate to exclude the debris. A high discriminator will result in falsely elevated S­phase estimates and will affect the accuracy of cell cycle analysis. The debris which is observed in channels below the diploid G1 peak is only one feature of this problem. Other debris will be present in channels which underlie S and G2M phase populations.

There is commercially available DNA modelling software containing several sophisticated approaches for assessing the effects of debris on the cell cycle23,24. Where debris accounts for >20% of total cells analysed, DNA modelling software should be used.


The presence of doublets will affect cell cycle analysis and must be excluded by appropriate gating. The manufacturers of the instruments all provide specific protocols for excluding/minimising doublet contamination. However, this minimising may result in the loss of valuable information.




In 1984, the Committee on Nomenclature of the Society of Analytical Cytology published guidelines for a Convention on Nomenclature for DNA Cytometry1. The recommended definitions were reinforced in the 1993 Guidelines for Implementation of Clinical DNA Cytometry5 and are encouraged by this subcommittee for adoption as standard nomenclature.

The terms "DNA diploid" and "DNA aneuploid" should be used, rather than the cytogenetic terminology (hypodiploid, etc.), as no direct measurement of changes in the number or composition of individual chromosomes has been made. The degree of DNA content abnormality is given as the DNA index. By definition a DNA diploid specimen has a DNA index of 1.0.

DNA Diploid

Only one G0/G1 peak is observed. A broad peak described by a large coefficient of variation may obscure a second peak. The coefficient of variation of the G0/G1 peak must be less than 5% for single-cell suspensions prepared from fresh/frozen tissues, and less than 8% for nuclear suspensions prepared from fixed, paraffin­embedded specimens. Where a diploid peak only is observed, one should ensure that tumour cells are present in the clinical sample analysed.

DNA Aneuploid

DNA aneuploidy is reported when at least two separate G0/G1 peaks are demonstrated. For some samples, the diploid/normal peak might be almost nonexistent; hence care should be taken to assign peaks (see Appendix, Histograms 3a and 3b). Descriptive aneuploid terms may be used for further clarification, but not in replacement of "DNA Aneuploid", i.e.:

Histograms are described as DNA Tetraploid when the G2/M fraction exceeds 15%, or at a value determined to be appropriate for a particular organ system. The presence or absence of the corresponding aneuploid G2/M population in the 8N position may be noted. If 6N peaks are noted without a major corresponding 3N peak, this may be an indicator of dumping (i.e. 6N due to triplets).

Cell Cycle Analysis

The presence of excessive debris, clumping of nuclei, multiploid distributions as well as broad peaks (described by large coefficients of variation) can lead to inaccurate S­phase measurements. There are a number of mathematical modelling programs available to analyse cell cycle compartments23,24

See the Appendix for examples of DNA histograms from solid tumours run on different flow cytometers.


In addition to the standard components of the interpretative report usually issued by the laboratory, include the following information:


1. Hiddemann W, Schumann J, Andreeff M et al. Convention on Nomenclature for DNA Cytometry. Cytometry 1984; 5:445­446

2. Bauer KD, Bagwell B, Giaretti W et al. Consensus Review of the Clinical Utility of DNA Cytometry in Colorectal Cancer. Cytometry 1993; 14: 486­491

3. Duque RE, Andreeff M, Braylan RC et al. Consensus Review of the Clinical Utility of DNA Cytometry in Neoplastic Hematopathology. Cytometry 1993; 14: 492­496

4. Hedley DW, Clark GM, Cornelisse CJ et al. Consensus Review of the Clinical Utility of DNA Cytometry in Carcinoma of the Breast. Cytometry 1993; 14: 482­485

5. Shankey TV, Rabinovitch PS, Bagwell B et al. Guidelines for Implementation of Clinical DNA Cytometry. Cytometry 1993; 14:472­477

6. Shankey TV, Kallioniemi O, Koslowski J et al. Consensus Review of the Clinical Utility of DNA Cytometry in Prostate Cancer. Cytometry 1993; 14: 497­500

7. Wheeless LL, Badalament RA, de Vere White RW, et al. Consensus Review of the Clinical Utility of DNA Cytometry in Bladder Cancer. Cytometry 1993; 14: 478­481

8. Bauer KD. Quality Control Issues in DNA Content Flow Cytometry. Annals New York Academy of Sciences 1993; 677:59­77

9. Australian Standards Ass 2243.3, 1991. Safety in Laboratories, Part 3: Microbiology.

10. Coon JS & Weinstein RS (Eds). Diagnostic Flow Cytometry. Techniques in Diagnostic Pathology. 1991. Academy of Pathology. USA.

11. Vielh P. Flow Cytometry Guide to Clinical Aspiration Biopsy . 1991. Igaku­Shoin Ltd, USA

12. Pallavicini MG, Taylor IW, Vindelov LL. Preparation of cell/nuclei suspensions from solid tumours for flow cytometry, in Melamed MR, Lindmo T, Mendelsohn ML eds. Flow Cytometry and Sorting. New York: Wiley-Liss,1990:187-194.

13. Bauer KD, Duque RE & Shankey TV (Eds). Clinical Flow Cytometry: Principles and Applications. 1993. Williams and Wilkins, USA.

14. Darzynkiewicz Z, Robinson JP & Crissman HA. Methods in Cell Biology : Flow Cytometry 1994: Vol 41, Part A (2nd ed.) Academic Press Inc. USA

15. Overton WR & McCoy JP. Reversing the Effect of Formalin on the Binding of Propidium Iodide to DNA. Cytometry 1994; 16 (4) : 351­356

16. Wersto RP, Liblit RL & Koss LG. Flow Cytometric DNA Analysis of Human Solid Tumours: A Review of the Interpretation of DNA Histograms. Human Pathology 1991: 22(11):1085­1098.

17. Foucar K, Chen I, Crago S. Organisation and Operation of a Flow Cytometric Immunophenotyping Laboratory. Seminars in Diagnostic Pathology 1989: 6:13-36

18. Riley RS, Mahin EJ & Ross W. Clinical Applications of Flow Cytometry. Igaku­Shoin, 1993, USA.

19. Robinson JP (Ed). Handbook of Flow Cytometry Methods 1993. Wiley­Liss, Inc., USA

20. Shapiro HM. Practical Flow Cytometry 1995 (3rd edition). Alan R. Liss Inc. USA

21. Givan AL. Flow Cytometry : First Principles 1992. Wiley­Liss Inc. USA

22. Vogt RF Jr, Cross GD, Henderson OL, Phillips. Model System Evaluating Fluorescein Labelled Microbeads as Internal Standards to Calibrate Fluorescence Intensity on Flow Cytometers. Cytometry 1989; 10:294-302.

23. Rabinovitch PS. Multicycle Enhanced DNA Content and Cell Cycle Analysis 1993. University of Washington Phoenix Flow Systems, USA

24. Verity: Mod Fit. Operations Manual. 1988­91. Verity Software House Inc., USA

APPENDIX: Examples of DNA histograms from frozen malignant solid tumours

The following histograms (nos 1 ­ 4) are paired. On the left hand side are the histograms from the tumour single cell suspension and on the right hand side the histograms derived from the tumour single cell suspension to which standard DNA diploid cells (PBMCs) have been added.

1(a) DNA Diploid ­ Breast

1(b) DNA Diploid ­ Breast with added PBMCs.

2(a) DNA Aneuploid (Hyperdiploid) ­ Breast

2(b) DNA Aneuploid (Hyperdiploid) ­ Breast with added PBMCs

3(a) DNA Aneuploid (Tetraploid) ­ Medulloblastoma*

3(b) DNA Aneuploid (Tetraploid) ­ Medulloblastoma with added PBMCs.

* This medulloblastoma specimen was a homogeneous tumour sample, with very few DNA diploid cells.

4(a) DNA Aneuploid (Multiploid) ­ Posterior fossa. The two aberrant sub­populations are calculated separately to produce the two different DIs.

4(b) DNA Aneuploid (Multiploid) ­ Posterior fossa with added PBMCs.

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CD-ROM Vol 3 was produced by Monica M. Shively and other staff at the Purdue University Cytometry Laboratories and distributed free of charge as an educational service to the cytometry community. If you have any comments please direct them to Dr. J. Paul Robinson, Professor & Director, PUCL, Purdue University, West Lafayette, IN 47907. Phone:(765) 494-0757; FAX (765) 494-0517; Web, EMAIL