DNA EVIDENCE IN THE COURTROOM24-Apr-2011 Law Article by: Geoff Harrison | Sydney Criminal Barrister | Sydney Criminal Lawyer | Published 24/04/2011
Deoxyribonucleic acid or DNA evidence can be somewhat confronting for solicitors and barristers let alone members of the jury. DNA evidence in jury trials has also been referred to as the ‘CSI effect’ as all jury members are no doubt familiar with prime time television crime shows - depicting investigators in white lab coats with a blue light. As the following passage demonstrates juries do place a considerable amount of weight upon DNA evidence:
Archival research revealed that juries were 23 times more likely to vote guilty in homicide cases and 33 times more likely to vote guilty in sexual assault cases when DNA evidence was admitted (Briody 2004). Concern has arisen that the safety of these verdicts may be compromised by widespread misconceptions about the infallibility of DNA evidence (Gans & Urbas 2002) by jurors who are ‘overawed by the scientific garb in which the evidence is presented and attach greater weight to it than it is capable of bearing’ (R v Duke 1979 22 SASSR 46 per King CJ: 48) .
In this article I will attempt to simplify what exactly is DNA evidence and the limitations of it. Unfortunately, this will require some biology revision relating to cells. DNA or deoxyribonucleic acid is the building block or template of life – it is responsible for not only replicating itself but also the making of proteins. DNA was first discovered by a Swiss biologist by the name of Friedrich Meischer in 1868 who extracted DNA from puss on a bandage. However, it was not until 1943 when Oswald Avery introduced DNA from the bacterium Streptococcus pneumonia into non-infectious bacteria of the same strand to make it infectious - which demonstrated that DNA was the molecule containing information within the cell.
In 1953 the structure of DNA was discovered by James D. Watson and Francis Crick – the double helix or spiral ladder. DNA was found to comprise of four nucleotides namely, Adenine, Cytonsie, Guanine and Thymine – where Adenine and Thymine always bond together as does cytosine and guanine (or base pairs). DNA is found in the nucleus of every cell (except for red blood cells) where the DNA molecule is packaged into thread-like structures called chromosomes. Each chromosome is made up of DNA tightly coiled many times around proteins called histones that support its structure. A human cell has 23 pairs of chromosomes (one set of the pair from a person’s mother and the other from the father) which consists of 22 linear autosomes and 1 pair of sex chromosome.
A gene is a stretch of DNA on the chromosome that codes for a type of protein that has a function for that organism. The region on the chromosome at which a particular gene is located is called its locus (or loci for plural). For example the amelogenin locus is usually used to determine sex ie. XX or XY. An allele is the form of a gene - given that we inherit one set from our mother and one from our father hence, the allele can be the same (monozygous) or different (heterozygous).
Collection of DNA
Cells/DNA can be deposited upon contact with an item - with some individuals having a greater propensity to shed cells than others; known as shedders. Possible sources to obtain DNA from include:
i. blood – white blood cells
x. Tissue – cells
xi. Vaginal secretions
As noted by Brian Hancock there are different success rates of obtaining DNA sample depending upon the nature of the source. “There are different rates of success of DNA analysis of evidentiary samples, depending on the source. For blood and semen, the approximate success rate is 90%; for saliva: on a cigarette butt, 70%; on a drink bottle, 40%; and on an alcohol bottle, 25%; for hair, 25%; for trace or contact samples: on clothing, 30%; on objects with extended contact (eg: mobile phones), 15%; on objects with limited contact (eg door handles), 10%; and on objects with single contact (eg: smudge), less than10%” .
While the majority of DNA doesn't differ from human to human, some 3 million base pairs of DNA - about 0.10 percent of your genome does vary from person to person. It is obviously the differences in the alleles that is targeted in DNA testing. What is specifically tested for at different loci are Short Tandem Repeats (STR) – which contain repeated nucleotide sequences where these repeated patterns occur differently on the same chromosome among individuals. It is these STR’s that are inspected by forensic scientists for the purpose of human identification. In any DNA test it is the number of repeats for this allele that is recorded for the pair – ie. from the mother and father. For example a base pair may repeat on one allele 15 times from the mother and 8 times from the father hence, the allele designation or profile would be 15, 8. The number of loci that are examined depends upon the test or profile that is used. In Australian forensic laboratories it is generally the Profiler Plus which examines nine different non-coding DNA at different loci as well as on the amelogenin locus to give an indication of sex.
For example, the D3 STR locus is a DNA segment that contains the letters AGAT repeated between 12 and 19 times in different people:
Some people will have 12 repeats of AGAT on one chromosome and have 16 repeats of this sequence on the paired chromosome
Other people may have 14 repeats of the letters AGAT in both copies of this STR locus .
The following figure shows how the results are generated automatically for three of the STR markers: D3, VWA and FGA .
Limitations of DNA
Even upon the finding of a DNA match between the suspect and the offender does not establish that the two are the one and the same. “It establishes no more than that the accused could be the offender” (per Hunt CJ at CL and Hiden J, R v Pantoja (1996) 88 A Crim R 554 (at 560)).
It should also be noted that DNA profiling is still based upon a statistical model. One example of where one person would have exactly the same DNA as another is homozygous twins. Other examples would include where the suspect comes from a genetically isolated population group – hence, a smaller gene pool and an increased probability of similar DNA profiles. Hence, in these cases some adjustment may be required to the probability ratio. One such case was R v Bropho  WADC 182 where in a rape case, a child to the complainant had the same DNA as the accused however, other close relatives were also suspects where there was a small number of loci used – the judge concluded he could not use the DNA evidence as reliable corroboration that the complainant had been raped.
In cases where the validity of the database (such as size of the database) supporting the low probability of the profile being a random match is challenged, it is the racial characteristics of the offender, not of the suspect, which dictates the validity of the database: per Hunt J, R v Pantoja (1996) 88 A Crim R 554 . Further, the judge should warn the jury not to approach the question of guilt strictly on the basis of a mathematical calculation: R v Galli  NSWCCA 405.
One other aspect that is worth mentioning is the Prosecutor’s fallacy – which relates to statistical reasoning. Given that the number of loci used and the statistical probability of the alleles being the same at each loci are multiplied together to give the probability of someone else in the community having the same DNA profile – probabilities can be extremely large even astronomical (such as 1 in 10 billion). Putting aside challenging the statistics based upon a possibly small gene pool - the prosecutor’s fallacy is to consider the unlikelihood of an event occurring in a given population and confusing this with the likelihood of it occurring without reference to the overall population. For example assuming that a suspect has the same DNA profile as the offender and the odds of someone else in the community having the same profile is 1 in 10,000. So either the offender committed the crime or the chances are that 1:10,000 persons have the same DNA. The fallacy would be to state that the probability of the offender being innocent is, 10,000:1. As assuming this crime occurred in a population of 1,000,000 people the odds of the offender being innocent is then actually 100:1.
At the end of the day the probability given of a particular profile merely represents the estimated frequency that a particular DNA profile could occur in a given population.
Forensic Procedure Act
The following is extracted from the Public Defenders site:
The Act operates as a facilitation mechanism for the collection of DNA and other forensic material. A good summary of the Act, particularly the provisions relating to taking samples from children or mentally ill people can be found in a decision of Simpson J - F V v Zeitler  NSWSC 333.
A Magistrate can order that a suspect provide a forensic sample if certain preconditions are met (s 24). There must be reasonable grounds to believe that the suspect has committed a prescribed offence, and there must be reasonable grounds to believe that the procedure might produce evidence tending to confirm or disprove that the suspect has committed the offence. The Magistrate must balance the public interest in obtaining evidence against the public interest in upholding the suspect’s physical integrity, having regard to the following:
(a) the gravity of the alleged offence,
(b) the seriousness of the circumstances in which the offence is alleged to have been committed,
(c) the degree to which the suspect is alleged to have participated in the commission of the offence,
(d) the age, cultural background and physical and mental health of the suspect, to the extent to which they are known,
(e) in the case of a suspect who is a child or an incapable person, the best interests of the child or person,
(f) such other practicable ways of obtaining evidence as to whether or not the suspect committed the alleged offence as are less intrusive,
(g) such reasons as the suspect may have given for refusing to consent to the carrying out of the forensic procedure concerned,
(h) in the case of a suspect who is in custody, the period for which the suspect has been in custody and the reasons for any delay in the making of an application for an order under this section,
(i) such other matters as the Magistrate considers relevant to the balancing of those interests.
The Act also allows police to request a suspect to undergo a forensic procedure. A senior police officer can order that a person under arrest provide a non-intimate sample (ss.17 to 21). The Act provides for the making of interim orders where consent is not given or is unable to be obtained and for final orders to be made by a Magistrate before the sample taken can be analysed.
The Act provides a Code for the taking of samples and other forensic evidence from a person. The Act is said to strike a necessary balance between the appropriate use of available scientific means for investigating suspected crime and the historic rights of citizens against self incrimination. Fawcett v Nimmo & Anor (2005) 156 A Crim R 431 Grove J at  In Orban v Bayliss  NSWSC 428, Justice Simpson pointed out that the Act requires a positive finding that the person to be tested is a “suspect”:
“The conditions that must be met, before an order can be made, demonstrate that the purpose of the legislation is not to enable investigating police (or other authorised persons) to identify a person as a suspect; it is to facilitate the procurement of evidence against a person who already is a suspect”(At ).
Before a sample can be requested there must be reasonable grounds to believe that the procedure will produce evidence that will prove the commission of an offence (s. 11(3)).
Where a Magistrate is asked to make an order or confirm an interim order, although the initial suspicion is that of the police investigator, the statute explicitly requires that the Magistrate be satisfied on the evidence before the Court, not the assertions of the police officer. Fawcett v Nimmo &Anor (2005) 156 A Crim R 431
A Magistrate considering an application under section 24 can take into account hearsay material L v Lyons (2002) 56 NSWLR 600 per Sully J.. The evidence does not have to be in admissible form or even strictly admissible (eg. hearsay is allowed) as long it is properly before the Court Hardy v Pinazza, unreported SCNSW, 18.4.2005, Adams J..
If the matter is reviewed by the Supreme Court (s. 115A) the question to be asked is whether it was open for the Magistrate to find, on the evidence before him or her, that there were reasonable grounds for suspecting Simpson J in Regina v. Rondo  NSW CCA 540 at par 53 summarised the law in relation to reasonable suspicion:
“(a) A reasonable suspicion involved less than a reasonable belief but more than a possibility. There must be some thing which would create in the mind of a reasonable person an apprehension or fear of one of the state of affairs cover by s 357E. A reason to suspect that a factor exists is more than a reason to consider or look into the possibility of its existence.
(b) Reasonable suspicion is not arbitrary. Some factual basis for the suspicion must be shown. A suspicion may be based on hearsay material or materials which may be inadmissible in evidence. The materials must have some probative value.
(c) What is important is the information in the mind of the police officer (undertaking the relevant course of action). Having ascertained that information the question is whether that information afforded reasonable grounds for the suspicion which the police officer formed. In answering that question regard must be had to the source of the information and its content, seen in the light of the whole of these surrounding circumstances.” See also Helen Maguire v Jason Beaton  NSWSC 1241 162 A Crim R 21, per Latham J that the person had committed the prescribed offence, and that the requested material would assist in the proof of that offence.
The Magistrate must articulate the basis on which he or she was satisfied that the plaintiff was a suspect or a challenge will succeed. Maguire v Beaton (2005)162 A Crim R 21, per Latham J Similarly, if the Magistrate fails to articulate the reason why an application was refused a challenge will succeed. Alessi v SE and Anor  NSWSC 909, Barr J
An example can be found in Maguire v Beaton (2005) 162 A Crim R 21, per Latham J. Her Honour set aside the Magistrate’s order for the taking of the plaintiff’s fingerprints and palm prints because there was insufficient evidence to justify making an order pursuant to s. 24:
“Police had arrested Mrs Maguire’s son in possession of suspicious items and found keys relating to a storage unit. During the execution of the search warrant on the unit, guns and drugs were found, so too were documents relating to the lease of the unit with Mrs Maguire’s name on them. Fingerprints implicated the son. Other prints were unidentified. The Magistrate required Mrs Maguire to give her fingerprints and palm prints.
The decision was challenged on the basis that the Magistrate’s determination that Mrs Maguire did not come within the definition of “suspect” for the purposes of s 25(a) of the Act and the Magistrate had not properly determination that there were reasonable grounds to believe that the suspect had committed an offence for the purposes of s 25(c).
Justice Latham held that the Magistrate could not have been satisfied as a matter of law that the plaintiff was a suspect as there was no evidence of anyone resembling her ever having attended storage unit, nor could she be identified from surveillance footage at the premises. Mrs Maguire had no criminal record, she was a woman in her late fifties who had been respectably employed for some time and she exhibited no trappings of unexplained wealth. At best there was a suspicion or mere speculation on the part of police that the plaintiff had leased the unit.
A police officer’s assertion of suspicion in the affidavit grounding the application was not enough nor was a suspicion that the plaintiff may have leased the unit.”
Again, in Hardy v Pinazza, SCNSW unreported, 18.4.2005 The judgment does not appear on the SC computer database., Justice Adams overturned the decision of the Magistrate because there was nothing in his reasons or the evidence that demonstrated he had reasonable grounds for believing the suspect had committed the relevant offence See also Maguire v Beaton,  SCNSWi241 per Latham J..
Another example is the decision of Hall J in Walker v Bugden (2005) 155 A Crim R 416. There his Honour held that before a Magistrate could be satisfied that there were reasonable grounds for believing that a forensic procedure might produce evidence, the factual foundation for that belief had to be established. In short, before a court can order DNA be taken from a suspect, there has to be some evidence there was DNA from the crime scene to which it could be compared.
Care must taken to ensure that the strict procedural requirements of the Act are followed and complied with. The Act is not a carte blanche to facilitate the placing of everyone’s DNA on a database. However, as long as there is evidence to support the conclusions reached and orders made and they are made in terms of the Act, a challenge to a Magistrate’s order will not succeed Jawasansher v Johnson LCM  NSWSC 872, per Barr J. F V v Zeitler  NSWSC 333. per Simpson J..
It is harder again to challenge interim orders. The provisions relating to interim orders do not have the safeguards that can be found in s.24 (final orders). Interim orders are intended to preserve evidence that may otherwise be lost and are by their very nature emergency measures where time is of the essence. No order (including analysis) may be made unless the requirements of s 24 are met and a final order applying all the safeguards is made. See JW v Detective Sergeant Karol Blackley & Anor (2007) 172 A Crim R 483, Simpson J
Generally, if there is some flaw in the process, this should be raised to argue against the admissibility of the evidence at trial: see s 82 and s 138 of the Evidence Act 1995. Obtaining a order to restrain testing is unlikely to succeed. Kerr v Commissioner of Police  NSWSC 637 per Studdert J and JW v Detective Sergeant Karol Blackley & Anor (2007) 172 A Crim R 483.
The Act cannot be used to compel a person to provide a sample or undergo a procedure, which is not authorised, e.g. a urine sample. Alessi v SE and Anor  NSWSC 909, Barr J
The Act can be abused. As a consequence it contains some protections. These are designed:
“To maintain a delicate balance between preserving the traditional rights of citizens and individuals, including those suspected of crimes, to decline to participate in investigations or to cooperate with investigating authorities, and the overall interests of the community and of justice in facilitating the investigation of crime and the administration of justice, in securing the conviction of the guilty and the non-prosecution or acquittal of the not guilty. The Act was a specific response to scientific and technological developments but in the context of valued traditional civil liberties.” Orban v Bayliss  NSWSC 428 Simpson J at .
The following judgement by His Honour Justice Mullighan of the South Australian Supreme Court is impressive in a number of respects and explains in detail how DNA is extracted, compared and analysed. The case itself related to a murder where two blood stains were located on the inside of the victim’s blouse. However, what is extracted relates to the extraction of DNA and the comparison of DNA samples.
R v KARGER No. SCCRM-98-224  SASC 64 (29 March 2001)
29 In early 1998 another system for DNA analysis was introduced into the relevant laboratory of Forensic Science Centre. It is known as the Profiler Plus system. All of the samples were tested for DNA using this system but no result was obtained with respect to KO22B, probably because all of the DNA had been extracted and used when the Quadruplex analysis was undertaken. The Quadruplex system inspects DNA at four loci and the Profiler Plus at ten loci, one of which is the same as a locus profiled by the Quadruplex system, known as vWA. The Profiler Plus inspects the amelogenin locus which indicates the gender of the donor of the sample, and eight other and different loci. As will be seen, a locus is a place or region on the DNA strand and loci is the plural of locus.
44 The first major development in DNA technology since the acceptance and use of PCR technology was the Short Tandem Repeat (STR) method of DNA analysis which was developed over the last ten years or so. It is now widely used around the world.
45 Before mentioning STR technology, it is appropriate to briefly describe the processes of extraction, quantification and amplification of DNA which are common to all current systems, including those employing silver staining which is a method of inspection used before fluorescence technology and which I shall later briefly describe.
46 DNA must be extracted from the relevant sample which may be a reference sample or a crime scene sample. There are differences in the process depending upon the nature of the sample, for example blood, urine, saliva or semen. In the present case the Forensic Science Centre was concerned with what were accepted as probably blood stains, some tissue and blood reference samples. The method of extraction used was the Chelex method which is widely used and accepted by forensic scientists. An extract from the sample is placed in a known volume of chelex with the result that DNA is extracted from that part of the sample. This procedure is undertaken in near sterile conditions using a biological safety cabinet and gloves and gowns which are, or should be, free of contamination. Dedicated sterile instruments are used. At the Forensic Science Centre the process occurs in one of three rooms designated for that purpose and the extracted DNA is kept in a sealed container in a refrigerator in a secure environment until required. Protocols and procedures are in place to avoid contamination. At the extraction stage, a control sample known as a reagent blank is also prepared. It is comprised of the reagents used in the extraction process but contains no DNA. It is run through the various stages of the analysis procedure so that it may be seen if the reagents are contaminated.
47 The next stage in the process is to attempt to quantify the amount of DNA which has been extracted, although not all laboratories undertake this step. It is desirable to know the quantity of DNA in the extract because there is an optimal level of DNA required for the amplification process, which is the next stage, so that the sample of amplified DNA submitted for analysis is not overloaded or saturated. If too much DNA is added, there is what is known as over-amplification or distortion which prevents or complicates interpretation at the analysis stage. If very low levels of DNA are amplified, a phenomenon known as "stochastic effect" occurs which may result in not all alleles being seen. Stochastic means random and is discussed later. The aim at the quantification stage is to provide an estimate of how much DNA is in the extract so that the amount of DNA added to the reaction mix at the next stage can be regulated. The systems used by the Forensic Science Centre in the present case are the QuantiBlot and ACES systems which are accepted and widely used by forensic scientists.
48 At the Forensic Science Centre quantification is undertaken in the main laboratory. A small amount of the extraction solution containing the DNA, about five microlitres, is taken and placed in a separate tube.
49 The DNA sample is placed on a membrane to which is added a probe labelled with, in the QuantiBlot system, a chemiluminescence detection system. The amount of chemiluminescence is proportional to the amount of DNA in the sample and is detected by an x-ray film. Control samples are run at the same time with known amounts of DNA as points of reference. The ACES system operates in much the same manner but a radioactive probe is used instead of chemiluminescence. The ACES system is regarded by some scientists as not as precise in measuring the quantity of DNA as the QuantiBlot system in that it tends to underestimate the amount of DNA in the sample.
50 Neither system is accurate. They are not particularly sensitive. Both tests can show no DNA to be present when it is present and a full profile may be obtained on analysis as occurred in the present case when using the Quadruplex to analyse the sample KO22B in 1998. I accept the evidence of Mr Pearman that the main purpose of quantification is to ensure that too much DNA is not amplified.
51 The next stage in the process is the amplification stage where extracted DNA is loaded into the reagents for the PCR. The sample is then loaded into a thermal cycler and heated and cooled at various stages using specified temperatures. This stage of the process occupies about two to three hours. This process mimics the copying process in the human body. A part of the extracted DNA duplicates, which is repeated time and time again until millions of copies have been made. Consequently there is usually ample DNA for analysis and profiling even when there was initially a low quantity of DNA in the sample. The copies are artificial but nevertheless accurate copies. The amplification process is also widely accepted and used by the forensic science community.
52 I now mention STR and fluorescence technology.
53 STR regions on the DNA in a chromosome are described as polymorphic DNA loci. They contain repeated nucleotide sequences. Nucleotides are base pairs and arrange themselves along the DNA molecule. The bases, A G T and C, only behave in a certain way in that A always pairs with T and G with C and at these types of loci they have identical repeat patterns along each strand of DNA. These repeat patterns occur differently on the same chromosome among individuals. They are particularly discriminating and are inspected by forensic scientists for the purpose of human identification. There are other regions of DNA which, by chemical reaction, dictate the characteristics of the human body and are consequently of interest to medical scientists. They tend not to differ much from person to person and are of little interest to forensic scientists.
54 STR loci consist of simple tandemly repeated sequences of one to six base pairs in length which may exhibit a high degree of length polymorphism due to variation in the number of repeat units displayed. They occur frequently throughout the DNA in the chromosome and have smaller repeat units than other regions of DNA. Because of their abundance, polymorphic nature and ease of amplification, they provide a source of highly imperative loci for use in human identification. The smaller size enables the PCR to amplify very small amounts of DNA for analysis. Because they are relatively short in size, up to about 350 to 400 base pairs, they are less susceptible to degradation than larger pieces of DNA. I accept that the "abundance, hypervariability and amenability" of STR loci to amplification by PCR "make them ideal markers for use in the identification of individuals".
55 The repeat sequence at one locus may be, for example, AATT and may be repeated four times, in which case it would be known as a four repeat unit. A sequence may be repeated five times and be known as a five repeat unit or there may be some other sequence. It is the repeat pattern which determines the length of the DNA fragment at a particular locus. One individual may have three tandem repeats at a particular locus inherited from one parent and eight tandem repeats inherited from the other parent or some other combination. These lengths of DNA are known as alleles and in this example are measured according to length, determined by the number of repeats. The allelic designations, or profile, at this locus would be 3 8. If the numbers of tandem repeats at each locus were eight and seven, the profile would be 8 7. In these two examples the alleles are of different length or size and the person is known as a heterozygote at that locus. Where the alleles are the same size, the person is known as a homozygote at that locus, and the profile would be a single digit, say 10.
56 Because the alleles are of different lengths, there is a technique to separate each of them, known as electrophoresis, which is mentioned shortly. Each locus is given a different name which identifies the particular chromosome and the precise location on that chromosome which is being described. An example is the D3S1358 locus. "D3" refers to the chromosome. "S1358" refers to the location on that chromosome. This designation and its significance are known to forensic scientists. A purpose of identifying the loci is so that anyone inspecting a particular locus is aware of the particular location on the chromosome which is being inspected.
57 Initially the inspection of STR loci was undertaken by what is described as the silver staining process. DNA is negatively charged. The amplified DNA is loaded onto a gel and the alleles are excited by an electric current through the electrophoresis process and move through the gel according to their size. The smaller pieces move faster than the larger pieces and are dispersed along the lane in the gel accordingly. An allelic ladder is loaded into the gel which is a sample containing the known alleles at the particular loci being inspected. Through the silver staining process, which need not be discussed in any detail because it is not relevant to any issue in the present case, the alleles appear as bands adjacent to the corresponding allelic size in the ladder and can be seen with the naked eye. That technology has been commonly used throughout the world. This system permits only one locus to be inspected at a time but various samples may be analysed simultaneously in the same gel.
58 The next development in DNA technology relevant for present purposes is fluorescence technology. At the PCR or amplification stage specially designed primers with fluorescent tags attach to the alleles or DNA fragments. They remain with the DNA in the gel and during the process of electrophoresis. Instruments have been developed to undertake the electrophoresis and detection processes. They are known as sequencers and enable the detection of alleles by the use of a laser which agitates the fluorescence in the primers which is captured by a camera and transmitted and recorded by a computer. The first of these sequencers is known as an AB1 373 DNA sequencer ("the 373"). Subsequent models are the AB1 Prism 373A sequencer ("the 373A"), AB1 Prism 310 sequencer ("the 310") and the AB1 Prism 377 sequencer ("the 377"). There are differences in the technology and process between the 310 and the others which need not be discussed as the 310 played no part in the DNA analyses in the present case. These sequencers were developed and manufactured by Perkin Elmer, a corporation in the United States of America, which has been prominent in the development of modern DNA technology. Other sequencers were developed by other manufacturers but they have no relevance to any issues in the present case.
59 The principle of electrophoresis in this technology is the same as with the silver staining process. As the electricity is applied, the fragments of DNA or alleles have moved according to their size. As has been mentioned, the fluorescent dye attached to the primer has become part of the amplified DNA so that there is a fluorescent tag attached to every piece of DNA. The primers are specific as to location. They bind to a particular locus of the DNA in accordance with their design and the dye attached to the primers is detected during the analysis process. The position of the allele is compared to an allelic ladder which is comprised of known alleles. The size of alleles is determined. The consequence is the designation of a profile at a particular locus.
60 Computer software was developed to assist in the interpretation of the data collected through the sequencers. Initially this software was known as genescan and later seems to have developed that name as a brand name, "Genescan", and I shall refer to it accordingly.
61 The Genescan analysis software converts the data obtained through the fluorescence process. It tracks each sample so as to ensure that the computer has analysed the correct portion of the sample in the particular lane. It produces a table of results and also shows them in a graphical format, called an electropherogram, showing peaks rising from the base line in the colours of the system which I mention later when discussing multiplex technology. The table of results includes the colour of the peak, the time of the run, the height and area of the peak, and also the Relative Fluorescent Unit ("RFU") value. Usually the greater the degree of fluorescence, the higher the peak on the electropherogram shown as an RFU. With Genescan it is at this stage of the process that the analysts interpret the results. Later, mention is made of artefacts and other issues which can arise in the interpretation of the results and the need for expertise of the scientist at the analysis stage. At this stage, it is sufficient to say that the analyst interprets the Genescan results and may manipulate the software so as to assist in that function.
62 When the laser excites the dye in the primer attached to the amplified DNA, the emitted light passes through a type of prism which separates out the light according to its wave length so that each specific wave length falls upon a designated portion of the detection camera. Usually a light wave, although basically of one of the particular colours, say blue, encompasses other light waves which spill over into another dye, say green. Whilst the majority of the light falls on its designated portion of the detection camera, and is detected as an allele, the portion of light which falls into another colour is picked up by other portions of the detection camera. The computer software will recognise that other portion of light and it may be represented in the data as a small peak in another colour. There is software in the system known as matrix which is established and adjusted when the system is installed and which is designed to take into account that portion of light which falls on to other parts of the detector. It effectively subtracts them from the collection software. However, there will be times when the matrix does not subtract all of that type of light and it will be shown as a small peak on another line on the electropherogram of the Genescan known as "pull up" which is mentioned later.
63 The next significant development in DNA technology for forensic scientists was the use of multiplex systems. Before this time, the DNA at each selected locus was amplified and inspected individually. Multiplex technology initially permitted amplification and analysis of more than one locus at a time using the techniques of electrophoresis and fluorescence and the collection software. Multiplex systems were developed to inspect different STR loci. Early such technology was known as a triplex which inspected the loci D21S11, FGA and the amelogenin gender locus. Another triplex system inspected the loci D3S1358, D21S11 and FGA.
64 Kits were produced by Perkin Elmer for these triplexes. They had different colours of dye being blue or green and were respectively known as the Blue Kit or the Green Kit each inspecting different loci.
65 These multiplex systems were further developed over the years by Perkin Elmer and, one of its competitors, Promega Corporation in the United States of America and the Forensic Science Service in the United Kingdom. The Forensic Science Service developed a quadruplex system in the early 1990's and Perkin Elmer developed the Quadruplex system which was used in tests in the present case. These systems were widely used by forensic scientists in the United States of America and the Forensic Science Service. They permitted the inspection of four loci in each DNA sample simultaneously known as THO1 and FES using blue dye in the primers and vWA and F13 using green dye.
Advantages of Fluorescence Technology
66 I accept the evidence of Mr Pearman that there are advantages in using fluorescence technology. It is described as a semi-quantitative technique which means that it is powerful in the interpretation of mixtures which occur when different people contribute DNA to the same stain or sample. The process removes some of the subjectivity of the scientist when looking at weak bands and deciding whether to designate such bands to be alleles. An internal sizing standard is used which offers a considerable level of precision. The process is able to correctly designate alleles at a locus which only vary by one base pair. The system removes the need for manual transcription of results and possible human error in cases involving contemporaneous testing of many samples.
360 When discussing evidence of Dr Davis, I mentioned the Forensic Science Centre establishing the Profiler Plus Caucasian database. The samples were used because it was accepted that the donors were of the Caucasian race either because of their names or because they had said so. This is known as the "self declaration method".
361 The size of this database varied a little from locus to locus ranging from 778 alleles at the D7 locus to 824 alleles at the D8 locus which variation is not unexpected. The method used was to include a homozygote at a locus as two alleles. As has been mentioned, this database was forwarded to Dr Weir and Dr Buckleton in about the middle of 1999 for opinions as to validity. Other Australian databases were also sent to them from time to time for the same purpose. They noticed an anomaly with respect to one profile which was, in fact, not part of a sample but of an allelic ladder. Also a mistyping at one locus of a sample from a member of staff was detected. It should have been a heterozygote but was typed as a homozygote. It was decided to re-appraise the whole database.
362 At the time this database was established, the reporting guidelines of the Forensic Science Centre for the Profiler Plus system had not been established. It will be remembered that these guidelines required a level of 100 RFU for homozygotes and 75 RFU for heterozygotes. Some alleles were weak and would not have been included in the database if the guidelines had been in place. Initially the reading level of 50 RFU used for the Quadruplex system was used. These samples were re-analysed and the results read using the guidelines and, where necessary, changes were made. The corrected database was sent to Dr Weir and Dr Buckleton for their consideration.
363 This database was reviewed in April 2000. Three profiles were removed because it was ascertained that the persons concerned were not Caucasian. Two other profiles were also removed because they had been mistyped. By this time the Profiler Plus had been in use for some time and 40 additional profiles were added.
364 Following a further report from Dr Weir and Dr Buckleton, there was another review of the database. Allelic designations were changed for 19 loci out of a total of 3269. With additions, this database was comprised of profiles from 414 persons. The changes to allelic designations occurred because errors were detected in the reading of results shown in electropherograms upon analysis of the samples.
365 It is this final database which the Crown sought to use at the trial.
366 The prosecution also proposed to use the national Quadruplex database. The National Institute of Forensic Science ("NIFS") decided in 1993 to establish a national database for use by all Australian forensic science laboratories. Samples from Red Cross donors were typed using the Quadruplex system by laboratories in Queensland, New South Wales and Victoria and the results were collated by NIFS and presented at a workshop in July 1998. The Queensland and New South Wales laboratories profiled all of the four loci with the samples they inspected but the Victorian laboratory only profiled the THO1 locus. This database was relatively small with 314 samples at THO1 and 223 samples at the other three loci.
367 I accepted the evidence of Mr Pearman and Dr Buckleton that both of the databases were of sufficient size to be used in the calculations which were made and which the Crown sought to prove.
588 Before mentioning the particular matters in issue, it is necessary to say a little more about the controls used in DNA testing. At the extraction stage, a reagent blank control is prepared. It is comprised of reagents used in the extraction procedure and so it is the same as the sample except that it does not contain any part of the DNA in the sample. At the PCR stage a positive control is prepared using the same reagents employed in that stage together with DNA of known profile. It is used in this stage in the same way as the extracted sample. A negative control is also used at the PCR stage. It is comprised of the same reagents but with distilled matter instead of the DNA in the positive control or in the extracted samples. The reagent blank is also passed through the PCR stage. The three controls are run with the sample to be tested through the analysis stage. If any of them do not produce the expected result, then the scientists know that something is amiss. The reagent blank and the negative control should not show the presence of DNA and the positive control should show the known profile.
Population Genetics and Statistics
617 I now turn to the challenge to the evidence which the Crown proposed to lead as to the weight to be given to the match between the DNA profile of the accused and of the stain KO22C on the blouse assuming that the jury found such a match and that the stain was left by the person who murdered Mrs Ostendorf.
618 It is recognised in the cases that once a jury concludes that there is a match between the DNA profiles of a sample at the crime scene and the accused, the case proceeds to the statistical evaluation stage provided there is an adequate evidential basis: see Jarrett, Pantoja. This is because a match does not establish that the accused left the crime scene sample. As the Court of Criminal Appeal observed in R v Doheny and Adams  1 CrAppR 369 at p373:
"As the art of [DNA] analysis progresses ... the stage may be reached when a match will be so comprehensive that it will be possible to construct a DNA profile that is unique and which proves the guilt of the defendant without any other evidence. So far as we are aware that stage has not yet been reached."
See also Pantoja and the cases therein referred to and, in particular, R v Green (NSW CCA, File No 60308 of 1991, 26th March 1993, unreported). As was said in Green, the evidence of a match, if accepted, means that the accused cannot be excluded and therefore it was "possible" that he was the person responsible for the items.
619 The following passage of the judgment of Abadee J in Pantoja expresses what then happens at p578:
"Once the match is declared the expert must make a decision as to the significance of the match by calculating the match probability. Essentially this involves assessing the probability of the match having occurred by chance. Because it is possible for a match to occur by coincidence a decision must be taken as to the significance of the match and this is typically done. The second stage is the final phase in the DNA profiling process. It involves the utilization of population genetics to estimate the probability that a person picked randomly from the population would have a DNA profile identical to the DNA profile generated from the forensic sample. The frequency with which a particular DNA pattern will occur in a given population is predicted by determining the frequency with which that patter occurs in database samples. Some commentators suggest that it is the probability favouring a random match that provides the telling and convincing evidence in the DNA testing exercise."
620 The Crown proposed to lead evidence from Mr Pearman and Dr Buckleton about this subject matter. For the evidence to be admissible, a number of matters must be proved with the onus resting upon the Crown. The databases used in the exercise must be shown to be valid. It is asserted by the Defence that they must be accurate and also have statistical validity. The method of calculating the match probability must be valid and accord with principles of population genetics. The expert making the calculation must be shown to have sufficient expertise to do so and must have undertaken the task correctly. The first and second of these matters were challenged by the Defence. There was no challenge to the expertise of Mr Pearman or Dr Buckleton.
Grounds of the Challenge
621 As the voir dire hearing progressed the particulars of the challenge to admissibility of this evidence were refined as follows:
"1 The accused challenges the validity of the database (D15(c)) and the National Caucasian (Quadruplex) database on the following grounds:
1.1 The racial/ethnic affiliation of the perpetrator being unknown, databases for each of the racial/ethnic groups represented in the relevant population must be used in order to derive the highest probability of seeing the profile.
1.2 An appropriate Fst/Theta factor for each of the relevant racial/ethnic groups must be calculated and applied. The proposed value for Fst/Theta (to adjust for dependence between alleles) is inapplicable.
1.3 Independence between loci in the sub-population of interest (comprising the perpetrator) must be established, but cannot be.
1.4 Independence between loci cannot be assumed as between the loci comprised in the national Caucasian Quad database and the loci comprised in the South Australian Caucasian Profiler Plus database - such as to justify multiplication of frequencies derived from those respective databases.
2 The accused challenges the use of the 'likelihood ratio' (LR) as an admissible method of representing the significance of the alleged profile match.
2.1 The LR is not a frequency, but the ratio of two conditional probabilities which functions as the multiplier in Bayes' Theorem to derive posterior odds from prior odds, and has no other relevant use.
2.2 The use of Bayes' Theorem by the jury is not permitted: the jury cannot make any mathematical estimate of the prior odds.
2.3 The use of conditional probabilities in deriving a LR without taking account of laboratory error rates is incomplete and misleading.
3 Alternatively, the evidence of opinion as to the LR should be excluded in the exercise of the court's discretion because its prejudicial effects outweigh any probative value."
622 The reference to the database is the South Australian Profiler Plus database established and used by the Forensic Science Centre when the DNA analyses have been undertaken using the Profiler Plus system.
623 Before turning to the issues raised in this part of the case, I mention the witnesses who gave evidence about them.
624 The Crown called Mr Pearman and Dr Buckleton. I have mentioned the qualifications, training and experience of Mr Pearman. In the course of his extensive experience in casework, he has made many calculations based upon accepted principles of the science of population genetics in order to give weight to the significance of a match of DNA profiles. He has undertaken reading and study of those principles. He has attended meetings and seminars at which they have been explained and discussed, including by Professor Weir, an acknowledged expert in this field of world renown, and Dr Buckleton. I was satisfied that Mr Pearman was sufficiently qualified to give expert evidence on this subject matter.
625 Dr Buckleton is a forensic scientist with a specialist interest in evidence interpretation. He was awarded a Master of Science Degree with first class honours and a Doctorate of Philosophy in chemistry by the University of Auckland in New Zealand. He has been working as a forensic scientist for about 16 years and is currently employed at the Mount Albert Science Centre of ESR in New Zealand which is accredited by ASCLD.
626 During three different periods, in 1988, 1993 and 1995 he worked at the Forensic Science Service in the United Kingdom in the Evidence Interpretation Research Unit, the head of which is Dr Ian Evett whose writings on DNA analysis and interpretation of profiles have been published widely in peer-reviewed journals. Whilst at the Forensic Science Service, Dr Buckleton specialised in the area of evidence interpretation including the interpretation of DNA profiles and was involved in a training and research programme in that country. He has since collaborated with Dr Evett in the field of evidence interpretation. He was involved in a training programme at the Forensic Science Centre in 1999.
627 In 1995 he worked with Professor Weir at the North Carolina State University. Professor Weir is a statistical geneticist and his writings in that field have also been published widely in peer-reviewed journals. Dr Buckleton has worked with him for some time in each year since 1995.
628 Dr Buckleton has published over 50 papers in peer reviewed journals and has lectured extensively in the United Kingdom, the United States of America, Australia and New Zealand in evidence interpretation. He has given evidence in courts in New Zealand and the United States of America and has undertaken extensive analysis of databases in the USA, UK and New Zealand and some such analysis in Australia.
629 This specialised area of expertise of evidence interpretation relating to DNA has been acknowledged and accepted by the courts. Once it has been established that there is in existence a reliable and valid database of DNA profiles, this type of expert may express an opinion as to the frequency with which the DNA profile matching the crime scene samples is likely to be found in the population at large. There has been much debate about how such an opinion should be expressed and the bases upon which it should formed, but there is no doubt that a suitably qualified expert can express the relevant opinion.
630 I have no doubt that Dr Buckleton, by reason of his training and experience, is suitably qualified as an expert to express a relevant opinion about that subject matter.
631 Also, the Crown proposed at the trial to lead evidence from Dr Buckleton as to the statistical validity of the Australian National Caucasian Quadruplex database and of the South Australian Profiler Plus database established in 1999 and amended in May 2000 and June 2000.
632 It is not only the size of the databases which is significant in order to establish statistical validity (see Pantoja) but also the manner in which they have been compiled, their statistical validity regardless of size and an acceptable method for statistical calculation in order to form the opinion. There are different views within the relevant scientific community about some of these matters, but there can be no doubt this subject matter forms part of a body of knowledge which is sufficiently organised and recognised to be accepted as a reliable body of knowledge: see Bonython at p47. Furthermore, the evidence clearly establishes that Dr Buckleton is well qualified on this subject matter, as is Mr Pearman.
633 Before turning to the principal issues raised by the challenge to this evidence, I mention the two witnesses called by the Defence, Dr Atchison and Dr Mitchell. I have referred to the qualifications, training and experience of Dr Atchison. I concluded that he was qualified to the subject matters relating to these issues and that he could give expert evidence about them.
634 Dr Mitchell is a population geneticist.
635 He was awarded a Bachelor of Geography degree with honours by the University of Durham in 1968 during the course of which he studied demography, human populations and statistics. He undertook a post-graduate degree in anthropology at the same University which included study of genetic aspects of race, human evolution, demography and population genetics which was described as the distribution of genes in populations and the causes of that distribution. He was awarded a Doctorate of Philosophy in 1974 by the same University. The subject of his thesis was population genetics. His post-graduate work has also involved the study of statistics. Dr Mitchell then took a position as post-doctoral fellow at the University of Newcastle in the United Kingdom for a period of two years. He came to Australia in 1974 and took a position of post-doctoral fellow at La Trobe University in the Department of Genetics and Human Variation. In 1975 Dr Mitchell became a lecturer at that University in mainly human genetics and biological anthropology. He has remained at the University and is now a senior lecturer working in the same fields. His work includes population genetics, DNA and human evolution.
636 His particular field of interest is human population genetics in which he has since worked extensively. It is unnecessary for present purposes to set out in any detail his subsequent fields of study and areas of work, as I accepted him as an expert in human population genetics and regarded him as qualified to express opinions about matters in issue.
637 He has undertaken studies of population groups in England and in Australia using inherited genetics markers of protein and blood groups and compiling databases for the populations under study. With the development of DNA technology, he changed from using those types of markers to the use of specific STR loci using PCR and silver staining technology. He is familiar with appropriate statistical tests for the validity of databases which he uses.
638 In his research and studies, Dr Mitchell has looked at inbreeding in that sense and calculated Fst values for the population groups he was studying.
639 This very brief description of his qualifications, training and experience does not do justice to his life's work in this specialised field, but it is adequate for present purposes. I found Dr Mitchell to be a truthful witness who was attempting to assist the Court. He was qualified to the relevant subject matters. I regarded him as an expert and I had regard to his opinions.
640 Once again, a substantial body of evidence was led in support of the challenge to the evidence proposed to be led by the Crown but it is not necessary to do more than briefly summarise the issues and the evidence led in support of the various contentions.
641 Forensic scientists tend to divide the population into three main varied groups - Caucasian, Asian and sub-Sahara African, as well as Indigenous in particular countries. In Australia the groups are Caucasian, Asian and Aboriginal. The evidence discloses that the Caucasian and Asian populations have sub-populations. For example, Italian and Scottish people are sub-populations of the Caucasian race. Thai, Vietnamese and Chinese people are sub-populations of the Asian race.
642 Mr Pearman reported that the chance of finding the profile of the accused in another person in the population is one in a million. In fact, his calculation is quite different, but it was the policy of the Forensic Science Centre to report in those terms even when the result of the calculation is one in a very much greater figure.
643 Having developed databases, the frequency of the presence of each allele at each locus in each database was calculated in percentage terms. Those frequencies were used in the calculations.
644 I accepted the evidence of Mr Pearman and Dr Buckleton that there are two acceptable methods. The first is what is known as the product rule and the second is known as a match probability or, as it is often called, Equation 4.10, because it is included in that paragraph of the report of the NRC Report II. The product rule method requires that relevant states of independence, or equilibrium, exist in the databases. There must be independence between alleles at each locus, which is known as Hardy Weinberg equilibrium and there must be independence between each locus and the other loci, which is known as linkage equilibrium.
645 One of the purposes of sending the databases to Professor Weir and Dr Buckleton was to see if those states of independence existed. After applying appropriate tests, which need not be described, they concluded that because of the limited power of the tests, they could not exclude that there may be mild disequilibrium between alleles at each locus and between loci. They suggested that the match probability or Equation 4.10 method be used which does not, in the opinion of Dr Buckleton, require either of these states of independence to exist. He said that the tests used, when applied to databases of a few hundred individuals, do not have sufficient power to show that the underlying population is not in Hardy-Weinberg equilibrium or is sub-structured or is admixed. He expressed the opinion that the history of human populations of forensic importance shows that they have been subject to admixture and are sub-structured.
646 I accepted the evidence of Dr Buckleton that forensic scientists use either the product rule or the match probability, or Equation 4.10, approach and the latter is used extensively in the British Isles, and in laboratories in the United States of America, New Zealand and some laboratories in Australia. The Equation 4.10 method is accepted by forensic scientists. It is the most conservative of the other methods of calculation available. Both Mr Pearman and Dr Mitchell accepted that the Equation 4.10 was an accepted approach.
647 The Forensic Science Centre used Equation 4.10 in the present case with an Fst value of three per cent and a confidence limit of 95 per cent. Using software, this match probability was one in 90.558 billion.
648 Fst is the measure of co-ancestry or relatedness of alleles and reflects the probability that alleles within a population have a common ancestor. It is necessary to know the level of that ancestral relationship between people. Population geneticists undertake that task by using an Fst value. Scientists have estimated this level of relatedness among Caucasians as less than one per cent. The use of three per cent is conservative. Dr Buckleton explained that an Fst value of three per cent is based upon the premise that all Caucasians are related to the level of second cousins, which is obviously factually incorrect and therefore conservative. According to Dr Buckleton, this percentage value easily accommodates for any degree of relatedness within the Caucasian community.
649 The confidence level of 95 per cent was explained by Mr Pearman and Dr Buckleton in this way. If 200 persons are profiled and allele frequencies are determined on that basis and the process is again undertaken with 200 different persons, slightly different values would be obtained for the allele frequencies simply because different people within the same population are being sampled. That sampling variation is taken into account by use of a confidence level which defines, with some certainty, that the true value lies between a common value and a rare value. This means that it is certain that 95 per cent of the time the true allele frequency will fall between the upper limit and the lower limit. In the present case the upper confidence limit was one in 90 billion and the lower confidence limit was one in 272 billion and so the figure adopted is the conservative and lower figure.
650 Mr Pearman presented this figure as a likelihood ratio which, he said, means that the probability or likelihood of seeing a second unrelated person with the same DNA profile is more rare than 1 in 90 billion which, in the present context, means that the crime scene stain KO22C is greater than 90 billion times more likely to match the profile of the accused if he left it, than if it was left by an unknown and unrelated person. Dr Buckleton put it this way. He said that it is about 90 billion times more likely if the accused donated the stain KO22C, than if it was donated by a random person.
651 Both Mr Pearman and Dr Buckleton said that the two databases were acceptable and valid for this purpose and that it was acceptable to combine the THO1, FES and F13 loci of the Quadruplex loci with the seven Profiler Plus loci at which the accused showed a profile. Both of these witnesses also said that the selection of a Caucasian database was appropriate as the accused is Caucasian and that the racial group where it is most likely to see a second profile, the same as the accused, is in the same racial group. Therefore, to use the race of a suspect is the more conservative database to use.
652 Also, both Mr Pearman and Dr Buckleton expressed the opinion that the frequency of alleles in both databases could be used in the calculation using Equation 4.10. Their evidence was that the creation of racial databases is accepted and is the usual practice by forensic scientists and is preferable to the creation of general databases.
 Brian Hancock, Barrister - http://www.lawlink.nsw.gov.au/lawlink/pdo/ll_pdo.nsf/pages/PDO_dnaevidenceconsidered