Nuclear DNA Analysis
What platforms and amplification kits are available for STR testing?
Bode offers STR amplification using every commercially available kit on the market for the generation of the core CODIS 13 loci, including both the Hitachi and Applied Biosystems platforms using Promega’s Powerplex® 16 and Powerplex® 16 BIO systems and the Applied Biosystems AmpFlSTR® ProfilerPlus®, COfiler®, Identifiler® and MiniFilerTM PCR amplification kits.
Does Bode offer miniSTR DNA analysis for casework?
How does this differ from standard STR analysis?
Yes, Bode is one of the first laboratories to process casework using miniSTR DNA analysis. MiniSTRs are designed to increase the likelihood of obtaining a full DNA profile from compromised samples. The miniSTR amplification kit targets the largest loci in the STR amplification kit that may not be identified with standard STR. Bode’s validation studies for miniSTRs show a full reportable profile with as little as 62pg of input DNA, compared to 200pg for standard STR.
Can hairs be tested for nuclear STR DNA analysis?
We can examine the hair for STR suitability. The suitability will depend on whether there is a root attached and the stage of growth of the hair. Based on our examination we will make a recommendation for nuclear or mitochondrial testing.
For very small samples, such as a drop of blood, that may have to be consumed during extraction which technology would you recommend?
Once the sample arrives we will do an assessment. We can extract and quant the sample. The quant value will give us an indication of whether miniSTR or standard STR will be necessary.
Could you give me an example of when Y-STR testing would be beneficial?
Y-STR testing would be beneficial in the case of a mixture with a major component female STR profile and a few alleles from a male contributor. A partial to full Y-STR profile would most likely be obtained because the Y-STR primers can focus on the male DNA without the female DNA interfering with the interpretation. Y-STR testing can be useful for samples believed to have originated from azospermic or vasectomized males as well as non-sexual samples such as mixed DNA profiles from touch evidence tested from fingernails, clothing, and guns.
How many sperm cells would be recommended in order to obtain a Y-STR profile from a sample?
1 sperm head contains approximately 3pg (picograms) of DNA. We target 500-1000pg of DNA to produce at least a low level YSTR profile, which is about 160 – 333 sperm cells. Ideally 100+ sperm cells will produce a full YSTR profile.
How should I collect a reference sample from either the victim or suspect to be compared to the evidence items?
Bode offers a reference sample collection kit that is designed with our patented Bode Buccal DNA Collector which easily collects a reference sample from the buccal (cheek) cells of the individual. Please contact our Technical Services Department at (866) 263-3443 x787 for more information, or to order a reference collection kit.
What other items or samples could be submitted for the reference sample if it is not possible to submit a blood or buccal sample?
Ideally anything that the individual’s saliva has come into contact with could be used as a reference sample. We would recommend items such as a discarded cigarette butt, chewing gum, a toothbrush, or soda can.
Are you able to test an envelope in order to identify the individual who mailed it?
Depending on how the envelope was sealed we can test for an individual that may have licked the seal. Generally from paper we would take small cuttings from areas such as the envelope flap and process them for DNA analysis in order to obtain the profile(s).
Is it possible to obtain a DNA profile from an item that an individual has touched or handled?
Bode uses a touch evidence procedure for processing samples from areas where you would expect to find DNA (in the form of skin cells) from a person who has come in contact with the item (for example, the handle of a murder weapon or a pair of pants that have been pulled down). The success of touch DNA depends on the sampling method, the type of material, and the shedding capabilities of the suspect (some people naturally leave behind more skin cells).
Would you suggest testing an item of clothing for touch DNA that has been laundered?
It is highly unlikely that the shed skin cells will remain on an item of clothing that has been laundered.
How does touch DNA processing differ from low copy number (LCN)?
LCN is used on items where only minimal contact has occurred or there are only small quantities of cells/DNA present. Differently from touch DNA processing these samples go through a higher number of PCR cycles which can obtain a DNA profile where conventional PCR would not. LCN work has to be done in special hoods and there is a higher chance of getting mixed profiles. LCN is usually only used on a sample that has already been processed, has an indication of DNA present, but cannot be re-worked any further using standard DNA methods.
Case Scenario: The suspect grabbed onto a sweatshirt that the victim was wearing and the victim was able to wiggle out and get away. The sweatshirt was left behind. Could this be tested for touch DNA?
Yes, it is best to send the entire sweatshirt and either provide a detailed description of where the attacker grabbed it, or mark the area on the clothing. We will take a sample from the clothing using the method that we deem suitable depending on the material type and size of contact area. We can also test for the wearer DNA in order to identify the individual who wore the clothing last. Since the item was not located on the victim, the actual wearer of the clothing may be disputed in court.
Is it possible to obtain a DNA profile from fingerprints?
Bode has had success in obtaining DNA results from fingerprints. These prints have been processed with Ninhydrin, DFO, Cyanoacrylate, and a variety of powders and we have found that they do not inhibit the DNA. The success rate is highly dependent on the number of cells that are associated with the fingerprints.
My agency has a number of samples that are up to 30 years old that have been stored as evidence. These samples have undergone routine heat fixation and have been stained, mounted, affixed with a cover slip and then stored. I understand that it is tricky to get quality DNA from such samples; however is Bode able to process such samples?
Yes, we have a specialized procedure for fixed/mounted slides and can easily remove the coverslip with little damage to the heat fixed cells on the slide. In terms of testing, we have found that the success rate depends on the condition of the slide and the number of cells on the actual slide.
Does Bode offer serology screening for unscreened cases?
Yes, Bode has available a number of methods of screening for the presence of biological fluids such as blood, semen, or saliva.
Case Scenario: I have one swab to submit for testing. I would like to know if semen is present and if so, proceed to DNA analysis. Is it possible to perform both the serology and DNA without consuming the sample?
Yes, this is possible. To conserve the sample we would do the extraction first and then look for spermatozoa in the extracted DNA. This way we are not taking a portion of the swab for serology up-front. If no spermatozoa are found in the extract we can perform our Y-Marker Screen for male DNA. If male DNA is found, the sample can proceed to DNA analysis. In the case of a vasectomized male we would not expect to find spermatozoa however there could be male DNA (i.e. in the form of skin cells) present in the extracted DNA.
Mitochondrial DNA Sequencing
Can a hair sample that does not contain follicular material be tested for mitochondrial DNA?
Yes, mitochondrial testing would be the only DNA testing option provided at Bode for this hair sample.
How long should a hair sample be in order to process it for mtDNA sequencing?
We recommend testing a hair that is at least 2 cm in length.
How are the results reported for 1 evidence item and 1 reference sample that are processed for comparison purposes using mtDNA sequencing?
The report will indicate whether the individual associated with the reference sample is consistent with (or cannot be excluded from) the sequence associated with the evidence item or will be excluded as a contributor to the evidence item.
Which bone would be best to submit for human DNA identification?
We would recommend sending the femur if available. If the femur is not an option, then a molar or the next largest load bearing bone available would be the best options. Bode has been successful with obtaining full DNA profiles from highly compromised bone fragments, including victims from Hurricane Katrina and the attack on the World Trade Center.
Is it possible to obtain DNA from the ashes of an individual that was cremated?
If the cremation temperature was lower than 1500C, teeth may have survived and could be processed for STR or mtDNA analysis.
I would like to submit samples for forensic paternity testing. Would you recommend sending in a sample from the biological mother as well?
Yes, using a 13 loci STR system, with the mother’s sample you will usually see a probability of paternity around 99.999%, while without the mother; you will see a probability of paternity around 99.9%.
How far along should a pregnancy have been in order to test fetal tissue for paternity determination?
We can perform the testing at any point, as long as the fetal tissue can be identified or has been isolated. 8 weeks is about the earliest that the fetus parts can be identified.
I would like to submit a forensic paternity case.I have a sample from the mother, child and the alleged father. How will the results be reported?
The results will include a Combined Paternity Index (CPI). This is reported as the number of times more likely that the alleged father is the biological father of the child rather than an unrelated individual in the population. If the CPI is1 it is suggested that he is the biological father, >100 it is a high probability that he is the biological father, and >1000 it can be considered scientifically proven that he is the biological father.
Does Bode allow visitors to observe laboratory procedures?
Clients may be given a tour of relevant laboratory areas while at the facility; however, clients will not be allowed to observe the testing of any casework or databanking samples.
Can Bode upload profiles to CODIS?
Currently private labs do not have the ability to upload profiles to CODIS however we routinely provide state labs with the relevant data that enables profiles generated at Bode to be uploaded to CODIS.
Where is DNA found?
The sources of biological material containing DNA that are tested at Bode include but are not limited to blood, saliva, semen (sperm cells), other bodily fluids containing white blood cells (i.e. mucus, spinal fluid), skin (epithelial cells), hair, tissue, teeth, and bones.