Editing DNA profiling (section)

==Issues with forensic DNA samples==
When people think of DNA analysis, they often think about television shows like ''[[NCIS (TV series)|NCIS]]'' or ''[[CSI: Crime Scene Investigation|CSI]]'', which portray DNA samples coming into a lab and being instantly analyzed, followed by the pulling up of a picture of the suspect within minutes⁠. However, the reality is quite different, and perfect DNA samples are often not collected from the scene of a crime. Homicide victims are frequently left exposed to harsh conditions before they are found, and objects that are used to commit crimes have often been handled by more than one person. The two most prevalent issues that forensic scientists encounter when analyzing DNA samples are degraded samples and DNA mixtures.<ref>{{cite journal | vauthors = Bieber FR, Buckleton JS, Budowle B, Butler JM, Coble MD | title = Evaluation of forensic DNA mixture evidence: protocol for evaluation, interpretation, and statistical calculations using the combined probability of inclusion | journal = BMC Genetics | volume = 17 | issue = 1 | pages = 125 | date = August 2016 | pmid = 27580588 | pmc = 5007818 | doi = 10.1186/s12863-016-0429-7 | doi-access = free }}</ref>

===Degraded DNA===
Before modern PCR methods existed, it was almost impossible to analyze degraded DNA samples. Methods like restriction fragment length polymorphism (RFLP), which was the first technique used for DNA analysis in forensic science, required high molecular weight DNA in the sample in order to get reliable data. High molecular weight DNA, however, is lacking in degraded samples, as the DNA is too fragmented to carry out RFLP accurately. It was only when polymerase chain reaction techniques were invented that analysis of degraded DNA samples were able to be carried out. Multiplex PCR in particular made it possible to isolate and to amplify the small fragments of DNA that are still left in degraded samples. When multiplex PCR methods are compared to the older methods like RFLP, a vast difference can be seen. Multiplex PCR can theoretically amplify less than 1&nbsp;ng of DNA, but RFLP had to have a least 100&nbsp;ng of DNA in order to carry out an analysis.<ref name="Forensic DNA Typing">{{cite book | vauthors = Butler J |title=Forensic DNA Typing |date=2001 |publisher=Academic Press | chapter = Chapter 7 |pages=99–115}}</ref>

===Low-Template DNA===
Low-template DNA can happen when there is less than 0.1&nbsp;ng(<ref>{{cite book |last1=Butler |first1=John M. |title=Forensic DNA typing : biology, technology, and genetics of STR markers |date=2005 |publisher=Elsevier Academic Press |location=Amsterdam |isbn=978-0-12-147952-7 |pages=68, 167–168 |edition=2nd}}</ref>) of DNA in a sample. This can lead to more stochastic effects (random events) such as allelic dropout or allelic drop-in which can alter the interpretation of a DNA profile. These stochastic effects can lead to the unequal amplification of the 2 alleles that come from a heterozygous individual. It is especially important to take low-template DNA into account when dealing with a mixture of DNA sample. This is because for one (or more) of the contributors in the mixture, they are more likely to have less than the optimal amount of DNA for the PCR reaction to work properly.<ref>{{cite book |last1=Butler |first1=John M. |title=Advanced topics in forensic DNA typing : interpretation |date=2015 |publisher=Academic Press |location=Oxford, England |isbn=978-0-12-405213-0 |pages=159–161}}</ref> Therefore, stochastic thresholds are developed for DNA profile interpretation. The stochastic threshold is the minimum peak height (RFU value), seen in an electropherogram where dropout occurs. If the peak height value is above this threshold, then it is reasonable to assume that allelic dropout has not occurred. For example, if only 1 peak is seen for a particular locus in the electropherogram but its peak height is above the stochastic threshold, then we can reasonably assume that this individual is homozygous and is not missing its heterozygous partner allele that otherwise would have dropped out due to having low-template DNA. Allelic dropout can occur when there is low-template DNA because there is such little DNA to start with that at this locus the contributor to the DNA sample (or mixture) is a true heterozygote but the other allele is not amplified and so it would be lost. Allelic drop-in<ref>{{cite journal |last1=Gittelson |first1=S |last2=Steffen |first2=CR |last3=Coble |first3=MD |title=Low-template DNA: A single DNA analysis or two replicates? |journal=Forensic Science International |date=July 2016 |volume=264 |pages=139–45 |doi=10.1016/j.forsciint.2016.04.012 |pmid=27131143 |pmc=5225751 }}</ref> can also occur when there is low-template DNA because sometimes the stutter peak can be amplified. The stutter is an artifact of PCR. During the PCR reaction, DNA Polymerase will come in and add nucleotides off of the primer, but this whole process is very dynamic, meaning that the DNA Polymerase is constantly binding, popping off and then rebinding. Therefore, sometimes DNA Polymerase will rejoin at the short tandem repeat ahead of it, leading to a short tandem repeat that is 1 repeat less than the template. During PCR, if DNA Polymerase happens to bind to a locus in stutter and starts to amplify it to make lots of copies, then this stutter product will appear randomly in the electropherogram, leading to allelic drop-in.

====MiniSTR analysis====
In instances in which DNA samples are degraded, like if there are intense fires or all that remains are bone fragments, standard STR testing on those samples can be inadequate. When standard STR testing is done on highly degraded samples, the larger STR loci often drop out, and only partial DNA profiles are obtained. Partial DNA profiles can be a powerful tool, but the probability of a random match is larger than if a full profile was obtained. One method that has been developed to analyse degraded DNA samples is to use miniSTR technology. In the new approach, primers are specially designed to bind closer to the STR region.<ref name="Coble 2005">{{cite journal | vauthors = Coble MD, Butler JM | title = Characterization of new miniSTR loci to aid analysis of degraded DNA | journal = Journal of Forensic Sciences | volume = 50 | issue = 1 | pages = 43–53 | date = January 2005 | pmid = 15830996 | doi = 10.1520/JFS2004216 | url = https://strbase.nist.gov/pub_pres/Coble2005miniSTR.pdf | access-date = 24 November 2018 | url-status = live | archive-url = https://web.archive.org/web/20170907224005/http://strbase.nist.gov/pub_pres/Coble2005miniSTR.pdf | archive-date = 7 September 2017}}</ref>

In normal STR testing, the primers bind to longer sequences that contain the STR region within the segment. MiniSTR analysis, however, targets only the STR location, which results in a DNA product that is much smaller.<ref name="Coble 2005"/>

By placing the primers closer to the actual STR regions, there is a higher chance that successful amplification of this region will occur. Successful amplification of those STR regions can now occur, and more complete DNA profiles can be obtained.  The success that smaller PCR products produce a higher success rate with highly degraded samples was first reported in 1995, when miniSTR technology was used to identify victims of the Waco fire.<ref>{{cite journal | vauthors = Whitaker JP, Clayton TM, Urquhart AJ, Millican ES, Downes TJ, Kimpton CP, Gill P | title = Short tandem repeat typing of bodies from a mass disaster: high success rate and characteristic amplification patterns in highly degraded samples | journal = BioTechniques | volume = 18 | issue = 4 | pages = 670–677 | date = April 1995 | pmid = 7598902 }}</ref>

===DNA mixtures===
Mixtures are another common issue faced by forensic scientists when they are analyzing unknown or questionable DNA samples. A mixture is defined as a DNA sample that contains two or more individual contributors.<ref name="Forensic DNA Typing"/> That can often occur when a DNA sample is swabbed from an item that is handled by more than one person or when a sample contains both the victim's and the assailant's DNA. The presence of more than one individual in a DNA sample can make it challenging to detect individual profiles, and interpretation of mixtures should be performed only by highly trained individuals. Mixtures that contain two or three individuals can be interpreted with difficulty. Mixtures that contain four or more individuals are much too convoluted to get individual profiles. One common scenario in which a mixture is often obtained is in the case of sexual assault. A sample may be collected that contains material from the victim, the victim's consensual sexual partners, and the perpetrator(s).<ref>{{cite journal | vauthors = Weir BS, Triggs CM, Starling L, Stowell LI, Walsh KA, Buckleton J | title = Interpreting DNA mixtures | journal = Journal of Forensic Sciences | volume = 42 | issue = 2 | pages = 213–222 | date = March 1997 | pmid = 9068179 | doi = 10.1520/JFS14100J | url = https://projects.nfstc.org/workshops/resources/articles/Interpreting%20DNA%20Mixtures.pdf | access-date = 25 October 2018 | url-status = live | archive-url = https://web.archive.org/web/20200429055409/https://projects.nfstc.org/workshops/resources/articles/Interpreting%20DNA%20Mixtures.pdf | archive-date = 29 April 2020}}</ref>

Mixtures can generally be sorted into three categories: Type A, Type B, and Type C.<ref>{{cite book |last1=Butler |first1=John M. |title=Advanced topics in forensic DNA typing : interpretation |date=2015 |publisher=Academic Press |location=Oxford, England |isbn=978-0-12-405213-0 |page=140}}</ref> Type A mixtures have alleles with similar peak-heights all around, so the contributors cannot be distinguished from each other. Type B mixtures can be deconvoluted by comparing peak-height ratios to determine which alleles were donated together. Type C mixtures cannot be safely interpreted with current technology because the samples were affected by DNA degradation or having too small a quantity of DNA present.

When looking at an electropherogram, it is possible to determine the number of contributors in less complex mixtures based on the number of peaks located in each locus. In comparison to a single source profile, which will only have one or two peaks at each locus, a mixture is when there are three or more peaks at two or more loci.<ref>{{cite book |last1=Butler |first1=John M. |title=Advanced topics in forensic DNA typing : interpretation |date=2015 |publisher=Academic Press |location=Oxford, England |isbn=978-0-12-405213-0 |page=134}}</ref> If there are three peaks at only a single locus, then it is possible to have a single contributor who is tri-allelic at that locus.<ref>{{cite web |title=Tri-Allelic Patterns |url=https://strbase.nist.gov/tri_tab.htm |website=strbase.nist.gov |publisher=National Institute of Standards and Technology |access-date=6 December 2022}}</ref> Two person mixtures will have between two and four peaks at each locus, and three person mixtures will have between three and six peaks at each locus. Mixtures become increasingly difficult to deconvolute as the number of contributors increases.

As detection methods in DNA profiling advance, forensic scientists are seeing more DNA samples that contain mixtures, as even the smallest contributor can now be detected by modern tests. The ease in which forensic scientists have in interpenetrating DNA mixtures largely depends on the ratio of DNA present from each individual, the genotype combinations, and the total amount of DNA amplified.<ref>{{cite book | vauthors = Butler J |title=Forensic DNA Typing |date=2001 |publisher=Academic Press |chapter=Chapter 7 |pages=99–119}}</ref> The DNA ratio is often the most important aspect to look at in determining whether a mixture can be interpreted. For example, if a DNA sample had two contributors, it would be easy to interpret individual profiles if the ratio of DNA contributed by one person was much higher than the second person. When a sample has three or more contributors, it becomes extremely difficult to determine individual profiles. Fortunately, advancements in probabilistic genotyping may make that sort of determination possible in the future. [[Probabilistic genotyping]] uses complex computer software to run through thousands of mathematical computations to produce statistical likelihoods of individual genotypes found in a mixture.<ref>{{cite web |last1=Indiana State Police Laboratory |title=Introduction to STRmix and Likelifood Ratios |url=https://www.in.gov/isp/labs/files/STRmix_and_Likelihood_Ratios_IPAC%20and_Defense_Council_Training_2017.pdf |website=In.gov |access-date=25 October 2018 |archive-date=25 October 2018 |archive-url=https://web.archive.org/web/20181025190514/https://www.in.gov/isp/labs/files/STRmix_and_Likelihood_Ratios_IPAC%20and_Defense_Council_Training_2017.pdf |url-status=live }}</ref>

<big>'''DNA profiling in plant:'''</big>

Plant DNA profiling (fingerprinting) is a method for identifying cultivars that uses molecular marker techniques. This method is gaining attention due to Trade Related Intellectual property rights (TRIPs) and the Convention on Biological Diversity (CBD).<ref>{{Cite web |title=Plant DNA fingerprinting: an overview |url=https://www.researchgate.net/publication/228559903}}</ref>

'''<big>Advantages of Plant DNA profiling:</big>'''

Identification, authentication, specific distinction, detecting adulteration and identifying phytoconstituents are all possible with DNA fingerprinting in medical plants.<ref name="DNA Fingerprinting">{{Cite web |title=Application of DNA Fingerprinting for Plant Identification |url=http://www.jairjp.com/MARCH%202017/02%20SELVAKUMARI%20REVIEW.pdf}}</ref>

DNA based markers are critical for these applications, determining the future of scientific study in pharmacognosy.<ref name="DNA Fingerprinting" />

It also helps with determining the traits (such as seed size and leaf color) are likely to improve the offspring or not.<ref>{{Cite web |title=DNA fingerprinting in Agricultural Genetics Programs |url=https://www.biotech.iastate.edu/publications/biotech_info_series/bio7.html}}</ref>