Editing DNA profiling (section)

==Profiling processes==

===DNA extraction===
{{Main|DNA extraction}}
When a sample such as [[blood]] or [[saliva]] is obtained, the DNA is only a small part of what is present in the sample. Before the DNA can be analyzed, it must be [[DNA extraction|extracted]] from the cells and purified. There are many ways this can be accomplished, but all methods follow the same basic procedure. The cell and nuclear membranes need to be broken up to allow the DNA to be free in solution. Once the DNA is free, it can be separated from all other cellular components. After the DNA has been separated in solution, the remaining cellular debris can then be removed from the solution and discarded, leaving only DNA. The most common methods of DNA extraction include [[phenol–chloroform extraction|organic extraction]] (also called [[phenol–chloroform extraction]]),<ref>{{Cite web |title=Phenol-Chloroform Extraction - an overview {{!}} ScienceDirect Topics |url=https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/phenol-chloroform-extraction |access-date=2023-10-28 |website=www.sciencedirect.com}}</ref> [[Chelex 100|Chelex extraction]], and [[solid-phase extraction]]. [[Differential extraction]] is a modified version of extraction in which DNA from two different types of cells can be separated from each other before being purified from the solution. Each method of extraction works well in the laboratory, but analysts typically select their preferred method based on factors such as the cost, the time involved, the quantity of DNA yielded, and the quality of DNA yielded.<ref>{{cite journal | url=https://journals.sagepub.com/doi/abs/10.1177/10815589251327503 | doi=10.1177/10815589251327503 | title=EXPRESS: Challenging Biological Samples and Strategies for DNA Extraction | date=2025 | last1=Rana | first1=Ajay Kumar | journal=Journal of Investigative Medicine | pmid=40033560 | url-access=subscription }}</ref><ref>{{Cite book|title=Forensic DNA typing: biology, technology, and genetics of STR markers| vauthors=Butler JM |date=2005 |publisher=Elsevier Academic Press|isbn=978-0080470610|edition=2nd|location=Amsterdam|oclc=123448124}}</ref>

===RFLP analysis===
[[File:Restriction Fragment Length Polymorphism.jpg|thumb|upright=1.5|Restriction Fragment Length Polymorphism]]
RFLP stands for restriction fragment length polymorphism and, in terms of DNA analysis, describes a DNA testing method which utilizes restriction [[Restriction enzyme|enzymes]] to "cut" the DNA at short and specific sequences throughout the sample. To start off processing in the laboratory, the sample has to first go through an extraction protocol, which may vary depending on the sample type or laboratory SOPs (Standard Operating Procedures). Once the DNA has been "extracted" from the cells within the sample and separated away from extraneous cellular materials and any nucleases that would degrade the DNA, the sample can then be introduced to the desired restriction enzymes to be cut up into discernable fragments. Following the enzyme digestion, a Southern Blot is performed. [[Southern blot|Southern Blots]] are a size-based separation method that are performed on a gel with either radioactive or chemiluminescent probes. RFLP could be conducted with single-locus or multi-locus probes (probes which target either one location on the DNA or multiple locations on the DNA). Incorporating the multi-locus probes allowed for higher discrimination power for the analysis, however completion of this process could take several days to a week for one sample due to the extreme amount of time required by each step required for visualization of the probes.{{Main|Restriction fragment length polymorphism}}

===Polymerase chain reaction (PCR) analysis===
This technique was developed in 1983 by Kary Mullis. PCR is now a common and important technique used in medical and biological research labs for a variety of applications.<ref>{{Cite journal |last1=Rahman |first1=Md Tahminur |last2=Uddin |first2=Muhammed Salah |last3=Sultana |first3=Razia |last4=Moue |first4=Arumina |last5=Setu |first5=Muntahina |date=2013-02-06 |title=Polymerase Chain Reaction (PCR): A Short Review |url=https://www.banglajol.info/index.php/AKMMCJ/article/view/13682 |journal=Anwer Khan Modern Medical College Journal |language=en |volume=4 |issue=1 |pages=30–36 |doi=10.3329/akmmcj.v4i1.13682 |issn=2304-5701|doi-access=free }}</ref>

PCR, or Polymerase Chain Reaction, is a widely used molecular biology technique to amplify a specific DNA sequence.
[[File:Polymerase chain reaction.svg|thumb|Steps of polymerase chain reaction]]
Amplification is achieved by a series of three steps:

'''1- Denaturation''' : In this step, the DNA is heated to 95 '''°C''' to dissociate the hydrogen bonds between the complementary base pairs of the double-stranded DNA.

'''2-Annealing''' : During this stage the reaction is cooled to 50-65 '''°C''' . This enables the primers to attach to a specific location on the single -stranded template DNA by way of hydrogen bonding.

'''3-Extension''' : A thermostable DNA polymerase which is Taq polymerase is commonly used at this step. This is done at a temperature of 72 '''°C''' . DNA polymerase adds nucleotides in the 5'-3' direction and synthesizes the complementary strand of the DNA template .

{{Main|Polymerase chain reaction}}

===STR analysis===
[[File:Short Tandem Repeat (STR) analysis.png|thumb|300px|Short Tandem Repeat (STR) analysis on a simplified model: First, a DNA sample undergoes [[polymerase chain reaction]] with [[Primer (molecular biology)|primers]] targeting certain STRs (which vary in lengths between individuals and their [[allele]]s). The resultant fragments are separated by size (such as [[electrophoresis]]).<ref>Image by Mikael Häggström, using following source image: [https://www.researchgate.net/figure/Principles-of-STR-analysis-STRs-loci-comprise-repetitive-sequences-of-2-7-bp-which-are_fig1_26513043 Figure 1 - available via license: Creative Commons Attribution 4.0 International"], from the following article:<br>{{cite journal|title=Using PCR for molecular monitoring of post-transplantation chimerism|url=https://www.researchgate.net/publication/26513043|first1=Roberta |last1=Sitnik|first2= Margareth Afonso|last2= Torres|first3= Nydia |last3=Strachman Bacal|first4= João Renato Rebello |last4=Pinho|journal=Einstein (Sao Paulo)|year=2006|volume=4|issue=2|s2cid=204763685}}</ref>]]
{{Main|STR analysis}}
The system of DNA profiling used today is based on [[polymerase chain reaction]] (PCR) and uses simple sequences.<ref name="Tautz2"/>

From country to country, different STR-based DNA-profiling systems are in use. In North America, systems that amplify the [[CODIS]] 20<ref>{{Cite web|url=https://www.fbi.gov/services/laboratory/biometric-analysis/codis|title=Combined DNA Index System (CODIS)|website=Federal Bureau of Investigation|language=en-us|access-date=20 April 2017|archive-date=29 April 2017|archive-url=https://web.archive.org/web/20170429154144/https://www.fbi.gov/services/laboratory/biometric-analysis/codis|url-status=live}}</ref> core loci are almost universal, whereas in the United Kingdom the [[DNA-17]] loci system is in use, and Australia uses 18 core markers.<ref>{{Cite news|url=https://theconversation.com/from-the-crime-scene-to-the-courtroom-the-journey-of-a-dna-sample-82250|title=From the crime scene to the courtroom: the journey of a DNA sample| vauthors = Curtis C, Hereward J |date=29 August 2017|work=The Conversastion|access-date=14 October 2017|archive-date=25 July 2018|archive-url= https://web.archive.org/web/20180725203821/http://theconversation.com/from-the-crime-scene-to-the-courtroom-the-journey-of-a-dna-sample-82250|url-status=live}}</ref>

The true power of [[STR analysis]] is in its statistical power of discrimination. Because the 20 loci that are currently used for discrimination in CODIS are [[independent assortment|independently assorted]] (having a certain number of repeats at one locus does not change the likelihood of having any number of repeats at any other locus), the [[Probability#Independent events|product rule for probabilities]] can be applied. This means that, if someone has the DNA type of ABC, where the three loci were independent, then the probability of that individual having that DNA type is the probability of having type A times the probability of having type B times the probability of having type C. This has resulted in the ability to generate match probabilities of 1 in a quintillion (1x10<sup>18</sup>) or more.{{explain|date=March 2022}} However, DNA database searches showed much more frequent than expected false DNA profile matches.<ref>{{Cite news| vauthors = Felch J |title = FBI resists scrutiny of 'matches'|newspaper = Los Angeles Times|pages = P8|date = 20 July 2008|url = https://www.latimes.com/archives/la-xpm-2008-jul-20-me-dna20-story.html|access-date = 18 March 2010|display-authors = etal|archive-date = 11 August 2011|archive-url = https://web.archive.org/web/20110811135116/http://articles.latimes.com/2008/jul/20/local/me-dna20|url-status = live}}</ref>

===Y-chromosome analysis===
Due to the paternal inheritance, Y-haplotypes provide information about the genetic ancestry of the male population. To investigate this population history, and to provide estimates for haplotype frequencies in criminal casework, the "Y haplotype reference database (YHRD)" has been created in 2000 as an online resource. It currently comprises more than 300,000 minimal (8 locus) haplotypes from world-wide populations.<ref>{{cite web |url=https://yhrd.org |title=Y haplotype reference database |access-date=19 April 2020 |archive-date=23 February 2021 |archive-url=https://web.archive.org/web/20210223175333/https://yhrd.org/ |url-status=live }}</ref>

===Mitochondrial analysis===
{{Main|Mitochondrial DNA}}
mtDNA can be obtained from such material as hair shafts and old bones/teeth.<ref>{{cite journal | vauthors = Ravikumar D, Gurunathan D, Gayathri R, Priya VV, Geetha RV | title = DNA profiling of ''Streptococcus mutans'' in children with and without black tooth stains: A polymerase chain reaction analysis | journal = Dental Research Journal | volume = 15 | issue = 5 | pages = 334–339 | date = 1 January 2018 | pmid = 30233653 | pmc = 6134728 | doi = 10.4103/1735-3327.240472 | doi-access = free }}</ref> Control mechanism based on interaction point with data. This can be determined by tooled placement in sample.<ref>{{cite journal| vauthors = Kashyap VK |date=2004|title=DNA profiling technologies in forensic analysis|url=http://krepublishers.com/02-Journals/IJHG/IJHG-04-0-000-000-2004-Web/IJHG-04-1-001-000-2004-Abst-PDF/IJHG-04-1-011-030-2004-Kashyap/IJHG-04-1-011-030-2004-Kashyap.pdf|journal=International Journal of Human Genetics|volume=4|issue=1|doi=10.31901/24566330.2004/04.01.02|doi-access=free|access-date=6 June 2021|archive-date=6 June 2021|archive-url=https://web.archive.org/web/20210606120729/http://krepublishers.com/02-Journals/IJHG/IJHG-04-0-000-000-2004-Web/IJHG-04-1-001-000-2004-Abst-PDF/IJHG-04-1-011-030-2004-Kashyap/IJHG-04-1-011-030-2004-Kashyap.pdf|url-status=live}}</ref>