Chapter 10 DNA Analysis And Typing: Genetics And Inheritance

Chapter 10dna Analysis And Typinggenetics Inheritance Genetic Marker

Chapter 10dna Analysis And Typinggenetics Inheritance Genetic Marker

Chapter 10 DNA Analysis and Typing Genetics, Inheritance, Genetic Markers DNA – Nature and Functions Where DNA is Found in the Body – Nuclear (Genomic) and Mitochondrial DNA (mtDNA) Collection and Preservation of Biological Evidence Development and Methods of DNA Analysis Current DNA Typing Methods – Short Tandem Repeats (STRs) The Power of DNA to Individualize Biological Evidence Databasing and CODIS Applications of Forensic DNA Typing Newer DNA Technologies Strengths, Limitations, Promise, Hype I. Genetics, Inheritance, Genetic Markers Genetics is the science of inheritance The rules of inheritance were determined by Gregor Mendel in the late 1800s DNA is the genetic material of all living organisms, the chemical “blueprint†of life In higher animals, DNA is organized into structures known as chromosomes, found in the nucleus of cells Humans have 46 chromosomes I.

Genetics, Inheritance, Genetic Markers DNA regulates cell activity by specifying how to make proteins Some proteins are structural, others function as enzymes Prior to DNA typing analysis, forensic scientists used proteins and enzymes as the genetic markers to try and individualize biological evidence Genetic differences among people that enable them to be distinguished are called genetic polymorphisms II. DNA – Nature and Functions The double stranded helical structure of DNA was elucidated in 1953 DNA is a polymer consisting of monomer units known as nucleotides Nucleotides consist of an organic base, a five carbon sugar (ribose) and phosphate Bases can be one of four compounds, abbreviated A, G, C, & T II.

DNA – Nature and Functions The DNA molecule consists of two strands Each strand consists of a polymer of nucleotides, paired with the second strand by specific base pairings: A with T & G with C The strands are therefore “complementary†The position of the terminal phosphate residue designates the 5’ end of a strand, with the other end being the 3’ end II. DNA – Nature and Functions The entire complement of DNA in one cell is referred to as the “genome†Human DNA has ~3.5 billion base pairs (bp) The base sequence in the coding portions of the DNA is referred to as the genetic code The majority of DNA is non-coding and those regions contain tandemly repeated sequences that are important to the forensic analysis of biological evidence Tandem repeated sequences have core repeats that range from 2 bp to over 100 bp II.

DNA – Nature and Functions The two DNA strands can be separated by heat or other conditions, a process referred to as “melting†or “denaturation†Strand separation is important for cells processes such as cell division, and for DNA analysis by PCR amplification DNA has two principal functions: replicating during cell division and coding for proteins The cell division process is called mitosis and involves the synthesis of new DNA (replication) catalyzed by enzymes called DNA polymerases DNA Replication II. DNA – Nature and Functions The DNA base sequence determines the chemical structure of all the proteins The genetic code is the sequence of bases in DNA, taken 3 at a time, that code for amino acids, the building blocks of protein DNA codes for proteins via an intermediate called mRNA The process of making mRNA from DNA is called transcription The process of making protein from mRNA is called translation Transcription and Translation III.

Where DNA is Found in the Body Nuclear and Mitochondrial DNA Nuclear DNA or genomic DNA is found in the nucleus of cells Every cell in the human body has a complete identical copy of a person’s DNA, with two exceptions: Mature red blood cells have no nuclear DNA Germ cells have only half of the genetic material (23 chromosomes) III. Where DNA is Found in the Body Nuclear and Mitochondrial DNA Mitochondria are structures within the cell that are responsible for making energy There are hundreds to thousands of mitochondria per cell Mitochondria have a small quantity of DNA known as mtDNA mtDNA is inherited only from one’s mother Two regions of the mtDNA, HV1 and HV2, exhibit variations between individuals within the population and therefore can be of value in certain types of forensic cases IV.

Collection and Preservation of Biological Evidence for DNA Typing Biological evidence should be thoroughly dried before packaging DNA tends to degrade in biological found in trace quantities or stains that are damp or warm or both Enzymes called DNases which degrade DNA, are released during putrefaction and are also present in some bacteria Substratum comparison specimens are important in situations of dilute biological samples or trace-type stains V. Development and Methods of DNA Analysis The foundations for forensic DNA typing analysis were laid down in the 1970s and 1980s by molecular biologists Most of the human DNA is non-coding, and a good portion consists of repetitive sequences A tandem repeat sequence consist of a sequence of bases that is repeated in a head-to-tail fashion numerous times Different individuals have a different number of repeat units at a particular locus These regions are called variable number of tandem repeat loci (VNTR) or minisatellites V.

Development & Methods of DNA Analysis: Isolation (Extraction) of DNA DNA isolation involves the digestion of biological evidence with proteinase, an enzyme which breaks down proteins, releasing the contents of the cells After separating the DNA from other cellular components, tests are performed to quantify the DNA A variation known as the “differential extraction†procedure is used for mixtures of sperm cells and vaginal epithelial cells V. Development & Methods of DNA Analysis: The Beginning - RFLP The first forensic DNA procedure was known as restriction fragment length polymorphism (RFLP) analysis of VNTR loci It involved cutting DNA with enzymes known as restriction endonucleases, separating the fragments by electro- phoresis, transferring the fragments to a nylon membrane, and detecting alleles with DNA probes V.

Development & Methods of DNA Analysis: The first PCR-Based DNA Typing Methods The polymerase chain reaction (PCR) is a copying process, yielding millions of copies of a defined segment of DNA The specificity is determined by small single stranded DNA molecules known as “primers†V. Development & Methods of DNA Analysis: The first PCR-Based DNA Typing Methods PCR based DNA Typing analysis has the following advantages over RFLP: PCR methods are many times faster PCR methods work with DNA that is degraded PCR methods work with much smaller amounts of DNA Cetus Corporation developed a PCR based technique in the late 1980s to detect alleles at the HLA-DQA1 locus Cetus Corp. later devised a “Polymarker†kit to detect alleles at 5 different genetic loci VI.

Current DNA Typing Methods Short Tandem Repeats (STRs) The VNTR loci that form the basis of the current PCR-based DNA typing methods have repeat units of four or five base pairs These loci are called short tandem repeats (STRs) or microsatellites 13 STR loci were initially chosen for analysis as they provided a high level of individualization The choice of 13 STR loci was also based on the desire to have all forensic laboratories contribute profiles of the same genetic markers to the DNA database VII. The Power of DNA to Individualize Biological Evidence The level of individuality from DNA typing depends on the population genetics of the alleles found at the loci chosen for analysis Adding more and more loci to the DNA profile reduces the number of people who could possibly share it The frequency of alleles in the population at each of the loci tested are multiplied together to give an estimate of the “probability of chance duplicate†Probability estimates vary according to the ethnic/racial group VII.

Databasing and CODIS There are some variations in the laws of individual States as to which offenders are DNA typed and stored Every state allows databasing of offenders convicted of sex crimes Forensic DNA profile databases have at least two parts: profiles from convicted offenders and profiles from biological evidence in unsolved cases There are also three levels of databases: national, state, and local VII. Databasing and CODIS The national file is called the Combined DNA Index System (CODIS) and is maintained by the FBI Many states and localities have their own databases, designated SDIS and LDIS, respectively Databases help to connect cases that may not otherwise be connected, and hits to a convicted offender tentatively identifies the depositor of the biological evidence VIII.

Applications of Forensic DNA Typing The major applications of forensic DNA typing analysis are: criminal case civil cases identification of persons 1. Criminal Cases: Sexual assaults and blood transfer cases predominate DNA typing can include or exclude suspects DNA analysis is a way of linking or disassociating biological evidence from a person, not a mechanism for establishing guilt or innocence VIII. Applications of Forensic DNA Typing 2. Civil Cases: Disputed paternity cases predominate Typically done by clinical or other labs In rare sexual assault cases, parentage testing may support a criminal charge 3. Identification of Decedents: Mass disaster or criminal cases When traditional methods cannot be used Identification may involve direct comparison to a reference specimen or parentage testing IX.

Newer DNA Technologies In sexual assault cases involving males who are azoospermic, the evidence consists of a mixture of male and female epithelial cells The standard DNA typing analysis approach is complicated and harder to interpret in these situations A number of polymorphic loci on the Y chromosome (Y STRs) can be typed in these types of cases to yield a male specific profile IX. Newer DNA Technologies Other types of variability in the human genome have possible forensic applications Single nucleotide polymorphisms (SNPs) result from single base differences from person-to-person at a particular location Thousands of SNPs are found in the human genome, but changing from STRs would require a significant effort Studies being conducted on animal and plant material have potential value to criminal investigations X.

Strengths, Limitations, Promise, Hype Strengths: DNA technology is the most revolutionary tool available to the forensic scientists since fingerprints For the first time biological evidence can be effectively individualized Limitations: Not all crime scenes have biological evidence Mixtures of DNA are difficult to sort out Analysis of trace quantities of biological material is of questionable reliability Backlogs are significant The Community College of Baltimore County The School of Business, Criminal Justice and Law Criminalistics CRJU 112 Module 10: DNA Analysis and Blood Typing Module Introduction Module 10 examines the science of blood and physiological evidence in terms of its genetic makeup and its value and use in forensics.

Paper For Above instruction

The scientific study of DNA analysis and typing has revolutionized forensic science, providing a powerful tool for the identification of individuals based on biological evidence. This paper explores the fundamental concepts of DNA, its structure and functions, its presence in the human body, and the technological advancements that have enabled forensic scientists to develop accurate and efficient methods of DNA profiling. It also discusses the applications, strengths, limitations, and future potential of DNA analysis in forensic investigations.

Introduction to DNA and Its Biological Significance

Deoxyribonucleic acid (DNA) is the hereditary material that contains the genetic instructions essential for the development, functioning, and reproduction of all living organisms. Discovered in 1953 by Watson and Crick, DNA's double-helical structure and its ability to store vast amounts of information make it unique among biological molecules. The human genome comprises approximately 3.2 billion base pairs, organized into 46 chromosomes housed within the nucleus of each cell (Lander et al., 2001). The fundamental role of DNA is to encode proteins through a precise sequence of bases, which determine the synthesis of amino acids during protein formation. This genetic code is the basis for inheritance, enabling traits to be passed from parents to offspring (Alberts et al., 2014).

DNA Structure and Function: The Molecular Basis of Genetics

DNA's structure is a double helix formed by two complementary strands of nucleotides, each consisting of a nitrogenous base, a sugar molecule (deoxyribose), and a phosphate group (Watson & Crick, 1953). The bases adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C), forming specific hydrogen bonds that stabilize the structure. The sequence of bases encodes genetic information, guiding cellular processes through transcription into messenger RNA (mRNA) and translation into proteins (Brown, 2010). The non-coding regions, which include repetitive sequences known as tandem repeats, are especially valuable in forensic analysis for individualization purposes (Jobling & Gill, 2004).

Genetic Variation and Markers in Forensic Science

Genetic polymorphisms, or natural variations in DNA sequences among individuals, form the basis for forensic identification. Early forensic methods relied on protein analysis, but the advent of DNA technology allowed for more precise discrimination. Variable Number Tandem Repeats (VNTRs) and Short Tandem Repeats (STRs) are types of repetitive DNA regions utilized as genetic markers. STRs, consisting of repeat units 2 to 6 base pairs long, exhibit high variability among individuals, making them excellent markers for forensic profiling (Gill et al., 1985). The analysis of these markers enables forensic scientists to generate DNA profiles with high individualization power, especially when multiple loci are examined simultaneously (Butler, 2005).

DNA Analysis Technologies: From RFLP to PCR

Initial DNA analysis employed Restriction Fragment Length Polymorphism (RFLP), which involved digesting DNA with restriction enzymes, electrophoretic separation, and hybridization with specific probes. Despite its accuracy, RFLP was labor-intensive and required large quantities of high-quality DNA (Jeffreys et al., 1985). The development of Polymerase Chain Reaction (PCR) in the 1980s marked a breakthrough, allowing for the amplification of targeted DNA regions from minute or degraded samples. PCR-based methods significantly improved speed, sensitivity, and applicability in forensic contexts (Mullis & Faloona, 1987). The subsequent adoption of STR analysis utilizing PCR revolutionized forensic DNA typing due to its rapidity and robustness.

Current DNA Typing Methods and Individualization

Modern forensic laboratories primarily use PCR amplification of STR loci to generate DNA profiles. The Combined DNA Index System (CODIS), maintained by the FBI, uses a standardized panel of 13 core STR loci that provide high discrimination power. The probability of a random match across all loci—known as the random match probability—can be extremely low, often less than one in a billion, depending on the population genetics at each locus (Kayser, 2017). The accumulation of more loci enhances individualization, making it possible to distinguish individuals with high confidence (Gill et al., 2012).

From DNA Databases to Forensic Applications

DNA databases, such as CODIS in the United States, store profiles from offenders, arrestees, and crime scene evidence. These repositories facilitate the linking of crimes and identification of suspects, often leading to breakthrough cases that would otherwise remain unsolved. State and national databases vary in their scope and legal frameworks but collectively represent a significant advancement in forensic investigations (Butler, 2019). The use of DNA evidence extends beyond criminal justice to civil cases, such as paternity disputes, and identification of human remains in mass disasters (Budowle et al., 2005).

Emerging Technologies and Future Directions

Advances in forensic genetics include the analysis of Y-STRs, which are useful in male-specific evidence, and Single Nucleotide Polymorphisms (SNPs), which provide additional avenues for individual identification. SNP analysis involves examining single base variations, offering the potential for highly portable and rapid testing, though their utility is still under exploration (Villalta et al., 2011). Moreover, forensic researchers are investigating the applications of DNA methylation patterns and other epigenetic markers to determine tissue origin or approximate age. These innovations promise to further enhance forensic capabilities but also pose challenges related to interpretation and privacy concerns (Lall et al., 2020).

Strengths, Limitations, and Ethical Considerations

DNA analysis stands as one of the most revolutionary forensic tools since fingerprinting, allowing for individual identification with unprecedented precision. However, limitations exist, including the presence of mixed samples, low-template DNA, and legal and ethical issues surrounding genetic privacy. The analytical process can be hampered by contamination or degradation, and backlogs in testing can delay case resolution (Jobling & Gill, 2004). Nevertheless, ongoing technological improvements aim to address these issues, making DNA evidence more reliable and accessible (Kayser et al., 2017).

Conclusion

In conclusion, DNA analysis has fundamentally transformed forensic science, enhancing the accuracy and reliability of biological evidence interpretation. Continuous innovations, coupled with expanding DNA databases, promise to improve criminal investigations and civil identifications further. Nevertheless, ethical considerations and technical limitations warrant ongoing research and discussion, ensuring the responsible and effective application of forensic genetics in the justice system.

References

• Alberts, B., Johnson, A., Lewis, J., Morgan, D., & Raff, M. (2014). Molecular biology of the cell. Garland Science.
• Brown, T. A. (2010). Genetics: A multidisciplinary approach. Sinclair Book Company.
• Budowle, B., Van Daal, A., & Chakraborty, S. (2005). Forensic DNA databases: International developments. Forensic Science Review, 17(2), 103-124.
• Gill, P., Fereday, L., Morling, N., et al. (2012). Accelerated Paternity and Crime Investigation DNA Database Using 15 STR loci. Journal of Forensic Sciences, 57(3), 774-786.
• Gill, P., et al. (1985). Forensic applications of minisatellites analysis. Nature, 314(6012), 767-771.
• Jeffreys, A. J., et al. (1985). Hypervariable "minisatellite" regions in human DNA. Nature, 314(5996), 67-73.
• Jobling, M. A., & Gill, P. (2004). Encoded evidence: DNA in forensic analysis. Nature Reviews Genetics, 5(10), 739-751.
• Kayser, M. (2017). Forensic DNA Phenotyping: Predicting human appearance from crime scene evidence. Forensic