Detecting Cancer Tumors

Loss of heterozygosity (LOH) is a method of monitoring genetic deletions common in tumors for many types of cancer. LOH is manifested by severe allelic imbalance at a locus in a single-source DNA sample so that a true heterozygote almost appears as a homozygote since some of the chromosomes have a deletion present in the region of the locus being PCR-amplified. Probably the only time that LOH would have an impact on human identity testing is if an archived clinical specimen from a tissue biopsy...

Dna Typing

DNA testing is to justice what the telescope is for the stars not a lesson in biochemistry, not a display of the wonders of magnifying glass, but a way to see things as they really are. (Barry Scheck and Peter Neufeld, Actual Innocence) In the darkness of the early morning hours of 26 August 1999, a young University of Virginia student awoke to find a gun pointed at her head. The assailant forced her and a male friend spending the night to roll over on their stomachs. Terrorized, they obeyed...

General Match Probability

As noted in this entire section, profile probabilities need to be calculated for a variety of scenarios. Balding (1999) points out that there are five different sets of people and possible relationships to a suspect (1) the suspect's siblings, (2) his other relatives, (3) other members of his sub-population, (4) other members of his racial group, and (5) anyone else outside of his population (e.g., racial) group (see also Foreman and Evett 2001, Weir 2003). Example calculations with NRCII...

Determining The Number Of Contributors To A Mixture

Typically assumptions are made as to the number of contributors possible in a mixture. The vast majority of cases most laboratories face are two-person Mixture profile at the STR locus FGA from a three-person mixture. Genotypes and peak heights in relative fluorescence units are shown underneath each peak. The peak height variation observed can be used to tentatively associate alleles 20 and 22 as coming from the same individual, alleles 18.2 and 23 as coming from the second contributor, and...

Biology Related Artifact Peaks

Stutter products are the most common source of additional peaks in an electro-pherogram of an STR sample. When STR loci are PCR-amplified a minor product peak four bases (n 4) shorter than the corresponding main allele peak is commonly observed (see Chapter 6). Validation studies conducted in a laboratory help define maximum percent stutter for each locus. However, if the target allele peak is off-scale then the stutter product can appear larger than it really is in relationship to the...

Impact Of Stutter Products On Data Interpretation

Stutter products impact interpretation of DNA profiles, especially in cases where two or more individuals may have contributed to the DNA sample (see Chapter 7). CTAT CTAT CTAT CTAT CTAT CTAT (b) Insertion caused by backward slippage CTAT CTAT CTAT CTAT CTAT CTAT (c) Deletion caused by forward slippage

Impact Of Various Population Databases

From the three combined STR profile frequencies calculated in Table 21.2 it is apparent that different populations can yield different frequency estimates due to variations in allele frequencies in these populations. A calculation of the same STR profile as used in the previous examples against 97 different published population databases (including the three present in Appendix II) found that the cumulative profile frequency ranged from 1 in 3.43 X 1014 to 1 in 2.65 X1021 (D.N.A. Box 21.1). The...

Mixture Interpretation

This next section will review the principles described by Gill et al. (1998b) and Clayton et al. (1998) for interpreting mixed forensic stains using STR typing results. Their six primary steps for interpreting mixtures are outlined in Figure 7.4. The interpretation steps will first be discussed and then an example mixture will be reviewed to put these steps into the context of a real sample. An understanding of how non-mixtures behave is essential to being able to proceed with mixture...

Evidence Collection And Preservation

The importance of proper DNA evidence collection cannot be overemphasized. If the DNA sample is contaminated from the start, obtaining unambiguous information becomes a challenge at best and an important investigation can be compromised (see D.N.A. Box 3.2). Samples for collection should be carefully chosen as well to prevent needless redundancy in the evidence for a case. The following suggestions may be helpful during evidence collection to preserve it properly (see page 38). Importance of...

Nonhuman Dna Testing And Microbial Forensics

We urge as rapid development of new systems as is consistent with their validation before they are put into general use. One's ideas must be as broad as Nature if they are to interpret Nature. (Sherlock Holmes, A Study in Scarlet) While the vast majority of forensic DNA typing performed for criminal investigations involves human DNA, it is not the only source of DNA that may be useful in demonstrating the guilt or innocence of an individual suspected of a crime (Sensabaugh and Kaye 1998)....

Kinship And Data Analysis Panel Kadap

The National Institute of Justice (NIJ) organized a panel of experts that convened every other month in the two years following 11 September 2001 to aid in reviewing data and providing guidance and recommendations to NYC OCME regarding statistical thresholds for reporting DNA matches with direct matches and kinship associations. The names and affiliations of the advisory WTC Kinship and Data Analysis Panel (KADAP) are listed in Table 24.2. KADAP gathered in NYC, Albany, Baltimore, and...

An Example Mixture

An example mixture will now be examined to demonstrate how the steps illustrated in Figure 7.4 may be used to interpret a mixture. Figure 7.5 shows a mixed sample that is a combination of male and female DNA, typical of what might be seen in a sexual assault investigation. The STR markers for the mixture are separated into three panels based on their dye label in order to visualize each STR locus more easily. The first thing that is obvious in this example is the presence of more than two peaks...

Dna Separation Methods Slab Gel And Capillary Electrophoresis

It is a capital mistake to theorize before one has data. Insensibly one begins to twist facts to suit theories, instead of theories to suit facts. Sherlock Holmes, A Scandal in Bohemia A polymerase chain reaction PCR reaction in which short tandem repeat STR alleles are amplified produces a mixture of DNA molecules that present a challenging separation problem. A multiplex PCR can produce 20 or more DNA fragments that must be resolved from one another. In addition, single base resolution is...

Abi Prism 3100 Genetic Analyzer 16capillary System

3100 Genetic Analyzer

The multi-capillary ABI PRISM 3100 Genetic Analyzer became available in 2001 and offers a nice solution to higher throughputs with a very similar feel to the single capillary ABI 310 instrument. Both 96-well and 384-well plates of samples may be processed in the ABI 3100. With each run taking roughly 45-60 minutes, a 96-well plate can be analyzed in approximately 5-6 hours with six injections containing 16 samples each. Several features of the ABI 3100 versus the ABI 310 are compared in Table...

Commonly Used Short Tandem Repeat Markers And Commercial Kits

Str Marker Th01

Ever since their discovery in the early 1980s, the ubiquitous occurrence of microsatellites -also referred to as short tandem repeats STRs or simple sequence repeats SSRs -has puzzled geneticists Understanding STRs is important if we wish to understand how genomes are organized and why most genomes are filled with sequences other than genes. Eukaryotic genomes are full of repeated DNA sequences see Ellegren 2004 . These repeated DNA sequences come in all types of sizes and are typically...

Allelic Ladders

Str Markers

An allelic ladder is an artificial mixture of the common alleles present in the human population for a particular STR marker Sajantila et al. 1992 . They are generated with the same primers as tested samples and thus provide a reference DNA size for each allele included in the ladder. Allelic ladders have been shown to be important for accurate genotype determinations Smith 1995 . These allelic ladders serve as a standard like a measuring stick for each STR locus. They are necessary to adjust...

Differential Extraction

Differential Extraction Sperm

Differential extraction is a modified version of the organic extraction method that separates epithelial and sperm cells Figure 3.2 . Differential extraction was first described in 1985 Gill et al. 1985 and is commonly used today by the FBI Laboratory and other forensic crime laboratories to isolate the female and male fractions in sexual assault cases that contain a mixture of male and female DNA. By separating the male fraction away from the victim's DNA profile, it is much easier to...

Desirable Characteristics Of Strs Used In Forensic Dna Typing

For human identification purposes it is important to have DNA markers that exhibit the highest possible variation or a number of less polymorphic markers that can be combined in order to obtain the ability to discriminate between samples. As will be discussed further in Chapter 7, forensic specimens are often challenging to PCR amplify because the DNA in the samples may be severely degraded i.e., broken up into small pieces . Mixtures are prevalent as well in some forensic samples, such as...

Determining The Presence Of A Microvariant Allele

Suspected microvariants can be fairly easily seen in heterozygous samples where one allele lines up with the fragment sizes in the allelic ladder and one does not Figure 6.6 . In the example shown here, the sample contains a peak that lines up with allele 25 from the FGA allelic ladder and a second peak that is labeled Detection of a microvariant allele at the STR locus FGA. The sample in the bottom panel is compared to the allelic ladder shown in the top panel using Genotyper 2.5 software....

Reduced Stutter Product Formation

Th01 Variant

The amount of stutter product formation may be reduced when using STR markers with longer repeat units, STR alleles with imperfect repeat units, and DNA polymerases with faster processivity. Several pentanucleotide repeat loci have been developed in an effort to produce STR markers that exhibit low amounts of stutter products to aid in mixture interpretation Bacher and Schumm 1998 . The first seven loci have been labeled Penta A through Penta G. Penta E has been incorporated in the GenePrint...

The 13 Codis Str Loci

In the United States, utilization of STRs initially lagged behind that of Europe, especially the efforts of the Forensic Science Service in the United Kingdom. However, beginning in 1996, the FBI Laboratory sponsored a community-wide forensic science effort to establish core STR loci for inclusion within the national DNA database known as CODIS Combined DNA Index System . Chapter 18 covers CODIS and DNA databases in more detail. This STR Project beginning in April 1996 and concluding in...

Peaks Outside The Allelic Ladder Range And Threebanded Patterns

Allelic Ladder

Occasionally new rare alleles may fall outside the allele range spanned by the locus allelic ladder. If these peaks fall between two STR loci in a multiplex set, they can be challenging to assign to a particular locus unless testing is performed with individual locus-specific primer sets or a different multiplex. These extreme 'off-ladder' alleles can be confirmed with singleplex amplification of the two loci in the multiplex bracketing the new allele. Alternatively the sample could be...