1. General DNA Background:
DNA Polymorphism (“many forms”: Regions of DNA which differ from person to person.
Locus (plural = loci) (Also referred to as a ”marker”: Site or location on a chromosome.
Allele: Variations which can exist at a locus.
DNA Profile: The combination of alleles for an individual.
CODIS: Combined DNA Index System.
CODIS uses two indexes to generate investigative leads in crimes for which biological evidence is recovered from a crime scene. The convicted offender index contains DNA profiles of individuals convicted of certain crimes ranging from certain misdemeanors to sexual assault and murder. Each State has different "qualifying offenses" for which persons convicted of them must submit a biological sample for inclusion in the DNA database.
The forensic index contains DNA profiles obtained from crime scene evidence, such as semen, saliva, or blood. CODIS uses computer software to automatically search across these indexes for a potential match. 10 of 13 loci must yield identifiable results for a forensic profile to be included in CODIS.
CODIS core loci: Thirteen STR sequences that have been selected for the Combined DNA Index System.
Partial profile: DNA evidence that does not yield identifiable results in all 13 core loci.
Amplification or PCR (Polymerase Chain Reaction): A technique for ‘replicating’ DNA in the laboratory (‘molecular Xeroxing’ Standard amplification is 28 cycles which produces nearly a billion copies. Ideal DNA test sample range is 0.5 – 2.0 nanograms.
Electrophoresis: A technique for separating molecules according to their size.
Electropherogram: A graph of results from an analysis done by electrophoresis.
STR: Short tandem repeat Describes a type of DNA polymorphism in which: a DNA sequence repeats over and over again and has a short (usually 4 base pair) repeat unit.
Testing introduced in ~1999
6 repeats: AATG AATG AATG AATG AATG AATG
5 repeats: AATG AATG AATG AATG AATG
4 repeats: AATG AATG AATG AATG etc.
Y-STR: Short Tandem Repeats found on the male-specific Y chromosome. Testing introduced in ~2002.Performing Y-STR testing can help to identify all males who have contributed to a sample.
Mini-STR: In cases where DNA evidence is limited, either in quantity or quality, such as highly degraded samples that are exposed to environmental insults or inhibitors, standard STR testing is often inadequate. Mini-STR primers “zoom in” on the STR locus so that the resulting DNA product is smaller, thereby increasing the chances of successful amplification.
Commercially available for forensics labs in ~2007.
LCN: Low copy number. DNA samples (typically skin cells) below ideal STR testing range, usually less than .25 nanograms (38 cells). (Tests can be run with as little as 5 to 20 cells.) To obtain a profile, special testing procedures must be used such increasing the the amplification cycles to greater than 28 – usually 34. There are a number of pitfalls, and it has not been well received in courts. Testing introduced in ~2001.
Touch DNA: Touch DNA samples (typically skin cells) are processed/amplified exactly the same way as blood, semen, saliva etc, and can stand up to scrutiny in court much better than LCN DNA. Testing introduced in ~2005.
Stutter: A testing artifact that appears as a peak, mimicking a true allele’s graph peak. Although they are generally <15% of a true allele peak and appear in predictable locations, stutters have been, and will continue to be, be interpreted as true peaks with the consequence of a false match or false exclusion.
Allelic dropout: Failure to detect an allele within a sample or failure to amplify an allele during PCR. Causes include sample degradation and low sample quantity.
Type of sample & Amount of DNA:
Blood = 30,000 ng/mL
stain 1 cm in area = 200 ng
stain 1 mm in area = 2 ng
Semen = 250,000 ng/mL
Postcoital vaginal swab = 0 - 3,000 ng
Hair
Plucked = 1 - 750 ng/hair
shed = 1 - 12 ng/hair
Saliva = 5,000 ng/mL
Urine = 1 - 20 ng/mL
http://www.bioforensics.com/downloads/KraneMAAFSDC.ppt
Amount of DNA & Number of Cells:
1ng = 152
0.5ng = 76
0.25ng = 38
0.125ng = 19
http://www.cstl.nist.gov/strbase/pub_pres/LCNintro_MAAFSworkshop_May2006.pdf
About 10,000 average-sized human cells can fit on the head of a pin.
A pinhead has a diameter of about 1mm
Grains of table salt vary slightly in size, a single grain is approximately 0.3 mm
The width (diameter) of a human hair ranges from very fine (0.017 mm) to very coarse (0.181 mm)
A human cheek cell is approximately 0.06mm
A human red blood cell is approximately 0.0075mm
Diameter of average human cell nucleus 0.0017mm
Nuclear DNA
Almost all cells in the body contain a nucleus (red blood cells are the exception). The genetic information coded for by nuclear DNA is carried in the chromosomes from one generation to the next, half of a person’s nuclear DNA being inherited from the mother and half from the father.
The nuclear DNA of identical twins is expected to be the same. Other siblings inherit different combinations of nuclear DNA from the same parents and their DNA is therefore somewhat different from one another. The DNA from unrelated individuals is likely to be even more different. Each generation of people is a new and different combination of genetic material from the previous generation.
From a forensic point of view, the interesting feature of an STR locus is that it consists of two alleles, one inherited from the mother and one from the father, and the number of repeats for each allele can vary independently of each other. Each allele has a name that reflects the number of repeats. “Allele 12” would indicate the presence of 12 repeats, “allele 14” would consist of 14 repeats, and so on.
So, at one locus, a person may be designated (12,14) for example - indicating that he/she has one allele of 12 repeats at that locus and another of 14 repeats. It is, of course, possible for a person to inherit an allele with the same number of repeats for a given locus from both parents, so a person who has inherited, for example, the allele with 11 repeats from both parents would have a locus designated (11,11).If the number of STR’s is the same, the person is said to be homozygous at that locus/marker. If the number of STR’s is different, the person is classified as heterozygous at that locus/marker. The possible combinations for children, if the mother is (8,12) and father is (6,12) at a locus/marker are: (6,12), (8,12), (6,8) and (8,8).
A full profile would be expected from items that are not degraded, such as reference blood samples, cheek scrapes and fresh samples from the scene of the crime. A partial DNA profile occurs when it has not been possible to obtain results for one or more of the STR loci or the gender marker. This can happen when the sample being analyzed has degraded after being exposed to the environment for a period of time, and/or when there is very little material available.
An example of a full 13 loci/marker profile that might be found in CODIS:
Locus: D3S1358, Vwa, FGA, D8S1179, D21S11, D18S51, D5S818
Genotype: (15, 18), (16, 16), (9, 24), (12, 13), (29, 31), (12, 13), (11, 13)
Locus: D13S317, D7S820, D16S539, THO1, TPOX, CSF1PO, AMEL
Genotype: (11, 11), (10, 10), (11, 11), (9, 9.3), (8,8), (11, 11), (X, Y)
References and further reading:
http://www.asis.org/Chapters/soasis/events/20040211.ppt
http://www.cps.gov.uk/legal/assets/uploads/files/lawyers'%20dna%20guide%20kswilliams%20190208%20(i).pdf
Continued below...
DNA Polymorphism (“many forms”: Regions of DNA which differ from person to person.
Locus (plural = loci) (Also referred to as a ”marker”: Site or location on a chromosome.
Allele: Variations which can exist at a locus.
DNA Profile: The combination of alleles for an individual.
CODIS: Combined DNA Index System.
CODIS uses two indexes to generate investigative leads in crimes for which biological evidence is recovered from a crime scene. The convicted offender index contains DNA profiles of individuals convicted of certain crimes ranging from certain misdemeanors to sexual assault and murder. Each State has different "qualifying offenses" for which persons convicted of them must submit a biological sample for inclusion in the DNA database.
The forensic index contains DNA profiles obtained from crime scene evidence, such as semen, saliva, or blood. CODIS uses computer software to automatically search across these indexes for a potential match. 10 of 13 loci must yield identifiable results for a forensic profile to be included in CODIS.
CODIS core loci: Thirteen STR sequences that have been selected for the Combined DNA Index System.
Partial profile: DNA evidence that does not yield identifiable results in all 13 core loci.
Amplification or PCR (Polymerase Chain Reaction): A technique for ‘replicating’ DNA in the laboratory (‘molecular Xeroxing’ Standard amplification is 28 cycles which produces nearly a billion copies. Ideal DNA test sample range is 0.5 – 2.0 nanograms.
Electrophoresis: A technique for separating molecules according to their size.
Electropherogram: A graph of results from an analysis done by electrophoresis.
STR: Short tandem repeat Describes a type of DNA polymorphism in which: a DNA sequence repeats over and over again and has a short (usually 4 base pair) repeat unit.
Testing introduced in ~1999
6 repeats: AATG AATG AATG AATG AATG AATG
5 repeats: AATG AATG AATG AATG AATG
4 repeats: AATG AATG AATG AATG etc.
Y-STR: Short Tandem Repeats found on the male-specific Y chromosome. Testing introduced in ~2002.Performing Y-STR testing can help to identify all males who have contributed to a sample.
Mini-STR: In cases where DNA evidence is limited, either in quantity or quality, such as highly degraded samples that are exposed to environmental insults or inhibitors, standard STR testing is often inadequate. Mini-STR primers “zoom in” on the STR locus so that the resulting DNA product is smaller, thereby increasing the chances of successful amplification.
Commercially available for forensics labs in ~2007.
LCN: Low copy number. DNA samples (typically skin cells) below ideal STR testing range, usually less than .25 nanograms (38 cells). (Tests can be run with as little as 5 to 20 cells.) To obtain a profile, special testing procedures must be used such increasing the the amplification cycles to greater than 28 – usually 34. There are a number of pitfalls, and it has not been well received in courts. Testing introduced in ~2001.
Touch DNA: Touch DNA samples (typically skin cells) are processed/amplified exactly the same way as blood, semen, saliva etc, and can stand up to scrutiny in court much better than LCN DNA. Testing introduced in ~2005.
Stutter: A testing artifact that appears as a peak, mimicking a true allele’s graph peak. Although they are generally <15% of a true allele peak and appear in predictable locations, stutters have been, and will continue to be, be interpreted as true peaks with the consequence of a false match or false exclusion.
Allelic dropout: Failure to detect an allele within a sample or failure to amplify an allele during PCR. Causes include sample degradation and low sample quantity.
Type of sample & Amount of DNA:
Blood = 30,000 ng/mL
stain 1 cm in area = 200 ng
stain 1 mm in area = 2 ng
Semen = 250,000 ng/mL
Postcoital vaginal swab = 0 - 3,000 ng
Hair
Plucked = 1 - 750 ng/hair
shed = 1 - 12 ng/hair
Saliva = 5,000 ng/mL
Urine = 1 - 20 ng/mL
http://www.bioforensics.com/downloads/KraneMAAFSDC.ppt
Amount of DNA & Number of Cells:
1ng = 152
0.5ng = 76
0.25ng = 38
0.125ng = 19
http://www.cstl.nist.gov/strbase/pub_pres/LCNintro_MAAFSworkshop_May2006.pdf
About 10,000 average-sized human cells can fit on the head of a pin.
A pinhead has a diameter of about 1mm
Grains of table salt vary slightly in size, a single grain is approximately 0.3 mm
The width (diameter) of a human hair ranges from very fine (0.017 mm) to very coarse (0.181 mm)
A human cheek cell is approximately 0.06mm
A human red blood cell is approximately 0.0075mm
Diameter of average human cell nucleus 0.0017mm
Nuclear DNA
Almost all cells in the body contain a nucleus (red blood cells are the exception). The genetic information coded for by nuclear DNA is carried in the chromosomes from one generation to the next, half of a person’s nuclear DNA being inherited from the mother and half from the father.
The nuclear DNA of identical twins is expected to be the same. Other siblings inherit different combinations of nuclear DNA from the same parents and their DNA is therefore somewhat different from one another. The DNA from unrelated individuals is likely to be even more different. Each generation of people is a new and different combination of genetic material from the previous generation.
From a forensic point of view, the interesting feature of an STR locus is that it consists of two alleles, one inherited from the mother and one from the father, and the number of repeats for each allele can vary independently of each other. Each allele has a name that reflects the number of repeats. “Allele 12” would indicate the presence of 12 repeats, “allele 14” would consist of 14 repeats, and so on.
So, at one locus, a person may be designated (12,14) for example - indicating that he/she has one allele of 12 repeats at that locus and another of 14 repeats. It is, of course, possible for a person to inherit an allele with the same number of repeats for a given locus from both parents, so a person who has inherited, for example, the allele with 11 repeats from both parents would have a locus designated (11,11).If the number of STR’s is the same, the person is said to be homozygous at that locus/marker. If the number of STR’s is different, the person is classified as heterozygous at that locus/marker. The possible combinations for children, if the mother is (8,12) and father is (6,12) at a locus/marker are: (6,12), (8,12), (6,8) and (8,8).
A full profile would be expected from items that are not degraded, such as reference blood samples, cheek scrapes and fresh samples from the scene of the crime. A partial DNA profile occurs when it has not been possible to obtain results for one or more of the STR loci or the gender marker. This can happen when the sample being analyzed has degraded after being exposed to the environment for a period of time, and/or when there is very little material available.
An example of a full 13 loci/marker profile that might be found in CODIS:
Locus: D3S1358, Vwa, FGA, D8S1179, D21S11, D18S51, D5S818
Genotype: (15, 18), (16, 16), (9, 24), (12, 13), (29, 31), (12, 13), (11, 13)
Locus: D13S317, D7S820, D16S539, THO1, TPOX, CSF1PO, AMEL
Genotype: (11, 11), (10, 10), (11, 11), (9, 9.3), (8,8), (11, 11), (X, Y)
References and further reading:
http://www.asis.org/Chapters/soasis/events/20040211.ppt
http://www.cps.gov.uk/legal/assets/uploads/files/lawyers'%20dna%20guide%20kswilliams%20190208%20(i).pdf
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