Second Generation Multiplex Plus
Encyclopedia
Second Generation Multiplex Plus (SGM Plus), is a DNA profiling system developed by Applied Biosystems
. It is an updated version of Second Generation Multiplex
. SGM Plus has been used by the UK National DNA Database
since 1998.
An SGM Plus profile consists of a list of 10 number pairs, one number pair for each of 10 genetic marker
s, along with two letters (XX or XY) which show the result of the gender test. Each number pair denotes the two allele
values for the marker - one value is inherited from each of the subject's parents. If both alleles are the same, then only a single number, rather than a pair, is recorded.
s (STRs). The markers used are: VWA, D8S1179, D21S11, D18S51, TH01, FGA, D3S1358, D16S539, D2S1338 and D19S433. Where a marker's designation begins with D, the digits immediately following the D indicate the chromosome
that contains the marker. For example, D21S11 is on chromosome 21
. SGM Plus also uses the Amelogenin
(Amelo) sex-indicating test.
SGM Plus differs from SGM in that SGM does not use the markers D3S1358, D16S539, D2S1338 and D19S433.
SGM Plus has eight markers in common with CODIS
FGA, TH01, VWA, D3S1358, D8S1179, D16S539, D18S51, and D21S11. It differs from CODIS in that it uses the additional markers D2S1338 and D19S433 and does not use the five markers CSF1PO, TPOX, D5S818, D7S820, D13S317.
The primers for each locus are arranged on the dyes in the following order, from low molecular weight to large molecular weight:
The dyes to which each primer is attached differ from those of the original SGM DNA profiling system.
paper is given below:
An SGM Plus profile retrieved from a DNA database would just list the allele values:
15,18; 6,9; 11,13; 22,22; 31,32.2; 14,17; 17,20; 11,12; 13,16.3; 15,16; XY
Each value is the number of tandem repeat
s within the allele. A non-standard repeat is designated by the number of complete repeat units and the number of base pairs of the partial repeat, separated by a decimal point.
Applied Biosystems estimates the probability of identity for SGM Plus to be approximately 1 in 13 trillion for African-Americans and 1 in 3.3 trillion Caucasian Americans.
The Human Genetics Commission
has reported that the random match probability is in the region of 1 in a trillion. However it stated "When the SGM Plus profiling system was first introduced, there was agreement within the scientific community that identifications with match probabilities lower than one in a billion would not be quoted in the courts of law, so as to avoid overstating the value of the DNA evidence to take into account that match probabilities are only estimates, and to make sure that the figure used was one that was meaningful to non-specialists."
The UK Crown Prosecution Service
states "SGM Plus DNA profiling is very discriminating between individuals. The probability of obtaining a match between the profiles of two unrelated individuals by chance is very low, of the order of 1 in a billion [note this is a UK billion, ie a US trillion]. However, it has not yet been possible to carry out the required statistical testing to be able to quote this match probability, and in practice a more conservative chance match figure of 1 in 1,000 million is used."
Applied Biosystems
Applied Biosystems, Inc. started as GeneCo , was the name of a pioneer biotechnology company founded in 1981 in Foster City, California, in the San Francisco Bay Area...
. It is an updated version of Second Generation Multiplex
Second Generation Multiplex
Second Generation Multiplex is a DNA profiling system used in the United Kingdom to set upthe UK National DNA Database in 1995. It is manufactured by ABI .It contains primers for the following STR loci....
. SGM Plus has been used by the UK National DNA Database
UK National DNA Database
The United Kingdom National DNA Database is a national DNA Database that was set up in 1995. As of the end of 2005, it carried the profiles of around 3.1 million people...
since 1998.
An SGM Plus profile consists of a list of 10 number pairs, one number pair for each of 10 genetic marker
Genetic marker
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify cells, individuals or species. It can be described as a variation that can be observed...
s, along with two letters (XX or XY) which show the result of the gender test. Each number pair denotes the two allele
Allele
An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...
values for the marker - one value is inherited from each of the subject's parents. If both alleles are the same, then only a single number, rather than a pair, is recorded.
Genetic Markers
The genetic markers (or loci) used by SGM Plus are all Short tandem repeatShort tandem repeat
A short tandem repeat in DNA occurs when a pattern of two or more nucleotides are repeated and the repeated sequences are directly adjacent to each other. The pattern can range in length from 2 to 5 base pairs and is typically in the non-coding intron region...
s (STRs). The markers used are: VWA, D8S1179, D21S11, D18S51, TH01, FGA, D3S1358, D16S539, D2S1338 and D19S433. Where a marker's designation begins with D, the digits immediately following the D indicate the chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
that contains the marker. For example, D21S11 is on chromosome 21
Chromosome 21 (human)
Chromosome 21 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. The trisomy of the 21st chromosome causes Down Syndrome...
. SGM Plus also uses the Amelogenin
Amelogenin
Amelogenin is a protein found in developing tooth enamel, and it belongs to a family of extracellular matrix proteins. Developing enamel contains about 30% protein, and 90% of this is amelogenins...
(Amelo) sex-indicating test.
SGM Plus differs from SGM in that SGM does not use the markers D3S1358, D16S539, D2S1338 and D19S433.
SGM Plus has eight markers in common with CODIS
Combined DNA Index System
The Combined DNA Index System is a DNA database funded by the United States Federal Bureau of Investigation . It is a computer system that stores DNA profiles created by federal, state, and local crime laboratories in the United States, with the ability to search the database to assist in the...
FGA, TH01, VWA, D3S1358, D8S1179, D16S539, D18S51, and D21S11. It differs from CODIS in that it uses the additional markers D2S1338 and D19S433 and does not use the five markers CSF1PO, TPOX, D5S818, D7S820, D13S317.
| Locus Designation |
Chromosome Location |
Common Sequence Motif | Allele range |
Size Range (bp) |
Dye Label |
|---|---|---|---|---|---|
| FGA | 4q28 | (TTTC)3TTTT TTCT (CTTT)n CTCC (TTCC)2 | 12.2-51.2 | 215–353 | NED |
| TH01 | 11p15.5 | (AATG)n | 3-14 | 165–204 | NED |
| VWA | 12p12-pter | TCTA(TCTG)3-4(TCTA)n | 10-25 | 157–209 | 5-FAM |
| D2S1338 | 2q35–37.1 | (TGCC)n(TTCC)n | 15-28 | 289–341 | 5-FAM |
| D3S1358 | 3p | TCTA (TCTG)1-3 (TCTA)n | 8-21 | 114–142 | 5-FAM |
| D8S117 | 8 | (TCTR)n | 7-20 | 128–172 | JOE |
| D16S539 | 16q24-qter | (AGAT)n | 5-16 | 234–274 | 5-FAM |
| D18S51 | 18q21.3 | (AGAA)n | 7-39.2 | 26–345 | JOE |
| D19S433 | 19q12–13.1 | (AAGG)(AAAG)(AAGG)(TAGG)(AAGG)n | 9-17.2 | 106–140 | NED |
| D21S11 | 21q11.2–q21 | (TCTA)n(TCTG)n[(TCTA)3TA(TCTA)3TCA (TCTA)2TCCA TA] (TCTA)n | 12-41.2 | 187–243 | JOE |
| Amelogenin | X: p22.1–22.3 Y: p11.2 |
— | — | 107 113 | JOE |
Dye tags
The primers are tagged with the following fluorescent dyes for detection under electrophoresis:- 5-FAM
- JOE
- NED
The primers for each locus are arranged on the dyes in the following order, from low molecular weight to large molecular weight:
- 5-FAM: D3, VWA, D16, D2
- JOE: Amelo, D8, D21, D18
- NED: D19, THO, FGA
The dyes to which each primer is attached differ from those of the original SGM DNA profiling system.
Example SGM Plus profile
The SGM Plus profile of subject GT36865 from a National Institute of Standards and TechnologyNational Institute of Standards and Technology
The National Institute of Standards and Technology , known between 1901 and 1988 as the National Bureau of Standards , is a measurement standards laboratory, otherwise known as a National Metrological Institute , which is a non-regulatory agency of the United States Department of Commerce...
paper is given below:
| Locus | Allele values |
|---|---|
| FGA | 22,22 |
| TH01 | 6,7 |
| VWA | 14,16 |
| D2S1338 | 19,24 |
| D3S1358 | 17,17 |
| D8S117 | 13,14 |
| D16S539 | 9,13 |
| D18S51 | 13,16 |
| D19S433 | 14,15 |
| D21S11 | 30,30 |
| Amelogenin | XX |
An SGM Plus profile retrieved from a DNA database would just list the allele values:
15,18; 6,9; 11,13; 22,22; 31,32.2; 14,17; 17,20; 11,12; 13,16.3; 15,16; XY
Each value is the number of tandem repeat
Tandem repeat
Tandem repeats occur in DNA when a pattern of two or more nucleotides is repeated and the repetitions are directly adjacent to each other. -Example:An example would be:in which the sequence A-T-T-C-G is repeated three times.-Terminology:...
s within the allele. A non-standard repeat is designated by the number of complete repeat units and the number of base pairs of the partial repeat, separated by a decimal point.
Probability of Identity
The probability of identify (also known as the random match probability) is the probability that two individuals selected at random will have an identical genetic profile.Applied Biosystems estimates the probability of identity for SGM Plus to be approximately 1 in 13 trillion for African-Americans and 1 in 3.3 trillion Caucasian Americans.
The Human Genetics Commission
Human Genetics Commission
The Human Genetics Commission is a non-departmental public body body that advises the UK government on the ethical and social aspects of genetics...
has reported that the random match probability is in the region of 1 in a trillion. However it stated "When the SGM Plus profiling system was first introduced, there was agreement within the scientific community that identifications with match probabilities lower than one in a billion would not be quoted in the courts of law, so as to avoid overstating the value of the DNA evidence to take into account that match probabilities are only estimates, and to make sure that the figure used was one that was meaningful to non-specialists."
The UK Crown Prosecution Service
Crown Prosecution Service
The Crown Prosecution Service, or CPS, is a non-ministerial department of the Government of the United Kingdom responsible for public prosecutions of people charged with criminal offences in England and Wales. Its role is similar to that of the longer-established Crown Office in Scotland, and the...
states "SGM Plus DNA profiling is very discriminating between individuals. The probability of obtaining a match between the profiles of two unrelated individuals by chance is very low, of the order of 1 in a billion [note this is a UK billion, ie a US trillion]. However, it has not yet been possible to carry out the required statistical testing to be able to quote this match probability, and in practice a more conservative chance match figure of 1 in 1,000 million is used."