Second Generation Multiplex Plus

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 markers, along with two letters (XX or XY) which show the result of the Amelogenin sex indicating 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.

Genetic markers

The genetic markers (or loci) used by SGM Plus are all short tandem repeats (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.[1]

Characteristics of alleles observed in the SGM Plus loci[1]
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
D8S1179 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 Technology paper is given below:[2]

SGM Plus profile of subject GT36865 [3]
Locus Allele values
FGA 22,22
TH01 6,7
VWA 14,16
D2S1338 19,24
D3S1358 17,17
D8S1179 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:[4]

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 repeats 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 identity (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.[5]

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." [6]

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. 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."[7]

See also

References

  1. ^ a b Core STR Review cstl.nist.gov [dead link‍]
  2. ^ "For the Record" (PDF). NIST. 17 October 2019.
  3. ^ JFS 2003 ID Results cstl.nist.gov
  4. ^ "NPIA: Basic Facts - FAQs". Archived from the original on 2010-03-03. Retrieved 2010-03-02.
  5. ^ AmpFlSTR SGM Plus PCR Amplification Kit User's Manual (PDF). pp. 14–12.
  6. ^ Human Genetics Commission. Nothing to hide, nothing to fear? p.49 (PDF) (Report).
  7. ^ The Crown Prosecution Service. "B4. Adventitious (chance) DNA Matches".