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The new Standard Reference Material® 2391c: PCR-based DNA profiling standard
Forensic Science International: Genetics Supplement Series 3 (2011) e355–e356
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
The new Standard Reference Material1 2391c: PCR-based DNA profiling standard M.C. Kline *, E.L.R. Butts, C.R. Hill, M.D. Coble, D.L. Duewer, J.M. Butler National Institute of Standards and Technology, Gaithersburg, MD 20899-8314, USA
A R T I C L E I N F O
A B S T R A C T
Article history: Received 25 August 2011 Accepted 15 September 2011
Standard Reference Material1 2391c (SRM 2391c) is the fourth generation certified reference material for PCR-based DNA profiling. The first generation SRM 2391 was released in 1995; the next two subsequent versions have had minor modifications in the type and number of loci certified but always used DNA from the same donors. SRM 2391c has been produced with an entirely new set of genomic DNA samples. In addition to four liquid samples, SRM 2391c has two dry storage matrices including FTA paper as well as 903 paper. SRM 2391c consists of six components: three are single source genomic DNA samples that are labeled A, B, and C, with the fourth genomic sample (component D) as a mixture of 3 parts of components A (female donor) to 1 part of component C (male donor). Component E consists of two 6 mm punches of 903 paper that have been spotted with approximately 75,000 cells/spot. Component F consists of two 6 mm punches of FTA paper that have been spotted with approximately 75,000 cells/spot of a different cell line. The six components representing five different DNA samples plus the mixture component have been analyzed using 22 commercially available STR typing kits, obtained from three different vendors, as well as the 26plex STR multiplex developed at NIST. In total there are data for 51 autosomal STRs and 17 YSTRs included in the certificate of analysis. Published by Elsevier Ireland Ltd.
Keywords: Certified Reference Material (CRM), Standard Reference Material (SRM) STR SRM 2391c
1. Introduction
2. Materials and methods
The PCR-based DNA profiling standard SRM 2391 was issued in 1995 and delivered four short tandem repeat (STR) loci genotypes for 12 single-donor source materials. Due to consistently high demand, the original standard was superseded by SRM 2391a in 1999 and SRM 2391b in 2003. SRM 2391a and 2391b were very similar in design to the original, using materials from the same donors but delivering genotypes for 21 and 48 STR loci, respectively. The fourth version of the series, SRM 2391c, has just (16-August-2011) been released for sale. Since evidence storage and mixture resolution have become increasingly pressing issues within the forensic community, SRM 2391c has been completely redesigned using materials from new source donors. Four of the six SRM 2391c components are DNA extracts, two from male donors, one from a female donor, and one an approximate 3:1 mixture of the female-source material with one of the male-sourced materials. The other components are cells spotted on two different paper storage media. All components have been genotyped at 51 autosomal STRs and 17 Y-STRs.
Component A was prepared at NIST by extracting the genomic DNA from Buffy coat white blood cells from a single source anonymous female. Components B and C were prepared from two cell line DNAs purchased from Coriell Cell Repositories (Camden, NJ): NA03469 and NA10451. Component D was prepared as a 3:1 mixture of the component A and C materials. (i.e., 3 parts of A to one part C). ‘‘Conventional’’ DNA concentrations, [DNA], of the materials used to prepare the SRM 2391c components A, B, and C were estimated from optical densities (ODs) at 260 nm [1]. NIST results from 22 commercial STR kits (Applied Biosystems: Identifiler, Identifiler Plus, NGM, NGM SElect, COfiler, Profiler, Profiler Plus, Profiler Plus ID, SGM Plus, SEfiler, MiniFiler, Yfiler; Promega Corp: PowerPlex 16, PowerPlex 16 HS, PowerPlex ESX 17, PowerPlex ESI 17, PowerPlex ES, PowerPlex S5, PowerPlex Y, FFFL; Qiagen: ESSplex, IDplex) and NIST-defined primer sets (26plex and miniSTRs [2–4]) were used to assign the genotypes. Results for many of these kits were confirmed by four cooperating laboratories. In addition, Promega provided information values for Penta C using their PowerPlex CS7 kit. Allele sequencing was performed on the SRM components at the D1S1656, D8S1115, D12S391, Penta D, Penta E, SE33, DYS448, DYS456, DYS458, DYS635, and Y GATA H4 loci. Prior to and after evaluating the candidate SRM 2391c materials, SRM 2031 Metal-on-Fused Silica Filters for Spectrophotometry and SRM 2034 Holmium Oxide Solution Wavelength from
* Corresponding author at: NIST, Biochemical Science Division, 100 Bureau Dr. M/ S 8314, Gaithersburg, MD 20899-8314, USA. Tel.: +1 301 975 3134; fax: +1 301 975 8505. E-mail address: [email protected] (M.C. Kline). 1875-1768/$ – see front matter . Published by Elsevier Ireland Ltd. doi:10.1016/j.fsigss.2011.09.040
e356
M.C. Kline et al. / Forensic Science International: Genetics Supplement Series 3 (2011) e355–e356
expressed as an expanded uncertainty, U. The expanded uncertainty is calculated as U = k uc, where uc is the combined uncertainty and the coverage factor k = 2.6 provides an approximately 95% level of confidence. Funding and disclaimers This work was funded in part through interagency agreement 2008-DN-R-121 between the National Institute of Justice and the NIST Office of Law Enforcement Standards. Points of view in this document are those of the authors and do not necessarily represent the official position or policies of the U.S. Department of Justice. Commercial equipment, instruments, and materials are identified in order to specify experimental procedures as completely as possible. In no case does such identification imply a recommendation or endorsement by the National Institute of Standards and Technology nor does it imply that any of the materials, instruments or equipment identified are necessarily the best available for the purpose. Fig. 1. Summary of mass ratio evidence for component D. The open circles represent the mean estimate for each of the lines of evidence, with bars spanning the full 95% level of confidence interval on the mean. Bars are not shown for the two loci characterized with only one multiplex. The ‘‘Peak Height Average’’ is the mean of the 140 discrete peak height ratios provided by the Applied Biosystems and Promega STR kits for 17 loci with unshared alleles for components A and C. The red horizontal lines bound the 3.1 0.1 95% level of confidence interval about the preparative value.
240 nm to 650 nm were used to verify the spectrophotometer’s absorbance and wavelength calibration. Once Components A and C were diluted to approximately 2 ng/mL these components were mixed by weight to create component D. The measured ODs and weights were used to establish the ratio of DNA from components A and C. Fig. 1 displays the verification of this preparative estimate using 140 discrete peak height ratios provided by 17 loci with unshared alleles amplified using 20 commercial kits and TrueAllele [5] results for six amplifications. 3. Results and discussion All genotype results for all six materials were concordant across STR kits and laboratories. The genotypes are available in the Certificate of Analysis, see: https://www-s.nist.gov/srmors/view_detail.cfm?srm=2391C. The certified mixture ratio of component D is: 3.1 0.1 component A [DNA]/component C [DNA]. The uncertainty in the value, calculated according to the method described in the Guide to the Expression of Uncertainty in Measurement (GUM) [6,7], is
Conflict of interest The National Institute of Standards and Technology, through the Measurement Service Division, sells Standard Reference Materials at the cost of production. Acknowledgements We thank the four laboratories selected to establish the commutability of the material comprising SRM 2391c: Palm Beach Sheriff’s Office (West Palm Beach, FL), Promega Corporation (Madison, WI), Applied Biosystems (Foster City, CA) and Bode Technology Group (Lorton, VA). References [1] J. Sambrook, D.W. Russell, Molecular Cloning a Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2001 (Chapter 6). [2] C.R. Hill, J.M. Butler, P.M. Vallone, A 26plex autosomal STR assay to aid human identity testing, J. Forensic Sci. 54 (5) (2009) 1008–1015. [3] M.D. Coble, J.M. Butler, Characterization of new miniSTR loci to aid analysis of degraded DNA, J. Forensic Sci. 50 (2005) 43–53. [4] C.R. Hill, M.C. Kline, M.D. Coble, et al., Characterization of 26 miniSTR loci for improved analysis of degraded DNA samples, J. Forensic Sci. 53 (1) (2008) 73–80. [5] M.W. Perlin, A. Sinelnikov, An information gap in DNA evidence interpretation, PLoS One 4 (12) (2009) e8327 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0008327. [6] JCGM 100:2008. Guide to the Expression of Uncertainty in Measurement (GUM). BIPM, Se`vres, France. http://www.bipm.org/utils/common/documents/jcgm/ JCGM_100_2008_E.pdf. [7] B.N. Taylor, C.E Kuyatt, Guidelines for Evaluating and Expressing the Uncertainty of NIST Measurement Results; NIST Technical Note 1297, U.S. Government Printing Office, Washington, DC, 1994. http://physics.nist.gov/Pubs/guidelines/TN1297/ tn1297s.pdf.
Contents lists available at ScienceDirect
Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/FSIGSS
The new Standard Reference Material1 2391c: PCR-based DNA profiling standard M.C. Kline *, E.L.R. Butts, C.R. Hill, M.D. Coble, D.L. Duewer, J.M. Butler National Institute of Standards and Technology, Gaithersburg, MD 20899-8314, USA
A R T I C L E I N F O
A B S T R A C T
Article history: Received 25 August 2011 Accepted 15 September 2011
Standard Reference Material1 2391c (SRM 2391c) is the fourth generation certified reference material for PCR-based DNA profiling. The first generation SRM 2391 was released in 1995; the next two subsequent versions have had minor modifications in the type and number of loci certified but always used DNA from the same donors. SRM 2391c has been produced with an entirely new set of genomic DNA samples. In addition to four liquid samples, SRM 2391c has two dry storage matrices including FTA paper as well as 903 paper. SRM 2391c consists of six components: three are single source genomic DNA samples that are labeled A, B, and C, with the fourth genomic sample (component D) as a mixture of 3 parts of components A (female donor) to 1 part of component C (male donor). Component E consists of two 6 mm punches of 903 paper that have been spotted with approximately 75,000 cells/spot. Component F consists of two 6 mm punches of FTA paper that have been spotted with approximately 75,000 cells/spot of a different cell line. The six components representing five different DNA samples plus the mixture component have been analyzed using 22 commercially available STR typing kits, obtained from three different vendors, as well as the 26plex STR multiplex developed at NIST. In total there are data for 51 autosomal STRs and 17 YSTRs included in the certificate of analysis. Published by Elsevier Ireland Ltd.
Keywords: Certified Reference Material (CRM), Standard Reference Material (SRM) STR SRM 2391c
1. Introduction
2. Materials and methods
The PCR-based DNA profiling standard SRM 2391 was issued in 1995 and delivered four short tandem repeat (STR) loci genotypes for 12 single-donor source materials. Due to consistently high demand, the original standard was superseded by SRM 2391a in 1999 and SRM 2391b in 2003. SRM 2391a and 2391b were very similar in design to the original, using materials from the same donors but delivering genotypes for 21 and 48 STR loci, respectively. The fourth version of the series, SRM 2391c, has just (16-August-2011) been released for sale. Since evidence storage and mixture resolution have become increasingly pressing issues within the forensic community, SRM 2391c has been completely redesigned using materials from new source donors. Four of the six SRM 2391c components are DNA extracts, two from male donors, one from a female donor, and one an approximate 3:1 mixture of the female-source material with one of the male-sourced materials. The other components are cells spotted on two different paper storage media. All components have been genotyped at 51 autosomal STRs and 17 Y-STRs.
Component A was prepared at NIST by extracting the genomic DNA from Buffy coat white blood cells from a single source anonymous female. Components B and C were prepared from two cell line DNAs purchased from Coriell Cell Repositories (Camden, NJ): NA03469 and NA10451. Component D was prepared as a 3:1 mixture of the component A and C materials. (i.e., 3 parts of A to one part C). ‘‘Conventional’’ DNA concentrations, [DNA], of the materials used to prepare the SRM 2391c components A, B, and C were estimated from optical densities (ODs) at 260 nm [1]. NIST results from 22 commercial STR kits (Applied Biosystems: Identifiler, Identifiler Plus, NGM, NGM SElect, COfiler, Profiler, Profiler Plus, Profiler Plus ID, SGM Plus, SEfiler, MiniFiler, Yfiler; Promega Corp: PowerPlex 16, PowerPlex 16 HS, PowerPlex ESX 17, PowerPlex ESI 17, PowerPlex ES, PowerPlex S5, PowerPlex Y, FFFL; Qiagen: ESSplex, IDplex) and NIST-defined primer sets (26plex and miniSTRs [2–4]) were used to assign the genotypes. Results for many of these kits were confirmed by four cooperating laboratories. In addition, Promega provided information values for Penta C using their PowerPlex CS7 kit. Allele sequencing was performed on the SRM components at the D1S1656, D8S1115, D12S391, Penta D, Penta E, SE33, DYS448, DYS456, DYS458, DYS635, and Y GATA H4 loci. Prior to and after evaluating the candidate SRM 2391c materials, SRM 2031 Metal-on-Fused Silica Filters for Spectrophotometry and SRM 2034 Holmium Oxide Solution Wavelength from
* Corresponding author at: NIST, Biochemical Science Division, 100 Bureau Dr. M/ S 8314, Gaithersburg, MD 20899-8314, USA. Tel.: +1 301 975 3134; fax: +1 301 975 8505. E-mail address: [email protected] (M.C. Kline). 1875-1768/$ – see front matter . Published by Elsevier Ireland Ltd. doi:10.1016/j.fsigss.2011.09.040
e356
M.C. Kline et al. / Forensic Science International: Genetics Supplement Series 3 (2011) e355–e356
expressed as an expanded uncertainty, U. The expanded uncertainty is calculated as U = k uc, where uc is the combined uncertainty and the coverage factor k = 2.6 provides an approximately 95% level of confidence. Funding and disclaimers This work was funded in part through interagency agreement 2008-DN-R-121 between the National Institute of Justice and the NIST Office of Law Enforcement Standards. Points of view in this document are those of the authors and do not necessarily represent the official position or policies of the U.S. Department of Justice. Commercial equipment, instruments, and materials are identified in order to specify experimental procedures as completely as possible. In no case does such identification imply a recommendation or endorsement by the National Institute of Standards and Technology nor does it imply that any of the materials, instruments or equipment identified are necessarily the best available for the purpose. Fig. 1. Summary of mass ratio evidence for component D. The open circles represent the mean estimate for each of the lines of evidence, with bars spanning the full 95% level of confidence interval on the mean. Bars are not shown for the two loci characterized with only one multiplex. The ‘‘Peak Height Average’’ is the mean of the 140 discrete peak height ratios provided by the Applied Biosystems and Promega STR kits for 17 loci with unshared alleles for components A and C. The red horizontal lines bound the 3.1 0.1 95% level of confidence interval about the preparative value.
240 nm to 650 nm were used to verify the spectrophotometer’s absorbance and wavelength calibration. Once Components A and C were diluted to approximately 2 ng/mL these components were mixed by weight to create component D. The measured ODs and weights were used to establish the ratio of DNA from components A and C. Fig. 1 displays the verification of this preparative estimate using 140 discrete peak height ratios provided by 17 loci with unshared alleles amplified using 20 commercial kits and TrueAllele [5] results for six amplifications. 3. Results and discussion All genotype results for all six materials were concordant across STR kits and laboratories. The genotypes are available in the Certificate of Analysis, see: https://www-s.nist.gov/srmors/view_detail.cfm?srm=2391C. The certified mixture ratio of component D is: 3.1 0.1 component A [DNA]/component C [DNA]. The uncertainty in the value, calculated according to the method described in the Guide to the Expression of Uncertainty in Measurement (GUM) [6,7], is
Conflict of interest The National Institute of Standards and Technology, through the Measurement Service Division, sells Standard Reference Materials at the cost of production. Acknowledgements We thank the four laboratories selected to establish the commutability of the material comprising SRM 2391c: Palm Beach Sheriff’s Office (West Palm Beach, FL), Promega Corporation (Madison, WI), Applied Biosystems (Foster City, CA) and Bode Technology Group (Lorton, VA). References [1] J. Sambrook, D.W. Russell, Molecular Cloning a Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2001 (Chapter 6). [2] C.R. Hill, J.M. Butler, P.M. Vallone, A 26plex autosomal STR assay to aid human identity testing, J. Forensic Sci. 54 (5) (2009) 1008–1015. [3] M.D. Coble, J.M. Butler, Characterization of new miniSTR loci to aid analysis of degraded DNA, J. Forensic Sci. 50 (2005) 43–53. [4] C.R. Hill, M.C. Kline, M.D. Coble, et al., Characterization of 26 miniSTR loci for improved analysis of degraded DNA samples, J. Forensic Sci. 53 (1) (2008) 73–80. [5] M.W. Perlin, A. Sinelnikov, An information gap in DNA evidence interpretation, PLoS One 4 (12) (2009) e8327 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0008327. [6] JCGM 100:2008. Guide to the Expression of Uncertainty in Measurement (GUM). BIPM, Se`vres, France. http://www.bipm.org/utils/common/documents/jcgm/ JCGM_100_2008_E.pdf. [7] B.N. Taylor, C.E Kuyatt, Guidelines for Evaluating and Expressing the Uncertainty of NIST Measurement Results; NIST Technical Note 1297, U.S. Government Printing Office, Washington, DC, 1994. http://physics.nist.gov/Pubs/guidelines/TN1297/ tn1297s.pdf.