TY - JOUR
T1 - Expanding beyond the current core STR loci
T2 - An exploration of 73 STR markers with increased diversity for enhanced DNA mixture deconvolution
AU - Novroski, Nicole M.M.
AU - Wendt, Frank R.
AU - Woerner, August E.
AU - Bus, Magdalena M.
AU - Coble, Michael
AU - Budowle, Bruce
N1 - Funding Information:
The authors would like to acknowledge Dr. Marty Flores and Dr. Bob Kolouch from Illumina, Inc. for their assistance and technical expertise in the design and troubleshooting of the AmpliSeq for Illumina multiplex. The authors would also like to thank Jerry Boonyaratanakornkit and Wahaj Zuberi from Exact Diagnostics for their technical assistance generating the AmpliSeq for Illumina sequencing data. This work was supported in part by award no. 2015-DN-BX-K067 (Enhancing Mixture Interpretation with Highly Informative STRs), awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice . The opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors, and do not necessarily reflect those of the U.S. Department of Justice. This work was also supported in part by the 2015-16 Lucas Grant (A Novel Intra-Allelic STR Variant Panel for Enhanced DNA Mixture De-Convolution), awarded by the Forensic Sciences Foundation, American Academy of Forensic Sciences .
Publisher Copyright:
© 2018 Elsevier B.V.
PY - 2019/1
Y1 - 2019/1
N2 - Current approaches to mixture deconvolution of complex biological samples at times do not have the capability to resolve component contributors in DNA evidence. Additional short tandem repeat (STR) loci were sought that may improve the forensic genetic analysis of mixtures. This study presents exploratory data of a multiplex comprised of 73 highly polymorphic STRs (referred herein as the 73Plex) that were selected because of their high diversity due to sequence variation. These STRs (or a subset of them) may be considered as candidates that may augment current core markers capabilities for DNA mixture deconvolution. Population genetics analyses were performed for each locus using DNA samples from 451 individuals comprising three U.S. populations. Sequence-based heterozygosities ranged from 72% to 98%, where only two loci (D10A97 and D6A7) fell below 80%. Mixture deconvolution capabilities for two-person mixtures were assessed based on complete allele resolution per locus (i.e., four alleles observed) of pairwise mixtures using in silico methods. A subset of 20 highly informative loci (referred herein as the 20Plex) from the 73Plex was compared to the 20 CODIS core loci on all population samples with full DNA profiles for both panels (i.e., no locus dropout; n = 443). Based on proportion of loci displaying four alleles, the 20Plex outperformed the CODIS core loci with increases of 82.6% and 89.3% using length-based and sequence-based alleles, respectively. A combination of 17 STR from the 20Plex and 3 CODIS loci gave the highest capacity for resolving allelic components per locus. These data illustrate the increased value of utilizing sequenced-based alleles of additional STR loci. Furthermore, there are a number of candidate STR loci that could notably augment the current core STR loci and enhance mixture interpretation capabilities.
AB - Current approaches to mixture deconvolution of complex biological samples at times do not have the capability to resolve component contributors in DNA evidence. Additional short tandem repeat (STR) loci were sought that may improve the forensic genetic analysis of mixtures. This study presents exploratory data of a multiplex comprised of 73 highly polymorphic STRs (referred herein as the 73Plex) that were selected because of their high diversity due to sequence variation. These STRs (or a subset of them) may be considered as candidates that may augment current core markers capabilities for DNA mixture deconvolution. Population genetics analyses were performed for each locus using DNA samples from 451 individuals comprising three U.S. populations. Sequence-based heterozygosities ranged from 72% to 98%, where only two loci (D10A97 and D6A7) fell below 80%. Mixture deconvolution capabilities for two-person mixtures were assessed based on complete allele resolution per locus (i.e., four alleles observed) of pairwise mixtures using in silico methods. A subset of 20 highly informative loci (referred herein as the 20Plex) from the 73Plex was compared to the 20 CODIS core loci on all population samples with full DNA profiles for both panels (i.e., no locus dropout; n = 443). Based on proportion of loci displaying four alleles, the 20Plex outperformed the CODIS core loci with increases of 82.6% and 89.3% using length-based and sequence-based alleles, respectively. A combination of 17 STR from the 20Plex and 3 CODIS loci gave the highest capacity for resolving allelic components per locus. These data illustrate the increased value of utilizing sequenced-based alleles of additional STR loci. Furthermore, there are a number of candidate STR loci that could notably augment the current core STR loci and enhance mixture interpretation capabilities.
KW - DNA mixtures
KW - Mixture deconvolution
KW - Sequence variation
KW - Short tandem repeats
UR - http://www.scopus.com/inward/record.url?scp=85055873864&partnerID=8YFLogxK
U2 - 10.1016/j.fsigen.2018.10.013
DO - 10.1016/j.fsigen.2018.10.013
M3 - Article
C2 - 30396008
AN - SCOPUS:85055873864
SN - 1872-4973
VL - 38
SP - 121
EP - 129
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
ER -