-
Something wrong with this record ?
Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise
C. Santos, M. Fondevila, D. Ballard, R. Banemann, AM. Bento, C. Børsting, W. Branicki, F. Brisighelli, M. Burrington, T. Capal, L. Chaitanya, R. Daniel, V. Decroyer, R. England, KB. Gettings, TE. Gross, C. Haas, J. Harteveld, P. Hoff-Olsen, A....
Language English Country Netherlands
Document type Journal Article, Research Support, Non-U.S. Gov't
- MeSH
- DNA genetics MeSH
- Electrophoresis, Capillary methods MeSH
- Genetic Markers * MeSH
- Genotype MeSH
- Polymorphism, Single Nucleotide MeSH
- Humans MeSH
- Forensic Genetics * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified.
Department of Forensic and Analytical Science Faculty of Life Science King's College London UK
Department of Forensic Biology Norwegian Institute of Public Health Oslo Norway
Department of Forensic Genetics Institute of Criminalistics Prague Czech Republic
Department of Human Biological Traces Netherlands Forensic Institute The Hague The Netherlands
ESR Private Bag 92021 Auckland New Zealand
Federal Criminal Police Office Wiesbaden Germany
Forensic Science Laboratory Dublin Ireland
Forensic Science Program The Pennsylvania State University University Park PA USA
Institute of Legal Medicine Faculty of Medicine University of Cologne Cologne Germany
Institute of Legal Medicine Medical University of Innsbruck Innsbruck Austria
Material Measurement Laboratory National Institute of Standards and Technology Gaithersburg MD USA
National Institute of Criminalistics and Criminology Chaussée de Vilvoorde 100 Brussels Belgium
Office of the Chief Forensic Scientist Forensic Services Department Victoria Police Australia
School of Biological Sciences Flinders University Adelaide South Australia 5042 Australia
Section of Forensic Genetics Institute of Forensic Research Kraków Poland
Zurich Institute of Forensic Medicine University of Zurich Zurich Switzerland
References provided by Crossref.org
- 000
- 00000naa a2200000 a 4500
- 001
- bmc16028405
- 003
- CZ-PrNML
- 005
- 20161021132147.0
- 007
- ta
- 008
- 161005s2015 ne f 000 0|eng||
- 009
- AR
- 024 7_
- $a 10.1016/j.fsigen.2015.06.004 $2 doi
- 024 7_
- $a 10.1016/j.fsigen.2015.06.004 $2 doi
- 035 __
- $a (PubMed)26122263
- 040 __
- $a ABA008 $b cze $d ABA008 $e AACR2
- 041 0_
- $a eng
- 044 __
- $a ne
- 100 1_
- $a Santos, C $u Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
- 245 10
- $a Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise / $c C. Santos, M. Fondevila, D. Ballard, R. Banemann, AM. Bento, C. Børsting, W. Branicki, F. Brisighelli, M. Burrington, T. Capal, L. Chaitanya, R. Daniel, V. Decroyer, R. England, KB. Gettings, TE. Gross, C. Haas, J. Harteveld, P. Hoff-Olsen, A. Hoffmann, M. Kayser, P. Kohler, A. Linacre, M. Mayr-Eduardoff, C. McGovern, N. Morling, G. O'Donnell, W. Parson, VL. Pascali, MJ. Porto, A. Roseth, PM. Schneider, T. Sijen, V. Stenzl, DS. Court, JE. Templeton, M. Turanska, PM. Vallone, RA. van Oorschot, L. Zatkalikova, Á. Carracedo, C. Phillips, . ,
- 520 9_
- $a There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified.
- 650 _2
- $a DNA $x genetika $7 D004247
- 650 _2
- $a elektroforéza kapilární $x metody $7 D019075
- 650 12
- $a soudní genetika $7 D053803
- 650 12
- $a genetické markery $7 D005819
- 650 _2
- $a genotyp $7 D005838
- 650 _2
- $a lidé $7 D006801
- 650 _2
- $a jednonukleotidový polymorfismus $7 D020641
- 655 _2
- $a časopisecké články $7 D016428
- 655 _2
- $a práce podpořená grantem $7 D013485
- 700 1_
- $a Fondevila, M $u Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
- 700 1_
- $a Ballard, D $u Department of Forensic and Analytical Science, Faculty of Life Science, King's College London, UK.
- 700 1_
- $a Banemann, R $u Federal Criminal Police Office, Wiesbaden, Germany.
- 700 1_
- $a Bento, A M $u Forensic Genetic and Biology Service, Centre Branch, National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal.
- 700 1_
- $a Børsting, C $u Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen, Denmark.
- 700 1_
- $a Branicki, W $u Section of Forensic Genetics, Institute of Forensic Research, Kraków, Poland.
- 700 1_
- $a Brisighelli, F $u Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy.
- 700 1_
- $a Burrington, M $u Forensic Science Laboratory, Dublin, Ireland.
- 700 1_
- $a Capal, T $u Department of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic.
- 700 1_
- $a Chaitanya, L $u Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands.
- 700 1_
- $a Daniel, R $u Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Australia.
- 700 1_
- $a Decroyer, V $u National Institute of Criminalistics and Criminology, Chaussée de Vilvoorde 100, Brussels, Belgium.
- 700 1_
- $a England, R $u ESR, Private Bag 92021, Auckland, New Zealand.
- 700 1_
- $a Gettings, K B $u Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
- 700 1_
- $a Gross, T E $u Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany.
- 700 1_
- $a Haas, C $u Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
- 700 1_
- $a Harteveld, J $u Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands.
- 700 1_
- $a Hoff-Olsen, P $u Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway.
- 700 1_
- $a Hoffmann, A $u Federal Criminal Police Office, Wiesbaden, Germany.
- 700 1_
- $a Kayser, M $u Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands.
- 700 1_
- $a Kohler, P $u Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway.
- 700 1_
- $a Linacre, A $u School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia.
- 700 1_
- $a Mayr-Eduardoff, M $u Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
- 700 1_
- $a McGovern, C $u ESR, Private Bag 92021, Auckland, New Zealand.
- 700 1_
- $a Morling, N $u Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen, Denmark; National Institute of Criminalistics and Criminology, Chaussée de Vilvoorde 100, Brussels, Belgium.
- 700 1_
- $a O'Donnell, G $u Forensic Science Laboratory, Dublin, Ireland.
- 700 1_
- $a Parson, W $u Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
- 700 1_
- $a Pascali, V L $u Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy.
- 700 1_
- $a Porto, M J $u Forensic Genetic and Biology Service, Centre Branch, National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal.
- 700 1_
- $a Roseth, A $u Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway.
- 700 1_
- $a Schneider, P M $u Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany.
- 700 1_
- $a Sijen, T $u Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands.
- 700 1_
- $a Stenzl, V $u Department of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic.
- 700 1_
- $a Court, D Syndercombe $u Department of Forensic and Analytical Science, Faculty of Life Science, King's College London, UK.
- 700 1_
- $a Templeton, J E $u School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia.
- 700 1_
- $a Turanska, M $u Institute of Forensic Science, Ministry of the Interior, Department of Biology and DNA Analysis, Slovenská Lupca, Slovakia.
- 700 1_
- $a Vallone, P M $u Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
- 700 1_
- $a van Oorschot, R A H $u Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Australia.
- 700 1_
- $a Zatkalikova, L $u Institute of Forensic Science, Ministry of the Interior, Department of Biology and DNA Analysis, Slovenská Lupca, Slovakia.
- 700 1_
- $a Carracedo, Á $u Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
- 700 1_
- $a Phillips, C $u Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain. Electronic address: c.phillips@mac.com.
- 700 1_
- $a ,
- 773 0_
- $w MED00166775 $t Forensic science international. Genetics $x 1878-0326 $g Roč. 19, č. - (2015), s. 56-67
- 856 41
- $u https://pubmed.ncbi.nlm.nih.gov/26122263 $y Pubmed
- 910 __
- $a ABA008 $b sig $c sign $y a $z 0
- 990 __
- $a 20161005 $b ABA008
- 991 __
- $a 20161021132555 $b ABA008
- 999 __
- $a ok $b bmc $g 1166719 $s 953035
- BAS __
- $a 3
- BAS __
- $a PreBMC
- BMC __
- $a 2015 $b 19 $c - $d 56-67 $e 20150615 $i 1878-0326 $m Forensic science international. Genetics $n Forensic Sci Int Genet $x MED00166775
- LZP __
- $a Pubmed-20161005
