Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results

Just, Rebecca S.; Irwin, Jodi A.

doi:10.1016/j.fsigen.2018.02.016

Title: Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results

Journal Article · 30 April 2018 · Forensic Science International. Genetics

DOI: https://doi.org/10.1016/j.fsigen.2018.02.016 · OSTI ID:1771201

; Irwin, Jodi A.

Not Available

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

OSTI ID:: 1771201

Journal Information:: Forensic Science International. Genetics, Journal Name: Forensic Science International. Genetics Journal Issue: C Vol. 34; ISSN 1872-4973

Publisher:: ElsevierCopyright Statement

Country of Publication:: Netherlands

Language:: English

References (68)

The next generation of DNA profiling - STR typing by multiplexed PCR - ion-pair RP LC-ESI time-of-flight MS Pitterl, Florian; Niederstätter, Harald; Huber, Gabriela ELECTROPHORESIS, Vol. 29, Issue 23 https://doi.org/10.1002/elps.200800209	journal	December 2008
An assessment of a massively parallel sequencing approach for the identification of individuals from mass graves of the Spanish Civil War (1936-1939): Nucleic Acids Calafell, Francesc; Anglada, Roger; Bonet, Núria ELECTROPHORESIS, Vol. 37, Issue 21 https://doi.org/10.1002/elps.201600180	journal	September 2016
Performance of the ForenSeq ^TM DNA Signature Prep kit on highly degraded samples: Nucleic Acids Fattorini, Paolo; Previderé, Carlo; Carboni, Ilaria ELECTROPHORESIS, Vol. 38, Issue 8 https://doi.org/10.1002/elps.201600290	journal	February 2017
Variation in Short Tandem Repeat sequences ?a survey of twelve microsatellite loci for use as forensic identification markers Urquhart, A.; Kimpton, C. P.; Downes, T. J. International Journal of Legal Medicine, Vol. 107, Issue 1 https://doi.org/10.1007/BF01247268	journal	January 1994
A highly variable STR at the D12S391 locus Lareu, M. V.; Pestoni, C.; Carracedo, A. International Journal of Legal Medicine, Vol. 109, Issue 3 https://doi.org/10.1007/BF01369673	journal	September 1996
Consistent treatment of length variants in the human mtDNA control region: a reappraisal Bandelt, H. -J.; Parson, W. International Journal of Legal Medicine, Vol. 122, Issue 1 https://doi.org/10.1007/s00414-006-0151-5	journal	March 2007
Sequence variation of a hypervariable short tandem repeat at the D12S391 locus Lareu, Maria Victoria; del Carmen Pestoni, Maria; Barros, Francisco Gene, Vol. 182, Issue 1-2 https://doi.org/10.1016/S0378-1119(96)00540-9	journal	December 1996
New alleles and mutational events in D12S391 and D8S1132: sequence data from an eastern German population Hering, Sandra; Müller, Erich Forensic Science International, Vol. 124, Issue 2-3 https://doi.org/10.1016/S0379-0738(01)00596-5	journal	December 2001
Recommendations for consistent treatment of length variants in the human mitochondrial DNA control region Wilson, Mark R.; Allard, Marc W.; Monson, Keith Forensic Science International, Vol. 129, Issue 1 https://doi.org/10.1016/S0379-0738(02)00206-2	journal	September 2002
Polymerase slippage in relation to the uniformity of tetrameric repeat stretches Klintschar, Michael; Wiegand, Peter Forensic Science International, Vol. 135, Issue 2 https://doi.org/10.1016/S0379-0738(03)00201-9	journal	August 2003
Additional variability at the D12S391 STR locus in an Austrian population sample: sequencing data and allele distribution Glock, Barbara; Dauber, Eva-Maria; Schwartz, Dieter W. M. Forensic Science International, Vol. 90, Issue 3 https://doi.org/10.1016/S0379-0738(97)00163-1	journal	December 1997
Polymorphism of the D12S391 microsatellite in a Japanese population sample Shigeta, Y.; Yamamoto, Y.; Doi, Y. Forensic Science International, Vol. 102, Issue 1 https://doi.org/10.1016/S0379-0738(99)00048-1	journal	May 1999
The low-template-DNA (stochastic) threshold—Its determination relative to risk analysis for national DNA databases Gill, Peter; Puch-Solis, Roberto; Curran, James Forensic Science International: Genetics, Vol. 3, Issue 2 https://doi.org/10.1016/j.fsigen.2008.11.009	journal	March 2009
Interpreting low template DNA profiles Balding, David J.; Buckleton, John Forensic Science International: Genetics, Vol. 4, Issue 1 https://doi.org/10.1016/j.fsigen.2009.03.003	journal	December 2009
Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel Phillips, C.; Fernandez-Formoso, L.; Garcia-Magariños, M. Forensic Science International: Genetics, Vol. 5, Issue 3 https://doi.org/10.1016/j.fsigen.2010.02.003	journal	June 2011
Forensim: An open-source initiative for the evaluation of statistical methods in forensic genetics Haned, Hinda Forensic Science International: Genetics, Vol. 5, Issue 4 https://doi.org/10.1016/j.fsigen.2010.03.017	journal	August 2011
STR sequence analysis for characterizing normal, variant, and null alleles Kline, Margaret C.; Hill, Carolyn R.; Decker, Amy E. Forensic Science International: Genetics, Vol. 5, Issue 4 https://doi.org/10.1016/j.fsigen.2010.09.005	journal	August 2011
SAM: String-based sequence search algorithm for mitochondrial DNA database queries Röck, Alexander; Irwin, Jodi; Dür, Arne Forensic Science International: Genetics, Vol. 5, Issue 2 https://doi.org/10.1016/j.fsigen.2010.10.006	journal	March 2011
Characterising stutter in forensic STR multiplexes Brookes, Clare; Bright, Jo-Anne; Harbison, SallyAnn Forensic Science International: Genetics, Vol. 6, Issue 1 https://doi.org/10.1016/j.fsigen.2011.02.001	journal	January 2012
Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry Planz, John V.; Sannes-Lowery, Kristen A.; Duncan, David D. Forensic Science International: Genetics, Vol. 6, Issue 5 https://doi.org/10.1016/j.fsigen.2012.02.002	journal	September 2012
Assessment of the stochastic threshold, back- and forward stutter filters and low template techniques for NGM Westen, Antoinette A.; Grol, Laurens J. W.; Harteveld, Joyce Forensic Science International: Genetics, Vol. 6, Issue 6 https://doi.org/10.1016/j.fsigen.2012.05.001	journal	December 2012
DNA commission of the International Society of Forensic Genetics: Recommendations on the evaluation of STR typing results that may include drop-out and/or drop-in using probabilistic methods Gill, P.; Gusmão, L.; Haned, H. Forensic Science International: Genetics, Vol. 6, Issue 6 https://doi.org/10.1016/j.fsigen.2012.06.002	journal	December 2012
Validation of a DNA mixture statistics tool incorporating allelic drop-out and drop-in Mitchell, Adele A.; Tamariz, Jeannie; O’Connell, Kathleen Forensic Science International: Genetics, Vol. 6, Issue 6 https://doi.org/10.1016/j.fsigen.2012.08.007	journal	December 2012
Exploratory data analysis for the interpretation of low template DNA mixtures Haned, H.; Slooten, K.; Gill, P. Forensic Science International: Genetics, Vol. 6, Issue 6 https://doi.org/10.1016/j.fsigen.2012.08.008	journal	December 2012
Developing allelic and stutter peak height models for a continuous method of DNA interpretation Bright, Jo-Anne; Taylor, Duncan; Curran, James M. Forensic Science International: Genetics, Vol. 7, Issue 2 https://doi.org/10.1016/j.fsigen.2012.11.013	journal	February 2013
STRait Razor: A length-based forensic STR allele-calling tool for use with second generation sequencing data Warshauer, David H.; Lin, David; Hari, Kumar Forensic Science International: Genetics, Vol. 7, Issue 4 https://doi.org/10.1016/j.fsigen.2013.04.005	journal	July 2013
Evaluating forensic DNA profiles using peak heights, allowing for multiple donors, allelic dropout and stutters Puch-Solis, Roberto; Rodgers, Lauren; Mazumder, Anjali Forensic Science International: Genetics, Vol. 7, Issue 5 https://doi.org/10.1016/j.fsigen.2013.05.009	journal	September 2013
The interpretation of single source and mixed DNA profiles Taylor, Duncan; Bright, Jo-Anne; Buckleton, John Forensic Science International: Genetics, Vol. 7, Issue 5 https://doi.org/10.1016/j.fsigen.2013.05.011	journal	September 2013
Characterising the STR locus D6S1043 and examination of its effect on stutter rates Bright, Jo-Anne; Stevenson, Kate E.; Coble, Michael D. Forensic Science International: Genetics, Vol. 8, Issue 1 https://doi.org/10.1016/j.fsigen.2013.06.012	journal	January 2014
Using continuous DNA interpretation methods to revisit likelihood ratio behaviour Taylor, Duncan Forensic Science International: Genetics, Vol. 11 https://doi.org/10.1016/j.fsigen.2014.03.008	journal	July 2014
Evidential evaluation of DNA profiles using a discrete statistical model implemented in the DNA LiRa software Puch-Solis, Roberto; Clayton, Tim Forensic Science International: Genetics, Vol. 11 https://doi.org/10.1016/j.fsigen.2014.04.005	journal	July 2014
Short tandem repeat typing on the 454 platform: Strategies and considerations for targeted sequencing of common forensic markers Scheible, Melissa; Loreille, Odile; Just, Rebecca Forensic Science International: Genetics, Vol. 12 https://doi.org/10.1016/j.fsigen.2014.04.010	journal	September 2014
STRait Razor v2.0: The improved STR Allele Identification Tool – Razor Warshauer, David H.; King, Jonathan L.; Budowle, Bruce Forensic Science International: Genetics, Vol. 14 https://doi.org/10.1016/j.fsigen.2014.10.011	journal	January 2015
Investigating a common approach to DNA profile interpretation using probabilistic software Cooper, Stuart; McGovern, Catherine; Bright, Jo-Anne Forensic Science International: Genetics, Vol. 16 https://doi.org/10.1016/j.fsigen.2014.12.009	journal	May 2015
Genotyping and interpretation of STR-DNA: Low-template, mixtures and database matches—Twenty years of research and development Gill, Peter; Haned, Hinda; Bleka, Oyvind Forensic Science International: Genetics, Vol. 18 https://doi.org/10.1016/j.fsigen.2015.03.014	journal	September 2015
STR allele sequence variation: Current knowledge and future issues Gettings, Katherine Butler; Aponte, Rachel A.; Vallone, Peter M. Forensic Science International: Genetics, Vol. 18 https://doi.org/10.1016/j.fsigen.2015.06.005	journal	September 2015
Evaluation of the Illumina ® Beta Version ForenSeq™ DNA Signature Prep Kit for use in genetic profiling Churchill, Jennifer D.; Schmedes, Sarah E.; King, Jonathan L. Forensic Science International: Genetics, Vol. 20 https://doi.org/10.1016/j.fsigen.2015.09.009	journal	January 2016
Sequence variation of 22 autosomal STR loci detected by next generation sequencing Gettings, Katherine Butler; Kiesler, Kevin M.; Faith, Seth A. Forensic Science International: Genetics, Vol. 21 https://doi.org/10.1016/j.fsigen.2015.11.005	journal	March 2016
Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs Friis, Susanne L.; Buchard, Anders; Rockenbauer, Eszter Forensic Science International: Genetics, Vol. 21 https://doi.org/10.1016/j.fsigen.2015.12.006	journal	March 2016
Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements Parson, Walther; Ballard, David; Budowle, Bruce Forensic Science International: Genetics, Vol. 22 https://doi.org/10.1016/j.fsigen.2016.01.009	journal	May 2016
Massively parallel sequencing of short tandem repeats—Population data and mixture analysis results for the PowerSeq™ system van der Gaag, Kristiaan J.; de Leeuw, Rick H.; Hoogenboom, Jerry Forensic Science International: Genetics, Vol. 24 https://doi.org/10.1016/j.fsigen.2016.05.016	journal	September 2016
A comparative study of qualitative and quantitative models used to interpret complex STR DNA profiles Bleka, Øyvind; Benschop, Corina C. G.; Storvik, Geir Forensic Science International: Genetics, Vol. 25 https://doi.org/10.1016/j.fsigen.2016.07.016	journal	November 2016
Characterization of genetic sequence variation of 58 STR loci in four major population groups Novroski, Nicole M. M.; King, Jonathan L.; Churchill, Jennifer D. Forensic Science International: Genetics, Vol. 25 https://doi.org/10.1016/j.fsigen.2016.09.007	journal	November 2016
FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise Hoogenboom, Jerry; van der Gaag, Kristiaan J.; de Leeuw, Rick H. Forensic Science International: Genetics, Vol. 27 https://doi.org/10.1016/j.fsigen.2016.11.007	journal	March 2017
Performance and concordance of the ForenSeq™ system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens Just, Rebecca S.; Moreno, Lilliana I.; Smerick, Jill B. Forensic Science International: Genetics, Vol. 28 https://doi.org/10.1016/j.fsigen.2017.01.001	journal	May 2017
Developmental validation of the MiSeq FGx Forensic Genomics System for Targeted Next Generation Sequencing in Forensic DNA Casework and Database Laboratories Jäger, Anne C.; Alvarez, Michelle L.; Davis, Carey P. Forensic Science International: Genetics, Vol. 28 https://doi.org/10.1016/j.fsigen.2017.01.011	journal	May 2017
Evaluation of the Illumina ForenSeq™ DNA Signature Prep Kit – MPS forensic application for the MiSeq FGx™ benchtop sequencer Xavier, Catarina; Parson, Walther Forensic Science International: Genetics, Vol. 28 https://doi.org/10.1016/j.fsigen.2017.02.018	journal	May 2017
Internal validation of STRmix™ for the interpretation of single source and mixed DNA profiles Moretti, Tamyra R.; Just, Rebecca S.; Kehl, Susannah C. Forensic Science International: Genetics, Vol. 29 https://doi.org/10.1016/j.fsigen.2017.04.004	journal	July 2017
European survey on forensic applications of massively parallel sequencing Alonso, Antonio; Müller, Petra; Roewer, Lutz Forensic Science International: Genetics, Vol. 29 https://doi.org/10.1016/j.fsigen.2017.04.017	journal	July 2017
Open source software EuroForMix can be used to analyse complex SNP mixtures Bleka, Øyvind; Eduardoff, Mayra; Santos, Carla Forensic Science International: Genetics, Vol. 31 https://doi.org/10.1016/j.fsigen.2017.08.001	journal	November 2017
Concordance of the ForenSeq™ system and characterisation of sequence-specific autosomal STR alleles across two major population groups Devesse, Laurence; Ballard, David; Davenport, Lucinda Forensic Science International: Genetics, Vol. 34 https://doi.org/10.1016/j.fsigen.2017.10.012	journal	May 2018
Short tandem repeat sequencing on the 454 platform Scheible, Melissa; Loreille, Odile; Just, Rebecca Forensic Science International: Genetics Supplement Series, Vol. 3, Issue 1 https://doi.org/10.1016/j.fsigss.2011.09.041	journal	December 2011
Assessing the potential of next generation sequencing technologies for missing persons identification efforts Irwin, Jodi; Just, Rebecca; Scheible, Melissa Forensic Science International: Genetics Supplement Series, Vol. 3, Issue 1 https://doi.org/10.1016/j.fsigss.2011.09.085	journal	December 2011
A comparison of statistical models for the analysis of complex forensic DNA profiles Kelly, Hannah; Bright, Jo-Anne; Buckleton, John S. Science & Justice, Vol. 54, Issue 1 https://doi.org/10.1016/j.scijus.2013.07.003	journal	January 2014
Analysis of Polymerase Chain Reaction Products by On-Line Liquid Chromatography−Mass Spectrometry for Genotyping of Polymorphic Short Tandem Repeat Loci Oberacher, Herbert; Parson, Walther; Mühlmann, Roswitha Analytical Chemistry, Vol. 73, Issue 21 https://doi.org/10.1021/ac010587f	journal	November 2001
Sequence Analysis and Characterization of Stutter Products at the Tetranucleotide Repeat Locus VWA Walsh, P. S.; Fildes, N. J.; Reynolds, R. Nucleic Acids Research, Vol. 24, Issue 14 https://doi.org/10.1093/nar/24.14.2807	journal	July 1996
Calculating the Weight of Evidence in Low-Template Forensic DNA Casework Lohmueller, Kirk E.; Rudin, Norah Journal of Forensic Sciences, Vol. 58 https://doi.org/10.1111/1556-4029.12017	journal	October 2012
Validating TrueAllele ^® DNA Mixture Interpretation* ^,† Perlin, Mark W.; Legler, Matthew M.; Spencer, Cara E. Journal of Forensic Sciences, Vol. 56, Issue 6 https://doi.org/10.1111/j.1556-4029.2011.01859.x	journal	November 2011
Population Genetic Comparisons among Eight Populations using Allele Frequency and Sequence Data from Three Microsatellite Loci Brinkmann, B. (a.); Sajantila, A. (b, c.); Goedde, H. W. (d.) European Journal of Human Genetics, Vol. 4, Issue 3 https://doi.org/10.1159/000472192	journal	January 1996
DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification Templeton, Jennifer E. L.; Brotherton, Paul M.; Llamas, Bastien Investigative Genetics, Vol. 4, Issue 1 https://doi.org/10.1186/2041-2223-4-26	journal	January 2013
Evaluation of forensic DNA mixture evidence: protocol for evaluation, interpretation, and statistical calculations using the combined probability of inclusion Bieber, Frederick R.; Buckleton, John S.; Budowle, Bruce BMC Genetics, Vol. 17, Issue 1 https://doi.org/10.1186/s12863-016-0429-7	journal	August 2016
More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing Ambers, Angie D.; Churchill, Jennifer D.; King, Jonathan L. BMC Genomics, Vol. 17, Issue S9 https://doi.org/10.1186/s12864-016-3087-2	journal	October 2016
A gamma model for {DNA} mixture analyses Cowell, R. G.; Lauritzen, S. L.; Mortera, J. Bayesian Analysis, Vol. 2, Issue 2 https://doi.org/10.1214/07-BA214	journal	June 2007
Validation of Short Tandem Repeats (STRs) for Forensic Usage: Performance Testing of Fluorescent Multiplex STR Systems and Analysis of Authentic and Simulated Forensic Samples Moretti, Tamyra R.; Baumstark, Anne L.; Defenbaugh, Debra A. Journal of Forensic Sciences, Vol. 46, Issue 3 https://doi.org/10.1520/JFS15018J	journal	May 2001
Validation of STR Typing by Capillary Electrophoresis Moretti, Tamyra R.; Baumstark, Anne L.; Defenbaugh, Debra A. Journal of Forensic Sciences, Vol. 46, Issue 3 https://doi.org/10.1520/JFS15019J	journal	May 2001
Taking Account of Peak Areas when Interpreting Mixed DNA Profiles Evett, Ian W.; Gill, Peter D.; Lambert, James A. Journal of Forensic Sciences, Vol. 43, Issue 1 https://doi.org/10.1520/JFS16091J	journal	January 1998
Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy Holland, Mitchell M.; McQuillan, Megan R.; O’Hanlon, Katherine A. Croatian Medical Journal, Vol. 52, Issue 3 https://doi.org/10.3325/cmj.2011.52.299	journal	June 2011
Flanking Variation Influences Rates of Stutter in Simple Repeats Woerner, August; King, Jonathan; Budowle, Bruce Genes, Vol. 8, Issue 11 https://doi.org/10.3390/genes8110329	journal	November 2017

Similar Records

LUS+: Extension of the LUS designator concept to differentiate most sequence alleles for 27 STR loci

Journal Article · 2020 · Forensic Science International: Reports · OSTI ID:1762557

Just, Rebecca S.; Le, Jennifer; Irwin, Jodi A.

Identification of the novel HLA-DPB1*5801 allele detected by sequenced based typing

Journal Article · 1995 · Immunogenetics · OSTI ID:75616

Versluis, L F; Zwan, A.W. van der; Tilanus, M G.J.; +3 more

Identification of the new HLA-DRB1{sup *}0812 allele detected by sequencing based typing

Journal Article · 1996 · Immunogenetics · OSTI ID:501876

Versluis, L F; Zwan, A.W. van der; Tilanus, M G.J.; +2 more

Title: Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results

Citation Formats

References (68)

Similar Records

Related Subjects