Highlights
- •A gentle introduction to the field of bioinformatics for forensic scientists.
- •Offers a review of the advancements that paved the way to the current state.
- •Describes the components of bioinformatic pipelines needed for the analyses of forensic MPS data.
Abstract
Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses
are three classes of markers which will play an important role in the future of forensic
DNA typing. The arrival of massively parallel sequencing platforms in forensic science
reveals new information such as insights into the complexity and variability of the
markers that were previously unseen, along with amounts of data too immense for analyses
by manual means. Along with the sequencing chemistries employed, bioinformatic methods
are required to process and interpret this new and extensive data. As more is learnt
about the use of these new technologies for forensic applications, development and
standardization of efficient, favourable tools for each stage of data processing is
being carried out, and faster, more accurate methods that improve on the original
approaches have been developed. As forensic laboratories search for the optimal pipeline
of tools, sequencer manufacturers have incorporated pipelines into sequencer software
to make analyses convenient. This review explores the current state of bioinformatic
methods and tools used for the analyses of forensic markers sequenced on the massively
parallel sequencing (MPS) platforms currently most widely used.
Keywords
To read this article in full you will need to make a payment
Purchase one-time access:
Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online accessOne-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribe:
Subscribe to Forensic Science International: GeneticsAlready a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
References
- More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing.BMC Genomics. 2016; 17https://doi.org/10.1186/s12864-016-3087-2
- Short-read, high-throughput sequencing technology for STR genotyping.Biotech Rapid Dispatches. 2012; 1–6
- Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA.Forensic Sci. Int. Genet. 2017; 26: 30-39https://doi.org/10.1016/j.fsigen.2016.10.008
- Analysis of DNA from post-blast pipe bomb fragments for identification and determination of ancestry.Forensic Sci. Int. Genet. 2017; 28: 195-202https://doi.org/10.1016/j.fsigen.2017.02.016
- High sensitivity multiplex short tandem repeat loci analyses with massively parallel sequencing.Forensic Sci. Int. Genet. 2015; 16: 38-47https://doi.org/10.1016/j.fsigen.2014.11.022
- Deep sequencing provides comprehensive multiplex capabilities.Forensic Sci. Int. Genet. Suppl. Ser. 2013; 4: e334-e335https://doi.org/10.1016/j.fsigss.2013.10.170
- Single nucleotide polymorphism typing with massively parallel sequencing for human identification.Int. J. Legal Med. 2013; 127: 1079-1086https://doi.org/10.1007/s00414-013-0879-7
- Next generation sequencing and its applications in forensic genetics.Forensic Sci. Int. Genet. 2015; 18: 78-89https://doi.org/10.1016/j.fsigen.2015.02.002
- Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.Nucleic Acids Res. 2013; 41: 1-7https://doi.org/10.1093/nar/gks981
- Analysis of the whole mitochondrial genome: translation of the Ion Torrent Personal Genome Machine system to the diagnostic bench?.Eur. J. Hum. Genet. 2014; : 1-8https://doi.org/10.1038/ejhg.2014.49
- A framework for variation discovery and genotyping using next- generation DNA sequencing data.Nat. Genet. 2011; 43: 491-498https://doi.org/10.1038/ng.806.A
- An analytical framework for optimizing variant discovery from personal genomes.Nat. Commun. 2015; 6: 6275https://doi.org/10.1038/ncomms7275
- 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.Forensic Sci. Int. Genet. 2017; 27: 27-40https://doi.org/10.1016/j.fsigen.2016.11.007
- My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing.Forensic Sci. Int. Genet. 2014; 9: 1-8https://doi.org/10.1016/j.fsigen.2013.10.012
- Fast STR allele identification with STRait razor 3.0.Forensic Sci. Int. Genet. 2017; 30: 18-23https://doi.org/10.1016/j.fsigen.2017.05.008
- 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.Forensic Sci. Int. Genet. 2016; 21: 68-75https://doi.org/10.1016/j.fsigen.2015.12.006
- AQME: a forensic mitochondrial DNA analysis tool for next-generation sequencing data.Forensic Sci. Int. Genet. 2017; 31: 189-197https://doi.org/10.1016/j.fsigen.2017.09.010
- Advanced Topics in Forensic DNA Typing: Methodology.2012https://doi.org/10.1016/B978-0-12-374513-2.00005-1
- Advanced Topics in Forensic DNA Typing: Interpretation.2015https://doi.org/10.1016/B978-0-12-405213-0.00015-4
- Multiplex pyrosequencing of InDel markers for forensic DNA analysis.Electrophoresis. 2016; 37: 3039-3045https://doi.org/10.1002/elps.201600255
- Genetic diversity of 38 insertion-deletion polymorphisms in Jewish populations.Forensic Sci. Int. Genet. 2016; 21: 1-4https://doi.org/10.1016/j.fsigen.2015.11.003
- Detection of insertion/deletion polymorphisms from challenged samples using the Investigator DIPplex® Kit.Forensic Sci. Int. Genet. 2015; 16: 29-37https://doi.org/10.1016/j.fsigen.2014.11.020
- DNA methylation and application in forensic sciences.Forensic Sci. Int. 2015; 249: 255-265https://doi.org/10.1016/j.forsciint.2015.01.037
- DNA methylation profiling for a confirmatory test for blood, saliva, semen, vaginal fluid and menstrual blood.Forensic Sci. Int. Genet. 2016; 24: 75-82https://doi.org/10.1016/j.fsigen.2016.06.007
- Developmental validation studies of epigenetic DNA methylation markers for the detection of blood, semen and saliva samples.Forensic Sci. Int. Genet. 2016; 23: 55-63https://doi.org/10.1016/j.fsigen.2016.01.017
- Epigenetic discrimination of identical twins from blood under the forensic scenario.Forensic Sci. Int. Genet. 2017; 0: 67-80https://doi.org/10.1016/j.fsigen.2017.07.014
- DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing.Forensic Sci. Int. Genet. 2017; 28: 225-236https://doi.org/10.1016/j.fsigen.2017.02.009
- Analysis of alu insertion polymorphism in South Morocco (Souss): use of markers in forensic science.Open Forensic Sci. J. 2009; 2: 1-5https://doi.org/10.2174/1874402800902010001
- Development of two highly sensitive forensic sex determination assays based on human DYZ1 and alu repetitive DNA elements.Electrophoresis. 2014; 35: 3028-3035https://doi.org/10.1002/elps.201400103
- INNULs: a novel design amplification strategy for retrotransposable elements for studying population variation.Hum. Heredity. 2012; 74: 27-35https://doi.org/10.1159/000343050
- Inference of human geographic origins using alu insertion polymorphisms.Forensic Sci. Int. 2005; 153: 117-124https://doi.org/10.1016/j.forsciint.2004.10.017
- Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science.Investig. Genet. 2014; 5: 16https://doi.org/10.1186/s13323-014-0016-5
- The human microbiome: an emerging tool in forensics.Microb. Biotechnol. 2017; 10: 228-230https://doi.org/10.1111/1751-7915.12699
- Random whole metagenomic sequencing for forensic discrimination of soils.PLoS One. 2014; 9https://doi.org/10.1371/journal.pone.0104996
- Forensic genetics and genomics: much more than just a human affair.PLoS Genet. 2017; 13: 1-28https://doi.org/10.1371/journal.pgen.1006960
- A global reference for human genetic variation.Nature. 2015; 526: 68-74https://doi.org/10.1038/nature15393
- An integrated map of structural variation in 2504 human genomes.Nature. 2015; 526: 75-81https://doi.org/10.1038/nature15394
- EMPOP-a forensic mtDNA database.Forensic Sci. Int. Genet. 2007; 1: 88-92https://doi.org/10.1016/j.fsigen.2007.01.018
- ALFRED: an allele frequency resource for research and teaching.Nucleic Acids Res. 2012; 40: 1-6https://doi.org/10.1093/nar/gkr924
- Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER).Forensic Sci. Int. Genet. 2016; 24: 97-102https://doi.org/10.1016/j.fsigen.2016.06.008
- STRSeq: a catalog of sequence diversity at human identification Short Tandem Repeat loci.Forensic Sci. Int. Genet. 2017; 31: 111-117https://doi.org/10.1016/j.fsigen.2017.08.017
- The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.Nucleic Acids Res. 2009; 38: 1767-1771https://doi.org/10.1093/nar/gkp1137
- A survey of tools for variant analysis of next-generation genome sequencing data.Brief. Bioinform. 2014; 15: 256-278https://doi.org/10.1093/bib/bbs086
- SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data.BMC Bioinf. 2010; 11: 485https://doi.org/10.1186/1471-2105-11-485
- Considering DNA damage when interpreting mtDNA heteroplasmy in deep sequencing data.Forensic Sci. Int. Genet. 2017; 26: 1-11https://doi.org/10.1016/j.fsigen.2016.09.008
- A comparison of variant calling pipelines using genome in a bottle as a reference.BioMed Res. Int. 2015; 2015https://doi.org/10.1155/2015/456479
- Systematic comparison of variant calling pipelines using gold standard personal exome variants.Sci. Rep. 2015; 5: 17875https://doi.org/10.1038/srep17875
- Nat. Methods. 2013; 9: 357-359https://doi.org/10.1038/nmeth.1923.Fast
H. Li, Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, arXiv Prepr. arXiv. 0 (2013) 3. arXiv:1303.3997 [q-bio.GN].
- Repetitive DNA and next-generation sequencing: computational challenges and solutions.Nat. Rev. Genet. 2013; 13: 36-46https://doi.org/10.1038/nrg3117.Repetitive
- Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.BMC Genomics. 2014; 15: 264https://doi.org/10.1186/1471-2164-15-264
- Tools for mapping high-throughput sequencing data.Bioinformatics. 2012; 28: 3169-3177https://doi.org/10.1093/bioinformatics/bts605
- The sequence alignment/map format and SAMtools.Bioinformatics. 2009; 25: 2078-2079https://doi.org/10.1093/bioinformatics/btp352
- The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.Genome Res. 2010; 20: 1297-1303https://doi.org/10.1101/gr.107524.110
- The variant call format and VCFtools.Bioinformatics. 2011; 27: 2156-2158https://doi.org/10.1093/bioinformatics/btr330
- The international HapMap project.Nature. 2003; 426: 789-796
- Forensically relevant SNP classes.Biotechniques. 2008; 44: 603-610https://doi.org/10.2144/000112806
- SNPs in forensic genetics: a review on SNP typing methodologies.Forensic Sci. Int. 2005; 154: 181-194https://doi.org/10.1016/j.forsciint.2004.10.020
Applied Biosystems, SNaPshot ® Multiplex System for SNP genotyping, (2012) 1–4. 10.1093/gbe/evt066.
- Forensically relevant SNaPshot® assays for human DNA SNP analysis: a review.Int. J. Legal Med. 2017; 131: 21-37https://doi.org/10.1007/s00414-016-1490-5
- Evaluation of the Genplex SNP typing system and a 49plex forensic marker panel.Forensic Sci. Int. Genet. 2007; 1: 180-185https://doi.org/10.1016/j.fsigen.2007.02.007
- McNevin: a SNaPshot of next generation sequencing for forensic SNP analysis.Forensic Sci. Int. Genet. 2015; 14: 50-60https://doi.org/10.1016/j.fsigen.2014.08.013
- Inter-laboratory evaluation of the EUROFORGEN global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.Forensic Sci. Int. Genet. 2016; 23: 178-189https://doi.org/10.1016/j.fsigen.2016.04.008
- A panel of 74 AISNPs: improved ancestry inference within Eastern Asia.Forensic Sci. Int. Genet. 2016; 23: 101-110https://doi.org/10.1016/j.fsigen.2016.04.002
- Developmental validation of the HIrisPlex system: DNA-based eye and hair colour prediction for forensic and anthropological usage.Forensic Sci. Int. Genet. 2014; 9: 150-161https://doi.org/10.1016/j.fsigen.2013.12.006
- Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region.Forensic Sci. Int. Genet. 2016; 20: 71-80https://doi.org/10.1016/j.fsigen.2015.10.003
- Developing a SNP panel for forensic identification of individualsi.Forensic Sci. Int. 2006; 164: 20-32https://doi.org/10.1016/j.forsciint.2005.11.017
- Developmental validation of a custom panel including 273 SNPs for forensic application using Ion Torrent PGM.Forensic Sci. Int. Genet. 2017; 27: 50-57https://doi.org/10.1016/j.fsigen.2016.12.003
- Development of a SNP-based panel for human identification for Indian populations.Forensic Sci. Int. Genet. 2017; 27: 58-66https://doi.org/10.1016/j.fsigen.2016.12.002
- Evaluation of the precision ID Ancestry Panel for crime case work: a SNP typing assay developed for typing of 165 ancestral informative markers.Forensic Sci. Int. Genet. 2017; 28: 138-145https://doi.org/10.1016/j.fsigen.2017.02.013
- STRs vs. SNPs: thoughts on the future of forensic DNA testing.Forensic Sci. Med. Pathol. 2007; 3: 200-205https://doi.org/10.1007/s12024-007-0018-1
- Microhaplotype loci are a powerful new type of forensic marker.Forensic Sci. Int. Genet. Suppl. Ser. 2013; 4: e123-e124https://doi.org/10.1016/j.fsigss.2013.10.063
- Criteria for selecting microhaplotypes: mixture detection and deconvolution.Investig. Genet. 2015; 6: 1https://doi.org/10.1186/s13323-014-0018-3
- Evaluating 130 microhaplotypes across a global set of 83 populations.Forensic Sci. Int. Genet. 2017; 29: 29-37https://doi.org/10.1016/j.fsigen.2017.03.014
- Inference of ancestry in forensic analysis II: analysis of genetic data.Methods Mol. Biol. U. S. 2016; : 255-285https://doi.org/10.1007/978-1-4939-3597-0_19
- Performance of a next generation sequencing SNP assay on degraded DNA.Forensic Sci. Int. Genet. 2015; 19: 1-9https://doi.org/10.1016/j.fsigen.2015.04.010
- Genetic analysis of the Yavapai Native Americans from West-Central Arizona using the Illumina MiSeq FGx™ forensic genomics system.Forensic Sci. Int. Genet. 2016; 24: 18-23https://doi.org/10.1016/j.fsigen.2016.05.008
- Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™.Forensic Sci. Int. Genet. 2015; 17: 110-121https://doi.org/10.1016/j.fsigen.2015.04.007
- Next generation sequencing: improved resolution for paternal/maternal duos analysis.Forensic Sci. Int. Genet. 2016; 24: 83-85https://doi.org/10.1016/j.fsigen.2016.05.015
- Developmental validation of the MiSeq FGx forensic genomics system for targeted next generation sequencing in forensic DNA casework and database laboratories.Forensic Sci. Int. Genet. 2017; 28: 52-70https://doi.org/10.1016/j.fsigen.2017.01.011
- Eye color and the prediction of complex phenotypes from genotypes.Curr. Biol. 2009; 19: R192-R193https://doi.org/10.1016/j.cub.2009.01.027
- The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA.Forensic Sci. Int. Genet. 2013; 7: 98-115https://doi.org/10.1016/j.fsigen.2012.07.005
- STRBase: a short tandem repeat DNA database for the human identity testing community.Nucleic Acids Res. 2001; 29: 320-322https://doi.org/10.1093/nar/29.1.320
- dbSNP: the NCBI database of genetic variation.Nucleic Acids Res. 2001; 29: 308-311https://doi.org/10.1093/nar/29.1.308
- Introducing the forensic research/reference on genetics knowledge base, FROG-kb.Investig. Genet. 2012; 3: 18https://doi.org/10.1186/2041-2223-3-18
- Short tandem repeat typing technologies used in human identity testing.Biotechniques. 2007; 43https://doi.org/10.2144/000112582
- Developmental validation of the GlobalFiler® express PCR amplification kit: a 6-dye multiplex assay for the direct amplification of reference samples.Forensic Sci. Int. Genet. 2015; 19: 148-155https://doi.org/10.1016/j.fsigen.2015.07.013
- Developmental validation of the PowerPlex® 21 system.Forensic Sci. Int. Genet. 2014; 9: 169-178https://doi.org/10.1016/j.fsigen.2013.12.005
- Developmental validation of QIAGEN Investigator ® 24plex QS Kit and Investigator ® 24plex GO! Kit: two 6-dye multiplex assays for the extended CODIS core loci.Forensic Sci. Int. Genet. 2017; 29: 9-20https://doi.org/10.1016/j.fsigen.2017.03.012
- Evaluation of the Illumina ® beta version ForenSeq™ DNA signature prep kit for use in genetic profiling.Forensic Sci. Int. Genet. 2016; 20: 20-29https://doi.org/10.1016/j.fsigen.2015.09.009
- An evaluation of the PowerSeq™ auto system: a multiplex short tandem repeat marker kit compatible with massively parallel sequencing.Forensic Sci. Int. Genet. 2015; 19: 172-179https://doi.org/10.1016/j.fsigen.2015.07.015
- Massively Parallel sequencing of short tandem repeats—population data and mixture analysis results for the PowerSeq™ system.Forensic Sci. Int. Genet. 2016; 24: 86-96https://doi.org/10.1016/j.fsigen.2016.05.016
- Effect of multiple allelic drop-outs in forensic RMNE calculations.Forensic Sci. Int. Genet. 2015; 19: 243-249https://doi.org/10.1016/j.fsigen.2015.08.001
- Towards simultaneous individual and tissue identification: a proof-of-principle study on parallel sequencing of STRs, amelogenin, and mRNAs with the Ion Torrent PGM.Forensic Sci. Int. Genet. 2015; 17: 122-128https://doi.org/10.1016/j.fsigen.2015.04.002
- Sequence variation of 22 autosomal STR loci detected by next generation sequencing.Forensic Sci. Int. Genet. 2016; 21: 15-21https://doi.org/10.1016/j.fsigen.2015.11.005
- Flanking region variation of ForenSeq™ DNA signature prep kit STR and SNP loci in Yavapai Native Americans.Forensic Sci. Int. Genet. 2017; 28: 146-154https://doi.org/10.1016/j.fsigen.2017.02.014
- Characterization of genetic sequence variation of 58 STR loci in four major population groups.Forensic Sci. Int. Genet. 2016; 25: 214-226https://doi.org/10.1016/j.fsigen.2016.09.007
- Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations.Forensic Sci. Int. Genet. 2017; 30: 66-70https://doi.org/10.1016/j.fsigen.2017.06.006
- lobSTR: a short tandem repeat profiler for personal genomes lobSTR: a short tandem repeat profiler for personal genomes.Genome Res. 2012; : 1154-1162https://doi.org/10.1101/gr.135780.111
- STRait razor: a length-based forensic STR allele-calling tool for use with second generation sequencing data.Forensic Sci. Int. Genet. 2013; 7: 409-417https://doi.org/10.1016/j.fsigen.2013.04.005
- STRait Razor v2s: advancing sequence-based STR allele reporting and beyond to other marker systems.Forensic Sci. Int. Genet. 2017; 29: 21-28https://doi.org/10.1016/j.fsigen.2017.03.013
- TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes.Bioinformatics. 2014; 30: 1651-1659https://doi.org/10.1093/bioinformatics/btu068
- SEQ Mapper: a DNA sequence searching tool for massively parallel sequencing data.Forensic Sci. Int. Genet. 2017; 26: 66-69https://doi.org/10.1016/j.fsigen.2016.10.006
- Forensic nomenclature for short tandem repeats updated for sequencing.Forensic Sci. Int. Genet. Suppl. Ser. 2015; 5: e542-e544https://doi.org/10.1016/j.fsigss.2015.09.214
- Massively parallel sequencing of forensic STRs: considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements.Forensic Sci. Int. Genet. 2016; 22: 54-63https://doi.org/10.1016/j.fsigen.2016.01.009
- Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons.Forensic Sci. Int. Genet. 2016; 22: 1-7https://doi.org/10.1016/j.fsigen.2016.01.001
- Evaluation of the early access STR kit v1 on the Ion Torrent PGM™ platform.Forensic Sci. Int. Genet. 2016; 23: 111-120https://doi.org/10.1016/j.fsigen.2016.04.004
- Characterization of human short tandem repeats (STRs) for individual identification using the Ion Torrent.BioChip J. 2015; 9: 164-172https://doi.org/10.1007/s13206-015-9210-7
- ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats.Bioinformatics. 2013; 29: 1734-1741https://doi.org/10.1093/bioinformatics/btt277
- STR-realigner: a realignment method for short tandem repeat regions.BMC Genomics. 2016; 17: 991https://doi.org/10.1186/s12864-016-3294-x
- Inferring short tandem repeat variation from paired-end short reads.Nucleic Acids Res. 2014; 42https://doi.org/10.1093/nar/gkt1313
- Short tandem repeat number estimation from paired-end reads for multiple individuals by considering coalescent tree.BMC Genomics. 2016; 17: 494https://doi.org/10.1186/s12864-016-2821-0
- Genome-wide profiling of heritable and de novo STR variations.Nat. Methods. 2017; 14: 590-592https://doi.org/10.1038/nmeth.4267
- STRait razor v2.0: the improved STR allele identification tool-razor.Forensic Sci. Int. Genet. 2015; 14: 182-186https://doi.org/10.1016/j.fsigen.2014.10.011
- Bpipe: a tool for running and managing bioinformatics pipelines.Bioinformatics. 2012; 28: 1525-1526https://doi.org/10.1093/bioinformatics/bts167
- Forensic massively parallel sequencing data analysis tool: implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application.Forensic Sci. Int. Genet. 2015; 15: 2-7https://doi.org/10.1016/j.fsigen.2014.10.006
- Development and validation of a new STR 25-plex typing system.Forensic Sci. Int. Genet. 2015; 17: 61-69https://doi.org/10.1016/j.fsigen.2015.03.008
- A high-throughput Sanger strategy for human mitochondrial genome sequencing.BMC Genomics. 2013; 14: 881https://doi.org/10.1186/1471-2164-14-881
- Sequence and organization of the human mitochondrial genome.Nature. 1981; 290: 457-465https://doi.org/10.1038/290457a0
- Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA.Nat. Genet. 1999; 23: 147https://doi.org/10.1038/13779
- A human mitochondrial DNA standard reference material for quality control in forensic identification, medical diagnosis, and mutation detection.Genomics. 1999; 55: 135-146https://doi.org/10.1006/geno.1998.5513
- Extended guidelines for mtDNA typing of population data in forensic science.Forensic Sci. Int. Genet. 2007; 1: 13-19https://doi.org/10.1016/j.fsigen.2006.11.003
- The mitochondrial landscape of African Americans: an examination of morethan 2500 control region haplotypes from 22 U.S. locations.Forensic Sci. Int. Genet. 2016; 22: 139-148https://doi.org/10.1016/j.fsigen.2016.01.002
- High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq.Forensic Sci. Int. Genet. 2014; 12: 128-135https://doi.org/10.1016/j.fsigen.2014.06.001
- DNA Commission of the International Society for Forensic Genetics: revised and extended guidelines for mitochondrial DNA typing.Forensic Sci. Int. Genet. 2014; 13: 134-142https://doi.org/10.1016/j.fsigen.2014.07.010
- Massively parallel sequencing of the entire control region and targeted coding region SNPs of degraded mtDNA using a simplified library preparation method.Forensic Sci. Int. Genet. 2016; 22: 37-43https://doi.org/10.1016/j.fsigen.2016.01.014
- Development of a control region-based mtDNA SNaPshot™ selection tool, integrated into a mini amplicon sequencing method.Sci. Justice. 2016; 56: 96-103https://doi.org/10.1016/j.scijus.2015.11.003
- Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples.Forensic Sci. Int. Genet. 2015; 15: 8-15https://doi.org/10.1016/j.fsigen.2014.11.009
- Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians.Int. J. Legal Med. 2004; 118: 137-146https://doi.org/10.1007/s00414-004-0427-6
- The use of mitochondrial DNA single nucleotide polymorphisms to assist in the resolution of three challenging forensic cases.J. Forensic Sci. 2009; 54: 887-891https://doi.org/10.1111/j.1556-4029.2009.01069.x
- Helena, the hidden beauty: resolving the most common West Eurasian mtDNA control region haplotype by massively parallel sequencing an Italian population sample.Forensic Sci. Int. Genet. 2015; 15: 21-26https://doi.org/10.1016/j.fsigen.2014.09.012
- Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing.Forensic Sci. Int. Genet. 2015; 18: 131-139https://doi.org/10.1016/j.fsigen.2015.05.003
- Heteroplasmic substitutions in the entire mitochondrial genomes of human colon cells detected by ultra-deep 454 sequencing.Forensic Sci. Int. Genet. 2015; 15: 16-20https://doi.org/10.1016/j.fsigen.2014.10.021
- MitoSAVE: mitochondrial sequence analysis of variants in Excel.Forensic Sci. Int. Genet. 2014; 12: 122-125https://doi.org/10.1016/j.fsigen.2014.05.013
- MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing.Bioinformatics. 2014; 30: 3115-3117https://doi.org/10.1093/bioinformatics/btu483
- Strategies for complete mitochondrial genome sequencing on Ion Torrent PGM™ platform in forensic sciences.Forensic Sci. Int. Genet. 2016; 22: 11-21https://doi.org/10.1016/j.fsigen.2016.01.004
- Concordance and reproducibility of a next generation mtGenome sequencing method for high-quality samples using the Illumina MiSeq.Forensic Sci. Int. Genet. 2016; 24: 103-111https://doi.org/10.1016/j.fsigen.2016.06.003
- Evaluation of GeneMarker ® HTS for improved alignment of mtDNA MPS data, haplotype determination, and heteroplasmy assessment.Forensic Sci. Int. Genet. 2017; 28: 90-98https://doi.org/10.1016/j.fsigen.2017.01.016
- Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics. 2009; 25: 1754-1760https://doi.org/10.1093/bioinformatics/btp324
- Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq.Forensic Sci. Int. Genet. 2014; 13: 20-29https://doi.org/10.1016/j.fsigen.2014.05.007
- Evaluation of next generation mtGenome sequencing using the Ion Torrent personal genome machine (PGM).Forensic Sci. Int. Genet. 2013; 7: 632-639https://doi.org/10.1016/j.fsigen.2013.09.007
- Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation.Hum. Mutat. 2009; 30: 386-394https://doi.org/10.1002/humu.20921
- HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups.Hum. Mutat. 2011; 32: 25-32https://doi.org/10.1002/humu.21382
- HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.Nucleic Acids Res. 2016; 44 (W58-63)https://doi.org/10.1093/nar/gkw233
- MitoTool: a web server for the analysis and retrieval of human mitochondrial DNA sequence variations.Mitochondrion. 2011; 11: 351-356https://doi.org/10.1016/j.mito.2010.09.013
- HmtDB: a genomic resource for mitochondrion-based human variability studies.Nucleic Acids Res. 2012; 40: 1150-1159https://doi.org/10.1093/nar/gkr1086
- mtDNAmanager: a web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences.BMC Bioinf. 2008; 9: 483https://doi.org/10.1186/1471-2105-9-483
- Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA).Forensic Sci. Int. Genet. 2013; 7: 601-609https://doi.org/10.1016/j.fsigen.2013.07.005
- SAM: string-based sequence search algorithm for mitochondrial DNA database queries.Forensic Sci. Int. Genet. 2011; 5: 126-132https://doi.org/10.1016/j.fsigen.2010.10.006
Article info
Publication history
Published online: December 12, 2017
Accepted:
December 10,
2017
Received in revised form:
November 30,
2017
Received:
September 13,
2017
Identification
Copyright
© 2017 Elsevier B.V. All rights reserved.
