SEQ Mapper: A DNA sequence searching tool for massively parallel sequencing data

Lee, James Chun-I; Tseng, Bill; Chang, Liang-Kai; Linacre, Adrian

doi:10.1016/j.fsigen.2016.10.006

Cited by 10 publications

(7 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…An optimal package for MPS data analysis needs to be accurate, time-saving and easy to operate. Several packages has been published to make this process convenient for forensic uses, such as TSSV 11 , STRait Razor 12,13 , STRinNGS 14 , SEQ Mapper 15 , FDStools 16 et al Sequencer manufacturers also carried out supplementary analysis packages to fit for the data produced by their sequencers, such as ForenSeq Universal Analysis Software 17 (UAS, Illumina, San Diego, CA) and Ion Torrent Suite Software Plugins 18 (Thermo Fisher Scientific, South San Francisco, CA).…”

mentioning

confidence: 99%

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Peng

Zhang

Ren

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Massively parallel sequencing (MPS) has rapidly become a promising method for forensic DNA typing, due to its ability to detect a large number of markers and samples simultaneously in a single reaction, and sequence information can be obtained directly. In the present study, two kinds of forensic genetic markers, short tandem repeat (STR) and identity-informative single nucleotide polymorphism (iiSNP) were analyzed simultaneously using ForenSeq DNA Signature Prep Kit, a commercially available kit on MPS platform. A total of 152 DNA markers, including 27 autosomal STR (A-STR) loci, 24 Y chromosomal STR (Y-STR) loci, 7 X chromosomal STR (X-STR) loci and 94 iiSNP loci were genotyped for 107 Tibetan individuals (53 males and 54 females). Compared with length-based STR typing methods, 112 more A-STR alleles, 41 more Y-STR alleles, and 24 more X-STR alleles were observed at 17 A-STRs, 9 Y-STRs, and 5 X-STRs using sequence-based approaches. Thirty-nine novel sequence variations were observed at 20 STR loci. When the flanking regions were also analyzed in addition to target SNPs at the 94 iiSNPs, 38 more alleles were identified. Our study provided an adequate genotype and frequencies data of the two types of genetic markers for forensic practice. Moreover, we also proved that this panel is highly polymorphic and informative in Tibetan population, and should be efficient in forensic kinship testing and personal identification cases. Several genetic markers have been introduced to forensic genetics to clarify the problems of kinship analysis and personal identification. Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are commonly used genetic markers in present forensic cases 1,2. STRs, usually 2-6 bp in length, are commonly typed with the amplified fragment length polymorphism (Amp-FLP) strategy combining fluorescently labelled multiplex PCR and capillary electrophoresis (CE) 3. Allele calling can thus be inferred from fragment length by comparison with a locus specific allelic ladder that has been previously sequenced, where the number of repeat units is distinct 2. Thus, each allele is regarded as a lengthbased (LB) allele using this approach. With the advancement of sequencing technologies over the last decade, the existence of sequence structure variations in alleles with the same length has been uncovered 4. SNPs, which could be amplified with smaller amplicons, are bi-allelic genetic markers with lower mutation rates compared with STRs 5. Several autosomal SNP marker sets and detection methods, such as single-base extension, chip-based microarrays, and allele-specific hybridization arrays, have been developed to compensate for the relatively weaker discrimination power of single loci caused by the bi-allelic nature of the human genome 5-7. However, these methods are not widely used in forensic practice due to the requirement of higher DNA inputs or the limited ability to detect a vast number of SNP loci in a single reaction 8. Different from detection methods mentioned above, massively paralle...

show abstract

mentioning

confidence: 99%

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Peng

Zhang

Ren

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Wykazano też, że techniki NGS odznaczają się wyższą czułością w porównaniu ze standardową analizą STR, nawet jeśli badane próbki entomologiczne zawierają minimalne ilości DNA lub materiał jest silnie zdegradowany [5,152]. Aby zwiększyć moc dyskryminacyjną, jako cele dla technik NGS można wykorzystywać STR i SNP [153]. Ponieważ niewiele wiadomo o zachowaniu owadów z dala od padliny, podejmowane są próby opracowania systemu profilowania mikrosatelitarnego przy wykorzystaniu NGS do analizy zachowań populacyjnych przy wyższej rozdzielczości [151].…”

Section: Microsatellites Markersunclassified

“…Moreover, it is revealed that NGS techniques have higher sensitivity in comparison to standard STR analysis, even with using low template and degraded entomological samples [5,152]. To maximize the power of discrimination, STRs and SNPs can be incorporated as targets for NGS [153]. Because of little information is known about insect behaviour away from carrion.…”

Section: Microsatellites Markersmentioning

confidence: 99%

Applications of forensic entomology: overview and update

Aly

Aldeyarbi

2020

amsik

View full text Add to dashboard Cite

Streszczenie Mimo ogromnych postępów w badaniach podstawowych i stosowanych entomologia sądowa stale się rozwija i jest uznawana za interdyscyplinarną dziedzinę wiedzy. W zestawieniu z innymi naukami prawnymi i biologicznymi publikacje z zakresu entomologii sądowej są jednak stosunkowo skromne, podobnie jak liczba entomologów sądowych. Głównym celem niniejszej pracy jest przedstawienie znaczenia entomologii sądowej przez omówienie jej zastosowań, czynności podejmowane przez entomologów mogą bowiem dostarczać istotnych informacji dotyczących czasu, miejsca i przyczyny śmierci, ułatwiać identyfikację sprawców i/lub ofiar przestępstwa, a w niektórych przypadkach także określać stan zaniedbania ofiar przed śmiercią. W pracy omówiono też możliwość wykorzystywania zdobyczy najnowocześniejszych technologii. Interdyscyplinarność prac badawczych umożliwi dalsze zgłębianie tej dziedziny, przyczyniając się do wytyczania nowych obszarów badań z korzyścią dla rozwoju nauki oraz zastosowań kryminalistycznych.

show abstract

“…Feedback emailed to strandwg@gmail.com will be distributed and discussed at future STRAND Working Group meetings. [35] http://forensic.mc.ntu.edu.tw:9000/SEQMapperWeb/Default.aspx STRait Razor v2s [3] STRait Razor 3.0 [36] https://www.unthsc.edu/graduate-school-of-biomedical-sciences/molecular-and-medical-genetics/laboratory-faculty-and-staff/strait-razor/ STRinNGS [37] Upon request from the University of Copenhagen ToaSTR [38] https://www.toastr.de/ Agnostic, for purchase…”

Section: Str Sequence Analysis Softwarementioning

confidence: 99%

Report from the STRAND Working Group on the 2019 STR sequence nomenclature meeting

Gettings

Ballard

Bodner

et al. 2019

Forensic Science International: Genetics

View full text Add to dashboard Cite

This report summarizes topics discussed at the STR sequence nomenclature meeting hosted by the STRAND Working Group in April 2019. Invited attendees for this meeting included researchers known-to-us to be developing STR sequence-based nomenclature schemata, scientific representatives from vendors developing STR sequence bioinformatic methods, DNA intelligence database curators, and academic experts in STR genomics. The goal of this meeting was to provide a forum for individuals developing nomenclature schemata to present and discuss their ideas, encouraging mutual awareness, identification of differences in approaches, opposing aspects, and opportunities for parallelization while some approaches are still under development.

show abstract

SEQ Mapper: A DNA sequence searching tool for massively parallel sequencing data

Cited by 10 publications

References 9 publications

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Applications of forensic entomology: overview and update

Report from the STRAND Working Group on the 2019 STR sequence nomenclature meeting

Contact Info

Product

Resources

About