A genomic audit of newly-adopted autosomal STRs for forensic identification

Phillips, C.

doi:10.1016/j.fsigen.2017.04.011

Cited by 33 publications

(22 citation statements)

References 33 publications

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“…It is likely that dragging errors in table preparation contributed to the latter. Even minimal nomenclature errors might lead to confusion with (upcoming) other STR loci, such as D2S4 4 1 vs. D2S4 1 1 [ 34 , 35 ]. In one submission, locus D5S2500 was incorrectly assigned by the typing kit manufacturer instead of D5S2800 [ 36 ].…”

Section: Results Of Strider Quality Controlmentioning

confidence: 99%

“…This is supported by more detailed proficiency test reports that specified manual allele calling errors, lacking separators between the two alleles at one locus, exchange of alleles between loci [ 75 ] and the tendency toward the concentration of errors in some “not so good” submissions [ 22 , 33 , 61 , 64 , 65 , 75 ]. Further analyses on (published) datasets confirmed the role of transcriptional errors [ 22 ] and found duplicate genotypes across database subsets [ 21 , 22 , 78 ], locus name misspelling [ 34 ], as well as allele swapping [ 26 ]. Information on errors and error rates in MPS STR typing is expected from ongoing collaborative exercises (P.A.…”

Section: Discussionmentioning

confidence: 99%

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The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets

Bodner

Parson

2020

Genes

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STRidER, the STRs for Identity ENFSI Reference Database, is a curated, freely publicly available online allele frequency database, quality control (QC) and software platform for autosomal Short Tandem Repeats (STRs) developed under the endorsement of the International Society for Forensic Genetics. Continuous updates comprise additional STR loci and populations in the frequency database and many further STR-related aspects. One significant innovation is the autosomal STR data QC provided prior to publication of datasets. Such scrutiny was lacking previously, leaving QC to authors, reviewers and editors, which led to an unacceptably high error rate in scientific papers. The results from scrutinizing 184 STR datasets containing >177,000 individual genotypes submitted in the first two years of STRidER QC since 2017 revealed that about two-thirds of the STR datasets were either being withdrawn by the authors after initial feedback or rejected based on a conservative error rate. Almost no error-free submissions were received, which clearly shows that centralized QC and data curation are essential to maintain the high-quality standard required in forensic genetics. While many errors had minor impact on the resulting allele frequencies, multiple error categories were commonly found within single datasets. Several datasets contained serious flaws. We discuss the factors that caused the errors to draw the attention to redundant pitfalls and thus contribute to better quality of autosomal STR datasets and allele frequency reports.

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Section: Results Of Strider Quality Controlmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets

Bodner

Parson

2020

Genes

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“…Precision ID GlobalFiler NGS STR Panel (Thermo Fisher Scientific). If new STR loci (see [16]) are targeted in commercially available assays launched in the future, additional records will be created.…”

Section: Samples and Submission Strategymentioning

confidence: 99%

STRSeq: A catalog of sequence diversity at human identification Short Tandem Repeat loci

Gettings

Borsuk

Ballard

et al. 2017

Forensic Science International: Genetics

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The STR Sequencing Project (STRSeq) was initiated to facilitate the description of sequence-based alleles at the Short Tandem Repeat (STR) loci targeted in human identification assays. This international collaborative effort, which has been endorsed by the ISFG DNA Commission, provides a framework for communication among laboratories. The initial data used to populate the project are the aggregate alleles observed in targeted sequencing studies across four laboratories: National Institute of Standards and Technology (N=1786), Kings College London (N=1043), University of North Texas Health Sciences Center (N=839), and University of Santiago de Compostela (N=944), for a total of 4612 individuals. STRSeq data are maintained as GenBank records at the U.S. National Center for Biotechnology Information (NCBI), which participates in a daily data exchange with the DNA DataBank of Japan (DDBJ) and the European Nucleotide Archive (ENA). Each GenBank record contains the observed sequence of a STR region, annotation ("bracketing") of the repeat region and flanking region polymorphisms, information regarding the sequencing assay and data quality, and backward compatible length-based allele designation. STRSeq GenBank records are organized within a BioProject at NCBI (https://www.ncbi.nlm.nih.gov/bioproject/380127), which is sub-divided into: commonly used autosomal STRs, alternate autosomal STRs, Y-chromosomal STRs, and X-chromosomal STRs. Each of these categories is further divided into locus-specific BioProjects. The BioProject hierarchy facilitates access to the GenBank records by browsing, BLAST searching, or ftp download. Future plans include user interface tools at strseq.nist.gov, a pathway for submission of additional allele records by laboratories performing population sample sequencing and interaction with the STRidER web portal for quality control (http://strider.online).

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“…2. Approximate position in the chromosome in mega bases from Phillips 201735 3. Calculated per diploid genome, in bit, details in the supporting information.…”

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confidence: 99%

Genomic encryption of digital data stored in synthetic DNA

Grass

Heckel

Dessimoz

et al. 2019

Preprint

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Today, we can read human genomes and store digital data robustly in synthetic DNA.Here we report a strategy to intertwine these two technologies to enable the secure storage of valuable information in synthetic DNA, protected with personalized keys. We show that genetic short tandem repeats (STRs) contain sufficient entropy to generate strong encryption keys, and that only one technology, DNA sequencing, is required to simultaneously read key and data. Using this approach, we experimentally generated 80 bit strong keys from human DNA, and used such a key to encrypt 17kB of digital information stored in synthetic DNA. Finally, the decrypted information was recovered perfectly from a single massively parallel sequencing run.

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A genomic audit of newly-adopted autosomal STRs for forensic identification

Cited by 33 publications

References 33 publications

The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets

The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets

STRSeq: A catalog of sequence diversity at human identification Short Tandem Repeat loci

Genomic encryption of digital data stored in synthetic DNA

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