scholarly journals Expanding the Swiss autosomal marker set to 32 STRs

2021 ◽  
Author(s):  
Martin Zieger ◽  
Alexandre Gouy ◽  
Silvia Utz
Keyword(s):  
Allele Frequency ◽  
Reference Database ◽  
High Quality ◽  
Autosomal Str ◽  
Autosomal Marker

AbstractBy genotyping 1198 individuals with the Qiagen Investigator® HDplex Kit, we expand the Swiss autosomal STR dataset to 32 loci, providing additional resources for complex kinship cases. We present the first high-quality allele frequency dataset for loci D2S1360, D5S2500, D7S1517, and D10S2325 that will be accessible through the ENFSI reference database STRidER. For loci D3S1744, D4S2366, D6S474, D8S1132, and D21S2055, we provide a first European STRidER dataset.

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

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 901
Author(s):  
Martin Bodner ◽  
Walther Parson
Keyword(s):  
Quality Control ◽  
Allele Frequency ◽  
Error Rate ◽  
Tandem Repeats ◽  
Forensic Genetics ◽  
Quality Standard ◽  
Reference Database ◽  
Autosomal Str ◽  
Scientific Papers ◽  
High Quality Standard

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in the first two years of STRidER QC since 2017 revealed that about two-thirds of the STR datasets were either being withdrawn by the authors after initial feedback or rejected based on a conservative error rate.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.

scholarly journals X-chromosomal STR based genetic polymorphisms and demographic history of Sri Lankan ethnicities and their relationship with global populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nandika Perera ◽  
Gayani Galhena ◽  
Gaya Ranawaka
Keyword(s):  
Allele Frequency ◽  
Demographic History ◽  
Evolutionary Genetics ◽  
Haplotype Frequency ◽  
Allele Frequency Distribution ◽  
Sri Lankan ◽  
Frequency Distributions ◽  
Autosomal Str ◽  
History Of ◽  
Multiplex System

AbstractA new 16 X-short tandem repeat (STR) multiplex PCR system has recently been developed for Sr Lankans, though its applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed. In this study, 838 unrelated individuals covering all four major ethnic groups (Sinhalese, Sri Lankan Tamils, Indian Tamils and Moors) in Sri Lanka were successfully genotyped using this new multiplex system. The results indicated a high forensic efficiency for the tested loci in all four ethnicities confirming its suitability for forensic applications of Sri Lankans. Allele frequency distribution of Indian Tamils showed subtle but statistically significant differences from those of Sinhalese and Moors, in contrast to frequency distributions previously reported for autosomal STR alleles. This suggest a sex biased demographic history among Sri Lankans requiring a separate X-STR allele frequency database for Indian Tamils. Substantial differences observed in the patterns of LD among the four groups demand the use of a separate haplotype frequency databases for each individual ethnicity. When analysed together with other 14 world populations, all Sri Lankan ethnicities except Indian Tamils clustered closely with populations from Indian Bhil tribe, Bangladesh and Europe reflecting their shared Indo-Aryan ancestry.

Allele frequency of 19 autosomal STR loci in the Bai population from the southwestern region of mainland China

2015 ◽  
Vol 36 (19) ◽  
pp. 2498-2503 ◽  
Author(s):  
Yi Li ◽  
Yine Hong ◽  
Xiujiang Li ◽  
Jinmeng Yang ◽  
Lanjiang Li ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Mainland China ◽  
Str Loci ◽  
Autosomal Str

Allele frequency distribution for 15 autosomal STR loci in Afridi Pathan population of Uttar Pradesh, India

2009 ◽  
Vol 11 (6) ◽  
pp. 308-311 ◽  
Author(s):  
Sabahat Noor ◽  
Shahnaz Ali ◽  
Muthukrishnan Eaaswarkhanth ◽  
Ikramul Haque
Keyword(s):  
Allele Frequency ◽  
Frequency Distribution ◽  
Uttar Pradesh ◽  
Allele Frequency Distribution ◽  
Str Loci ◽  
Autosomal Str

Allele frequency and forensic efficiency of 15 autosomal STR loci in the Sardinian population (Italy)

2019 ◽  
Vol 41 ◽  
pp. e26-e29 ◽  
Author(s):  
Maria Elena Ghiani ◽  
Alessandro Mameli ◽  
Renato Robledo ◽  
Carla Maria Calò
Keyword(s):  
Allele Frequency ◽  
Str Loci ◽  
Autosomal Str ◽  
Forensic Efficiency ◽  
Sardinian Population

scholarly journals Update of an on-line autosomal STR and Y-STR reference database of Argentina

2009 ◽  
Vol 2 (1) ◽  
pp. 382-383 ◽  
Author(s):  
Evguenia Alechine ◽  
Miguel Marino ◽  
Andrea Sala ◽  
Maria Cecilia Bobillo ◽  
Mariela Caputo ◽  
...  
Keyword(s):  
Reference Database ◽  
Autosomal Str ◽  
On Line

scholarly journals Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT

2019 ◽  
Author(s):  
F.A. Bastiaan von Meijenfeldt ◽  
Ksenia Arkhipova ◽  
Diego D. Cambuy ◽  
Felipe H. Coutinho ◽  
Bas E. Dutilh
Keyword(s):  
Dna Sequences ◽  
Real World ◽  
Taxonomic Classification ◽  
Reference Database ◽  
Annotation Tool ◽  
High Quality

ABSTRACTCurrent-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high-quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity. In a real-world challenge, we apply BAT to over 900 MAGs from a recent rumen metagenomics study and classified 97% consistently with prior phylogeny-based classifications, but in a fully automated fashion.

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