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in the first two years of STRidER QC since 2017 revealed that about two-thirds of the STR datasets were either being withdrawn by the authors after initial feedback or rejected based on a conservative error rate.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 Analysis of allele frequencies of the selected 15 autosomal STR markers in Tikrit population – Iraq with comparison to Middle Eastern, African, and Europeans

2021 ◽  
pp. 75-84
Author(s):  
Maan Hasan Salih ◽  
Akeel Hussain Ali Al-Assie ◽  
Majeed Arsheed Sabbah
Keyword(s):  
Tandem Repeats ◽  
Human Genetics ◽  
Forensic Genetics ◽  
Middle Eastern ◽  
Allele Frequencies ◽  
Match Probability ◽  
Discrimination Power ◽  
Str Loci ◽  
Dna Database ◽  
Autosomal Str

Short tandem repeats (STRs) have been recommended as the highest polymorphic loci among the humana DNA regions. Therefore, STRs are agreeable to many genetic fields like forensic, population genetics and anthropological studies. The main aim of this research is to evaluate the autosomal STRs in Tikrit city-Iraq, to expand the human genetics database and forensic genetics analysis. The DNA database was obtained from 306 unrelated volunteers from native Tikrit population-Iraq, using 15 autosomal STR loci. The current study determined the allele frequencies in the Tikrit population and then compared them with other national Iraqi populations as well as with populations in the Middle East, Africa, and Europe. The highest level of heterozygosity was observed in D8S1179 and TH01 loci (0.797), while the less level was shown by CSF1PO (0.48). The departure from HWE Equilibrium was recorded in only 3 STR loci from a total of 15 loci analyzed (p<0.003). The Combined Match Probability (CMP) for 15 autosomal STR was 1 in 7.89208×10-19 and the Combined Discrimination Power (CDP) was 0.9999999997. The discrimination power (DP) was especially high in D2S1338, D18S51, D19S433 and D21S11. Based on the results observed in a Dendrogram, Tikrit population was clustered with other populations, likely reflecting the historical and geographical factors. D2S1338, D18S51, D19S433 and D21S11 markers were recognized as suitable for forensic genetics analysis in Tikrit population. Also, the 15 STRs markers provide information for the studies of genetic distances between the current study and other included populations to be compared with this study.

scholarly journals Comparative analysis of allele variation using allele frequencies according to sample size in Korean population

2021 ◽  
Vol 43 (11) ◽  
pp. 1301-1305
Author(s):  
Hyun-Chul Park ◽  
Eu-Ree Ahn ◽  
Sang-Cheul Shin
Keyword(s):  
Comparative Analysis ◽  
Sample Size ◽  
Allele Frequency ◽  
Tandem Repeats ◽  
Population Studies ◽  
Forensic Genetics ◽  
Sampling Bias ◽  
Allele Frequencies ◽  
Rare Alleles ◽  
Allele Variation

Abstract Background Allele frequency using short tandem repeats (STRs) is used to calculate likelihood ratio for database match, to interpret DNA mixture and to estimate ethnic groups in forensic genetics. In Korea, three population studies for 23 STR loci have been conducted with different sample size for forensic purposes. Objective We performed comparative analysis to determine how the difference of sample size affects the allele frequency and allele variation within same ethnic population (i.e. Korean). Furthermore, this study was conducted to check how the sampling group and multiplex kit also affect allele variation such as rare alleles and population specific alleles. Methods To compare allele variation, we used allele frequencies of three population data published from three Korean forensic research groups. Allele frequencies were calculated using different sample sizes and multiplex kits: 526, 1000, and 2000 individuals, respectively. Results The results showed the different distribution of allele frequencies in some loci. There was also a difference in the number of rare alleles observed by the sample size and sampling bias. In particular, an allele of 9.1 in the D2S441 locus was not observed in population study with 526 individuals due to multiplex kits. Conclusion Because the allele frequencies play an important role in forensic genetics, even if the samples are derived from the same population, it is important to consider the effects of sample size, sampling bias, and selection of multiplex kits in population studies.

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 A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wendell Jones ◽  
Binsheng Gong ◽  
Natalia Novoradovskaya ◽  
Dan Li ◽  
Rebecca Kusko ◽  
...  
Keyword(s):  
Quality Control ◽  
Allele Frequency ◽  
Liquid Biopsy ◽  
Limit Of Detection ◽  
Reference Sample ◽  
Digital Pcr ◽  
Detection Sensitivity ◽  
Analytical Accuracy ◽  
And Performance ◽  
Reference Samples

Abstract Background Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance. Results In reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5–100× more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels. Conclusion These new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.

scholarly journals Comparative Study of Iran and the UK national curriculum based on the principles of Mind, Brain and Education

2019 ◽  
Vol 8 (1) ◽  
pp. 46
Author(s):  
Nazanin Reza Zadeh Mottaghi ◽  
Mahmoud Talkhabi
Keyword(s):  
Educational System ◽  
Teaching And Learning ◽  
National Curriculum ◽  
Quality Standard ◽  
Thinking Skills ◽  
Reflective Practices ◽  
Science Of Mind ◽  
High Quality Standard ◽  
The Uk ◽  
Collaborative Activities

This study compares the national curriculum of Iran and the UK to find out how the educational system indeveloping countries such as Iran can be improved. Because of implementing thinking skills and cognitive education,the educational system in the UK benefits from a high-quality standard. The science of mind, brain, educationintroduces some principles to improve teaching and learning methods and provide thoughtful and lifelong learnersfor the societies. In this study, we specified the main parts of the national curriculum in both countries and selectedsome of the principles to determine whether these two countries apply them in their national curriculum. Some ofthese principles focus on some significant issues: teaching models, the use of Meta-discipline and HolisticTechniques, authentic learning experiences, use of products, processing and progressing Evaluations, developingexplicit learning objectives, how to benefit from thinking and reflective practices, using collaborative and democraticactivities, preparing students to set personal objectives, giving themselves feedbacks, technology and flippedclassrooms, and beginning Year- Round Schooling. The results show that Iran needs more precise and detailedlearning objectives in its curriculum, use of democratic and collaborative activities with academics and students,develop thinking and reflective practices which play vital roles in upgrading the educational system. Moreover, it issuggested that the UK and Iran should consider embedded evaluations and flipped classrooms to meet the needs ofnew generation of learners.

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.

scholarly journals Comparison of the Allelic Alterations between InDel and STR Markers in Tumoral Tissues Used for Forensic Purposes

Medicina ◽  
2021 ◽  
Vol 57 (3) ◽  
pp. 226
Author(s):  
Pamela Tozzo ◽  
Arianna Delicati ◽  
Anna Chiara Frigo ◽  
Luciana Caenazzo
Keyword(s):  
Colorectal Cancer ◽  
Genomic Instability ◽  
Tandem Repeats ◽  
Forensic Genetics ◽  
Tumor Type ◽  
Forensic Dna ◽  
Dna Identification ◽  
Human Dna ◽  
Tumor Transformation ◽  
Paternity Tests

Background and objectives: Over the last two decades, human DNA identification and kinship tests have been conducted mainly through the analysis of short tandem repeats (STRs). However, other types of markers, such as insertion/deletion polymorphisms (InDels), may be required when DNA is highly degraded. In forensic genetics, tumor samples may sometimes be used in some cases of human DNA identification and in paternity tests. Nevertheless, tumor genomic instability related to forensic DNA markers should be considered in forensic analyses since it can compromise genotype attribution. Therefore, it is useful to know what impact tumor transformation may have on the forensic interpretation of the results obtained from the analysis of these polymorphisms. Materials and Methods: The aim of this study was to investigate the genomic instability of InDels and STRs through the analysis of 55 markers in healthy tissue and tumor samples (hepatic, gastric, breast, and colorectal cancer) in 66 patients. The evaluation of genomic instability was performed comparing InDel and STR genotypes of tumor samples with those of their healthy counterparts. Results: With regard to STRs, colorectal cancer was found to be the tumor type affected by the highest number of mutations, whereas in the case of InDels the amount of genetic mutations turned out to be independent of the tumor type. However, the phenomena of genomic instability, such as loss of heterozygosity (LOH) and microsatellite instability (MSI), seem to affect InDels more than STRs hampering genotype attribution. Conclusion: We suggest that the use of STRs rather than InDels could be more suitable in forensic genotyping analyses given that InDels seem to be more affected than STRs by mutation events capable of compromising genotype attribution.

scholarly journals Accurate measurement of microsatellite length by disrupting its tandem repeat structure

2021 ◽  
Author(s):  
Dan Levy ◽  
Zihua Wang ◽  
Andrea Moffitt ◽  
Michael H. Wigler
Keyword(s):  
Tandem Repeat ◽  
Error Rate ◽  
Tandem Repeats ◽  
Clinical Applications ◽  
Error Rates ◽  
Sequence Motifs ◽  
High Error Rate ◽  
Repeat Structure ◽  
Flanking Regions ◽  
Simple Sequence

Replication of tandem repeats of simple sequence motifs, also known as microsatellites, is error prone and variable lengths frequently occur during population expansions. Therefore, microsatellite length variations could serve as markers for cancer. However, accurate error-free quantitation of microsatellite lengths is difficult with current methods because of a high error rate during amplification and sequencing. We have solved this problem by using partial mutagenesis to disrupt enough of the repeat structure so that it can replicate faithfully, yet not so much that the flanking regions cannot be reliably identified. In this work we use bisulfite mutagenesis to convert a C to a U, later read as T. Compared to untreated templates, we achieve three orders of magnitude reduction in the error rate per round of replication. By requiring two independent first copies of an initial template, we reach error rates below one in a million. We discuss potential clinical applications of this method.

scholarly journals A structural analysis in seismic archaeology: the walls of Noto and the 1693 earthquake

1995 ◽  
Vol 38 (5-6) ◽  
Author(s):  
E. Guidoboni ◽  
P. Riva ◽  
V. Petrini ◽  
A. Madini Moretti ◽  
G. Lombardini
Keyword(s):  
Finite Element ◽  
Research Programme ◽  
Historical Earthquakes ◽  
Quality Standard ◽  
Seismic Effects ◽  
Ground Acceleration ◽  
Element Analysis ◽  
Second Development ◽  
High Quality Standard ◽  
The One

A crucial problenl for seismic archeology is how to recognize seismic effects and how to date them. On an experimental basis. we proposed that the problem be reversed, and that we begin at the other end: i.e. by analyzing already known seismic effects on ancient structures, testified by written sources. to be able to .calibrate>> the types or possible observations and any subsequent elaborations. The choice of the walls of Noto was suggested by the fact that Noto was abandoned following the earthquake of l693 (I,= XI MCS. Me 7.5) which had already been studied in depth as part of an ING research programme (1988-92). Moreover, just after recent research, this event proved to be reconstructed with a high quality standard. Photogrammetric measurements were made on several parts of the town walls to plot a numerical model aimed at ascertaining specific aspects of the earthquake damage. An estimate of the ground acceleration during the earthquake has been attempted via non-linear finite-element analyses of a building located by the main city gate. The analyses show that. in order to obtain the building vault collapse, a ground acceleration of 0.5 to 0.7 g had to be reached during the earthquake. This result, typical of a strong earthquake such as the one of 1693, proves that an approach based on finite element analysis and a sound engineering judgment Inay be systematically applied to historical earthquake sites to obtain some estimates of ground acceleration in historical earthquakes. On the whole, this work aimed at starting up the second development phase of the great event of 1693 of which the macroseismic erfects are known. In the meantime, some possibilities of tackling structural analyses in seismic archaeology are being explored.

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