Discordance of STR typing results can be expected between kits that employ different primers for amplification. The complex motif of the SE33 locus and its flanking regions can contribute to the degree of discordant results. Sequence-dependent conformational changes can manifest as length differences under certain electrophoretic conditions and/or use of different primers. The AmpFlSTR® NGM SElect™ PCR Amplification Kit (Life Technologies, Carlsbad, CA), PowerPlex® ESX 17 system (Promega Corporation, Madison, WI), and PowerPlex® ESI 17 system (Promega Corporation) were compared for concordance of allele calls for the SE33 marker in selected samples. A total of 16 samples were identified that were discordant at one of the SE33 alleles by an apparent one nucleotide in size. While the ESX 17 and NGM SElect™ kits yielded concordant results for these 16 samples, the ESI 17 kit generated alleles that differed. The discordant alleles were observed in individuals of African and European descent. Sequence analysis revealed that the one-base difference in size is not due to an indel but is instead the result of a single nucleotide polymorphism (SNP) in the flanking region of the SE33 repeat region. Three different SNPs were observed, one of which is novel. Although these migration anomalies were observed only with the ESI 17 kit, one cannot preclude that a similar phenomenon may occur with the other kits as data sets increase. The type and degree of discordance of STR allele calls among STR kits is an important issue when comparing STR profiles among laboratories and when determining search parameters for identifying candidate associations in national databases.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.fsigen.2011.12.002 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Impact on natural history of atypical meningioma after changes in 2016 edition of the world health organization (WHO) classification of central nervous system tumors: a literature review.
Neurosurg Rev
September 2024
Laboratory of Molecular and Cellular Biology (LIM15), Department of Neurology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Avenida Dr Arnaldo, 455/ 4º andar/ sala 4110, São Paulo, SP, 01246-903, Brazil.
Article Synopsis
- Meningiomas, particularly atypical grade 2 tumors, are challenging to classify due to significant interobserver discordance; the WHO 2016 guidelines introduced brain invasion as a critical factor for diagnosis.
- * A study analyzed data from 3445 patients worldwide between 2017 and 2024, highlighting that most cases involved patients around the average age of 52, with 67.8% of tumors located on the convexity of the brain.
- * Despite a high rate of gross total resection (71.25%), the recurrence rate for atypical meningiomas was 35.44%, indicating a need for improved understanding of their molecular mechanisms for better treatment options.*
Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium.
Ann Bot
December 2024
Princess Therese von Bayern chair of Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Menzinger Str. 67, Munich 80638, Germany.
Background And Aims: Cypripedium is the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny of Cypripedium and explore its evolutionary history using target capture data for the first time.
View Article and Find Full Text PDFCharacterization of sequence variations in the extended flanking regions using massively parallel sequencing in 21 A-STRs and 21 Y-STRs.
BMC Genomics
September 2024
Shanghai Medical College, Fudan University, Shanghai, 200032, China.
Article Synopsis
- This study explores the advantages of using massively parallel sequencing (MPS) over conventional capillary electrophoresis (CE) for analyzing short tandem repeats (STRs) in forensic genetics, especially by investigating both the core repeat regions and their flanking regions.
- A new MPS system was developed that genotyped 350 male individuals from the Chinese Han population, focusing on 42 commonly used autosomal and Y-chromosomal STRs, and categorized them based on various sequence and length metrics.
- The findings indicated that sequence variations, particularly in A-STRs, significantly enhance identification capabilities, with 58 observed variations in the flanking regions mostly affecting A-STR analysis; the concordance between MPS and CE methods
Discordance of Penta D x.4 microvariant alleles results between three capillary electrophoresis and one massively parallel sequencing short tandem repeat kits.
Forensic Sci Int Genet
November 2024
Forensic Biology Laboratory, PathWest Laboratory Medicine WA, Locked Bag 2009, Nedlands, Western Australia 6009, Australia.
Forensic Biology is contingent upon matching DNA profiles between a crime sample and a reference sample. There are several capillary electrophoresis kits available to generate a short tandem repeat (STR) profile from DNA samples, while newer methods using massively parallel sequencing are slowly being implemented in forensic laboratories worldwide. During evaluation of a newer capillary electrophoresis kit, Applied Biosystems™ VeriFiler™ Plus, a discordance was observed in the Penta D locus.
View Article and Find Full Text PDF"I didn't even wonder why I was on the floor" - mixed methods exploration of stroke awareness and help-seeking behaviour at stroke symptom onset.
BMC Health Serv Res
August 2024
Department of Neurology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.
Introduction: To better target stroke awareness efforts (pre and post first stroke) and thereby decrease the time window for help-seeking, this study aims to assess quantitatively whether stroke awareness is associated with appropriate help-seeking at symptom onset, and to investigate qualitatively why this may (not) be the case.
Methods: This study conducted in a German regional stroke network comprises a convergent quantitative-dominant, hypothesis-driven mixed methods design including 462 quantitative patient questionnaires combined with qualitative interviews with 28 patients and seven relatives. Quantitative associations were identified using Pearson's correlation analysis.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!