Microsatellites or short tandem repeats (STRs) are abundant in the human genome with easily assayed polymorphisms, providing powerful genetic tools for mapping both Mendelian and complex traits. Microsatellite genotyping requires detection of the products of polymerase chain reaction (PCR) amplification by electrophoresis, and analysis of the peak data for discrimination of the true allele. A high-throughput genotyping approach requires computer-based automation at both the detection and analysis phases. In order to achieve this, complicated peak patterns from individual alleles must be interpreted in order to assign alleles. Previous methods consider limited types of noise peaks and cannot provide enough accuracy. By pattern recognition of various types of noise peaks, such as stutter peaks and additional peaks, we have achieved an overall average accuracy of 94% for allele calling in our actual data. Our algorithm is crucial for a high-throughput genotyping system for microsatellite markers by reducing manual editing and human errors.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC534627 | PMC |
| http://dx.doi.org/10.1093/nar/gkh946 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Detection of cervical precancerous lesions and cancer by small-scale RT-qPCR analysis of oppositely deregulated mRNAs pairs in cytological smears.
Front Oncol
January 2025
AO Vector-Best, Novosibirsk, Russia.
Background: Cervical screening, aimed at detecting precancerous lesions and preventing cancer, is based on cytology and HPV testing. Both methods have limitations, the main ones being the variable diagnostic sensitivity of cytology and the moderate specificity of HPV testing. Various molecular biomarkers are proposed in recent years to improve cervical cancer management, including a number of mRNAs encoded by human genes involved in carcinogenesis.
View Article and Find Full Text PDFHigh-throughput method characterizes hundreds of previously unknown antibiotic resistance mutations.
Nat Commun
January 2025
Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK.
A fundamental obstacle to tackling the antimicrobial resistance crisis is identifying mutations that lead to resistance in a given genomic background and environment. We present a high-throughput technique - Quantitative Mutational Scan sequencing (QMS-seq) - that enables quantitative comparison of which genes are under antibiotic selection and captures how genetic background influences resistance evolution. We compare four E.
View Article and Find Full Text PDFA next-generation sequencing-based universal target panel and algorithm for one-stop detection of copy number alterations and single-nucleotide variations in the HBB gene cluster for rapid diagnosis of β-thalassemia.
Mol Biol Rep
January 2025
Department of Zoology, The University of Burdwan, Bardhaman, West Bengal, 713104, India.
Background: This study aimed to develop and validate a targeted next-generation sequencing (NGS) panel along with a data analysis algorithm capable of detecting single-nucleotide variants (SNVs) and copy number variations (CNVs) within the beta-globin gene cluster. The aim was to reduce the turnaround time in conventional genotyping methods and provide a rapid and comprehensive solution for prenatal diagnosis, carrier screening, and genotyping of β-thalassemia patients.
Methods And Results: We devised a targeted NGS panel spanning an 80.
Detection of low frequency artemisinin resistance mutations, C469Y, P553L and A675V, and fixed antifolate resistance mutations in asymptomatic primary school children in Kenya.
BMC Infect Dis
January 2025
Centre for Geographic Medicine Research (Coast), Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.
Background: To understand the emergence and spread of drug-resistant parasites in malaria-endemic areas, accurate assessment and monitoring of antimalarial drug resistance markers is critical. Recent advances in next-generation sequencing (NGS) technologies have enabled the tracking of drug-resistant malaria parasites.
Methods: In this study, we used Targeted Amplicon Deep Sequencing (TADS) to characterise the genetic diversity of the Pfk13, Pfdhfr, Pfdhps, and Pfmdr1 genes among primary school-going children in 15 counties in Kenya (Bungoma, Busia, Homa Bay, Migori, Kakamega, Kilifi, Kirinyaga, Kisii, Kisumu, Kwale, Siaya, Tana River, Turkana, Vihiga and West Pokot).
High clinical utility of long-read sequencing for precise diagnosis of congenital adrenal hyperplasia in 322 probands.
Hum Genomics
January 2025
Department of Endocrine and Metabolic Diseases, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.
Background: The molecular genetic diagnosis of congenital adrenal hyperplasia (CAH) is very challenging due to the high homology between the CYP21A2 gene and its pseudogene CYP21A1P.
Methodology: This study aims to assess the clinical efficacy of targeted long-read sequencing (T-LRS) by comparing it with a control method based on the combined assay (NGS, Multiplex ligation-dependent probe amplification and Sanger sequencing) and to introduce T-LRS as a first-tier diagnostic test for suspected CAH patients to improve the precise diagnosis of CAH.
Results: A large cohort of 562 participants including 322 probands and 240 family members was enrolled for the perspective (96 probands) and prospective study (226 probands).
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!