An assay for variable fragment length allele-specific genotyping

Ruslan Kalendar; Vladislav Shevtsov; Aisulu Ismailova

doi:10.1007/978-1-0716-4642-7_1

An assay for variable fragment length allele-specific genotyping

Ruslan Kalendar
, Vladislav Shevtsov
, Aisulu Ismailova

Laboratory of bioinformatics and systems biology

S. Seifullin Kazakh Agrotechnical Research University
National Center for Biotechnology
Ministry of Education and Science of the Republic of Kazakhstan

Research output: Chapter in Book/Report/Conference proceeding › Chapter

1 Citation (Scopus)

17 Downloads (Pure)

Abstract

Polymerase chain reaction (PCR) is a quick and easy technique used to detect nucleotide polymorphisms and sequence variations in various fields such as medicine, agriculture, and basic research. There exists a set of PCR variants, collectively called allele-specific PCR, which use competitive reactions in the presence of allele-specific primers to amplify only specific alleles. In this chapter , we present protocols for a bioinformatics tool that can be used to design PCR-based genotyping assays for variable fragment length allele-specific genotyping. This assay is designed in both directions and can target single nucleotide polymorphisms and insertion/deletions. This chapter provides a step-by-step guide to design a multiplexed primer assay for variable fragment length allele-specific genotyping.

Original language	English
Title of host publication	Methods in Molecular Biology
Editors	Anthony Torres
Publisher	Humana Press Inc.
Chapter	1
Pages	1-17
Number of pages	17
Volume	2943
Edition	1
ISBN (Electronic)	978-1-0716-4642-7
ISBN (Print)	978-1-0716-4641-0
DOIs	https://doi.org/10.1007/978-1-0716-4642-7_1
Publication status	Published - Jun 29 2025

Publication series

Name	Methods in Molecular Biology
Volume	2943
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Funding

This research has been funded by the Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan (Grant No. AP19678041 and BR24993023, BR24992881, BR27199879, BR24992841).

Funders	Funder number
Ministry of Education and Science of the Republic of Kazakhstan	AP19678041, BR24993023, BR24992881, BR27199879, BR24992841

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 1 No Poverty
SDG 6 Clean Water and Sanitation
SDG 12 Responsible Consumption and Production

Keywords

Genotyping assay design software
Genotyping system
Insertion-deletion polymorphism (InDel)
Multiplex
Multiplex Ligation-dependent Probe Amplification (MLPA)
Single-nucleotide polymorphism (SNP)
SNaPshot

ASJC Scopus subject areas

Molecular Biology
Genetics

Access to Document

10.1007/978-1-0716-4642-7_1Licence: CC BY-ND

https://link.springer.com/protocol/10.1007/978-1-0716-4642-7_1Licence: CC BY-ND

Cite this

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An assay for variable fragment length allele-specific genotyping

Abstract

Publication series

Funding

UN SDGs

Keywords

ASJC Scopus subject areas

Access to Document

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Cite this