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Brief Summary of the Most Important Molecular Genetic Methods (PCR, qPCR, Microarray, Next-Generation Sequencing, etc.)

  • Henriett Butz
  • Attila PatócsEmail author
Chapter
  • 273 Downloads
Part of the Experientia Supplementum book series (EXS, volume 111)

Abstract

Molecular genetic methods have become an organic part of everyday clinical practice. In the past, molecular diagnostic tests were carried out for genetic diagnosis of a particular monogenic disease. In these situations the tests itself were used for identification of one particular genetic alteration (e.g., point mutation or deletion) of the gene of interest. Later, parallel with the development of the technology, the focus has shifted by allowing investigating at once targeted gene panels and even the whole exome/genome behind a suspected genetic disorder. Historically for these purposes, array-based methods (oligonucleotide arrays) and then next-generation sequencing-based methods have been used. High-throughput methods have been fundamentally transforming the everyday, routine genetic diagnostics, but older molecular techniques still have a role in clinical genetics. Here, we summarize the most important molecular genetic methods and shed light to the advantages and disadvantages of their application in routine diagnostics. We mainly focus on methods used for detection of germline alterations.

Keywords

Mutation Genetic testing Sequencing Next-generation sequencing Polymerase chain reaction 

List of Abbreviations

aCGH

Array comparative genomic hybridization

ARMS

Amplification refractory mutation system

AS-PCR

Allele-specific PCR

cDNA

Complementary DNA

CGH

Comparative genomic hybridization

CNV

Copy number variations

cT

Cycle threshold

DDGE

denaturing gradient gel electrophoresis

ddNTP

Dideoxyribonucleotide triphosphate

DNA

Deoxyribonucleic acid

dNTP

Deoxyribonucleotide triphosphate (adenine, cytosine, guanine, and thymine triphosphate: dATP, dCTP, dGTP, and dTTP, respectively)

dPCR

Digital polymerase chain reaction

dsDNA

Double-stranded DNA

EDTA

Ethylenediaminetetraacetic acid

FRET

Fluorescence resonance energy transfer

HA

Heteroduplex analysis

HRM

High-resolution melting analysis

IVD

In vitro diagnosis

MLPA

Multiplex ligation-dependent probe amplification

NGS

Next-generation sequencing

OD

Optical density

PASA

PCR amplification of specific alleles

PCR

Polymerase chain reaction

qPCR

Quantitative polymerase chain reaction

RFLP

Restriction fragment length polymorphism

RT-qPCR

Reverse transcription quantitative polymerase chain reaction

SNP

Single-nucleotide polymorphism

SNV

Single-nucleotide variants

SSCP

Single-strand conformation polymorphism (SSCP)

STR

Small tandem repeat

UPD

Uniparental disomy

VAF

Variant allele frequency

VUS

Variant of uncertain significance

WES

Whole-exome sequencing

WGS

Whole-genome sequencing

Notes

Acknowledgments

This work has been supported by the National Excellence Program to Attila Patócs and ÚNKP-18-4-SE-8 New National Excellence Program of The Ministry of Human Capacities to Henriett Butz. Henriett Butz is a recipient of Bolyai Research Fellowship of Hungarian Academy of Sciences.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Laboratory Medicine, Faculty of MedicineSemmelweis UniversityBudapestHungary
  2. 2.“Lendület” Hereditary Endocrine Tumors Research GroupHungarian Academy of Sciences and Semmelweis UniversityBudapestHungary
  3. 3.Department of Molecular GeneticsNational Institute of OncologyBudapestHungary

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