Nobody is perfect: comparison of the accuracy of PCR-RFLP and KASP (TM) method for genotyping. ADH1B and FTO polymorphisms as examples

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F75010330%3A_____%2F15%3A00011211" target="_blank" >RIV/75010330:_____/15:00011211 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00023001:_____/15:00059501

Výsledek na webu

<a href="http://fb.cuni.cz/file/5786/fb2015a0021.pdf" target="_blank" >http://fb.cuni.cz/file/5786/fb2015a0021.pdf</a>

DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Nobody is perfect: comparison of the accuracy of PCR-RFLP and KASP (TM) method for genotyping. ADH1B and FTO polymorphisms as examples

Popis výsledku v původním jazyce

DNA genotyping is among the most common analyses currently performed in scientific research. Two high-throughput genotyping techniques are widely used - the "classic" PCR-RFLP and probe-based methods such as TaqMan (R) PCR assay or KASP (TM) genotyping. The probe-based techniques are claimed to be more accurate than PCR-RFLP; however, the evidence for this claim is sparse. We have directly compared results of genotyping of two SNPs (rs1229984 and rs17817449) obtained by the PCR-RFLP and KASP (TM) in 1,502 adult Caucasians. The results were identical in 97.3 % and 95.9 % cases, respectively. Discrepancies (either different results or result obtained with one but not with the other method) were addressed by confirmatory analysis using direct sequencing. The sequencing revealed that both methods can give incorrect results, but the frequency of incorrect genotyping of rs1229984 and rs17817449 was very low for both methods - 0.1 % and 0.5 %, respectively, for PCR-RFLP and 0.1 % and 0.3 %, respectively, for KASP (TM). These results confirm that the KASP (TM) technique is slightly more accurate, but it achieves slightly lower call rates than PCR-RFLP. When carefully set up, both PCR-RFLP and KASP (TM) could have accuracy of 99.5 % or higher.

Název v anglickém jazyce

Nobody is perfect: comparison of the accuracy of PCR-RFLP and KASP (TM) method for genotyping. ADH1B and FTO polymorphisms as examples

Popis výsledku anglicky

DNA genotyping is among the most common analyses currently performed in scientific research. Two high-throughput genotyping techniques are widely used - the "classic" PCR-RFLP and probe-based methods such as TaqMan (R) PCR assay or KASP (TM) genotyping. The probe-based techniques are claimed to be more accurate than PCR-RFLP; however, the evidence for this claim is sparse. We have directly compared results of genotyping of two SNPs (rs1229984 and rs17817449) obtained by the PCR-RFLP and KASP (TM) in 1,502 adult Caucasians. The results were identical in 97.3 % and 95.9 % cases, respectively. Discrepancies (either different results or result obtained with one but not with the other method) were addressed by confirmatory analysis using direct sequencing. The sequencing revealed that both methods can give incorrect results, but the frequency of incorrect genotyping of rs1229984 and rs17817449 was very low for both methods - 0.1 % and 0.5 %, respectively, for PCR-RFLP and 0.1 % and 0.3 %, respectively, for KASP (TM). These results confirm that the KASP (TM) technique is slightly more accurate, but it achieves slightly lower call rates than PCR-RFLP. When carefully set up, both PCR-RFLP and KASP (TM) could have accuracy of 99.5 % or higher.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

EB - Genetika a molekulární biologie

OECD FORD obor

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Projekt

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Návaznosti

V - Vyzkumna aktivita podporovana z jinych verejnych zdroju

Rok uplatnění

2015

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Folia Biologica

ISSN

0015-5500

e-ISSN

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Svazek periodika

61

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

CZ - Česká republika

Počet stran výsledku

5

Strana od-do

156-160

Kód UT WoS článku

000367178500005

EID výsledku v databázi Scopus

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