Detail
Article
Online article
FT
Medvik - BMC
  • Something wrong with this record ?

Parallel optimization and genotyping of multiple single-nucleotide polymorphism markers by sample pooling approach using cycling-gradient CE with multiple injections

M Minarik, L Benesova, L Fantova, J Horacek, J Heracek, A Loukola

. 2006 ; 27 (19) : 3856-3863.

Language English Country Germany

Document type Research Support, Non-U.S. Gov't, Validation Study

Persistent link   https://www.medvik.cz/link/bmc13026506

Grant support
NR8039 MZ0 CEP Register

Increasing importance of single-nucleotide polymorphisms (SNPs) in determination of disease susceptibility or in prediction of therapy response brings attention of many molecular diagnostic laboratories to simple and low-cost SNP genotyping methodologies. We have recently introduced a mutation detection technique based on analysis of homo- and heteroduplex PCR fragments resolved in cycling temperature gradient conditions on a conventional multicapillary-array DNA sequencer. The main advantage of this technique is in its simplicity with no requirement for sample cleanup prior to the analysis. In this report we present a practical application of the technology for genotyping of SNP markers in two separate clinical projects resulting in a combined set of 44 markers screened in over 500 patients. Initially, a design of PCR primers and conditions was performed for each SNP marker. Then, optimization of CE running conditions (limited just to the proper selection of temperature cycling) was performed on pools of 20 DNA samples to increase the probability of having each of the two allele types represented in the sample. After selecting the optimum conditions, screening of markers in patients was performed using a multiple-injection approach for further acceleration of the sample throughput. The rate of successful optimization of experimental conditions without any pre-selection based on the SNP sequence or melting characteristics was 80% from the initial SNP marker candidates. By studying the failed markers, we attempt to identify critical factors enabling successful typing. The presented technique is very useful for low to medium sized SNP genotyping projects mostly applied in pharmacogenomic research as well as in clinical diagnostics. The main advantages include low cost, simple setup and validation of SNP markers.

References provided by Crossref.org

Bibliography, etc.

Literatura

000      
00000naa a2200000 a 4500
001      
bmc13026506
003      
CZ-PrNML
005      
20140107105417.0
007      
ta
008      
130812s2006 gw a f 000 0|eng||
009      
AR
024    7_
$a 10.1002/elps.200600289 $2 doi
035    __
$a (PubMed)16972303
040    __
$a ABA008 $d ABA008 $e AACR2 $b cze
041    0_
$a eng
044    __
$a gw
100    1_
$a Minárik, Marek, $d 1970- $7 xx0071043 $u Genomac International, Laboratory for Molecular Genetics, Prague, Czech Republic
245    10
$a Parallel optimization and genotyping of multiple single-nucleotide polymorphism markers by sample pooling approach using cycling-gradient CE with multiple injections / $c M Minarik, L Benesova, L Fantova, J Horacek, J Heracek, A Loukola
504    __
$a Literatura
520    9_
$a Increasing importance of single-nucleotide polymorphisms (SNPs) in determination of disease susceptibility or in prediction of therapy response brings attention of many molecular diagnostic laboratories to simple and low-cost SNP genotyping methodologies. We have recently introduced a mutation detection technique based on analysis of homo- and heteroduplex PCR fragments resolved in cycling temperature gradient conditions on a conventional multicapillary-array DNA sequencer. The main advantage of this technique is in its simplicity with no requirement for sample cleanup prior to the analysis. In this report we present a practical application of the technology for genotyping of SNP markers in two separate clinical projects resulting in a combined set of 44 markers screened in over 500 patients. Initially, a design of PCR primers and conditions was performed for each SNP marker. Then, optimization of CE running conditions (limited just to the proper selection of temperature cycling) was performed on pools of 20 DNA samples to increase the probability of having each of the two allele types represented in the sample. After selecting the optimum conditions, screening of markers in patients was performed using a multiple-injection approach for further acceleration of the sample throughput. The rate of successful optimization of experimental conditions without any pre-selection based on the SNP sequence or melting characteristics was 80% from the initial SNP marker candidates. By studying the failed markers, we attempt to identify critical factors enabling successful typing. The presented technique is very useful for low to medium sized SNP genotyping projects mostly applied in pharmacogenomic research as well as in clinical diagnostics. The main advantages include low cost, simple setup and validation of SNP markers.
590    __
$a bohemika - dle Pubmed
650    12
$a elektroforéza kapilární $x metody $7 D019075
650    02
$a průtoková injekční analýza $7 D017022
650    02
$a genetické markery $x genetika $7 D005819
650    12
$a genetická predispozice k nemoci $x genetika $7 D020022
650    12
$a genetické testování $x metody $7 D005820
650    02
$a genotyp $7 D005838
650    02
$a lidé $7 D006801
650    12
$a jednonukleotidový polymorfismus $7 D020641
650    02
$a schizofrenie $x genetika $7 D012559
650    12
$a sekvenční analýza DNA $x metody $7 D017422
655    _2
$a práce podpořená grantem $7 D013485
655    _2
$a validační studie $7 D023361
700    1_
$a Mináriková, Lucie, $7 xx0105258 $u Genomac International, Laboratory for Molecular Genetics, Prague, Czech Republic $d 1974-
700    1_
$a Fantová, Lucie $7 _BN001709 $u Genomac International, Laboratory for Molecular Genetics, Prague, Czech Republic
700    1_
$a Horáček, Jiří, $d 1966- $7 jo2002152353 $u 3rd Faculty of Medicine, Charles University, Center for Neuropsychiatric Studies, Prague, Czech Republic
700    1_
$a Heráček, Jiří, $d 1969- $7 nlk20050170272 $u Faculty Hospital, Department of Urology, Prague, Czech Republic
700    1_
$a Loukola, Anu $u National Public Health Institute, Department of Molecular Medicine, Helsinki, Finland
773    0_
$t Electrophoresis $x 0173-0835 $g Roč. 27, č. 19 (2006), s. 3856-3863 $p Electrophoresis $w MED00001508
773    0_
$p Electrophoresis $g 27(19):3856-63, 2006 Oct $x 0173-0835
910    __
$a ABA008 $y 4 $z 0
990    __
$a 20130812111825 $b ABA008
991    __
$a 20140107110117 $b ABA008
999    __
$a ok $b bmc $g 990353 $s 824928
BAS    __
$a 3
BMC    __
$a 2006 $b 27 $c 19 $d 3856-3863 $i 0173-0835 $m Electrophoresis $x MED00001508 $n Electrophoresis
GRA    __
$a NR8039 $p MZ0
LZP    __
$a 2013-07/išbo
Back

Find record

Citation metrics

Archiving options