Genotyping Technologies

Cristi R. King; Sharon Marsh

doi:10.1017/CBO9781139051194.004

2 - Genotyping Technologies

from I - Critical Concepts

Published online by Cambridge University Press: 05 June 2012

Cristi R. King and

Edited by

David Flockhart and

Russ B. Altman: Affiliation:
Stanford University, California
David Flockhart: Affiliation:
Indiana University
David B. Goldstein: Affiliation:
Duke University, North Carolina

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Summary

With the release of the Human Genome Mapping Project data (1) and the subsequent International HapMap Project (2), a wealth of genotype information is now publically available to researchers. Pharmacogenomics can utilize this information to its advantage by screening patient samples for known functional or tagging polymorphisms and deriving associations with drug outcome and toxicity. In addition, where no known functional polymorphisms have been identified in genes involved in drug pathways, technologies have emerged to perform whole-genome screens to find novel genome regions for further study.

Often considered the “gold standard” of genotyping, Sanger sequencing performed on the same DNA region in multiple individuals (resequencing) can be used to identify both new and previously reported polymorphisms. However, this process is not cost-effective, and analysis time can be slow. Consequently, it is often used as a quality-control step to confirm genotypes reported through the various technologies discussed later in this chapter.

Type: Chapter
Information: Principles of Pharmacogenetics and Pharmacogenomics , pp. 12 - 20

DOI: https://doi.org/10.1017/CBO9781139051194.004 [Opens in a new window]

Publisher: Cambridge University Press

Print publication year: 2012

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References

Sachidanandam, RWeissman, DSchmidt, SCA map of human genome sequence variation containing 1.42 million single nucleotide polymorphismsNature 2001 409 928Google Scholar

Altshuler, DBrooks, LDChakravarti, AA haplotype map of the human genomeNature 2005 437 1299Google Scholar

Horie, NAiba, HOguro, KFunctional analysis and DNA polymorphism of the tandemly repeated sequences in the 5′-terminal regulatory region of the human gene for thymidylate synthaseCell Struct Funct 1995 20 191Google Scholar

Rose, CMMarsh, SAmeyaw, MMPharmacogenetic analysis of clinically relevant genetic polymorphismsMethods Mol Med 2003 85 225Google Scholar

Voso, MTD’Alo, FPutzulu, RNegative prognostic value of glutathione S-transferase (GSTM1 and GSTT1) deletions in adult acute myeloid leukemiaBlood 2002 100 2703Google Scholar

Freimuth, RRAmeyaw, M-MPritchard, SCHigh-throughput genotyping methods for pharmacogenomic studiesCurr Pharmacogenomics 2004 2 21Google Scholar

King, CRPorche-Sorbet, RMGage, BFPerformance of commercial platforms for rapid genotyping of polymorphisms affecting warfarin doseAm J Clin Pathol 2008 129 876Google Scholar

Vairavan, RAutoGenomics, IncPharmacogenomics 2004 5 585Google Scholar

Kim, SMisra, ASNP genotyping: technologies and biomedical applicationsAnnu Rev Biomed Eng 2007 9 289Google Scholar

Bortolin, SBlack, MModi, HAnalytical validation of the tag-it high-throughput microsphere-based universal array genotyping platform: application to the multiplex detection of a panel of thrombophilia-associated single-nucleotide polymorphismsClin Chem 2004 50 2028Google Scholar

Strom, CMJaneczko, RAAnderson, BTechnical validation of a multiplex platform to detect thirty mutations in eight genetic diseases prevalent in individuals of Ashkenazi Jewish descentGenet Med 2005 7 633Google Scholar

Ugozzoli, LWahlqvist, JMEhsani, ADetection of specific alleles by using allele-specific primer extension followed by capture on solid supportGenet Anal Tech Appl 1992 9 107Google Scholar

King, CRScott-Horton, TPyrosequencing(R): a simple method for accurate genotypingMethods Mol Biol 2006 373 39Google Scholar

Marsh, SKing, CRGarsa, AAPyrosequencing of clinically relevant polymorphismsMethods Mol Biol 2005 311 97Google Scholar

Ronaghi, MPyrosequencing sheds light on DNA sequencingGenome Res 2001 11 3Google Scholar

Isler, JAVesterqvist, OEBurczynski, MEAnalytical validation of genotyping assays in the biomarker laboratoryPharmacogenomics 2007 8 353Google Scholar

Ronaghi, MUhlen, MNyren, PA sequencing method based on real-time pyrophosphateScience 1998 281Google Scholar

Marsh, SPyrosequencing applicationsMethods Mol Biol 2007 373 15Google Scholar

Lyamichev, VMast, ALHall, JGPolymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probesNat Biotechnol 1999 17 292Google Scholar

Hall, JGEis, PSLaw, SMSensitive detection of DNA polymorphisms by the serial invasive signal amplification reactionProc Natl Acad Sci U S A 2000 97 8272Google Scholar

de Arruda, MLyamichev, VIEis, PSInvader technology for DNA and RNA analysis: principles and applicationsExpert Rev Mol Diagn 2002 2 487Google Scholar

Wang, DGFan, JBSiao, CJLarge-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genomeScience 1998 280 1077Google Scholar

Pusch, WWurmbach, JHThiele, HMALDI-TOF mass spectrometry-based SNP genotypingPharmacogenomics 2002 3 537Google Scholar

Fei, ZOno, TSmith, LMMALDI-TOF mass spectrometric typing of single nucleotide polymorphisms with mass-tagged ddNTPsNucleic Acids Res 1998 26 2827Google Scholar

Braun, ALittle, DPKoster, HDetecting CFTR gene mutations by using primer oligo base extension and mass spectrometryClin Chem 1997 43 1151Google Scholar

Gabriel, SZiaugra, LTabbaa, DSNP genotyping using the Sequenom MassARRAY iPLEX platformCurr Protoc Hum Genet 2009Google Scholar

Oeth, PBeaulieu, MPark, Chttp://www.agrf.org.au/docstore/snp/iPlex.pdf

Michael, KLTaylor, LCSchultz, SLRandomly ordered addressable high-density optical sensor arraysAnal Chem 1998 70 1242Google Scholar

Steemers, FJFerguson, JAWalt, DRScreening unlabeled DNA targets with randomly ordered fiber-optic gene arraysNat Biotechnol 2000 18 91Google Scholar

Kennedy, GCMatsuzaki, HDong, SLarge-scale genotyping of complex DNANat Biotechnol 2003 21 1233Google Scholar

Bushman, FDHoffmann, CRonen, KMassively parallel pyrosequencing in HIV researchAIDS 2008 22 1411Google Scholar

Voelkerding, KVDames, SADurtschi, JDNext-generation sequencing: from basic research to diagnosticsClin Chem 2009 55 641Google Scholar

Huse, SMHuber, JAMorrison, HGAccuracy and quality of massively parallel DNA pyrosequencingGenome Biol 2007 8Google Scholar

Wheeler, DASrinivasan, MEgholm, MThe complete genome of an individual by massively parallel DNA sequencingNature 2008 452 872Google Scholar

Miller, WDrautz, DIRatan, ASequencing the nuclear genome of the extinct woolly mammothNature 2008 456 387Google Scholar

Ley, TJMardis, ERDing, LDNA sequencing of a cytogenetically normal acute myeloid leukaemia genomeNature 2008 456 66Google Scholar

Milos, PEmergence of single-molecule sequencing and potential for molecular diagnostic applicationsExp Rev Mol Diag 2009 9 659Google Scholar

Eid, JFehr, AGray, JReal-Time dna sequencing from single polymerase moleculesScience 2009 323 133Google Scholar

Drmanac, RSparks, ABCallow, MJHuman genome sequencing using unchained base reads on self-assembling DNA nanoarraysScience 2010 327 78Google Scholar

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