Home > Research > Publications & Outputs > Investigation into the ability of SNP chipsets ...

Research

Links

Text available via DOI:

Keywords

View graph of relations

Investigation into the ability of SNP chipsets and microsatellites to detect association with a disease locus

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Published

Standard

Investigation into the ability of SNP chipsets and microsatellites to detect association with a disease locus. / Curtis, D.; Vine, A. E.; Knight, Jo.
In: Annals of Human Genetics, Vol. 72, No. 4, 07.2008, p. 547-556.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Harvard

Curtis, D, Vine, AE & Knight, J 2008, 'Investigation into the ability of SNP chipsets and microsatellites to detect association with a disease locus', Annals of Human Genetics, vol. 72, no. 4, pp. 547-556. https://doi.org/10.1111/j.1469-1809.2008.00434.x

APA

Curtis, D., Vine, A. E., & Knight, J. (2008). Investigation into the ability of SNP chipsets and microsatellites to detect association with a disease locus. Annals of Human Genetics, 72(4), 547-556. https://doi.org/10.1111/j.1469-1809.2008.00434.x

Vancouver

Curtis D, Vine AE, Knight J. Investigation into the ability of SNP chipsets and microsatellites to detect association with a disease locus. Annals of Human Genetics. 2008 Jul;72(4):547-556. doi: 10.1111/j.1469-1809.2008.00434.x

Author

Curtis, D. ; Vine, A. E. ; Knight, Jo. / Investigation into the ability of SNP chipsets and microsatellites to detect association with a disease locus. In: Annals of Human Genetics. 2008 ; Vol. 72, No. 4. pp. 547-556.

Bibtex

@article{98295a9a6ea54d47957b80cb7d447459,
title = "Investigation into the ability of SNP chipsets and microsatellites to detect association with a disease locus",
abstract = "We wished to investigate the ability of different SNP chipsets to detect association with a disease and to investigate the linkage disequilibrium (LD) relationships between microsatellites and nearby SNPs in order to assess their potential usefulness to detect association. SNP genotypes were obtained from HapMap and microsatellite genotypes from CEPH. 5000 SNPs were simulated as disease genes which increased penetrance from 0.01 to 0.02 in a sample of 400 cases and 400 controls. The power of flanking SNPs to detect association was tested using sets of 1, 2, 3 or 4 markers analysed with haplotype analysis or logistic regression and using either all HapMap markers or those from the Affymetrix 500K, Illumina 300K or Illumina 550K chipsets. Additionally, LD relationships between 10 microsatellites and SNPs within 2Mb of each other were studied. The power for one of the markers to detect association at p = 0.001 was around 0.4. Power was slightly better for logistic regression than haplotype analysis and for two-marker as opposed to single marker analysis but analysing with larger numbers markers had little benefit. The Illumina 550K marker set was better able to detect association than the other two and was almost as powerful as using all HapMap markers. Microsatellites had detectable LD with only a small number of nearby SNPs and the pattern of LD was very variable. Available chipsets have quite good ability to detect association although obviously results will be critically dependent on the nature of the genetic effect on risk, sample size and the actual LD relationships of the susceptibility polymorphisms involved. Microsatellites seem ill-suited for systematic studies to detect association.",
keywords = "Genetic Predisposition to Disease, Genotype, Haplotypes, Humans, Linkage Disequilibrium, Logistic Models, Microsatellite Repeats, Oligonucleotide Array Sequence Analysis, Phenotype, Polymorphism, Single Nucleotide",
author = "D. Curtis and Vine, {A. E.} and Jo Knight",
year = "2008",
month = jul,
doi = "10.1111/j.1469-1809.2008.00434.x",
language = "English",
volume = "72",
pages = "547--556",
journal = "Annals of Human Genetics",
issn = "0003-4800",
publisher = "Wiley-Blackwell",
number = "4",

}

RIS

TY - JOUR

T1 - Investigation into the ability of SNP chipsets and microsatellites to detect association with a disease locus

AU - Curtis, D.

AU - Vine, A. E.

AU - Knight, Jo

PY - 2008/7

Y1 - 2008/7

N2 - We wished to investigate the ability of different SNP chipsets to detect association with a disease and to investigate the linkage disequilibrium (LD) relationships between microsatellites and nearby SNPs in order to assess their potential usefulness to detect association. SNP genotypes were obtained from HapMap and microsatellite genotypes from CEPH. 5000 SNPs were simulated as disease genes which increased penetrance from 0.01 to 0.02 in a sample of 400 cases and 400 controls. The power of flanking SNPs to detect association was tested using sets of 1, 2, 3 or 4 markers analysed with haplotype analysis or logistic regression and using either all HapMap markers or those from the Affymetrix 500K, Illumina 300K or Illumina 550K chipsets. Additionally, LD relationships between 10 microsatellites and SNPs within 2Mb of each other were studied. The power for one of the markers to detect association at p = 0.001 was around 0.4. Power was slightly better for logistic regression than haplotype analysis and for two-marker as opposed to single marker analysis but analysing with larger numbers markers had little benefit. The Illumina 550K marker set was better able to detect association than the other two and was almost as powerful as using all HapMap markers. Microsatellites had detectable LD with only a small number of nearby SNPs and the pattern of LD was very variable. Available chipsets have quite good ability to detect association although obviously results will be critically dependent on the nature of the genetic effect on risk, sample size and the actual LD relationships of the susceptibility polymorphisms involved. Microsatellites seem ill-suited for systematic studies to detect association.

AB - We wished to investigate the ability of different SNP chipsets to detect association with a disease and to investigate the linkage disequilibrium (LD) relationships between microsatellites and nearby SNPs in order to assess their potential usefulness to detect association. SNP genotypes were obtained from HapMap and microsatellite genotypes from CEPH. 5000 SNPs were simulated as disease genes which increased penetrance from 0.01 to 0.02 in a sample of 400 cases and 400 controls. The power of flanking SNPs to detect association was tested using sets of 1, 2, 3 or 4 markers analysed with haplotype analysis or logistic regression and using either all HapMap markers or those from the Affymetrix 500K, Illumina 300K or Illumina 550K chipsets. Additionally, LD relationships between 10 microsatellites and SNPs within 2Mb of each other were studied. The power for one of the markers to detect association at p = 0.001 was around 0.4. Power was slightly better for logistic regression than haplotype analysis and for two-marker as opposed to single marker analysis but analysing with larger numbers markers had little benefit. The Illumina 550K marker set was better able to detect association than the other two and was almost as powerful as using all HapMap markers. Microsatellites had detectable LD with only a small number of nearby SNPs and the pattern of LD was very variable. Available chipsets have quite good ability to detect association although obviously results will be critically dependent on the nature of the genetic effect on risk, sample size and the actual LD relationships of the susceptibility polymorphisms involved. Microsatellites seem ill-suited for systematic studies to detect association.

KW - Genetic Predisposition to Disease

KW - Genotype

KW - Haplotypes

KW - Humans

KW - Linkage Disequilibrium

KW - Logistic Models

KW - Microsatellite Repeats

KW - Oligonucleotide Array Sequence Analysis

KW - Phenotype

KW - Polymorphism, Single Nucleotide

U2 - 10.1111/j.1469-1809.2008.00434.x

DO - 10.1111/j.1469-1809.2008.00434.x

M3 - Journal article

C2 - 18355389

VL - 72

SP - 547

EP - 556

JO - Annals of Human Genetics

JF - Annals of Human Genetics

SN - 0003-4800

IS - 4

ER -