From genotypes to genes: doubling the sample size - PubMed (original) (raw)
. 1997 Dec;53(4):1253-61.
Affiliations
- PMID: 9423247
From genotypes to genes: doubling the sample size
P D Sasieni. Biometrics. 1997 Dec.
Abstract
This paper considers the analysis of genetic case-control data. One approach considers the allele frequency in cases and controls. Because each individual has two alleles at any autosomal locus, there will be twice as many alleles as people. Another approach considers the risk of the disease in those who do not have the allele of interest (A), those who have a single copy (heterozygous), and those who are homozygous for A. A third approach does not differentiate between individuals with one or two copies of A. This was common when alleles were determined serologically and one could not distinguish between homozygotes and those with one copy of A and one of an unknown allele. All three approaches have been used in the literature, but this is the first systematic comparison of them. The different interpretations of the odds ratios from such analyses are explored and conditions are given under which the first two approaches are asymptotically equivalent. The chi-squared statistics from the three approaches are discussed. Both the odds ratio and the chi-squared statistic from the analysis that treats alleles rather than genotypes as individual entities are appropriate only when the Hardy-Weinberg equilibrium holds. When the equilibrium holds, the allele-based test statistic is asymptotically equivalent to the test for trend using the genotype data. Thus, analyses that treat alleles rather than people as observations should not be used. Instead, we recommend that such data should be analyzed by genotype.
Similar articles
- HLA-DQ alpha allele and genotype frequencies in a native Kuwaiti population.
al-Nassar KE, Mathew J, Thomas N, Fatania HR. al-Nassar KE, et al. Forensic Sci Int. 1995 Mar 21;72(1):65-9. doi: 10.1016/0379-0738(94)01618-f. Forensic Sci Int. 1995. PMID: 7705737 - Biased tests of association: comparisons of allele frequencies when departing from Hardy-Weinberg proportions.
Schaid DJ, Jacobsen SJ. Schaid DJ, et al. Am J Epidemiol. 1999 Apr 15;149(8):706-11. doi: 10.1093/oxfordjournals.aje.a009878. Am J Epidemiol. 1999. PMID: 10206619 - High frequency of HLA-DQB1 non-Asp(57) alleles in Kuwaiti children with insulin-dependent diabetes mellitus.
Haider MZ, Shaltout A, Alsaeid K, Al-Khawari M, Dorman JS. Haider MZ, et al. Hum Hered. 2000 Jul-Aug;50(4):242-6. doi: 10.1159/000022923. Hum Hered. 2000. PMID: 10782017 - DNA locus HLA-DQ alpha polymorphism in human population of the north-eastern Poland.
Pepiński W, Skawrońska M, Janica J. Pepiński W, et al. Rocz Akad Med Bialymst. 1996;41(2):277-83. Rocz Akad Med Bialymst. 1996. PMID: 9020539 - Distribution of the HLA-DQ alpha alleles and genotypes in a sample of a population from Barcelona (Spain).
Huguet E, Gené M, Corbella J, Moreno P. Huguet E, et al. Hum Hered. 1993 Sep-Oct;43(5):326-8. doi: 10.1159/000154153. Hum Hered. 1993. PMID: 8406523
Cited by
- Increase in power by obtaining 10 or more controls per case when type-1 error is small in large-scale association studies.
Katki HA, Berndt SI, Machiela MJ, Stewart DR, Garcia-Closas M, Kim J, Shi J, Yu K, Rothman N. Katki HA, et al. BMC Med Res Methodol. 2023 Jun 29;23(1):153. doi: 10.1186/s12874-023-01973-x. BMC Med Res Methodol. 2023. PMID: 37386403 Free PMC article. - Screening properties of trend tests in genetic association studies.
Jiang Z, Guo H, Wang J. Jiang Z, et al. Sci Rep. 2023 Jun 5;13(1):9139. doi: 10.1038/s41598-023-35929-4. Sci Rep. 2023. PMID: 37277435 Free PMC article. - Genome-wide association testing in malaria studies in the presence of overdominance.
Akoth M, Odhiambo J, Omolo B. Akoth M, et al. Malar J. 2023 Apr 10;22(1):119. doi: 10.1186/s12936-023-04533-2. Malar J. 2023. PMID: 37038187 Free PMC article. - A nonparametric alternative to the Cochran-Armitage trend test in genetic case-control association studies: The Jonckheere-Terpstra trend test.
Manning SE, Ku HC, Dluzen DF, Xing C, Zhou Z. Manning SE, et al. PLoS One. 2023 Feb 2;18(2):e0280809. doi: 10.1371/journal.pone.0280809. eCollection 2023. PLoS One. 2023. PMID: 36730335 Free PMC article. - Health-related behavioral changes and incidence of chronic kidney disease: The Japan Specific Health Checkups (J-SHC) Study.
Kimura H, Asahi K, Tanaka K, Iseki K, Moriyama T, Yamagata K, Tsuruya K, Fujimoto S, Narita I, Konta T, Kondo M, Kasahara M, Shibagaki Y, Watanabe T, Kazama JJ. Kimura H, et al. Sci Rep. 2022 Sep 29;12(1):16319. doi: 10.1038/s41598-022-20807-2. Sci Rep. 2022. PMID: 36175537 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Other Literature Sources
Medical