Linkage analysis merging replicate phenotypes: an application to three quantitative phenotypes in two African samples.
- Authors
- Hinrichs, Anthony L; Culverhouse, Robert C; Suarez, Brian K
- Year
- 2011
- Journal
- BMC proceedings
- PMID
- 22373343
- DOI
- 10.1186/1753-6561-5-S9-S81
- PMCID
- PMC3287922
We report two approaches for linkage analysis of data consisting of replicate phenotypes. The first approach is specifically designed for the unusual (in human data) replicate structure of the Genetic Analysis Workshop 17 pedigree data. The second approach consists of a standard linkage analysis that, although not specifically tailored to data consisting of replicate genotypes, was envisioned as providing a sounding board against which our novel approach could be assessed. Both approaches are applied to the analysis of three quantitative phenotypes (Q1, Q2, and Q4) in two sets of African families. All analyses were carried out blind to the generating model (i.e., the "answers"). Using both methods, we found numerous significant linkage signals for Q1, although population colocalization was absent for most of these signals. The linkage analysis of Q2 and Q4 failed to reveal any strong linkage signals.
First three principal components from an Eigenstrat analysis of two African populations
Linkage analysis for Q1 for families 2, 3, and 4 of the Luhya pedigree. Genome-wide results of Fisher’s method and GLMM analyses of the Q1 quantitative phenotype in the three Luhya pedigrees. To make the figure more readable, the ratio of the chromosome lengths is not to scale.
Linkage analysis for Q1 for families 5 and 6 of the Yoruba pedigree. Genome-wide results of Fisher’s method and GLMM analyses of the Q1 quantitative phenotype in the two Yoruban pedigrees. To make the figure more readable, the ratio of the chromosome lengths is not to scale.
Subset of pedigree 5 Segment of pedigree 5 showing the cosegregation at C8S775 and C13S434.
| Name | Type |
|---|---|
| 1000 Genomes Project | cohort |
| African groups local | cohort |
| African samples | cohort |
| age | phenotype |
| Animal local | cohort |
| C13S434 local | variant |
| C8S775 local | variant |
| CDCA2 local | gene |
| Chinese samples | cohort |
| derived phenotype local | phenotype |
| DICER1 | gene |
| East Africans local | cohort |
| F1 hybrids local | cohort |
| family data set local | cohort |
| FLT1 local | gene |
| founder 2005 local | cohort |
| founder 4021 local | cohort |
| founders | cohort |
| genes | gene |
| Genetic Analysis Workshop 17 local | cohort |
| genetic heterogeneity | phenotype |
| genetic homogeneity local | phenotype |
| genetic variants | cohort |
| Homozygous inbred strains local | cohort |
| human | cohort |
| Japanese | cohort |
| kindred group A local | cohort |
| kindred group B local | cohort |
| linkage signals local | variant |
| LOC643659 local | gene |
| Longitudinal phenotype data local | phenotype |
| Luhya local | cohort |
| Luhya pedigrees local | cohort |
| Luhya population local | cohort |
| Luhya sample local | cohort |
| novel quantitative phenotype local | phenotype |
| pedigree 2 local | cohort |
| pedigree 3 local | cohort |
| pedigree 4 local | cohort |
| pedigree 5 local | cohort |
| pedigree 6 local | cohort |
| pedigrees | cohort |
| pilot3 study local | cohort |
| Plant local | cohort |
| PLAT local | gene |
| pleuropulmonary blastoma local | phenotype |
| population | cohort |
| Q1 local | phenotype |
| Q2 local | phenotype |
| Q4 local | phenotype |
| quantitative phenotypes | phenotype |
| RNF145 local | gene |
| sex | phenotype |
| single-nucleotide polymorphisms | variant |
| smoking | phenotype |
| smoking status | phenotype |
| SNP | cohort |
| SREBF1 | gene |
| trait | phenotype |
| Tuscan local | cohort |
| Twin cohort | cohort |
| unrelated individuals | cohort |
| Unrelated individuals data set local | cohort |
| West Africans local | cohort |
| Yoruba | cohort |
| Yoruba kindred local | cohort |
| Yoruba pedigrees local | cohort |
No uploaded files.
| Citation | PMID | DOI | Status |
|---|---|---|---|
| AlmasyLBlangeroJMultipoint quantitative trait linkage analysis in general pedigreesAm J Hum Genet1998621198121110.1086/3018449545414PMC1377101 | — | — | — |
| CulverhouseRHinrichsALSuarezBKStratify or adjust? Dealing with multiple populations when evaluating rare variantsBMC Proc20115suppl 9S10110.1186/1753-6561-5-S9-S101PMC328782422373399 | — | — | — |
| EntineJTaboo: why black athletes dominate sports and why we are afraid to talk about it2000New York, Public Affairs11234647 | — | — | — |
| HillDAIvanovichJPriestJRGurnettCADehnerLPDesruisseauDJarzembowskiJAWikenheiser-BrokampKASuarezBKWhelanAJDICER1 mutations in familial pleuropulmonary blastomaScience200932596510.1126/science.117433419556464PMC3098036 | — | — | — |
| MortonNEThe detection and estimation of linkage between the genes for elliptocytosis and the Rh blood typeAm J Hum Genet19568809613313518PMC1716663 | — | — | — |
| PriceALPattersonNJPlengeRMWeinblattMEShadickNAReichDPrincipal components analysis corrects for stratification in genome-wide association studiesNat Genet20063890490910.1038/ng184716862161 | — | — | — |
| ProvinceMAThe significance of not finding a geneAm J Hum Genet20016966066310.1086/32331611481587PMC1235495 | — | — | — |
| SAS Institute IncCary, NCSAS 9.22008SAS Institute Inc | — | — | — |
| SuarezBKDuanJSandersARHinrichsALJinCHHouCBuccolaNGHaleNWeilbaecherANNertneyDAGenomewide linkage scan of 409 European-ancestry and African American families with schizophrenia: suggestive evidence of linkage at 8p23.3–p21.2 and 11p13.1–q14.1 in the combined sampleAm J Hum Genet20067831533310.1086/50027216400611PMC1380238 | — | — | — |
No papers in this knowledge base cite this source.
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| Identifying cryptic population structure in multigenerational pedigrees in a Mexican American sample. | Culverhouse RC et al. | — | 2014 | → |
| Application of Bayesian network structure learning to identify causal variant SNPs from resequencing data. | Schlosberg CE et al. | — | 2011 | → |
| Incorporating linkage information into a common disease/rare variant framework. | Hinrichs AL et al. | — | 2011 | → |
| Stratify or adjust? Dealing with multiple populations when evaluating rare variants. | Culverhouse RC et al. | — | 2011 | → |