ArticleGenetic epidemiology2011
Optimum designs for next-generation sequencing to discover rare variants for common complex disease.
Article in Genetic epidemiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed.
- Identification of novel sarcoma risk genes using a two-stage genome wide DNA sequencing strategy in cancer cluster families and population case and control cohorts.BMC medical genetics · 2019Article
- On the association analysis of CNV data: a fast and robust family-based association method.BMC bioinformatics · 2017Article
- Family-Based Rare Variant Association Analysis: A Fast and Efficient Method of Multivariate Phenotype Association Analysis.Genetic epidemiology · 2016Article
- Exome-based case-control association study using extreme phenotype design reveals novel candidates with protective effect in diabetic retinopathy.Human genetics · 2016Article
- A novel statistical method for rare-variant association studies in general pedigrees.BMC proceedings · 2016Article
- The contribution of rare and common variants in 30 genes to risk nicotine dependence.Molecular psychiatry · 2015Article
- On the design and analysis of next-generation sequencing genotyping for a cohort with haplotype-informative reads.Methods (San Diego, Calif.) · 2015Article
- Test of rare variant association based on affected sib-pairs.European journal of human genetics : EJHG · 2015Article
- Two-stage family-based designs for sequencing studies.BMC proceedings · 2014Article
- Visualization of haplotype sharing patterns in pedigree samples.Human heredity · 2014Article
- Two-phase and family-based designs for next-generation sequencing studies.Frontiers in genetics · 2013Review
- Detecting association of rare variants by testing an optimally weighted combination of variants for quantitative traits in general families.Annals of human genetics · 2013Article
- Identification of novel variants in colorectal cancer families by high-throughput exome sequencing.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2013Article
- Using genetic prediction from known complex disease Loci to guide the design of next-generation sequencing experiments.PloS one · 2013Article
- Prevalence and correlates of low medication adherence in apparent treatment-resistant hypertension.Journal of clinical hypertension (Greenwich, Conn.) · 2012Article
- Quantitative trait locus analysis for next-generation sequencing with the functional linear models.Journal of medical genetics · 2012Article
- Rare PPARA variants and extreme response to fenofibrate in the Genetics of Lipid-Lowering Drugs and Diet Network Study.Pharmacogenetics and genomics · 2012Article
- Genetic epidemiology with a capital E: where will we be in another 10 years?Genetic epidemiology · 2012Article
- Between candidate genes and whole genomes: time for alternative approaches in blood pressure genetics.Current hypertension reports · 2012Review
- Whole-exome sequencing and an iPSC-derived cardiomyocyte model provides a powerful platform for gene discovery in left ventricular hypertrophy.Frontiers in genetics · 2012Article
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Abstract
Recent advances in next-generation sequencing technologies make it affordable to search for rare and functional variants for common complex diseases systematically. We investigated strategies for enriching rare variants in the samples selected for sequencing so as to optimize the power for their discovery. In particular, we investigated the roles of alternative sources of enrichment in families through computer simulations. We showed that linkage information, extreme phenotype, and nonrandom ascertainment, such as multiply affected families, constitute different sources for enriching rare and functional variants in a sequencing study design. Linkage is well known to have limited power for detecting small genetic effects, and hence not considered to be a powerful tool for discovering variants for common complex diseases. However, those families with some degree of family-specific linkage evidence provide an effective sampling strategy to sub-select the most linkage-informative families for sequencing. Compared with selecting subjects with extreme phenotypes, linkage evidence performs better with larger families, while extreme-phenotype method is more efficient with smaller families. Families with multiple affected siblings were found to provide the largest enrichment of rare variants. Finally, we showed that combined strategies, such as selecting linkage-informative families from multiply affected families, provide much higher enrichment of rare functional variants than either strategy alone.
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