ArticleGenome research2007
Intra- and interpopulation genotype reconstruction from tagging SNPs.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- Genetic history of the population of Crete.Annals of human genetics · 2019Article
- Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks.European journal of human genetics : EJHG · 2017Article
- Tic symptom dimensions and their heritabilities in Tourette's syndrome.Psychiatric genetics · 2015Article
- Maritime route of colonization of Europe.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- MultiFacTV: module detection from higher-order time series biological data.BMC genomics · 2013Article
- rCUR: an R package for CUR matrix decomposition.BMC bioinformatics · 2012Article
- Genome-wide compatible SNP intervals and their properties.The 2010 ACM International Conference on Bioinformatics and Computational Biology : ACM-BCB 2010 : Niagara Falls, New York, U.S.A., August 2-4, 2010. ACM International Conference on Bioinformatics and Computational Biology (1st : 2010 :... · 2010Article
- CUR matrix decompositions for improved data analysis.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Tracing sub-structure in the European American population with PCA-informative markers.PLoS genetics · 2008Article
- Article
- PCA-correlated SNPs for structure identification in worldwide human populations.PLoS genetics · 2007Article
- Comparison of ENCODE region SNPs between Cebu Filipino and Asian HapMap samples.Journal of human genetics · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
The optimal method to be used for tSNP selection, the applicability of a reference LD map to unassayed populations, and the scalability of these methods to genome-wide analysis, all remain subjects of debate. We propose novel, scalable matrix algorithms that address these issues and we evaluate them on genotypic data from 38 populations and four genomic regions (248 SNPs typed for approximately 2000 individuals). We also evaluate these algorithms on a second data set consisting of genotypes available from the HapMap database (1336 SNPs for four populations) over the same genomic regions. Furthermore, we test these methods in the setting of a real association study using a publicly available family data set. The algorithms we use for tSNP selection and unassayed SNP reconstruction do not require haplotype inference and they are, in principle, scalable even to genome-wide analysis. Moreover, they are greedy variants of recently developed matrix algorithms with provable performance guarantees. Using a small set of carefully selected tSNPs, we achieve very good reconstruction accuracy of "untyped" genotypes for most of the populations studied. Additionally, we demonstrate in a quantitative manner that the chosen tSNPs exhibit substantial transferability, both within and across different geographic regions. Finally, we show that reconstruction can be applied to retrieve significant SNP associations with disease, with important genotyping savings.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.