Gene- or region-based association study via kernel principal component analysis

January 2011
BMC Genetics;2011, Vol. 12 Issue 1, p75
Academic Journal
The article presents a study detecting the correlation between genetic variations and disease by using a kernel principal component analysis combined with logistic regression test (KPCA-LRT). The KPCA-LRT model has been used in this study to avoid the multicolinearity. The study found that KPCA-LRT is a valid and powerful gene- or region-based method for the analysis of genome-wide association studies (GWAS) data set.


Related Articles

  • Rare DNA copy number variants in cardiovascular malformations with extracardiac abnormalities. Lalani, Seema R; Shaw, Chad; Wang, Xueqing; Patel, Ankita; Patterson, Lance W; Kolodziejska, Katarzyna; Szafranski, Przemyslaw; Ou, Zhishuo; Tian, Qi; Kang, Sung-Hae L; Jinnah, Amina; Ali, Sophia; Malik, Aamir; Hixson, Patricia; Potocki, Lorraine; Lupski, James R; Stankiewicz, Pawel; Bacino, Carlos A; Dawson, Brian; Beaudet, Arthur L // European Journal of Human Genetics;Feb2013, Vol. 21 Issue 2, p173 

    Clinically significant cardiovascular malformations (CVMs) occur in 5-8 per 1000 live births. Recurrent copy number variations (CNVs) are among the known causes of syndromic CVMs, accounting for an important fraction of cases. We hypothesized that many additional rare CNVs also cause CVMs and...

  • Association between copy number variation of complement component C4 and Graves' disease.  // Journal of Biomedical Science;2011, Vol. 18 Issue 1, p71 

    The article offers information on the study conducted by the authors related to association between copy number variation of complement component C4 and Graves' disease. It states that gene copy number of complement component C4, which varies among individuals, may determine the intrinsic...

  • Many sequence variants affecting diversity of adult human height. Gudbjartsson, Daniel F.; Walters, G. Bragi; Thorleifsson, Gudmar; Stefansson, Hreinn; Halldorsson, Bjarni V.; Zusmanovich, Pasha; Sulem, Patrick; Thorlacius, Steinunn; Gylfason, Arnaldur; Steinberg, Stacy; Helgadottir, Anna; Ingason, Andres; Steinthorsdottir, Valgerdur; Olafsdottir, Elinborg J.; Olafsdottir, Gudridur H.; Jonsson, Thorvaldur; Borch-Johnsen, Knut; Hansen, Torben; Andersen, Gitte; Jorgensen, Torben // Nature Genetics;May2008, Vol. 40 Issue 5, p609 

    Adult human height is one of the classical complex human traits. We searched for sequence variants that affect height by scanning the genomes of 25,174 Icelanders, 2,876 Dutch, 1,770 European Americans and 1,148 African Americans. We then combined these results with previously published results...

  • Incremental value of rare genetic variants for the prediction of multifactorial diseases. Mihaescu, Raluca; Pencina, Michael J.; Alonso, Alvaro; Lunetta, Kathryn L.; Heckbert, Susan R.; Benjamin, Emelia J.; Janssens, A. Cecile J. W. // Genome Medicine;2013, Vol. 5 Issue 8, p1 

    Background: It is often assumed that rare genetic variants will improve available risk prediction scores. We aimed to estimate the added predictive ability of rare variants for risk prediction of common diseases in hypothetical scenarios. Methods: In simulated data, we constructed risk models...

  • Toward Inclusive Genomics. JOON-HO YU; BURKE, WYLIE // GeneWatch;Jul/Aug2012, Vol. 25 Issue 4, p11 

    The article discusses the underrepresentation of minority populations in the human genetics research, the Human Genome Project. This underrepresentation may reportedly present an incomplete picture of human genetic variation. Recruitment strategies and procedures that consider the perspectives...

  • Genetics and social identity after the HapMap. Foster, Morris W. // Nature Reviews Genetics;Dec2005, Vol. 6 Issue 12, p879 

    The article looks at the possible implication of project HapMap, the haplotype map of the human genome, for human genetic variation and social identity. HapMap revealed that there are common variants that are found across populations and that there are differences in frequencies of those...

  • Detection of rare functional variants using group ISIS. Niu, Yue S.; Ning Hao; An, Lingling // BMC Proceedings;2011 Supplement 9, Vol. 5 Issue Suppl 9, p1 

    Genome-wide association studies have been firmly established in investigations of the associations between common genetic variants and complex traits or diseases. However, a large portion of complex traits and diseases cannot be explained well by common variants. Detecting rare functional...

  • Genome-wide case-control study in GAW17 using coalesced rare variants. Libo Wang; Pungpapong, Vitara; Yanzhu Lin; Dabao Zhang // BMC Proceedings;2011 Supplement 9, Vol. 5 Issue Suppl 9, p1 

    Genome-wide association studies have successfully identified numerous loci at which common variants influence disease risks or quantitative traits of interest. Despite these successes, the variants identified by these studies have generally explained only a small fraction of the variations in...

  • Comparison of collapsing methods for the statistical analysis of rare variants. Dering, Carmen; Ziegler, Andreas; K├Ânig, Inke R.; Hemmelmann, Claudia // BMC Proceedings;2011 Supplement 9, Vol. 5 Issue Suppl 9, p1 

    Novel technologies allow sequencing of whole genomes and are considered as an emerging approach for the identification of rare disease-associated variants. Recent studies have shown that multiple rare variants can explain a particular proportion of the genetic basis for disease. Following this...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics