Rare Variant Association Testing for Sequencing Data Using the Sequence Kernel Association Test ( SKAT )

*These authors contributed equally to this work. 1 Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA 2 Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA 3 Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA 4 Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA

[1]  Xihong Lin Variance component testing in generalised linear models with random effects , 1997 .

[2]  Tong Zhang,et al.  An Introduction to Support Vector Machines and Other Kernel-Based Learning Methods , 2001, AI Mag..

[3]  F. Fleuret,et al.  Scale-Invariance of Support Vector Machines based on the Triangular Kernel , 2001 .

[4]  P. Bork,et al.  Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.

[5]  S. Gabriel,et al.  Calibrating a coalescent simulation of human genome sequence variation. , 2005, Genome research.

[6]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[7]  D. Reich,et al.  Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.

[8]  W. Thilly,et al.  A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). , 2007, Mutation research.

[9]  Xihong Lin,et al.  Semiparametric Regression of Multidimensional Genetic Pathway Data: Least‐Squares Kernel Machines and Linear Mixed Models , 2007, Biometrics.

[10]  S. Leal,et al.  Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. , 2008, American journal of human genetics.

[11]  Dawei Liu,et al.  Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models , 2008, BMC Bioinformatics.

[12]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[13]  Xihong Lin,et al.  A powerful and flexible multilocus association test for quantitative traits. , 2008, American journal of human genetics.

[14]  Amy E. Hawkins,et al.  DNA sequencing of a cytogenetically normal acute myeloid leukemia genome , 2008, Nature.

[15]  E. Mardis Next-generation DNA sequencing methods. , 2008, Annual review of genomics and human genetics.

[16]  Suzanne M. Leal,et al.  Discovery of Rare Variants via Sequencing: Implications for the Design of Complex Trait Association Studies , 2009, PLoS genetics.

[17]  K. Frazer,et al.  Common vs. rare allele hypotheses for complex diseases. , 2009, Current opinion in genetics & development.

[18]  Huan Liu,et al.  A new chi-square approximation to the distribution of non-negative definite quadratic forms in non-central normal variables , 2009, Comput. Stat. Data Anal..

[19]  S. Browning,et al.  A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic , 2009, PLoS genetics.

[20]  W. Ansorge Next-generation DNA sequencing techniques. , 2009, New biotechnology.

[21]  Huanming Yang,et al.  SNP detection for massively parallel whole-genome resequencing. , 2009, Genome research.

[22]  Eric Boerwinkle,et al.  Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. , 2008, The Journal of clinical investigation.

[23]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

[24]  Wei Pan,et al.  Asymptotic tests of association with multiple SNPs in linkage disequilibrium , 2009, Genetic epidemiology.

[25]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[26]  Yun Li,et al.  Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. , 2010, American journal of human genetics.

[27]  L. Carvajal-Carmona,et al.  Challenges in the identification and use of rare disease-associated predisposition variants. , 2010, Current opinion in genetics & development.

[28]  Shamil R Sunyaev,et al.  Pooled association tests for rare variants in exon-resequencing studies. , 2010, American journal of human genetics.

[29]  Jason H. Moore,et al.  Missing heritability and strategies for finding the underlying causes of complex disease , 2010, Nature Reviews Genetics.

[30]  Eleftheria Zeggini,et al.  Rare variant association analysis methods for complex traits. , 2010, Annual review of genetics.

[31]  E. Zeggini,et al.  An Evaluation of Statistical Approaches to Rare Variant Analysis in Genetic Association Studies , 2009, Genetic epidemiology.

[32]  Olivier Harismendy,et al.  Accurate detection and genotyping of SNPs utilizing population sequencing data. , 2010, Genome research.

[33]  Pierre Lafaye de Micheaux,et al.  Computing the distribution of quadratic forms: Further comparisons between the Liu-Tang-Zhang approximation and exact methods , 2010, Comput. Stat. Data Anal..

[34]  Deanne M. Taylor,et al.  Powerful SNP-set analysis for case-control genome-wide association studies. , 2010, American journal of human genetics.

[35]  Wei Pan,et al.  A Data-Adaptive Sum Test for Disease Association with Multiple Common or Rare Variants , 2010, Human Heredity.

[36]  Kathryn Roeder,et al.  Testing for an Unusual Distribution of Rare Variants , 2011, PLoS genetics.

[37]  Emmanouil Collab A map of human genome variation from population-scale sequencing , 2011, Nature.

[38]  Power and sample size calculations for designing rare variant sequencing association studies , 2011 .