MOTIVATION Recently, structural genomic variants have come to the forefront as a significant source of variation in the human population, but the identification of these variants in a large genome remains a challenge. The complete sequencing of a human individual is prohibitive at current costs, while current polymorphism detection technologies, such as SNP arrays, are not able to identify many...

We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication tests show that these predictors capture, respectively, ∼40, 20, and 9 percent of total variance for the three traits. For example, predicted heights correla...

SNPServer is a real-time flexible tool for the discovery of SNPs (single nucleotide polymorphisms) within DNA sequence data. The program uses BLAST, to identify related sequences, and CAP3, to cluster and align these sequences. The alignments are parsed to the SNP discovery software autoSNP, a program that detects SNPs and insertion/deletion polymorphisms (indels). Alternatively, lists of relat...

This research provides an analytical tool, fuzzy decision support system (FDSS), to find the precedence of jeopardy in occupations spawning shoulder and neck pain (SNP), an important musculoskeletal disorder and the most ubiquitous pain complaint in an occupational environment. FDSS evaluates and prioritizes the relative importance of the imprecise, uncertain and vague nature of risk factors ca...

CHAPTER 1 GENERAL INTRODUCTION 1

The analysis of next-generation sequence (NGS) data is often a fragmented step-wise process. For example, multiple pieces of software are typically needed to map NGS reads, extract variant sites, and construct a DNA sequence matrix containing only single nucleotide polymorphisms (i.e., a SNP matrix) for a set of individuals. The management and chaining of these software pieces and their outputs...

Abstract The Netherlands’ field genebank collection of European wild apple ( Malus sylvestris ), consisting 115 accessions, was studied in order to determine whether duplicates and mistakes had been introduced, develop a strategy optimize the planting design as seed orchard. We used 20K Infinium single nucleotide polymorphism (SNP) array, developed M. domestica , for first time genotyping . cou...

Title: The effects of linkage disequilibrium in large scale SNP datasets for MDR

Reproduction traits are important but difficult to improve in sheep because they are lowly heritable and are recorded later in life. Genomic information can be used for genomic prediction of breeding values to increase the accuracy of selection. Alternatively, genomic information can be used to identify recessive lethal mutations, which cause embryonic losses. We investigated both uses of genom...

1 Some phylogenetic datasets omit data matrix positions at which all taxa share the same state. 2 For sequence data this may be because of a focus on single nucleotide polymorphisms (SNPs) 3 or the use of a technique such as restriction site-associated DNA sequencing (RADseq) that 4 concentrates attention onto regions of differences. With morphological data, it is common to 5 omit states that s...