Cryptic relationships such as first-degree relatives often appear in studies that collect population samples such as the case–control genome-wide association studies (GWAS). Cryptic relatedness not only creates increased type 1 error rate but also affects other aspects of GWAS, su ...
The Hardy–Weinberg principle, one of the most important principles in population genetics, was originally developed for the study of allele frequency changes in a population over generations. It is now, however, widely used in studies of human diseases to detect inbreeding, populations ...
Methods of estimating allele frequencies from data on unrelated and related individuals are described in this chapter. For samples of unrelated individuals with simple codominant markers, the natural estimator of allele frequencies can be used. For genetic data on related individu ...
Gametic phase disequilibrium (GPD) is the nonrandom association of alleles within gametes. Linkage disequilibrium (LD) describes the special case of deviation from independence between alleles at two linked genetic loci. Estimation of allelic LD requires knowledge of haplotyp ...
Beyond calculating parameter estimates to characterize the distribution of genetic features of populations (frequencies of mutations in various regions of the genome, allele frequencies, measures of Hardy–Weinberg disequilibrium), genetic epidemiology aims to identi ...
This chapter describes how the heritability of a trait can be estimated using data collected from pairs of twins. The principles of the classical twin design are described, followed by the assumptions and possible extensions of the design. In the second part of this chapter, two example scripts are ...
The array CGH technique (array comparative genome hybridization) has been developed to detect chromosomal copy number changes on a genome-wide and/or high-resolution scale. Here, we present validated protocols using in-house spotted oligonucleotide libraries for array CGH. Th ...
Recently developed microarray-based copy number measurement assays have drastically improved the accuracy and resolution to which DNA copy number alterations can be detected. As with any microarray assay, those designed to measure genome copy number produce large data sets for each ...
Genome sequencing has revealed the remarkable amount of genetic diversity that can be encountered in bacterial genomes. In particular, the comparison of genome sequences from closely related strains has uncovered significant differences in gene content, hinting at the dynamic na ...
The ability to analyze a large number of genetic markers consisting of single nucleotide polymorphisms (SNPs) may bring about significant advance in understanding human biology. Recent development of several high-throughput genotyping approaches has significantly facil ...
DNA microarrays can be used to detect polymorphic loci in addition to identifying genes or regions that are absent within a genome. A survey such as this offers greater insight into the level of diversification within a species or population, which is useful in organisms that have nearidentical g ...
Single nucleotide polymorphisms (SNPs) are the most frequent form of DNA variation present in the human genome, and millions of SNPs have been identified (http://www.ncbi.nlm.nih.gov/SNP/). Because of their abundance, even spacing, and stability across the genome, SNPs have significa ...
We have described molecular inversion probe technologies for large-scale genetic analyses. This technique provides a comprehensive and powerful tool for the analysis of genetic variation and enables affordable, large-scale studies that will help uncover the genetic basis of com ...
The same high-throughput techniques used to make genomic sequences generally available, are also useful in mapping the genetic differences between individuals. Resequencing of a genomic region in a set of individuals is considered the golden standard for the discovery of sequence va ...
Sites in the DNA sequences where two homologous chromosomes differ at a single DNA base are called single nucleotide polymorphisms (SNPs). The human genome contains at least 10 million SNPs, making them the most abundant genetic “lampposts” for pinpointing causal variants underlying hu ...
Identification and characterization of nucleotide substitutions in DNA sequences for single nucleotide polymorphism or point mutation detection can be a time consuming and sometimes inaccurate process, particularly in relatively low-throughput situations where fully ...
The National Center for Biotechnology Information (NCBI) has developed several web-based mini-courses (http://www.ncbi.nlm.nih.gov/Class/minicourses) illustrating the applications of NCBI resources. This chapter describes the problem-based minicourse called “ ...
Analysis of bacterial genomes revealed a high percentage of DNA consisting of repeats, in which DNA motifs existed in multiple copies. Study of these DNA motifs has resulted in the development of variable number tandem repeat (VNTR) or multilocus variant-repeat analysis (MLVA) assays, whi ...
Genetic mapping with DNA sequence polymorphisms allows for map-based positional cloning of mutations at any required resolution. Numerous methods have been worked out to assay single nucleotide polymorphisms (SNPs), the most common type of molecular polymorphisms. However, SNP g ...
High-resolution and reproducible whole genome methodologies are needed as tools for rapid and cost-effective analysis of genetic diversity within bacterial genomes. These should be useful for a broad range of applications such as identification and subtyping of microorganisms ...
