The International HapMap Project was an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation. HapMap is used to find genetic variants affecting health, disease and responses to drugs and environmental factors. The information produced by the project is made freely available for research.
A DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is identical by descent (IBD) in two or more individuals if they have inherited it from a common ancestor without recombination, that is, the segment has the same ancestral origin in these individuals. DNA segments that are IBD are IBS per definition, but segments that are not IBD can still be IBS due to the same mutations in different individuals or recombinations that do not alter the segment.
In genomics, a genome-wide association study, is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. GWA studies typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other genetic variants and any other organisms.
Population structure is the presence of a systematic difference in allele frequencies between subpopulations. In a randomly mating population, allele frequencies are expected to be roughly similar between groups. However, mating tends to be non-random to some degree, causing structure to arise. For example, a barrier like a river can separate two groups of the same species and make it difficult for potential mates to cross; if a mutation occurs, over many generations it can spread and become common in one subpopulation while being completely absent in the other.
Gilean Alistair Tristram McVean is a professor of statistical genetics at the University of Oxford, fellow of Linacre College, Oxford and co-founder and director of Genomics plc. He also co-chaired the 1000 Genomes Project analysis group.
C-type lectin domain family 16, also known as CLEC16A, is a protein that in humans is encoded by the CLEC16A gene.
In genetics, association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link phenotypes to genotypes, uncovering genetic associations.
Sir Michael Rudolf Stratton, is a British clinical scientist and the third director of the Wellcome Trust Sanger Institute. He currently heads the Cancer Genome Project and is a leader of the International Cancer Genome Consortium.
Zinc finger protein 300 is a protein that in humans is encoded by the ZNF300 gene. The protein encoded by this gene is a C2H2-type zinc finger DNA binding protein and a likely transcription factor.
Jonathan Karl Pritchard is an English-born professor of genetics at Stanford University, best known for his development of the STRUCTURE algorithm for studying population structure and his work on human genetic variation and evolution. His research interests lie in the study of human evolution, in particular in understanding the association between genetic variation among human individuals and human traits.
Andrew B. Singleton is a British neurogeneticist currently working in the USA. He was born in Guernsey, the Channel Islands in 1972, where he lived until he was 18 years old. His secondary education was conducted at the Guernsey Grammar School. He earned a first class degree in Applied Physiology from Sunderland University and his PhD in neuroscience from the University of Newcastle upon Tyne where he studied the genetics of Alzheimer's disease and other dementias at the Medical Research Council (MRC) Neurochemical Pathology Unit. He moved to the United States in 1999, where he began working at the Mayo Clinic in Jacksonville, Florida studying the genetic basis of Parkinson's disease, ataxia, and dystonia. He moved to the National Institutes of Health in 2001 to head the newly formed Molecular Genetics unit within the Laboratory of Neurogenetics. In 2006 he took over as Chief of the Laboratory of Neurogenetics and became an NIH Distinguished Investigator in the intramural program at the National Institute on Aging (NIA) in 2017. In 2020 he stepped down as the Chief of the Laboratory of Neurogenetics and became the Acting Director of the newly formed Center for Alzheimer's and Related Dementias at the NIA. In 2021 he became the Director of CARD.
In genetics, haplotype estimation refers to the process of statistical estimation of haplotypes from genotype data. The most common situation arises when genotypes are collected at a set of polymorphic sites from a group of individuals. For example in human genetics, genome-wide association studies collect genotypes in thousands of individuals at between 200,000-5,000,000 SNPs using microarrays. Haplotype estimation methods are used in the analysis of these datasets and allow genotype imputation of alleles from reference databases such as the HapMap Project and the 1000 Genomes Project.
Imputation in genetics refers to the statistical inference of unobserved genotypes. It is achieved by using known haplotypes in a population, for instance from the HapMap or the 1000 Genomes Project in humans, thereby allowing to test for association between a trait of interest and experimentally untyped genetic variants, but whose genotypes have been statistically inferred ("imputed"). Genotype imputation is usually performed on SNPs, the most common kind of genetic variation.
Gonçalo Rocha Abecasis is a Portuguese American biomedical researcher at the University of Michigan and was chair of the Department of Biostatistics in the School of Public Health. He leads a group at the Center for Statistical Genetics in the Department of Biostatistics, where he is also the Felix E. Moore Collegiate Professor of Biostatistics and director of the Michigan Genomic Initiative. His group develops statistical tools to analyze the genetics of human disease.
Mega2 allows the applied statistical geneticist to convert one's data from several input formats to a large number output formats suitable for analysis by commonly used software packages. In a typical human genetics study, the analyst often needs to use a variety of different software programs to analyze the data, and these programs usually require that the data be formatted to their precise input specifications. Conversion of one's data into these multiple different formats can be tedious, time-consuming, and error-prone. Mega2, by providing validated conversion pipelines, can accelerate the analyses while reducing errors.
Sabera Nazneen Rahman is a geneticist who specialises in cancer research and is a non-executive director for Astra Zeneca. She was previously head of Genetics and Epidemiology at the Institute of Cancer Research.
A multilocus genotype is the combination of alleles found at two or more loci in a single individual.
The Wellcome Trust Case Control Consortium is a collaboration between fifty research groups in the United Kingdom in the field of human genetics. Established in 2005, the WTCCC aims to conduct genome-wide association studies (GWASs) to shed light on the genetic architecture of common human diseases. The founding chairman of the consortium was University of Oxford statistician Peter Donnelly. The consortium was funded by £9 million from the Wellcome Trust. According to the consortium's website, it has identified "approximately 90" new susceptibility loci for common human diseases.
In genetics, a haplotype block is a region of an organism's genome in which there is little evidence of a history of genetic recombination, and which contain only a small number of distinct haplotypes. According to the haplotype-block model, such blocks should show high levels of linkage disequilibrium and be separated from one another by numerous recombination events. The boundaries of haplotype blocks cannot be directly observed; they must instead be inferred indirectly through the use of algorithms. However, some evidence suggests that different algorithms for identifying haplotype blocks give very different results when used on the same data, though another study suggests that their results are generally consistent. The National Institutes of Health funded the HapMap project to catalog haplotype blocks throughout the human genome.
Human genetic clustering refers to patterns of relative genetic similarity among human individuals and populations, as well as the wide range of scientific and statistical methods used to study this aspect of human genetic variation.
