Lecture

Genomics: SNP Detection & Population Stratification

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In course

BIO-373: Genetics and genomics

The theoretical part of this course covers classical genetics and contemporary genomics. Because bioinformatics has become important for genomic research, the course also includes practical applications to genomic analyses using Python, including group pro ...

Description

This lecture covers the detection of single nucleotide polymorphisms (SNPs) using high-density oligonucleotide arrays, the SNP database, and the concept of linkage disequilibrium. It also discusses the estimation of SNPs in the human genome, the use of LD bins to capture common SNPs, and the application of genomics in elucidating human history through Neanderthal genome comparisons.

Instructors (2)

Bart Deplancke

Bart Deplancke graduated as a Biochemical Engineer at Ghent University (Belgium, 1998) after which he pursued doctoral studies in Immunobiology at the University of Illinois (USA) and postdoctoral work in regulatory genomics at the Harvard and UMass Medical Schools (USA). In 2007, he established his lab at the EPFL School of Life Sciences where he is now a Full Professor and former Vice-Dean of Innovation. There, he is developing new, often single cell-related technologies to study how the genome mediates c

Jacques Fellay

Jacques Fellay is a medical scientist with expertise in infectious diseases and human genomics. He obtained his MD from the University of Lausanne in 2002 and his PhD from University of Utrecht. After a clinical training in infectious diseases in Switzerland and a 4-years postdoctoral fellowship at Duke University, he joined the EPFL in April 2011 with an SNF Professorship. On top of his EPFL affiliation, Jacques is also Head of Precision Medicine at the University Hospital (CHUV) in Lausanne, Group Leader at the Swiss Institute of Bioinformatics, and Co-director of the Health2030 Genome Center at Campus Biotech in Geneva.

Official source

Related concepts (15)

Human history

Human history is the narrative of humankind's past. Humans evolved in Africa 300,000 years ago and initially lived as hunter-gatherers. Humans migrated out of Africa during the Last Glacial Period (Ice Age) and had populated most of the Earth by the time the Ice Age ended 12,000 years ago. The Agricultural Revolution began soon afterwards in fertile river valleys of the Near East: humans began the systematic husbandry of plants and animals, and many humans transitioned from a nomadic life to a sedentary existence as farmers in permanent settlements.

Human genome

The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA, such as that for ribosomal RNA, transfer RNA, ribozymes, small nuclear RNAs, and several types of regulatory RNAs.

Neanderthal

Neanderthals (niˈændə(r)ˌtɑːl,neɪ-,-ˌθɑːl; Homo neanderthalensis or H. sapiens neanderthalensis), also written as Neandertals, are an extinct species or subspecies of archaic humans who lived in Eurasia until about 40,000 years ago. The reasons for Neanderthal extinction are disputed. Theories for their extinction include demographic factors such as small population size and inbreeding, competitive replacement, interbreeding and assimilation with modern humans, climate change, disease, or a combination of these factors.

Linkage disequilibrium

In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than expected if the loci were independent and associated randomly. Linkage disequilibrium is influenced by many factors, including selection, the rate of genetic recombination, mutation rate, genetic drift, the system of mating, population structure, and genetic linkage.

Human

Humans, or modern humans (Homo sapiens), are the most common and widespread species of primate. A great ape characterized by their hairlessness, bipedalism, and high intelligence, humans have a large brain and resulting cognitive skills that enable them to thrive in varied environments and develop complex societies and civilizations. Humans are highly social and tend to live in complex social structures composed of many cooperating and competing groups, from families and kinship networks to political states.

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