Human Population Genomics: Introduction to Essential Concepts and Applications

ISBN-13: 9783030616441 / Angielski / Twarda / 2021 / 234 str.

Kirk E. Lohmueller; Rasmus Nielsen

Recenzje

"This book is likely to be most useful to PhD students in the early stages of their graduate degree ... . By reading this edited volume, researchers will feel empowered and be able to interpret complex human genomic datasets. ... Human Population Genomics: Introduction to Essential Concepts and Applications would be a valuable addition to the bookshelf of any research group that studies this topic." (Joseph Lachance, The Quarterly Review of Biology, Vol. 97 (3), September, 2022)

Spis treści

​Section 1:  Population genetic theory 

1. Coalescent models (all the basics)  (John Wakeley: wakeley@fas.harvard.edu) 

2. Linkage disequilibrium (Monty Slatkin: slatkin@berkeley.edu) 

a. r^2, D’

b. LD and population history

c. Recombination and LD

3. Analysis of population structure (Per Sjödin, Lucie Gattepaille, Pontus Skoglund, Carina Schlebusch, and Mattias Jakobsson): mattias.jakobsson@ebc.uu.se) 

d. How do we quantify population structure?

e. PCA

f. Estimating Trees

g. Likelihood based genealogical approaches

h. FST

i. Estimation of parameters based on SFS

j. STRUCTURE analyses

k. Admixture HMMs

l. D statistics?

 

4. Inferring selection from population genetic DNA sequence data (David Enard) 

m. Frequency spectrum-based approaches

. Haplotype-based approaches

o. Multi-population-based approaches

Section 2:  Association studies and medical genetics

5. Methods for association studies (John Witte and Rebecca Graff) 

a. Case-control studies

b. Family based studies

c. Quantitative traits

d. Controlling for stratification

. Multiple testing, etc. 

6. IBD Mapping for complex traits (Elizabeth Thompson: eathomp@u.washington.edu) 

7. What have we learned from GWAS? (Ben Voight: bvoight@broadinstitute.org) 

p. Effect sizes

q. Missing heritability 

Section 3:  Human evolutionary population genetics

8. Human origins and ancient human demographic history (Jeff Wall: WallJ@humgen.ucsf.edu) 

9. Evidence and examples of selective sweeps across the human genome (Leslie S. Emery and Josh Akey: akeyj@uw.edu) 

O autorze

Kirk E. Lohmueller is an Associate Professor in the Department of Ecology and Evolutionary Biology as well as Human Genetics at UCLA. He received his PhD from Cornell University in 2010 and then was a Miller Fellow at UC Berkeley till 2013 when he joined the faculty at UCLA. Dr. Lohmueller is a population geneticist who studies a wide range of organisms, including humans, mice, dogs, wolves, foxes, birds, sea otters, and plants. A major focus of his research is understanding how deleterious mutations impact genomes and complex traits. He has received several awards including a Sloan Research Fellowship, Searle Scholar Award, and the Hellman Faculty Fellowship. His research has been supported by the National Institutes of Health, National Science Foundation, and National Institute of Justice.

Rasmus Nielsen is a Professor of computational biology in the Department of Integrative Biology and the Department of Statistics at the UC Berkeley, a position he has held since 2008.  He obtained his PhD from UC Berkeley in 1998, did a two-year postdoc at Harvard University 1998-2000, was an Assistant Professor at Cornell University 2000-2004 and has also been a Professor at University of Copenhagen since 2004.  His work focuses on statistical and computational methods in genetics, including methods for elucidating human history using genomic data. He has received multiple fellowships and awards for his work including a Fulbright fellowship, a Sloan Research Fellowship, the AAAS Newcomb Clevealand Price, and the Villum Kann Rasmussen Annual Award. He has published more than 300 peer reviewed publications which have been cited by other researchers more than 75,000 times.

Blurb

This textbook provides a concise introduction and useful overview of the field of human population genomics, making the highly technical and contemporary aspects more accessible to students and researchers from various fields.

Over the past decade, there has been a deluge of genetic variation data from the entire genome of individuals from many populations. These data have allowed an unprecedented look at human history and how natural selection has impacted humans during this journey. Simultaneously, there have been increased efforts to determine how genetic variation affects complex traits in humans. Due to technological and methodological advances, progress has been made at determining the architecture of complex traits. 

Split in three parts, the book starts with the basics, followed by more advanced and current research. The first part provides an introduction to essential concepts in population genetics, which are relevant for any organism. The second part covers the genetics of complex traits in humans. The third part focuses on applying these techniques and concepts to genetic variation data to learn about demographic history and natural selection in humans.

This new textbook aims to serve as a gateway to modern human population genetics research for those new to the field. It provides an indispensable resource for students, researchers and practitioners from disparate areas of expertise.