Human Population Genomics

Resolución CD Nº0737, Expte Nº503.400/2014

  • Duración: 9 semanas, 18 días, 90 hs.
  • Desde – Hasta: 15/08/2014 – 15/10/2014
  • Teóricas: Mi y Vi de 16:30 a 18:30. Aula 12-PB, y Aula 6-Subsuelo. Pab. 2.
  • Prácticas: Mi y Vi de 13:00 a 16:00 hs.  Lab. 4,  y Lab. 5 de Cc. Computación. Pab. 1.
  • Docentes: Hernán Dopazo, Cristian Rohr y docentes invitados.
  • Pre-inscripción: Hasta el 11 de julio de 2014 inclusive.
  • Notificación de Aceptación25 de julio de 2014
  • Capacidad: Mínimo 10, máximo 25 estudiantes
  • Programa de Doctorado: 3 puntos
  • Arancel: 300$ para los estudiantes externos al Programa de Doctorado de la FCEN-UBA
  • InteresadosCompletar formulario de pre-inscripción al final de esta página
  • Inscripción Definitiva: Hasta el 29/08/14. Sólo para los alumnos que han sido confirmados. Instrucciones
  • Evaluación de los Estudiantes sobre el Curso 2014:

 grafico_evaluacion_final

Program

Module I: Human Genomes

Theme 1. Personal Genomes & NGS Technologies: The Human Genome Project (Public and Private). Diploid Genomes: Venter, & Watson. Comparing Genomes: Europeans, Asians, and Africans. NGS Technologies: Roche, Illumina, Helicos, Pacific Bioscience, Ion Torrent/Proton and Oxford Nanopore. Paired-end & Mate-Pair libraries. Multiplex sequencing. Genomic Enrichment Strategies. The Big-Data Storage Problem.

Theme 2. Genomics of Transcription: ENCODE Project. Phase I & II.  Results & Technologies: Chip-chip, Tilling array, RACE, CAGE, PET, DNase-seq, FAIRE-seq, Chip-seq, RNA-seq  & 5C. The post-encode gene’s definition. Ultra-conserved elements in the genome. Neutral vs Adaptive Gene Expression. 80% Functional or Still Junk ? Neutral Ecology of Genomes.

Theme 3. Structural Variants and Populations: Structural Variants (SVs) in the Human Genome. Genotyping and NGS Methods. Mapping Strategies of NGS-SVs. CNVs formation mechanisms. The SVs Databases. SVs in Human Populations. Population Genetic of SVs. The Human Pan-Genome Concept.

Module II: Population Genomics

Theme 4. Human Genome Variability: On Human Variation. Single Nucleotide Polymorphisms (SNPs).  Tag-SNPs. Haplotypes and Linkage Disequilibrium in the Human Genome. Haplotype Blocks. Recombination Hotspots. The HapMap Project. Phase I, II & III. Genotype imputation. The 1,000 Genomes Project: Pilot, and Phase II.

Theme 5. Population Structure and Demography: Shared & Private population variants. Demographic Explosion of Human Populations. Deep sequencing in humans. Genetic Structure and Demography of Human Populations. Evidences from Africa, Europe, Asia, Australia, Oceania and America. The Genetic Atlas of Human Admixture History.

Module III: Selection, Ancestral Genomes, and Continental Peopling

Theme 6. Tests of Neutrality and Signatures of Selection: Tajima’s D; Fay & Wu’s H; MK; dN/dS and LRH test. Ancient and Recent Signatures of Selection in the Human Genome. Natural Selection on Functional Modules. Evidences of Ongoing Selection.

Theme 7. Ancestral Hominin Genomes: Time to the most recent common ancestor (TMRCA): Genomic’s Distribution. Models of Human Origins. Neanderthal, and Denisovan Genomes. Inferring ancient population size change over time. Ancient Introgression between hominins. Altai-Neanderthal Imbreeding. Inferring human derived features from archaic hominin genomes.

Theme 8. Continental Peopling: The Out-of-Africa Serial Founder Effect Model. Historical Information form mtDNA and Y chromosomes. Genomic Evidences for a South African Origin of Modern Humans. The Multiple Dispersals with Isolation (MDI) Model.  American Peopling. Human Races: What they mean?  How culture shaped human genome ?

Hands-on Computer Exercises

TP1. Lessons on Linux OS using UBUNTU. The Linux shell. Basic shell commands. Overview of the Linux file system. Linux users, groups and permissions. Basic scripting. Running Local Blast example.

TP2: Exploring and Downloading Human Genome Data. Genomic databases. Ensembl structure and use for variants search. Find disease genes and mutations using NCBI. Access and data retrieve using BioMart.

TP3. NGS Methods & NGS Quality Control. Introduction & technical evolution of Next Generation Sequencing. Quality control of NGS reads using FastQC. Processing of reads using FASTX-toolkit.

TP4. Human mtDNA chromosome assembly. Introduction to NGS data assembly (strategies, methods, common errors, k-mer spectra, and de bruijn graphs). Assembly with ABYSS. Parameters estimation and assembly with VELVET. Alignment to reference using BOWTIE2.

TP5. Exploring the Encode and the Database of Genomic Variants. Access to ENCODE data through UCSC browser. Comparison of structural variants databases. Access to variants in the Database of Genomic Variants. Structural variants prediction and visualization using inGAP-sv.

TP6. Population Genomics with HapMap & 1,000 Human Genomes Project. Access to HapMap. Visualization and download: Linkage disequilibrium, Tagging SNP’s, Phased Haplotypes. Data manipulation using Haploview. Data access and download with HapMart. Exploring the 1000G browser. Variant Call File (VCF) format. Download and analysis of 1000G data with tabix and VCF tools.

TP7. Human Population Structure. Filter SNPs in LD. Explore HW predictions. Computing and plotting MAF frequency spectra. Estimation of ancestries using ADMIXTURE. Principal components analysis. Phenotype association and Manhattan plots. 

TP8. Signatures of Selection in the Human Genome. Statistical Analysis of Adaptation using DnaSP. The 1,000 Genomes Selection Browser.

Pre-Inscripción: Human Population Genomics. CERRADA !

  • Complete todos los campos y describa en no mas de 3 párrafos las razones por las que este curso le resulta de interés.
  • Una vez enviado solo observará en su pantalla: Message Sent !!
  • No espere la recepción de un mail de confirmación.