Human Population Genomics & Diseases (2017)

“Human genetics, as a field of genetics that lacks the benefit of an experimental system, therefore has a special reliance on population genetic theory”.  


  • Resolución CD Nº 1830/16, Exped. Nº506.158/16
  • Duración: 90 hs.
  • Desde – Hasta:  14/08/2017 – 30/10/2017.
  • Prácticas:  Lunes y Jueves de 13.30 a 16.30. Lab 1. Pab1.
    • Lunes 18/09 y 25/09 de 14.00 a 17.00
  • Teóricas: Lunes y Jueves de 17.00 a 19.00. Aula 12-Pab2-Lunes, Aula E24-Pab1- Jueves.
  • Docente Responsable: Hernán Dopazo
  • Docentes Colaboradores: Juan Berros, Nicolás Moreyra, Diego de Panis y Jeremias Zubrzycki.
  • Pre-inscripción: Desde el 01/07/2017  hasta el 01/08/2017.
  • Interesados: Completar formulario de pre-inscripción al final de esta página.
  • Capacidad: Mínimo 10, máximo 25 estudiantes.
  • Notificación de Aceptación: 03/08/2017
  • Programa de Doctorado: 3 puntos.
  • Arancel: 300$ para los estudiantes externos al Programa de Doctorado de la FCEN-UBA.
  • Inscripción en la FCEyN: Desde el 04/08/2017 hasta el 03/09/2017. Sólo para los alumnos que han sido seleccionados y confirmados. Instrucciones
  • Cronograma de prácticas y teóricas (aquí)

Program

Module I: Human Population Genomics

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/454, 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. 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, Phase II and III. The Encode Project Phase I and II. Criticisms.

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 Genetics of SVs. The Human Pan-Genome Concept.

Module II:  Demography & Natural Selection

Theme 4. Human Demography and Population Structure: Shared & Private population variants. Deep sequencing projects.Demographic Explosion of Human Populations.   Models of Modern Human Origins. Genomic Evidences of the Out-of-Africa Serial Founder Effect Model. Population Genetic Structure of Africans, Europeans and Americans. Human Races: What they mean?

Theme 5. 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. Archaic Adaptive Introgression in Humans. Natural Selection on Functional Modules. 

Module III: Genomics of Simple and Complex Diseases

Theme 6. Genomics and Human Diseases:  Genetic Diseases. Relative Risk. Odds-Ratio. Parametric Linkage Analysis. LOD Score. Sensitivity & Specificity. Population & Family Association Studies. Population Stratification.  The Genetic Architecture of Human Diseases. Loss-of-Function (LoF) Variants. The Distribution of the Fitness Effects. The Human Disease Network and the Interactome. 

Theme 7. Genome-Wide Association Studies: Heritability. Common Disease / Common Variants Hypothesis. GWAS. Common and Rare variant association studies.  Replicability. The Enigma of the Hidden Heritability. Prioritising Candidate Genes.

Theme 8. Personalized Medical Genomics:  The Molecular Medical Diagnostic (MDx) Landscape. Direct to Consumer (DTC) Testing. Heterozygous Carries of Mendelian Diseases. Pre-implantational Genetic Screening (PGS) & Diagnostic (PGD). Karyomapping. Prenatal & Postnatal Genomic Tests. Gene Panels. Exome Sequencing. Non-Invasive Genomic Tests. Single Cell Genomics.


MAR01
SAILING A SEA OF ZEROES AND ONES

Hands-on Computer Exercises

TP1. Introduction to Linux with UBUNTU. Overview of the file system. Users, groups and permissions. The command-line interface. Basic commands and scripting. Running Local Blast example.

TP2: Exploring and Downloading Human Genome Data. Genomic databases. Ensembl structure and use for variants search. Using NCBI MapViewer browser. Access and data retrieve using BioMart, and the basic uses of the Perl Application Program Interfaces (API).

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 & cutadapt.

TP4. Introduction to Genome Assembly using NGS data. Strategies and methods. De novo assembly and evaluation. Reference’s data alignment and visualization.

TP5. Introduction to RNAseq. Strategies and methods. Transcriptome assembly. Mapping and counting. Differential expression analysis.

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 1KG 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. Find Signatures of Selection in the Human Genome using DnaSP and the 1000 Genomes Selection Browser.

TP9. GWAS Using Plink.

TP10: Variant Calling & Annotation. GATK Best Practices Pipeline: data pre proccesing, local realignment around indels, base quality score recalibration, variant discovery.


Pre-Inscripción on-line … 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.

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