Human Population Genomics and Diseases (2015)

Resolución CD Nº 1088, Expte Nº504.785/2015

  • Duración: 90 hs.
  • Desde – Hasta:  28/09/2015 – 14/12/2015. 
  • Prácticas:  Lunes y Jueves de 13.00 a 16.00. Pab. 1. Lab 2.
  • Teóricas: Lunes y Jueves de 16.30 a 18.30. Pab. 2. Aula 10.
  • Docentes: Hernán Dopazo, Cristian Rohr. Prof. Invitados (A. Navarro y J. Oliver)
  • Pre-inscripción: Desde 3 de Julio hasta el 14 Agosto de 2015 inclusive.
  • InteresadosINSCRIPCION CERRADA Completar formulario de pre-inscripción al final de esta página. 
  • CapacidadMínimo 10, máximo 25 estudiantes
  • Notificación de Aceptación: 28 de Agosto 2015
  • Programa de Doctorado: 3 puntos
  • Arancel: 300$ para los estudiantes externos al Programa de Doctorado de la FCEN-UBA
  • Inscripción Definitiva en la FCEyN: Desde el 01/09/2015 hasta el 15/09/2015. Sólo para los alumnos que han sido seleccionados y confirmadosInstrucciones

Descargue el cronograma de prácticos y teóricas aquí

Video y Canción Oficial

cancion

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

Fin de Curso 2015

20151126_180254
Festejando el Fin de Curso

20151130_184133


evaluacion2015
Satisfacción media 2015

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. 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.

Theme 3. 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.

Module II: Demography and Natural Selection 

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

Theme 5. Tests of Neutrality and Signatures of SelectionTajima’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.

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. Using NCBI MapViewer browser. 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 & cutadapt.

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 Database of Genomic Variants. 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. 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.

 

Anuncios