MIT-OCW Health Sciences & Technology 508/510 Harvard Biophysics 101 EconomicsEconomics, Public Policy, Business, Health PolicyPublic PolicyBusinessHealth.

Slides:

Advertisements

Similar presentations

applications of genome sequencing projects

Advertisements

Genome+Environment = Traits, [diseases], (treatments) Hair: Baldness [alopecia](minoxidil) Eyes: [Near/Far-sightedness](glasses) Iris color [ARMD] (glasses)

Review of main points from last week Medical costs escalating largely due to new technology This is an ethical/social problem with major conseq. Many new.

Single Nucleotide Polymorphism And Association Studies Stat 115 Dec 12, 2006.

Charles He, Jessica McClendon, Kaelin Priger, and Wangshu Yang Group B2 Genes and Mutations.

But what if we test more than one locus? The future of genetic studies of complex human diseases. RefRef (Note above graphs are active spreadsheets --

Genetic research designs in the real world Vishwajit L Nimgaonkar MD, PhD University of Pittsburgh

Sampling distributions of alleles under models of neutral evolution.

Genetic Screening for Alzheimer’s Disease Thorstensen: Genetic Screening for Alzheimer's Disease 1.

Ferdinand van ’t Hooft Cardiovascular Genetics and Genomics Group Karolinska Institutet, Stockholm, Sweden Genome-Wide Association Study GWAS

Office hours Wednesday 3-4pm 304A Stanley Hall. Fig Association mapping (qualitative)

CS177 Lecture 9 SNPs and Human Genetic Variation Tom Madej

Dr. Almut Nebel Dept. of Human Genetics University of the Witwatersrand Johannesburg South Africa Significance of SNPs for human disease.

MIT-OCW Health Sciences & Technology 508/510 Harvard Biophysics 101 EconomicsEconomics, Public Policy, Business, Health PolicyPublic PolicyBusinessHealth.

Admixture Mapping Qunyuan Zhang Division of Statistical Genomics GEMS Course M Computational Statistical Genetics Computational Statistical Genetics.

Biology and Bioinformatics Gabor T. Marth Department of Biology, Boston College BI820 – Seminar in Quantitative and Computational Problems.

MIT-OCW Health Sciences & Technology 508/510 Harvard Biophysics 101 EconomicsEconomics, Public Policy, Business, Health PolicyPublic PolicyBusinessHealth.

March 2006Vineet Bafna CSE280b: Population Genetics Vineet Bafna/Pavel Pevzner

MIT-OCW Health Sciences & Technology 508/510 Harvard Biophysics 101 EconomicsEconomics, Public Policy, Business, Health PolicyPublic PolicyBusinessHealth.

Positional Cloning LOD Sib pairs Chromosome Region Association Study Genetics Genomics Physical Mapping/ Sequencing Candidate Gene Selection/ Polymorphism.

CSE 291: Advanced Topics in Computational Biology Vineet Bafna/Pavel Pevzner

MIT-OCW Health Sciences & Technology 508/510 Harvard Biophysics 101 EconomicsEconomics, Public Policy, Business, Health PolicyPublic PolicyBusinessHealth.

MIT-OCW Health Sciences & Technology 508/510 Harvard Biophysics 101 EconomicsEconomics, Public Policy, Business, Health PolicyPublic PolicyBusinessHealth.

Inference of Genealogies for Recombinant SNP Sequences in Populations Yufeng Wu Computer Science and Engineering Department University of Connecticut

BioVision Alexandria 2010 Linking Genes to Disease: Leveraging the Human Genome Doug Brutlag Professor Emeritus Biochemistry & Medicine (by courtesy)

Does knowing personal genomic information change behavior? Nate Cira Gene 210 6/5/2012.

Population Genetics 101 CSE280Vineet Bafna. Personalized genomics April’08Bafna.

Georgia Wiesner, MD CREC June 20, GATACAATGCATCATATG TATCAGATGCAATATATC ATTGTATCATGTATCATG TATCATGTATCATGTATC ATGTATCATGTCTCCAGA TGCTATGGATCTTATGTA.

Bernard Keavney Institute of Human Genetics University of Newcastle, UK. Recent developments in genetic epidemiology relevant to PURE.

Modes of selection on quantitative traits. Directional selection The population responds to selection when the mean value changes in one direction Here,

1 Thanks to: Biophysics 101, Tue 8-Sep-2009 Genomics, Computing, Economics Azco RBH.

A)High rate of mutation b)Founder effect c)Bottleneck effect d)Cats with extra toes are better at catching mice e)Extra toes are sexually appealing to.

Introduction to BST775: Statistical Methods for Genetic Analysis I Course master: Degui Zhi, Ph.D. Assistant professor Section on Statistical Genetics.

10 AM Tue 13-Feb Genomics, Computing, Economics Harvard Biophysics 101 (MIT-OCW Health Sciences & Technology 508)MIT-OCW Health Sciences & Technology 508.

The evolution of HIV Why is HIV fatal?. Lethal strains are favored, due to “Short sighted” evolution within hosts Transmission rate advantages.

Computational research for medical discovery at Boston College Biology Gabor T. Marth Boston College Department of Biology

Harvard Biophysics 101 (MIT-OCW Health Sciences & Technology 508)MIT-OCW Health Sciences & Technology 508

Population Genetics: Chapter 3 Epidemiology 217 January 16, 2011.

The Complexities of Data Analysis in Human Genetics Marylyn DeRiggi Ritchie, Ph.D. Center for Human Genetics Research Vanderbilt University Nashville,

The medical relevance of genome variability Gabor T. Marth, D.Sc. Department of Biology, Boston College Medical Genomics Course – Debrecen,

Conservation of genomic segments (haplotypes): The “HapMap” n In populations, it appears the the linear order of alleles (“haplotype”) is conserved in.

Harvard Biophysics 101 (MIT-OCW Health Sciences & Technology 508)MIT-OCW Health Sciences & Technology 508

From Genome-Wide Association Studies to Medicine Florian Schmitzberger - CS 374 – 4/28/2009 Stanford University Biomedical Informatics

Host genetic diversity Genome-wide approaches. Affected sib analysis Take full sibs, preferably of the same sex should share many environmental variables.

ABC for the AEA Basic biological concepts for genetic epidemiology Martin Kennedy Department of Pathology Christchurch School of Medicine.

Lecture 6. Functional Genomics: DNA microarrays and re-sequencing individual genomes by hybridization.

MEME homework: probability of finding GAGTCA at a given position in the yeast genome, based on a background model of A = 0.3, T = 0.3, G = 0.2, C = 0.2.

H.J. Muller. T. Dobzhansky Mutation Rates at Human STR Loci, Measured in Paternity Tests STR SystemMaternal Meioses (%)Paternal Meioses (%) TH015/42100.

10 AM Tue 20-Feb Genomics, Computing, Economics Harvard Biophysics 101 (MIT-OCW Health Sciences & Technology 508)MIT-OCW Health Sciences & Technology 508.

Linear Reduction Method for Tag SNPs Selection Jingwu He Alex Zelikovsky.

An quick overview of human genetic linkage analysis

Association analysis Genetics for Computer Scientists Biomedicum & Department of Computer Science, Helsinki Päivi Onkamo.

In The Name of GOD Genetic Polymorphism M.Dianatpour MLD,PHD.

Complex Adaptive Systems and Human Health: Statistical Approaches in Pharmacogenomics Kim E. Zerba, Ph.D. Bristol-Myers Squibb FDA/Industry Statistics.

Coalescent theory CSE280Vineet Bafna Expectation, and deviance Statements such as the ones below can be made only if we have an underlying model that.

Computational Biology and Genomics at Boston College Biology Gabor T. Marth Department of Biology, Boston College

Admixture Mapping Controlled Crosses Are Often Used to Determine the Genetic Basis of Differences Between Populations. When controlled crosses are not.

1 Finding disease genes: A challenge for Medicine, Mathematics and Computer Science Andrew Collins, Professor of Genetic Epidemiology and Bioinformatics.

Lecture 3 - Concepts of Marine Ecology and Evolution II 3) Detecting evolution: HW Equilibrium Principle -Calculating allele frequencies, predicting genotypes.

Date of download: 7/2/2016 Copyright © 2016 American Medical Association. All rights reserved. From: How to Interpret a Genome-wide Association Study JAMA.

Evolutionary Mechanisms Biological evolution: change in genetic composition of a population over time How can the gene pool of a population be characterized.

BEYOND THE HUMAN GENOME

High level GWAS analysis

Epidemiology 101 Epidemiology is the study of the distribution and determinants of health-related states in populations Study design is a key component.

DNA to Genes to Genomes J.W. Prokop et al Physiological Genomics 2018, 50,

Host genetic diversity

Hunting for Celiac Disease Genes

The principles of genetic association

Schematic representation of an MR analysis.

Genome wide association study for T2D-related loci

Presentation transcript:

MIT-OCW Health Sciences & Technology 508/510 Harvard Biophysics 101 EconomicsEconomics, Public Policy, Business, Health PolicyPublic PolicyBusinessHealth Policy For more info see: 10 AM Tue 11-Oct 2005 Fairchild 177 week 4 of 14 Genomics, Computing, Economics & Society

Class outline (1) Topic priorities for homework since last class (2) Quantitative exercises: psycho-statistics, combinatorials, random/compression, exponential/logistic, bits, association & multi- hypotheses (3) Project level presentation & discussion (4) Sub-project reports & discussion: Personalized Medicine & Energy Metabolism (5) Discuss communication/presentation tools (6) Topic priorities for homework for next class

Common Disease – Common Variant Theory. How common? ApoE allele  4 : Alzheimer’s dementia, & hypercholesterolemia 20% in humans, >97% in chimps>97% in chimps HbS 17% & G6PD 40% in a Saudi sample CCR5  32 : resistance to HIV 9% in caucasians

SNPs & Covariance in proteins e4 20% ApoE e3 80% Ancestral = Arg 112 Thr 61

One form of HIV-1 Resistance

Association test for CCR-5 & HIV resistance Samson et al. Nature :722-5Nature :722-5

But what if we test more than one locus? The future of genetic studies of complex human diseases. RefRef (Note above graphs are active spreadsheets -- just click) GRR = Genotypic relative risk

How many "new" mutations? G= generations of exponential population growth = 5000 N'= population size = 6 x 10 9 now; N= 10 4 pre-G m= mutation rate per bp per generation = to (ref)(ref) L= diploid genome = 6 x 10 9 bp e kG = N'/N; so k= Av # new mutations <   Le kt m = 4 x 10 3 to 4 x 10 4 per genome t=1 to 5000 Take home: "High genomic deleterious mutation rates in hominids" accumulate over 5000 generations & confound linkage methods And common (causative) allele assumptions.

Class outline (1) Topic priorities for homework since last class (2) Quantitative exercise (3) Project level presentation & discussion (4) Sub-project reports & discussion (5) Discuss communication/presentation tools (6) Topic priorities, homework for next class