Chapter 15 The Human Genome Project and Genomics

Genomics • Is the study of all genes in a genome • Relies on

Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Linkage refers to the transmission of two genes on the same chromosome How was

Fig. 5. 11 Dihybrid Cross: purple flower Fig. P: 5. 11 L: long pollen,

Fig. 5. 11 Two extremes Chapter 15 Human Heredity by Michael Cummings © 2006

Crossing over Disrupts Linkage and creates new combination of alleles (recombinants) Figure 5. 10

Gene Linkage • Two or more genes do not show independent assortment • They

Recombination Frequency (RF) = # of recombinant gametes/ total # of gametes - •

Linkage Maps. Linear maps from RF data RF of 1% between two genes: =

Genetic Mapping • Find linkages between genes • Measuring the frequency of crossing over

General rules ØRecombination frequency is constant between two genes. ØRecombination frequency varies between different

Linked Genes Fig. 15. 3 Chapter 15 Human Heredity by Michael Cummings © 2006

Positional Cloning • Recombinant DNA-based method for mapping and cloning genes • No prior

Genes ID-ed by Positional Cloning Chapter 15 Human Heredity by Michael Cummings © 2006

Chromosome 1 Fig. 15. 4 Chapter 15 Human Heredity by Michael Cummings © 2006

Human Genome Project • Arose from methods developed for basic research recombinant DNA technology

Goals of Genomics Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Timeline of HGP Fig. 15. 5 Chapter 15 Human Heredity by Michael Cummings ©

Gene Sequencing Computers Fig. 15. 7 Chapter 15 Human Heredity by Michael Cummings ©

Sequencing a Genome Clone-by-Clone Method (used by public project) • A genomic library (a

Clone-by. Clone Method Fig. 15. 9 a Chapter 15 Human Heredity by Michael Cummings

How We Sequence a Genome Shear add plasmid vector+ Subclone Chapter 15 Human Heredity

How We Sequence a Genome Transform into bacteria Grow bacteria Purify DNA Sequence DNA

How We Sequence a Genome Sequence read Feed all 30 M reads to assembly

How to Do 30 M Sequence Reads 30 M reads, that’s a lot. Need

Sequencing a Genome Shotgun Cloning (used by private project) • Genomic library prepared •

Sequence of Beta-Globin Gene • Open reading frames (ORFs) are exons labeled in blue

Facts About the Human Genome • Diploid, 23 chromosome pairs • 3 x 109

Functions of Human Genes Fig. 15. 12 Chapter 15 Human Heredity by Michael Cummings

Selected Genomes Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Genomics and Human Genetic Disorders Important questions that must be answered include • Where

Bioinformatics • Comparative genomics – Compares genomes • Structural genomics – Derives 3 -D

Comparative Genomics *Using genomes of related species as keys to understanding genome evolution and

Evolution of Humans Mammals Increased Genomic and Developmental Complexity Chordate Body Plan Primates (Human)

Mouse and Human Genomes Very similar biology Separated by ~75 million years of evolution

Syntenic Regions Between Human and Mouse • Identify sequences that are highly similar •

Humans have low rate of genetic variation ~100, 000 BC, 104 humans 3000 generations

Proteomics Study of expressed proteins in a cell • Important in – Understanding gene

Studying Proteins in a Cell Fig. 15 Chapter 15 Human Heredity by Michael Cummings

Ethical, Legal, and Social Implications (ELSI) Chapter 15 Human Heredity by Michael Cummings ©

Future Issues • Resources – Genome sequences – Libraries of cloned DNA sequences •

Future Issues • Training – Scientists, physicians and scholars • Ethical, Legal, and Social

All members of a group get the same grade Chapter 15 Human Heredity by

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Genomics • Is the study of all genes in a genome • Relies on interconnected databases and software to analyze sequenced genomes and to identify genes • Impacts basic research in biology and generates new methods of diagnosis and treatment of disease Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Linkage refers to the transmission of two genes on the same chromosome How was linkage discovered? Standard dihybrid cross Find that observed ratios in the F 2 progeny do not follow mendelian ratios. Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Fig. 5. 11 Dihybrid Cross: purple flower Fig. P: 5. 11 L: long pollen, p: white flower l: round pollen P_L_: P_ll: pp. L_ : ppll 9: 3 : 1 Observed: hi low Hypothesis: These two genes are somehow linked, and do not assort independently Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning hi

Gene Linkage • Two or more genes do not show independent assortment • They tend to be inherited together • Located on the same chromosome • A measure of the degree of recombination gives relative distance between them Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Recombination Frequency (RF) = # of recombinant gametes/ total # of gametes - • RF for a set of genes is proportional to the distance between the genes Figure 5. 12 Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Genetic Mapping • Find linkages between genes • Measuring the frequency of crossing over to determine the relative distance between the genes • Linkage analysis is difficult to do in humans: only 5 human linkage groups were identified by 1969 • Unit of measure is a centimorgan (c. M) 1 c. M = frequency of 1% recombination Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

General rules ØRecombination frequency is constant between two genes. ØRecombination frequency varies between different genes. NO Recombination = genes are very closely linked. Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Positional Cloning • Recombinant DNA-based method for mapping and cloning genes • No prior information about the gene product or its function is required • Maps cloned DNA sequences; most are markers not genes • 3, 500 genes and markers identified in the late 1980 s Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Human Genome Project • Arose from methods developed for basic research recombinant DNA technology and DNA sequencing • It is an extension of genetic mapping by recombination frequencies • Took 13 years and $3 billion to complete Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Sequencing a Genome Clone-by-Clone Method (used by public project) • A genomic library (a collection of clones) is developed • Physical maps are prepared • Clones are organized into overlapping groups • DNA cut with restriction enzymes • Each clone is sequenced and software assembles sequence from the libraries Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

How We Sequence a Genome Sequence read Feed all 30 M reads to assembly software Software compares all reads Assembles them together into consensus sequence Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Sequencing a Genome Shotgun Cloning (used by private project) • Genomic library prepared • No genetic or physical maps are created • Restriction enzymes are used to cut DNA, and overlapping fragments are created • Clones selected at random from each library and sequenced • Assembler software programs organize information into genomic sequences Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Sequence of Beta-Globin Gene • Open reading frames (ORFs) are exons labeled in blue • Green indicates where transcription begins Fig. 15. 10 Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Facts About the Human Genome • Diploid, 23 chromosome pairs • 3 x 109 bases • ~30, 000 genes • Genes represent ~1. 5 -2% of genome sequence • Non-genic functional sequences = ? ? • Repetitive DNA = ~50% • 8% present in large recent duplications Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Genomics and Human Genetic Disorders Important questions that must be answered include • Where is the gene located? • What is the normal function of the protein encoded by this gene? • How does the mutant gene or protein produce the disease phenotype? Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Bioinformatics • Comparative genomics – Compares genomes • Structural genomics – Derives 3 -D structures for proteins • Pharmacogenomics – Analyzes genes and proteins for therapeutic use Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Comparative Genomics *Using genomes of related species as keys to understanding genome evolution and function Key tools: Conserved sequences (both genes and not) Conserved order of sequences Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Evolution of Humans Mammals Increased Genomic and Developmental Complexity Chordate Body Plan Primates (Human) Rodents (Mouse) Reptiles Birds Amphibians Bony fish (Tetraodon) Cartilaginous fish Jawless vertebrates Cephalochordates Urochordates (Ciona) Hemichordates Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Mouse and Human Genomes Very similar biology Separated by ~75 million years of evolution Similarity at nucleotide level ~83% in genes ~60% between genes Shared gene content: 99% similar genes 96% similar genes in similar location Synteny- regions of genomes that share order of conserved features Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Syntenic Regions Between Human and Mouse • Identify sequences that are highly similar • Find their locations in each genome • Syntenic blocks: conserved order over long stretches • ~200 syntenic blocks between mouse and human • Span 95% of genome Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Humans have low rate of genetic variation ~100, 000 BC, 104 humans 3000 generations Present day, 6 x 109 humans • Humans: small species that grew large rapidly • Amount of variation implies 10, 000 founders • Current variation in population ~10, 000 individuals Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Proteomics Study of expressed proteins in a cell • Important in – Understanding gene function and its changing role in development and aging – Identifying proteins that are markers for diseases – Finding proteins that are targets for drugs in order to treat diseases and genetic disorders Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Future Issues • Resources – Genome sequences – Libraries of cloned DNA sequences • Technology – New sequencing methods – Techniques of monitoring gene expression – Links to disease • Software for computational biology – Reveal protein-protein interactions in disease – Evaluate environmental factors on health Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning

Future Issues • Training – Scientists, physicians and scholars • Ethical, Legal, and Social Implications – Protection of human subjects and genomic information • Education – Healthcare professionals – Public – Develop reliable resources Chapter 15 Human Heredity by Michael Cummings © 2006 Brooks/Cole-Thomson Learning