lecture1.pdf

Genome Guided Medicine Prof. Lotfi Chouchane  Case Report 35 year- old investment banker presents to your office for his routine yearly examination He is healthy, but smokes cigars, is about 15 lbs overweight, exercises infrequently He read an art...

Genome Guided Medicine Prof. Lotfi Chouchane  Case Report 35 year- old investment banker presents to your office for his routine yearly examination He is healthy, but smokes cigars, is about 15 lbs overweight, exercises infrequently He read an article in the newspaper regarding genetic testing and, at the suggestion of his wife, sent a saliva sample to a consumer predictive genetic testing company Consumer Predictive Genetic Testing Increased risk  Emphysema  Coronary artery disease  Allergy to penicillin-type antibiotics  Colon cancer  Early onset Alzheimer's  Case Report He wants your advice – he is worried, does not know whether to share the information with his wife, and he wants you to tell him - what does he do now?  February, 2001 Sequencing of the Human Genome International Human Genome Sequencing Consortium Celera Genomics Why Should You Be Interested in Your Patient’s Genome?  Within your genes lie the details of your ancestry and the predictions of your future  Mutations slumber in your cells; from your genome you may learn what diseases you will get, how you may die and how you may respond to diet, surgery, medical devices, environment and drugs  Your genome provides a roadmap to prevent and treat disease  The Human Nuclear Genome  Composed of DNA - 3.1 billion letters that represent our genetic footprint  Our genomes are distributed on 2 sets of 23 chromosomes inherited from our parents  Codes for 25,000 genes that tell our cells how to function  Protein coding sequences only represent 1.5% of the genome  Not All Genes are on Nuclear Chromosomes  Mitochondria have DNA that functions autonomously from nuclear chromosomes  Ova are rich in mitochondria while sperm are not, thus mitochondrial DNA is inherited from the mother  Mitochondrial Genome  16.5 kb human mitochondrial genome encodes 13 polypeptides essential for oxidative phosphorylation and 24 RNAs (22 tRNAs and two rRNAs) essential for local protein synthesis using a mitochondria-specific genetic code  Maternal inheritance  Mitochondrial genome (about 0.001% of the nuclear genome) is responsible for ~1% of human genetic diseases (1/17,000), most commonly affecting organs that use a lot of energy (skeletal muscle, heart, nervous system)  How Many Genes in the Human Genome - How Do You Count Genes? Signposts - motifs Translation Splice sites Translation CpG islands Promoter start stop ATG Exons Humans have approximately 25,000 genes  How Do 25,000 Genes Make Humans?  Epigenetic controls – methylation and histone modifications turns genes on and off  Promoters control which genes are expressed in specific tissues at specific times  Alternative splicing yields 100,000 different proteins  Post translational modifications Functions of Human Genes Diversity of the Human Genome  Unrelated humans share 99.9% of their DNA sequences  90% of human heterozygosity is attributable to ~10 to 15x106 SNPs that arose during human evolution in Africa, and are shared around the world  Human Genetic Variation  Sites in the genome where one or more individuals differ from the reference genome  40 million known variant sites in NCBI database (dbSNP) - single nucleotide polymorphisms (1 base) - indels (2-100 bases) - copy number variants (1 kb – several Mb) - chromosomal variants (several Mb – whole chromosomes)  What is a SNP? …G G T A A C T G… Human Genome has 3 billion DNA Polymorphic base-pairs …G G C A A C T G... Some people have a different base at a given location: This is a Single Nucleotide Polymorphism or SNP Single Nucleotide Polymorphisms  Tolerated SNPs – in a DNA non-coding, non-regulatory region or coding for the same amino acid or an amino acid that does not mRNA change protein function  Deleterious SNPs - alter the function or level of the Protein protein Analysis of Single Nucleotide Polymorphisms  Isolate DNA from blood, buccal smear, saliva  Amplify DNA, hybridize with DNA probes to identify variation  Depending on technology, assess 1 to 106 Gene chip SNPs/sample  What Is the Cost and Effort to Sequence the Human Genome? 2001  $2.3 billion, 5x coverage  Took many years, 100’s of investigators 2024  Complete genome - $500, 30-50x coverage  From blood sample to DNA sequence 1-3 days  70% Q1  n=452 Qatari genomes >70% Q2  500,000 genome-wide SNPs used >70% Q3 to identify 48 SNPs that separate Admixed Qataris into 3 distinct populations - Q1 Arab - Q2 Persian - Q3 African Q3 Q2 1.0 % population 0.8 0.6 Q3 Q2 Q1 0.4 0.2 0.0 One subject per column (n=452) Qataris: a multi-ancestry Middle Eastern population 0.025 PAR GAR AFR SAS 0.020 WEP ADM 0.015 0.010 PC2 0.005 0.000 -0.005 -0.010 -0.030 -0.025 -0.020 -0.015 -0.010 -0.005 0.000 0.005 -0.025 -0.020 -0.015 -0.010 -0.005 -0.000 0.005 0.010 0.015 PC1 PC3 Whole Genome Sequencing of more than 6,000 subjects  Extent of Inbreeding in the European vs Qatari Populations 30 Frequency 20 10 0 -0.1 0.0 0.1 0.2 European inbreeding coefficient, F 6 Frequency 4 2 0 -0.1 0.0 0.1 0.2 Qatari inbreeding coefficient, F  Copy Number Variations 1 Submicroscopic genetic variations of kb to mb DNA segments consisting of deletions, insertions, duplications and complex multi-site variants Can be simple (e.g., tandem duplication) or may involve complete gain or loss of homologous sequences at multiple sites Importance – can influence gene expression and phenotypic variation by disrupting genes or altering gene dosage 1 Redon, R et al, Global Variation in Copy Number in the Human Genome. Nature 444, 444-454, 2006 Quantity of Gene Expression is Important  Variable phenotype – for some genes, low expression gives a very different phenotype than high expression Genetic Variation and the Risk for Disease Monogenic recessive, Complex, dominant and multigenic X-linked disorders disorders  Mechanisms of Monogenic Inheritance Common  Autosomal recessive  Autosomal dominant  X-linked Rare  Mitochondrial  Imprinting  Uniparental disomy  Expanding trinucleotide repeats  Incidence of Monogenic Disorders  Hereditary hemochromotosis (1 in 300)  Cystic fibrosis (1 in 3000)  Neurofibromatosis (1 in 3000)  a1-antitrypsin deficiency (1 in 7000)  Modifier Genes Disease  Genes that modify the gene genome A effects of another gene  Based on the genetic background of the genome B individual  Responsible for much genome C of the observed variation in genotype- phenotype relationships Complex, Multigenic Disorders  Disorders based, in part, on the contribution of many genes  Examples – cardiovascular, diabetes, cancer, chronic obstructive lung disease, psychiatric, rheumatoid disorders Low Prevalence Alleles With High Penetrance Associated with the Complex Genetic Disorders  BRCA1 and 2 – breast and ovarian cancer  HNPCC – hereditary non-polyposis colorectal cancer  MODY1, 2, and 3 – diabetes  a-synuclein – Parkinson’s disease High Prevalence Alleles With Low Penetrance Associated with the Complex Genetic Disorders  APC - increased risk for colorectal cancer  Factor V Leiden - increased risk for thrombosis  Complex Genetic Disorders with Both High and Low Prevalance Alleles Alzheimer’s  Rare mutation (