Genetic analysis in human disease

1. Nataly Manjarrez Orduño, PhD Assistant Investigator, Feinstein Institute for Medical Research nmanjarrez@nshs.edu Genetic Analysis in Human Disease Genetic analysis in human disease Nataly Manjarrez, PhD

3. Outline • Intro and genetics vocabulary. • Single & polygenic genetic disorders. • Omics in the clinical practice. • Outlook

4. Aim • Talk and understand genetics. • Understand quality control in publications. • Incorporate it to practice. Your patients may be talking genetics already.

5. Genetic diseases in pediatrics Genetic disorders and birth defects account for ~12% of pediatric admissions in the US. There are around 7000 rare diseases identified in the US, with 80% of genetic origin. 30% of rare disease patients die before the age of 5.

6. It is all about DNA Owald T. Avery MD, Colin McCLeod MD, Macylin McCarty MD Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III J. Exp Med, 1944

7. Genome • Locus/Loci SNP

8. Common Genetic Terms Dominant: Condition phenotypically expressed in someone carrying one copy of a mutant gene Recessive: Condition phenotypically expressed only in someone with two copies of the mutant gene. Carrier: has recessive gene but no disease. • Expressivity: Qualitative characteristic trait expressed in various ways. • Penetrance: Quantitativecharacteristicdegree or severity of the abnormality Genotype: An individual’s genetic makeup - forms of a particular gene at a given locus Phenotype: The observable expression of a genotype Allele: one of the forms of the same gene/locus/SNP. Homozygous: Identical forms of a particular gene Heterozygous: Different forms of a gene– CARRIER if one normal and one abnormal.

9. Family History • Reflects the consequences of genetic susceptibilities, shared environment and common behaviors. • Allows us to identify potentially inherited disorders in families. • Is an independent risk factor for most chronic diseases of public health significance. In this day and age, family history is still one of the strongest genetic tools.

10. Common Genetic Terms What if “Attached earlobes” this is a disease? Is Ee completely healthy (carrier) or is there a degree of Expressivity? Does everyone with ee gets the disease? What about penetrance?

11. Male / boy Female / girl This line is used to show parents who are divorced/not together Adopted • What if there is limited information • about family members? • If you do not know names and ages of familymembers, but do know the number of boys andthe number of girls, you can do this: • If you do not know the number of boysand the number of girls, use diamond with number inside it (if total is known) or “?”. The diagonal line is used to show that the person has died. Pregnancy loss. Include number of weeks, if known. Example: This shows that there are 5 boys and 3 girls. 3 5 SB stands for stillbirth. Include number of weeks, if known. SB 8 Example: This shows that there are 8 children.

13. Single Gene Traits/Disorders • Traits that are determined by one particular gene • Characterized by their transmission pattern in families – PEDIGREE ANALYSIS. • Able to determine risks for particular family members if know mode of inheritance

14. Autosomal Dominant Diseases • Physically expressed if only one copy of gene is present. • An affected parent has a 50% chance of passing the gene to a child. • Some are due to new mutations.

15. Autosomal Recessive Diseases • Physically expressed only if both chromosomes carry a copy of the gene Rare diseases may fall mostly in this category.

16. X-linked inheritance

17. Chromosomal disorders

19. Genetics of complex traits and disease

20. The spectrum of genetic effects in complex diseases

21. Disease Causation: The Big Picture Chance/Fate Phenotype Genotype Environment

22. If we think a disease or trait has a genetic component, how can we find identify the relevant genetic variation?

23. SNP diversity between any two unrelated individuals: ~ 3 million base pairs Human Genetic Variation, NIH

24. Association in population samples Where effects are probabilistic, must measure frequency in affected and control populations Controls Affecteds

25. Most of the genome does not encode genes It is a matter of probability.

26. Lots of genes/genetic regions discovered for autoimmune disease – most in the last 3-4 years using genome wide association studies (GWAS) CD40 CCl21 CD244 PIP4K2C IL2RA PRKCQ IL2RB AFF3 TNFRSF14 REL BLK TAGAP CD28 TRAF6 PTPRC FCGR2A PRDM1 CD2/CD58 SIAE SPRED2 RBPJ CCR6 IRF5 PXK IL6S TNFAIP3 STAT4 TRAF1/C5 IL2-IL21 HLA “shared epitope” hypothesis HLA- DR4 PADI4 PTPN22 CTLA4 1978 1987 2003 2004 2005 2007 2008 2009 2010 Timeline for discovery in rheumatoid arthritis

27. The strength of each genetic association is modest, generally odds ratios <2 (with exception of HLA) Top GWAS hits in T1 diabetes Concannon, Rich, Nepom Genetics of Type 1A Diabetes N Engl J Med 2009;360:1646-54.

28. GWAS – where are the hits? • 3800 SNPs identified for 427 diseases and traits • Only 7% in coding regions • >50% in DNAse sensitive sites, presumed regulatory regions Genotyping, not sequencing! Science 232:1031, 2011 Stamatoyannopoulos, Cold Spring Harbor, May 2011

29. Omics and medicine Genome: Epigenome Transcriptome: Microbiome: • Whole genome sequencing • Exome sequencing. • Analysis of the “marks” in the DNA • RNA sequencing. • Sequencing for microorganism ID.

30. Genomes, genomes • First genome $2,700,000,000 15 years, • Current $5,000 One week

31. Whole vsexome sequencing

32. Whole genome sequencing • Reserved for individuals in whom – the likelihood of success is high – reasonable clinical testing has not achieved answer – molecular diagnosis has the potential to advance clinical decision making

33. The omics landscape Modified from Genome Res, 2009 19:521-532.

34. Rare and orphan diseases • > 5,000 monogenic disorders have been identified with more being discovered. • Most humans have about 6-8 defective genes, most being recessive & therefore not expressed. • Sequencing might help to uncover not only the cause of a disorder but also other potential mutations.

36. The real picture FAMILY HISTORY!!! SciTransl Med 3, 87re3 (2011);

37. Genetics and the future of medicine • Complete definition of genetic variation of individuals at reasonable cost is only a few years away • The interpretation of these data are going to be major challenge • Large populations need to be studied to connect phenotypic/disease state to genetic variation • Regulatory variation in the genome (ENCODE project) is going to be key to understanding • Data mining in the context of large health will be crucial to the success of this effort