Personalized Genomics

1. Personalized Genomics • Genetic testing status and prospects • Types of human variation • Detection of human genomic variation • GWAS limitations • Nextgen sequencing • Challenges • Ethical questions J.M. Sikela, Ph.D. April 7, 2011

2. Types of Genetic Testing • Scientific Research • Between species: phylogenetics • Within human species • Medical • Diagnostic, predictive, carrier, prenatal, newborn • Identification: DNA Fingerprinting • Military/large scale disasters • Identification of remains • Paternity • Forensic • Criminal investigations • DNA Databases: UK; USA • Exoneration of wrongfully convicted

3. Genetic Testing: Concerns • Uncertainties surrounding test interpretation • -The tests give only a probability for developing the disorder • Lack of available medical options for some of these diseases • The tests' potential for provoking anxiety; family issues • Risks for discrimination and social stigmatization • -Legislative progress: GINA

4. GINA • Genetic Information Non-discrimination Act: Passed into law May 2008 • Prohibits group health plans and health insurers from denying coverage to a healthy individual or charging that person higher premiums based solely on a genetic predisposition to developing a disease in the future • Bars employers from using individuals’ genetic information when making hiring, firing, job placement, or promotion decisions

7. Genetic research on specific human populations • deCODE model • Uses DNA from over 100,000 Icelandic people • Medical/genealogical records date back to 1,000 years ago • Extensive informed consent/privacy measures implemented

8. Process of IVF • Hyper ovulation • Egg Retrieval • Artificial Insemination • Embryo Transfer

9. Pre-implantation Genetic Diagnosis (PGD):Genetic testing performed prior to embryo transfer “The debate [around PGD] has been building since the late 1980s, when doctors at London's Hammersmith Hospital learned how to tease a cell from a 3-day-old embryo and study its chromosomes for gender.” (Zitner 2002) • Adds $2000 to IVF • Reduces rate of miscarriages from 23% to 10% • Does not increase chance of pregnancy

10. Preimplantation Genetic Diagnosis (PGD) • Gender selection • Prenatal genetic diagnosis • -Spinal muscular atrophy (deletions in SMA gene) • -Huntington’s Disease • -CF: mutations that represent 75% of known CF mutations • -Chromosomal translocations (single cell FISH) • Future: fetal genome sequencing??? • IVF & PGD • - selection of bone marrow matched offspring (Nash family) • - other medical/non-medical uses

11. (taken from Genetics and IVF Institute Website) • PGD for Family Balancing* • Preimplantation Genetic Diagnosis (PGD) may be used to obtain cells for genetic analysis from embryos created by in vitro fertilization (IVF). GIVF offers PGD for gender selection for the purpose of family balancing for couples that meet qualifying criteria. Initial qualifications are:  • Couple is married • Have at least one child • Desire a child of the less represented sex of children in the family • *italics added

12. Genomic variation & their effects • Single gene defects (rare) - e.g., CF, Huntington’s • Multigenic diseases (more common) - e.g., diabetes, heart disease, schizophrenia • Non-disease conditions (all) - enhancements: immune system, cognition, physical ability, appearance

13. Direct-to-Consumer Marketing • Companies: • Use of genetic profiling to “guide” diet/lifestyle • Lack of regulation • Research: • Direct web-based solicitation of volunteers with specific diseases/traits • Avoidance of red-tape; greater scope

14. GAO 'Sting' 'Doesn't Bode Well' for DTC Industry • July 23, 2010 • The United States Government Accountability Office dealt a blow to several direct-to-consumer genetic testing firms • Issued a 33-page report outlining the group's investigation of the "deceptive" marketing claims made by four DTC firms. • GAO team sent 10 saliva samples to each of the four companies — not named in the report — from volunteer donors, and submitted along with them both accurate and fictitious health information. • The GAO team received "test results that are misleading and of little or no practical use," and found "10 egregious examples of deceptive marketing • including claims made by four companies that “a consumer’s DNA could be used to create personalized supplement to cure diseases," according to the report • A customer service representative at one of the companies told a GAO volunteer that "an above average risk prediction for breast cancer meant she was 'in the high risk of pretty much getting' the disease."

15. Personal Genomics: Current Status & Prospects • Sequencing cost and speed: • Nextgen sequencing: advantages & limitations • Strong motivation ($$) to get even better • Personal Genome Project (PGP): George Church • “Public availability” experiment • See book: “Here is a human being” Misha Angrist • Privacy issues:Can DNA really be “deidentified”? • 1000 Genomes Project • Genome sequences from different human populations: HapMap Phase II

16. Studies on human height Heritability of height is 0.8 (80% of variation in height is due to genetic factors) 3 GWAS studies genotyped 63,000 individuals at 500,000 loci (biggest cohort analyzed to date) 54 loci explain ~4% of the variance. What explains the remaining 96%?

17. Lessons from GWAS for understanding common traits or diseases Chip-based, not sequencing-based GWAS only analyzes common known variants (that you put on the chip) Lander: Some regions of the genome are not “HapMap-able” i.e. cannot be typed by SNP technology Consequence: potentially important genomic regions are unexamined Also a problem for current sequencing technology

18. What did GWAS studies find • Mostly low associations of common SNPs with diseases/traits • Height = 80-90% genetic  GWAS explains <5% • Autism = 90% genetic  GWAS explains <5% • GWAS studies have found significant associations, with over 400 genes IDed from different studies • Cumulative effects of all these explain very little phenotype variation though • Two options: GWAS missed them or they are not there

19. GWAS Limitations Missing Heritability & Strategies for Finding the Underlying Causes of Complex Disease Nat Rev Gen 2010 – Eichler, et al The Case of the Missing Heritability Nature 2008 – Brendan Maher Genetic Mapping in Human Disease Science 2009 – Altschuler, Daly, Lander G

20. One Possible Explanation: Non-SNP Variants Important • GWAS ignored all but SNPs – no structural or copy-number variants (CNVs): • Detection of CNVs using SNP arrays is very limited • These have been shown important in schizophrenia, autism, microcephaly, heart disease…many more. • Also, we know major genome differences between humans (even monozygotic twins) • Good evidence that these regions are very dynamic, i.e. non-Mendelian

21. The 1,000 Genomes Project • Currently being sequenced using 35-mer illumina reads • If you get a rare variant, may not be able to map the read to the genome - “Reference genome” vs “de novo” assembly • Structural/CNVs –very unlikely to catch much of these. Difficult to ID these with 35-mers… • Strategy being explored: Read-depth proportional to copy number (e.g. MrFast; SUNs) • Helped by long-read sequencing: e.gPacBio • May only be good at catching rare SNPs or structural variants that are small (maybe 10 or less bp)

22. Structural variations among human genomes

24. “Good genes & bad genes”: the value of a gene/allele is context-dependent • Effect on the individual • -extensive/some/no knowledge • Genetic background of the individual • -between 2 individuals, 1 change every 1,000 bp • -99.9% identical = 3 million DNA differences • Environment • -geographic (e.g. malarial region or not) • -social issues (culture, customs, laws) • -medical (status of non-genetic interventions • e.g., PKU vs. HD) • Effect on the species • -homogeneity vs. diversity

25. Good genes and bad genes (cont.) • Example of a good gene: - the globin gene variant that, when heterozygous, protects against malaria • Example of a bad gene: -the globin gene variant that, when homozygous, produces sickle-cell anemia -they are the same gene!