Contemplating the End of the Beginning

1. Contemplating the End of the Beginning Francis S. Collins, M.D., Ph.D. HGM 2003 Cancun, Mexico April 29, 2003

7. Characteristics of the Human Genome Sequence • 99% of euchromatin (2.85 Gb) is covered • Error rate: <<1:10,000 bp • <400 unclonable gaps • A randomly chosen nucleotide sits on a stretch of 27 Mb of continuous sequence • All data is freely accessible without restriction

8. WE DID IT!

9. Empowerment of Gene Discovery by the Human Genome Project:A Recent Vignette Identification of a gene involved in human aging Maria Eriksson, Ph.D.

10. Affected child

11. Case #1 46,XY UPD (1)(p11.2;qter) Case #2 46,XX UPD (1)(q22;qter) NA NA NA 96 102 173 173 255 255 148 148 206 206 272 272 111 111 304 108 108 149 149 332 332 172 172 124 124 159 159 260 260 109 109 259 259 169 169 219 219 153 153 246 246 1p13.1 D1S252 1p11.2 D1S2696 1q21.1 D1S2344 1q21.2 D1S2222 1q21.3 D1S498 1q21.3 D1S2347 1q21.3 D1S2346 1q22 D1S1153 1q23.1 D1S1653 1q23.2 D1S2635 1q24.2 D1S196 1q25.2 D1S2791 1q25.3 D1S2127 1q31.1 D1S191 1q31.3 D1S413 1q32.2 D1S2685 1q41 D1S2141 1q42.12 D1S2763 1q42.2 D1S2800 1q43 D1S2850 1q44 D1S2836 92 106 167 169 253 255 148 148 198 202 272 284 99 107 305 305 104 104 146 146 330 330 172 172 128 128 163 163 260 260 115 115 263 263 169 169 215 215 155 155 249 249 1p11.2 1q22

12. Paternal deletion in sample C8803 96 100 232 230 145 147 99 99 216 220 309 313 135 143 100 112 232 244 149 146 106 92 238 230 145 145 93 99 218 216 297 287 139 139 108 108 240 228 153 144 1p13.1 D1S252 1q21.1 D1S442 1q21.3 D1S2345 1q21.3 D1S2346 Pdi3 1q22 D1S1153 1q23.1 D1S506 1q23.1 D1S1653 Dtetra46 1q23.2 D1S2635 C8803 & C8803b P4 1p13.1 D1S252 1q21.1 D1S442 1q21.3 D1S2345 1q21.3 D1S2346 Pdi3 1q22 D1S1153 1q23.1 D1S506 1q23.1 D1S1653 Dtetra46 1q23.2 D1S2635 106 100 238 230 145 147 93 99 218 218 297 297 139 139 108 108 240 240 153 146

13. LMNA Paternal deletion in C8803 1p 1q Dtetra46 Pdi3 1q23.2 D1S2635 1q21.3 D1S2346 RP1-140J1 RP11-66D17 RP11-120D12 RP11-91G5 RP11-137P24 RP11-110J1 Deletion 5.66 Mb Maximum deletion 5.9 Mb UPD case #1 UPD case #2

14. R.D. Goldman et al., Genes and Development 16: 533-547, 2002

15. Sequencing exon 11 of LMNA Normal GTG GGC GGA Progeria GTG GG GGA Mother GTG GGC GGA Father GTG GGC GGA C T

16. Nearly all cases of progeria have a de novo mutation in codon 608 of the lamin A/C gene Normal GTG GGC GGA Progeria GTG GG GGA 18/20 GTG GC GGA 1/20 607 608 609 C T G A

17. How can the observed mutations cause progeria? Splice donor sequence A A G G G T T G Normal sequence G G T G G G C G G T G G G T Mutation 1 G G T G A G C Mutation 2 Normal 3’UTR 12 Exon 11 Mutant

18. RT-PCR experiment Exon 10 3’UTR Exon 11 12 Normal Exon 10 3’UTR Mutant 1 & 2 Ex 12 639 489 Mutant 1 Mutant 2

19. Western and immunofluorescence with lamin A/C antibody lamin A/C mito- chondria Lamin A del 50 prelamin A unaffected father Lamin C Mutant 1 Mutant 2 classical HGPS

20. Conclusions about progeria • Point mutations in LMNA are the cause of Hutchinson-Gilford progeria syndrome • The mutant protein lacks 50 aa near the C-terminus • Two cases of segmental UPD from fibroblast DNA do not show the mutation -- we postulate that this is a somatic rescue event (in vitro or in vivo) • These results suggest the possibility that other variants in LMNA might contribute to normal aging • Identification of the molecular basis of this disease could never have been achieved without the HGP

21. All of the original goals of the Human Genome Project have been accomplished What’s next?

22. NHGRI Planning Process 2001 - 2003 Comprehensive Extraction of Biological Information from Genomic Sequence Jul. 23-24 Genomics to Health Oct. 7-9 Sequencing and Re-Sequencing the Biome Jul. 23 Special Council Meeting Oct. 9 Bioethics and Humanities Research: Genetics and Worldviews Jul. 2 Council Feb. 10-11 Race, Ethnicity, Genetics, and Health Disparities Aug. 7 Proteomics Apr. 25-26 Airlie I Dec. 12-14, 2001 Publish Plan April 2003 APR MAY JUL AUG SEP OCT JUN NOV DEC JAN FEB Education & Public Engagement Jun. 10 Exploring the Ethical Boundaries on Genomic and Genetic Research Jul. 22 Council Sept. 9-10 Patenting Roundtable Dec. 4 Relating Genetic Variation to Health and Disease Aug. 8-9 Non-Medical Applications of GenomicsJul. 11 Airlie II Nov. 18-20 http://www.genome.gov/Pages/About/Planning/

24. Genomics to Biology • Define the structure of human variation: the human haplotype map • Sequence lots of additional genomes • Develop new technologies for sequencing, genotyping, expression analysis, and proteomics • Identify all functional elements of the genome • Identify all the proteins of the cell, and their interactions • Develop a computational model of the cell

25. A Haplotype Map of Human Variation • Goal is to define all common haplotypes in the human genome • Genome-wide association studies can then be done with 30 – 50 times less work • Project is international (9 labs in 5 countries); was initiated in October 2002, using samples of African, Asian, and European origin

27. Quantum Leaps in Technology • Genotyping at very low cost, allowing whole genome association studies on thousands of DNA samples for $10,000 or less • Genome sequencing at $1000 or less for a mammalian genome • Synthesis of any DNA molecule at high accuracy for $0.01 or less per base • Determination of methylation status of all the DNA in a single cell • Determination of the abundance and modification state of all proteins in a single cell in a single experiment

28. Genomics to Health • Identify the genetic and environmental risk factors for all common disease • Develop “sentinel systems” for early detection of disease and molecular taxonomy of illness • Develop and deploy high-throughput robotic screening of small molecules for academic researchers • Catalyze development of large human cohorts for genotype-phenotype correlations • Elucidate the role that genomics can play in reducing health disparities • Utilize genomics to improve health in the developing world

29. Automation Technology Compound Brokers Combinatorial Chemistry HGP Ability to screen Abundance of targets Availability of compounds Public sector screening and chemistry initiative Small molecule initiative is enabled by recent developments in biology and chemistry • Fundamentally new paradigm for assigning function to the genome • Access to small molecules for fundamental biology is currently limited • Four convergent developments in last 5 yrs make a new initiative possible

30. Genomics to Society • Enhance genetic privacy and protection against genetic discrimination • Encourage appropriate patenting and licensing practices to benefit the public • Understand the relationship of genomics, race, and ethnicity, and bring this to bear usefully on the often contentious dialog about race • Assess the ramifications of advances in understanding genetic factors that influence behavior • Define boundaries of the appropriate application of genomics in the non-medical arena

33. www.genome.gov