Reconstructing Genomic Architectures of Tumor Genomes

Pavel Pevzner and Ben Raphael

Department of Computer Science & Engineering University of California, San Diego

(joint work with Colin Collins lab at UCSF Cancer Center)

Chromosome Painting: Normal Cells

Chromosome Painting: Tumor Cells

Rearrangements in Tumors

• GleevecTM (Novartis 2001) targets BCR-ABL oncogene.

• Change gene structure and regulatory “wiring” of the genome.

• Create “bad” novel fusion genes and break “good” old genes.

• Example: translocation in leukemia.

promoter

promoter ABL gene

BCR genepromoter

Chromosome 9

Chromosome 22

BCR-ABL oncogene

Complex Tumor Genomes

1) What are detailed architectures of tumor genomes?

2) What rearrangements/duplications produce these architectures and what is the order of these events?

3) What are the novel fusion genes and old “broken” genes?

• What are the the “architectural blocks” forming the existing genomes and how to find them?

• What is the architecture of the ancestral genome?• What is the evolutionary scenario for transforming

one genome into the other?

Unknown ancestor~ 80 million yearsago

Mouse (X chrom.)

Human (X chrom.)

Genome rearrangements

History of Chromosome X

Rat Consortium, Nature, 2004

Inversions

• Blocks represent conserved genes.• In the course of evolution or in a clinical context,

blocks 1,2,…,10 could be misread as:

1, 2, 3, -8, -7, -6, -5, -4, 9, 10.

1 32

4

10

56

8

9

7

1, 2, 3, 4, 5, 6, 7, 8, 9, 10

Inversions1 32

4

10

56

8

9

7

1, 2, 3, -8, -7, -6, -5, -4, 9, 10

Blocks represent conserved genes. In the course of evolution or in a clinical context, blocks

1,…,10 could be misread as 1, 2, 3, -8, -7, -6, -5, -4, 9, 10.

Evolution: occurred one-two times every million years. Cancer: may occur every month.

End Sequence Profiling (ESP)C. Collins et al. (UCSF Cancer Center)

1) Pieces of tumor genome: clones (100-250kb).

Human DNA

2) Sequence ends of clones (500bp).

3) Map end sequences to human genome.

Tumor DNA

Each clone corresponds to pair of end sequences (ES pair) (x,y).

yx

Human genome(known)

Tumor genome(unknown)

Unknown sequence of rearrangements

Location of ES pairsin human genome.(known)

Map ES pairs tohuman genome.

-C -D EA B

B C EA D

x2 y2x3 x4 y1 x5 y5 y4 y3x1

Tumor Genome Reconstruction Puzzle

Reconstruct tumor genome

B C EA D

-C

-D

E

A

B

Tumor

Human

Tumor Genome Reconstruction

B C EA D

-C

-D

E

A

B

Tumor

Human

Tumor Genome Reconstruction

B C EA D

-C

-D

E

A

B

Tumor (x2,y2)

(x3,y3)

(x4,y4)

(x1,y1)

y4 y3x1 x2 x3 x4 y1 y2

Tumor Genome Reconstruction

B

C

E

A

D

Human

B C EA D

2D Representation of ESP Data

• Each point is ES pair.• Can we reconstruct the tumor genome from the positions of the ES pairs?

(x2,y2)

(x3,y3)

(x4,y4)

(x1,y1)

ESP Plot

Human

B

C

E

A

D

Human

Human

B C EA D

2D Representation of ESP Data

• Each point is ES pair.• Can we reconstruct the tumor genome from the positions of the ES pairs?

B

C

E

A

D

Human

Human

B C EA D

2D Representation of ESP Data

• Each point is ES pair.• Can we reconstruct the tumor genome from the positions of the ES pairs?

B

C

E

A

D

Human

Human

B C EA D

2D Representation of ESP Data

• Each point is ES pair.• Can we reconstruct the tumor genome from the positions of the ES pairs?

B

C

E

A

D

Human

Human

B C EA D

2D Representation of ESP Data

• Each point is ES pair.• Can we reconstruct the tumor genome from the positions of the ES pairs?

B

C

E

A

D

Human

Human

B C EA D

2D Representation of ESP Data

• Each point is ES pair.• Can we reconstruct the tumor genome from the positions of the ES pairs?

B

C

E

A

D

Human

Human

B C EA D

2D Representation of ESP Data

• Each point is ES pair.• Can we reconstruct the tumor genome from the positions of the ES pairs?

B

C

E

A

D

Human

Human

B C EA D

2D Representation of ESP Data

• Each point is ES pair.• Can we reconstruct the tumor genome from the positions of the ES pairs?

B

C

E

A

D

Human

Human

B C EA D

2D Representation of ESP Data

• Each point is ES pair.• Can we reconstruct the tumor genome from the positions of the ES pairs?

B

C

E

A

D

Human

Human

B

-D

E

A

DA C

E

-C

B

-C -D EA B

ReconstructedTumor Genome

Real data noisy and incomplete!

Breast Cancer MCF7 Cell Line

Human chromosomes MCF7 chromosomes5 inversions

15 translocations

Raphael et al. 2003.

33/70 clustersTotal length: 31Mb

Complications with MCF7: Chromosomes 1,3,17, 20

sA

tC-B

sA

tCB inversion

Human

uA B

uA

wDB C D

vE

wC D

vE

duplication/transposition

uA B

wC

vE ????

Rearrangement Signatures Tumor

sA

t

-Bs

At

-CB DC D translocation

Complex Tumor Genomes

Tumor Amplisomes

33 clustersTotal length: 31Mb

17 201 3

Reconstructed MCF7 amplisome

Chromosomecolors

Explains 24/33 invalid clusters.

Raphael and Pevzner, 2004.

Sequencing Tumor Clones Confirms Complex Mosaic Structure

What’s Next?

• Human Genome Project, 2001• Mouse Genome Project, 2002• Rat Genome Project, 2003• Chicken Genome Project, 2004• Chimp Genome Project, 2005• ???

Tumor Genomes Projects

Tumor genomeHuman genome

1) Identify recurrent aberrations2) Identify temporal sequence of aberrations3) Use these data for tumor diagnostics and therapeutics

Mutation, selection

Tumor genome 2

Tumor genome 4

Tumor genome 3