1. Mouse Genome Sequencing
10/15/2002
Wei Yuan
Mouse Genome Sequencing
---Sequencing strategy and the Physical Map
Reference:
1) Gregory, et al. A physical map of the mouse genome. Nature, , 418,
2) Green, ED, Strategies for the systematic sequencing of complex genomes. Nature reviews Genetics, 2001, 2,

2. Strategies for the systematic sequencing of complex genomes
First Part
Strategies for the systematic sequencing of complex genomes

7. Strategies for Complex Genomes sequencing
clone-by-clone shotgun sequencing
whole-genome shotgun sequencing
hybrid strategies for shotgun sequencing
Contig: overlapping series of clones or sequences reads (for a clone contig or sequencing contig, respectively) that corresponds to a contiguous segment of the source genome.

8. Two main shotgun-sequencing strategies
clone-by-clone
whole-genome

9. For clone-by-clone, a sequence-ready BAC contig map is required
Sequence-ready BAC contig map. A collection of overlapping bacterial artificial chromosome (BAC) clones that contain human DNA was subjected to restriction enzyme digest-based fingerprint analysis. The resulting data was analysed using the program FPC, which constructed the depicted BAC contig map that spans >1 Mb.
Minimal Tiling Path: a minimal set of overlapping clones that together provides complete coverage across a genomic region. (The 11 clones outlined in red, which provide a minimal tiling path across the corresponding genomic region, were selected for sequencing. )

10. The probability of two clones overlapping is based on the similarity of their fragments, performed by the program FPC.
FPC uses an algorithm to cluster clones into contigs based on their probability of coincidence score. For each contig, it builds a consensus band (CB) map which is similar to a restriction map; but it does not try to resolve all the errors. The CB map is used to assign coordinates to the clones based on their alignment to the map and to provide a detailed visualization of the clone overlap.
two clones are considered to overlap if the following score is below a user supplied cutoff:
M is the number of shared bands, nL and nH are the lowest and highest number of bands in the two clones, respectively, t is the tolerance, gellen is approximately the number of possible values, b = 2t/gellen, and p = (1 b)nH,.

11. Shotgun-sequence assembly
---display from the program Consed

12. Hybrid shotgun-sequencing approach

13. Hybrid shotgun-sequencing approach
take benefits of both clone-by-clone and whole-genome shotgun
whole-genome shotgun: provides rapid insight about the sequence of the entire genome
clone-by-clone shotgun: simplifies the process of sequence assembly to individual clone-sized genomic segments, thereby minimizing the likelihood of serious misassemblies
Used by NIH in mouse genome sequencing. (Celera is using whole genome shotgun)

14. Construction of a physical map of the mouse genome
Second Part
Construction of a physical map of the mouse genome

15. Physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA.
It provides:
a framework for assembly of whole-genome shotgun sequence data
a tile path of clones for generation of the reference sequence

16. Strategy: Using the human sequence as a framework!
Benefit:
1. Give a better level of resolution
2. Accelerate the process of constructing the mouse clone map

17. Because they are similar in sequence organization!
But why to choose human sequence?
Because they are similar in sequence organization!
180 conserved synteny (a region where the chromosomal location of multiple genes is conserved)
conserved segment/linkage (a region where the order of multiple genes on a single chromosome segment is the same in both species)

19. Comparing Human and Mouse DNA
Most human genes have mouse orthologs
Coding exons usually correspond 1-1
Coding sequence similarity ~ 85%

20. Let’s go back to an old slide

21. How to construct a physical clone map of the mouse genome
Two Phases:
Phase I: Generation of a human-mouse homology clone map
Compared restriction digest patterns (‘fingerprint’) of 305,716 BAC clones. Identified overlaps between clones on the basis of similarity between fingerprints and use this information to construct 7,587 contigs of overlapping clones.
----Done by the program FPC, under high strigency conditions at a probability of 1x10-16 and a match tolerance of seven
Align the mouse BAC contigs to the human genome sequence by BES (BAC end sequences). Extend and join contigs where possible after re-examing the fingerprint data (p>1x10-12).
---- Done by BLASTN (with a blast score>700)

22. Phase II: Generation of a mouse clone map
Use a set of independently mapped mouse markers (available in existing genetic and radiation hybrid maps of the mouse) to position the BAC contigs in the mouse genome.
---Markers were added to the map either by electronic PCR, or by hybridization using probes
After further manual contig editing was carried out (p>1x10-10), a mouse clone map comprising 296 contigs was generated.

23. Construction of human–mouse homology clone map
Alignment between part of human chromosome 6 (Hsa6) and mouse chromosome 4 (Mmu4). A 1.6-Mb interval is enlarged, showing part of Hsa6q16.1 aligned to a 1.3-Mb mouse BAC contig.
11 of the 15 segments of human sequence match to 29 of the BESs within a mouse BAC contig

24. Summary statistics of human-mouse homology clone map

25. Summary statistics of mouse physical clone map by chromosome

26. More details about the mouse physical map
found 51,486 homologous crosslinks btw two genomes
Of the clones in the human genome tile path, 88% are collinear with the mouse BAC map. For individual human chromosomes, coverage by aligned mouse contigs exceeds 80% on all except chromosome 19 (61%) and the Y chromosome (0%).
Of the total coverage of the mouse BAC map (in 211 contigs), 97% (2,658 Mb) is aligned to the human genome sequence.
Most mouse BAC contigs contained multiple mouse markers (average 57 markers per contig).
coverage of the mouse genome (2.8 Gb) in mapped BACs is virtually complete: 296 contigs of average size 9.3 Mb cover an estimated 2,739 Mb. (~98%)
275 gaps due to breaks in synteny btw the two genomes.

28. Future Work for Mouse Genome Sequencing
Finish sequencing by 2005
Analysis
Sequence comparisons
Annotation
Gene Expression analysis
Global genomic analysis

29. The End