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- 1. Assembly Understanding the human reference genome Deanna M. Church Staff Scientist, NCBI 26 Mar 2013
- 5. The Reference Assembly is NOT Static NCBI35 (hg17) NCBI36 (hg18) GRCh37 (hg19) GRCh37.p10
- 10. An assembly is a MODEL of the genome
- 12. GeT-RM http://www.ncbi.nlm.nih.gov/projects/variation/get-rm NC_000012.11:g.22066016delA Missed in ARUP Exome, but not covered by capture probes
- 15. Kidd et al, 2007 APOBEC cluster BLACK: Deletion White: Insertion
- 16. IHGSC, Nature 2004 Clones Clones
- 17. Build sequence contigs based on contigs defined in TPF (Tiling Path File). Check for orientation consistencies Select switch points Instantiate sequence for further analysis Switch point Representative chromosome sequence
- 18. RP11-34P13 64E8 RP4-669L17 RP5-857K21 RP11-206L10 RP11-54O7 Gaps
- 19. NCBI35 (Assembly described in last HGP paper) chrX:g.153054447G>A chrX TKTL1:c.31G>A TKTL1 CXorf2 153,019,779 153,044,285 153,054,417 153,079,546 chrX:g.153533600G>A TKTL1:c.135-74G>A GRCh37 (current reference assembly) TKTL1:c.-90G>A chrX TKTL1:c.135-56G>A 153,498,930 153,523,564 153,524,027 153,558,713
- 20. Data tracking ABC14-1065514J1 Date Gaps Length FP565796.1 21-Oct-2009 1 FP565796.2 14-Oct-2010 0 FP565796.3 07-Nov-2010 0
- 21. NCBI35 (Assembly described in last HGP paper) chrX chrX:g.153054447G>A NC_000023.8:g.153054447G>A GRCh37 (current reference assembly) chrX chrX:g.153533600G>A NC_000023.10:g.153533600G>A
- 22. NM_012253.3 NM_001145933.1 TKTL1 NM_001145934.1 NM_001145933.1:c.135-74G>A NM_00114594.1:c.-90G>A NM_012253.3:c.135-56G>A
- 23. GRCh37 (current reference assembly) chrX Preview of GRCh38 (scheduled Fall 2013) TEX28 TKTL1 LOC101060233 LOC101060234 (opsin related) (TEX28 related)
- 25. The human reference assembly is a COMPOSITE of many individuals The human reference assembly is NOT static Accession.versions are KEY to data management When the reference assembly updates: Your favorite region may have the same SEQUENCE but different COORDINATES Your favorite region may CHANGE significantly We have the TOOLS to help! http://www.ncbi.nlm.nih.gov/variation
Hinweis der Redaktion
- Alignments refer to pairs of sequence. Once you know how a pair of sequences go together, you can look at stringing the pairs along into a contig. The contig is essentially the consensus sequence that is produced from the components.To create a contig, we use the steps shown on this slide.What are switch points? As you create the consensus sequence of the contig, the switch points tell you where to stop using the sequence from one component and begin using the sequence from the next.