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My talk on how the human reference assembly is produced. Given http://www.palmettogba.com/ngssummit

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  • 1. AssemblyUnderstanding the human reference genome Deanna M. Church Staff Scientist, NCBI26 Mar 2013

2. Valerie Schneiderhttp://genomereference.org 3. The Reference Assembly is NOT StaticNCBI35 (hg17)NCBI36 (hg18)GRCh37 (hg19)GRCh37.p10 4. An assembly is a MODEL of the genome 5. CD1Echr1:g.158324425A>GCD1E:c.317A>G 6. GeT-RMhttp://www.ncbi.nlm.nih.gov/projects/variation/get-rmNC_000012.11:g.22066016delAMissed in ARUP Exome, but not covered by capture probes 7. Kidd et al, 2007 APOBEC clusterBLACK: DeletionWhite: Insertion 8. IHGSC, Nature 2004ClonesClones 9. Build sequence contigs based on contigsdefined in TPF (Tiling Path File). Check for orientation consistencies Select switch points Instantiate sequence for further analysis Switch pointRepresentative chromosome sequence 10. RP11-34P13 64E8 RP4-669L17 RP5-857K21 RP11-206L10 RP11-54O7 Gaps 11. NCBI35 (Assembly described in last HGP paper) chrX:g.153054447G>AchrXTKTL1:c.31G>A TKTL1 CXorf2153,019,779 153,044,285153,054,417 153,079,546chrX:g.153533600G>ATKTL1:c.135-74G>AGRCh37 (current reference assembly) TKTL1:c.-90G>AchrXTKTL1:c.135-56G>A153,498,930 153,523,564 153,524,027153,558,713 12. Data trackingABC14-1065514J1Date GapsLengthFP565796.1 21-Oct-20091FP565796.2 14-Oct-20100FP565796.3 07-Nov-20100 13. NCBI35 (Assembly described in last HGP paper)chrXchrX:g.153054447G>ANC_000023.8:g.153054447G>AGRCh37 (current reference assembly)chrXchrX:g.153533600G>ANC_000023.10:g.153533600G>A 14. NM_012253.3NM_001145933.1 TKTL1NM_001145934.1 NM_001145933.1:c.135-74G>A NM_00114594.1:c.-90G>A NM_012253.3:c.135-56G>A 15. GRCh37 (current reference assembly)chrXPreview of GRCh38 (scheduled Fall 2013) TEX28 TKTL1LOC101060233LOC101060234(opsin related)(TEX28 related) 16. http://genomereference.org 17. The human reference assembly is a COMPOSITE of many individualsThe human reference assembly is NOT staticAccession.versions are KEY to data managementWhen the reference assembly updates:Your favorite region may have the same SEQUENCE but different COORDINATESYour favorite region may CHANGE significantlyWe have the TOOLS to help!http://www.ncbi.nlm.nih.gov/variation