Church ngs

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

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  • 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.
  • Church ngs

    1. 1. AssemblyUnderstanding the human reference genome Deanna M. Church Staff Scientist, NCBI 26 Mar 2013
    2. 2. Valerie Schneiderhttp://genomereference.org
    3. 3. The Reference Assembly is NOT Static NCBI35 (hg17) NCBI36 (hg18) GRCh37 (hg19) GRCh37.p10
    4. 4. An assembly is a MODEL of the genome
    5. 5. CD1Echr1:g.158324425A>GCD1E:c.317A>G
    6. 6. GeT-RM http://www.ncbi.nlm.nih.gov/projects/variation/get-rmNC_000012.11:g.22066016delA Missed in ARUP Exome, but not covered by capture probes
    7. 7. Kidd et al, 2007 APOBEC clusterBLACK: DeletionWhite: Insertion
    8. 8. IHGSC, Nature 2004 ClonesClones
    9. 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 point Representative chromosome sequence
    10. 10. RP11-34P13 64E8 RP4-669L17 RP5-857K21 RP11-206L10 RP11-54O7 Gaps
    11. 11. NCBI35 (Assembly described in last HGP paper) chrX:g.153054447G>AchrX TKTL1:c.31G>A TKTL1 CXorf2153,019,779 153,044,285 153,054,417 153,079,546 chrX:g.153533600G>A TKTL1:c.135-74G>AGRCh37 (current reference assembly) TKTL1:c.-90G>AchrX TKTL1:c.135-56G>A153,498,930 153,523,564 153,524,027 153,558,713
    12. 12. Data trackingABC14-1065514J1 Date Gaps LengthFP565796.1 21-Oct-2009 1FP565796.2 14-Oct-2010 0FP565796.3 07-Nov-2010 0
    13. 13. NCBI35 (Assembly described in last HGP paper)chrX chrX:g.153054447G>A NC_000023.8:g.153054447G>AGRCh37 (current reference assembly)chrX chrX:g.153533600G>A NC_000023.10:g.153533600G>A
    14. 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. 15. GRCh37 (current reference assembly)chrXPreview of GRCh38 (scheduled Fall 2013) TEX28 TKTL1 LOC101060233 LOC101060234 (opsin related) (TEX28 related)
    16. 16. http://genomereference.org
    17. 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 COORDINATES Your favorite region may CHANGE significantly We have the TOOLS to help! http://www.ncbi.nlm.nih.gov/variation

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