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Deanna Church

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

Tecnología

Assembly
Understanding the human reference genome

Deanna M. Church
Staff Scientist, NCBI
26 Mar 2013

Valerie Schneider

http://genomereference.org

The Reference Assembly
is NOT Static
NCBI35 (hg17)
NCBI36 (hg18)
GRCh37 (hg19)
GRCh37.p10

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

Kidd et al, 2007 APOBEC cluster

BLACK: Deletion
White: Insertion

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

RP11-34P13 64E8 RP4-669L17 RP5-857K21 RP11-206L10 RP11-54O7

Gaps

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

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

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

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

GRCh37 (current reference assembly)
chrX

Preview of GRCh38 (scheduled Fall 2013)

TEX28 TKTL1

LOC101060233 LOC101060234
(opsin related) (TEX28 related)

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

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Church ngs

1. Assembly Understanding the human reference genome Deanna M. Church Staff Scientist, NCBI 26 Mar 2013

4. Valerie Schneider http://genomereference.org

5. The Reference Assembly is NOT Static NCBI35 (hg17) NCBI36 (hg18) GRCh37 (hg19) GRCh37.p10

10. An assembly is a MODEL of the genome

11. CD1E chr1:g.158324425A>G CD1E:c.317A>G

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

13.

14.

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)

24. http://genomereference.org

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

Notas del editor

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.

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