Church ngs
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derstanding the human reference geno Deanna M. Church Staff Scientist, NCBI 26 Mar 2013 Assembly
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My talk on how the human reference assembly is produced. Given http://www.palmettogba.com/ngssummit
Transcript of Church ngs
Understanding the human reference genome
Deanna M. ChurchStaff Scientist, NCBI
26 Mar 2013
Assembly
http://genomereference.org
Valerie Schneider
The Reference Assembly is NOT Static
NCBI35 (hg17)NCBI36 (hg18)GRCh37 (hg19)GRCh37.p10
An assembly is a MODEL of the genome
chr1:g.158324425A>GCD1E:c.317A>G
CD1E
NC_000012.11:g.22066016delA
Missed in ARUP Exome, but not covered by capture probes
http://www.ncbi.nlm.nih.gov/projects/variation/get-rmGeT-RM
Kidd et al, 2007 APOBEC cluster
BLACK: DeletionWhite: Insertion
Clones
Clones
IHGSC, Nature 2004
Build sequence contigs based on contigs defined in TPF (Tiling Path File).
Check for orientation consistenciesSelect switch pointsInstantiate sequence for further analysis
Switch point
Representative chromosome sequence
RP11-34P13 64E8 RP4-669L17 RP5-857K21 RP11-206L10 RP11-54O7
Gaps
CXorf2 TKTL1
NCBI35 (Assembly described in last HGP paper)
153,019,779
chrX
153,044,285 153,054,417 153,079,546
chrX:g.153054447G>ATKTL1:c.31G>A
GRCh37 (current reference assembly)chrX
153,498,930 153,523,564 153,524,027 153,558,713
chrX:g.153533600G>ATKTL1:c.135-74G>ATKTL1:c.-90G>ATKTL1:c.135-56G>A
Data tracking
ABC14-1065514J1Gaps LengthDate
FP565796.1 121-Oct-2009
FP565796.2 014-Oct-2010
FP565796.3 007-Nov-2010
NCBI35 (Assembly described in last HGP paper)chrX
chrX:g.153054447G>ANC_000023.8:g.153054447G>A
GRCh37 (current reference assembly)chrX
chrX:g.153533600G>ANC_000023.10:g.153533600G>A
NM_012253.3NM_001145933.1NM_001145934.1
TKTL1
NM_001145933.1:c.135-74G>ANM_00114594.1:c.-90G>ANM_012253.3:c.135-56G>A
Preview of GRCh38 (scheduled Fall 2013)
TEX28 TKTL1
LOC101060233(opsin related)
LOC101060234(TEX28 related)
GRCh37 (current reference assembly)chrX
http://genomereference.org
The human reference assembly is a COMPOSITE of many individuals
The human reference assembly is NOT static
When the reference assembly updates:
Accession.versions are KEY to data management
Your favorite region may have the same SEQUENCE but different COORDINATESYour favorite region may CHANGE significantly
We have the TOOLS to help!
http://www.ncbi.nlm.nih.gov/variation
