Ashg2017 workshop schneider

GRC/GIAB Workshop:Getting the Most from the Reference

Assembly and Reference MaterialsOct 17: 1-4 pm

Valerie Schneider (NCBI): GRCh38 assembly basics and updatesTina Lindsay (MGI): Reference-grade human assemblies

Karen Miga (UCSC): Centromere assembliesBREAK (15 min)

Benedict Paten (UCSC): Building human variation graphsFritz Sedlazeck (BCM): Structural Variation Characterization Across the Human Genome and Populations

Justin Zook (NIST): GIAB benchmarks for difficult variants

GRCh38 assembly basics and updates

Valerie Schneider, Ph.D.NCBI

17 October 2017

https://genomereference.org


Twitter: @GenomeRef

Announcements: [email protected]

• Assembly basics• GRCh38 updates• Taking advantage of the data

Outline

Assembly Basics

Reference Assembly Basics

(For updated assemblies, only date of initial submission is counted)

Other assemblies

GRCh38(reference)

Sanger-seq’d, clone-based assembly BAC insertBAC vector

Shotgun sequence clone

Assemble clone

GAPS

Finish (via PCR)

Minimal Clone Tiling Path

Define consensus from switch points of adjacent clones

Consequences:• Highly contiguous• High sequence accuracy (<10-5)• Haploid mosaic

Ordering the Path

Fingerprint maps

Genetic linkage maps

Radiation hybrid maps


HuRef

SOAPdenovoNA12878

ALLPATHSNA12878

Lander and Waterman

(1988) Genomics

SequencedNot sequenced

1X Coverage

5X Coverage

10X Coverage

37% 63%

0.6% 99.4%

0.005% 99.995%

The likelihood a base is seq’d.Coverage

Contig N50

MHAPCHM1

Chaisson and Eichler (2015), with modification

Measure of contiguity. Half of the assembly is in contigs this length or greater.


AK1

HX1NA12878_prelim

Why all this matters:Longer haplotype blocks

Fewer collapsed repeats & segmental duplicationsBetter annotation

More robust mapping target


Today’s reference assembly does not represent:1.The most common allele/haplotype

2.The longest allele/haplotype3.The ancestral allele/haplotype

It represents the sequence available from the HGP


Gene1 Gene2

Gene1

Sample

Ref

Assembly

Reference assembly influence

Slide Credit: Deanna Church Reference Assembly Basics

75 % off-target alignments

25% no alignment

chromosome

variant

PLoS Biology (Jul 5, 2011)

Sequences from haplotype 1

Sequences from haplotype 2


Original assembly model:compress into a consensus

falsegap

chromosome

Current assembly model:represent both haplotypes

alt loci scaffold

chromosomemanyGene1 Gene2

Sample

Gene2

Gene1chromosome

alt scaffold

Reference

GRCh38 (Dec. 2013)• 178 regions with alt loci: 2% of chromosome

sequence (61.9 Mb)

• 261 Alt Loci: 3.6 Mb novel sequence relative to

chromosomes

• Average alt length = 400 kb, max = ~5 Mb

• >150 genes only represented on alt loci



• Closed gaps• Targeted base fixes• Corrected path errors• Addition of missing paralogs• Better representation of variation• Better annotation• Modeled centromeres• Genome Research 27(5):849-864

(2017)• PubMed: 28396521

GRCh38

• Changed coordinates• Remapping challenges

• Alt Loci Usability• Allelic duplication/Aligners• Reporting multiple locations• Variant analysis

• Clinical validation

2016Growth in SRA submission

over prior year

GRCh38

GRCh37

Outline


GRCh38 Updates

GRCh38: Dec. 2013

(n=1797)

(n=1396) (n=401)

GRCh38 Updates

(rare allele analysis)

GRCh38 Updates

chromosome

novel patch scaffold

alt loci scaffold

chromosome

fix patch scaffold

Patch release: No change to chromosome coordinatesAssembly nomenclature: GRCh38.p$

GRCh38.p11• 64 FIX, 59 NOVEL

• Added >1.5 Mb novel

sequence

• >20 genes affected

GRCh38 Updates

GRCh38: 5S rRNA cluster under-represented (19 copies)

GRCh38 patch: 5S rRNA cluster valid representation (35 copies)

Poster 423F (11:30-12:30)Updates to the human

reference genome assemblyTayebeh Rezaie

GRCh38 Updates

• Ideals:• Chromosome context for any

common human sequence >500 bp• Unambiguous data interpretation at

all clinically relevant loci• No systematic error/bias in

genome-wide analyses

• Real-World:• Community interest• Resources for curation

• GRCh39• Substantial added value• User must-haves

Outline

• Assembly basics• GRCh38 & updates• Taking advantage of the data

Accessing the Data

Assembly Stats


Accessing the Data

Accessing the Data

Accessing the Data

https://www.ncbi.nlm.nih.gov/genome/gdv/

Learn more about GDV:

Data CoLab #159 Weds 10:30-11:00

Poster 1531WWeds 2:00-3:00

Accessing the Data

Assembly Support Track Set

Accessing the Data

http://www.ensembl.org/GRC Tracks

http://www.ensembl.org/

Accessing the Data

ftp://ngs.sanger.ac.uk/production/grit/track_hub/hub.txt

Outline


Credits

GRCh38 Collaborators• NCBI RefSeq and gpipe annotation team• Havana annotators• Karen Miga• Karyn Meltz Steinberg• David Schwartz• Steve Goldstein• Mario Caceres• Giulio Genovese• Jeff Kidd• Peter Lansdorp• Mark Hills• David Page• Jim Knight• Stephan Schuster• 1000 Genomes

GRC SAB• Rick Myers• Granger Sutton• Evan Eichler• Jim Kent• Roderic Guigo• Carol Bult• Derek Stemple• Jan Korbel• Liz Worthey• Matthew Hurles• Richard Gibbs

GRCTina Graves-LindsayTayebeh RezaieKerstin HoweRichard DurbinPaul FlicekLaura ClarkeDeanna ChurchCurators!Developers!

Health & Medicine

Ashg2017 workshop schneider