ìDiversity and Genome AnalysisDeannaM.ChurchSeniorDirectorofApplications, 10xGenomics

• Howdoesdiversityaffectassembly?

• Howdoesdiversityaffectassembly?• Whyisitimportanttorepresentthis?

• Howdoesdiversityaffectassembly?• Whyisitimportanttorepresentthis?• Improvingindividualgenomeanalysis

ìHow does diversity affect assembly

Old Assembly ModelsSequencesfromhaplotype1Sequencesfromhaplotype2

Old Assembly ModelsSequencesfromhaplotype1Sequencesfromhaplotype2

Old Assembly ModelsSequencesfromhaplotype1Sequencesfromhaplotype2

New Assembly ModelsSequencesfromhaplotype1Sequencesfromhaplotype2

GRCh37

New Reference Assembly ModelsSequencesfromhaplotype1Sequencesfromhaplotype2

Improving the modelCCL3: region: GRCh37

NC_000017.10 (chr17): 34,442,621-35,005,379

Improving the modelNC_000017.10 (chr17): 34,442,621-35,005,379

CCL3: region: GRCh37

Alternate LociCCL5-TBC1D3 region: GRCh38NC_000017.11 (chr17): 36,032,574-36,269,924

NT_187661.1

100 Kb deletion on chromosome

Steinberg et al., 2014 http://dx.doi.org/10.1101/006841

Diversity and the assembly

• Complexdiversitycanleadtoassemblyerrors

Diversity and the assembly

• Complexdiversitycanleadtoassemblyerrors• Haploidconsensusleadstomissinginformation

ìWhy is this important?

Allelic diversity

10.1038/nrg3933

MAPT locus

MHC (chr6)Chr 6representation(PGF)

Alt_Ref_Locus_2(COX)

MHC (chr6)Chr 6representation(PGF)

Alt_Ref_Locus_2(COX)

MHC (chr6)Chr 6representation(PGF)

Alt_Ref_Locus_2(COX)

Assembly Representation

75Mbnewsequence>2000newproteincodingtranscripts

178RegionswithAlternateLoci3.6MbuniquesequencetoAlts

153genesuniquetoalts

GRCh38

• Missingsequenceleadsto• MissingHaplotypeConfiguration• MissingGeneModels• MissingKnowledge

ìImproving individual genome analysis

Analysis challenges: alignments

Primary Assembly

Paralogous duplicationAllelic duplication

AltLocus

MapQ

Analysis challenges: alignments

Primary Assembly

Paralogous duplicationAllelic duplication

Alt Locus

MapQ

Alt Loci and Genes

Medically Interpretable Genes (MIG) ~8,000

Primary Assembly

Alt Locus

6.4%

6.2%0.18%

Impact on reference based analysis

De Novo Local Assembly of HLA-A RegionExample of analysis from Linked-Reads

CallandphaseHLAgenes,intronsandinterveningMHCsequenceValerieSchneider,Friday7:50pmDavidJaffe,Friday8:30pmKaryn Meltz Steinberg,Friday9:10

http://www.pathology.washington.edu/galleries/Cytogallery/main.php?file=human%20karyotypes

The reference assembly and genome interpretation

KCNE1

Parting thoughts

Outwiththeoldandinwiththenew

Parting thoughts

Outwiththeoldandinwiththenew

• Oldassemblymodelsleadtoanalysisholes

Parting thoughts

Outwiththeoldandinwiththenew

• Oldassemblymodelsleadtoanalysisholes• Improvedreferencecanhelpreferencebased

analysis

Parting thoughts

Outwiththeoldandinwiththenew

• Oldassemblymodelsleadtoanalysisholes• Improvedreferencecanhelpreferencebased

analysis• Individualdenovoassemblyisthefuture• Stillneedreferencetointerpret• Needtooldevelopment