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ìDiversity and Genome Analysis
Deanna	M.	Church	
Senior	Director	of	Applications,	 10x	Genomics
• How	does	diversity	affect	assembly?
• How	does	diversity	affect	assembly?
• Why	is	it	important	to	represent	this?
• How	does	diversity	affect	assembly?
• Why	is	it	important	to	represent	this?
• Improving	individual	genome	analysis
ì
How does diversity affect assembly
OldAssembly Models
Sequences	from	haplotype	1
Sequences	from	haplotype	2
OldAssembly Models
Sequences	from	haplotype	1
Sequences	from	haplotype	2
OldAssembly Models
Sequences	from	haplotype	1
Sequences	from	haplotype	2
New Assembly Models
Sequences	from	haplotype	1
Sequences	from	haplotype	2
GRCh37
New Reference Assembly Models
Sequences	from	haplotype	1
Sequences	from	haplotype	2
Improving the modelCCL3: region: GRCh37
NC_000017.10 (chr17): 34,442,621-35,005,379
Improving the model
NC_000017.10 (chr17): 34,442,621-35,005,379
CCL3: region: GRCh37
Alternate LociCCL5-TBC1D3 region: GRCh38
NC_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
• Complex	diversity	can	lead	to	assembly	errors
Diversity and the assembly
• Complex	diversity	can	lead	to	assembly	errors
• Haploid	consensus	leads	to	missing	information
ì
Why is this important?
Allelic diversity
10.1038/nrg3933
MAPT locus
MHC (chr6)
Chr 6	representation	(PGF)
Alt_Ref_Locus_2	(COX)
MHC (chr6)
Chr 6	representation	(PGF)
Alt_Ref_Locus_2	(COX)
MHC (chr6)
Chr 6	representation	(PGF)
Alt_Ref_Locus_2	(COX)
Assembly Representation
75Mb	new	sequence
>2000	new	protein	coding	transcripts
178	Regions	with	Alternate	Loci
3.6	Mb	unique	sequence	to	Alts
153	genes	unique	to	alts
GRCh38
• Missing	sequence	leads	to
• Missing	Haplotype	Configuration
• Missing	Gene	Models
• Missing	Knowledge
ì
Improving individual genome analysis
Analysis challenges: alignments
Primary Assembly
Paralogous duplication
Allelic duplication
Alt	Locus
MapQ
Analysis challenges: alignments
Primary Assembly
Paralogous duplication
Allelic duplication
Alt Locus
MapQ
Alt Loci andGenes
Medically Interpretable Genes (MIG) ~8,000
Primary Assembly
Alt Locus
6.4%
6.2%0.18%
Impact on reference based analysis
De Novo LocalAssembly of HLA-A Region
Example of analysis from Linked-Reads
Call	and	phase	HLA	genes,	introns	and	intervening	MHC	sequence
Valerie	Schneider,	Friday	7:50	pm
David	Jaffe,	Friday	8:30pm	
Karyn Meltz Steinberg,	Friday	9:10
http://www.pathology.washington.edu/galleries/Cytogallery/main.php?f
ile=human%20karyotypes
The reference assembly and genome interpretation
KCNE1
Parting thoughts
Out	with	the	old	and	in	with	the	new
Parting thoughts
Out	with	the	old	and	in	with	the	new
• Old	assembly	models	lead	to	analysis	holes
Parting thoughts
Out	with	the	old	and	in	with	the	new
• Old	assembly	models	lead	to	analysis	holes
• Improved	reference	can	help	reference	based
analysis
Parting thoughts
Out	with	the	old	and	in	with	the	new
• Old	assembly	models	lead	to	analysis	holes
• Improved	reference	can	help	reference	based
analysis
• Individual	de	novo	assembly	is	the	future
• Still	need	reference	to	interpret
• Need	tool	development

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