Identifying Structural Variation, component issues, and other sequence artifacts by integrating long range genome maps in a web-based genome browser.

1. Identifying structural variation, component issues and other sequence
artifacts by integrating long range genome maps in a web-based genome
browser
William Chow, and Kerstin Howe
Wellcome Trust Sanger Institute, Cambridge, UK.
Applications
Identifying and Capturing Variation
The
Ashkenazim
and
CHS
trio
maps
were
generated
using
Bionano
Haplotype
Aware
so;ware
(unpublished).
The
poten@al
inheritance
paBern
of
the
child
can
be
deduced
from
the
maps
of
the
parents.
Primary
Assembly
(NC_00018)
Alternate
Locus
Representa@on
(NT_187618)
There
are
two
nickase
labeled
groups
seen.
#
blocks
Total
size
Orange
blocks
2
~32kb
Red
blocks
4
~38kb
Allele
1
with
Primary
Assembly
(NC_00018)
Allele
2
with
Alternate
Assembly
(NT_187618)
Human
(GRCh38)
–
Chr
18:
43,724,697-43,768,880
CAST/EiJ
BALB/cJ
GRCm38
PWK/PhJ
PWK/PhJ
Mouse
(PWK/PhJ)
–
Chr
8:
106,309,962-­‐106,509,961
Assembly Evaluation
There are two observations from this region of PWK/PhJ (above):
A. there is genome map discordance. (Mapà~10kb. BspQIà~60kb)
B. all the transcript mappings are green, but pmfbp1 looks like there is a very long suspicious intron caused by
middle component ScRybd3_121_120.
Comparative alignments between PWK/PhJ and CAST/EiJ, BALB/cJ, GRCm38 (right):
C. ScRybd3_121_120 has no alignments to the other mouse assemblies, providing evidence that perhaps this
component is creating an expansion of the region.
C
CB
A
Compara@ve
Assembly
View:
Mouse
(PWK/PhJ)
against
3
other
Mouse
Assemblies
The gEVAL Browser
gEVAL is a modern, scrollable and dynamic genome browser, allowing the user to view pre-calculated analyses or attach data as tracks specifically tailored for
assembly evaluation. It also includes comparative analyses of different assembly builds for each species as well as automated lists created to facilitate
identification of and navigation to issues or regions of interest.
Public
Repository
DENOVO
ASSEMBLY
CONSENSUS
MAPS
Example
of
data
used
Clone
Library
Ends
Transcripts/cDNAs
Assembly
Self
Comparisons
GRC
Issues
tracker
Markers
Pacbio
reads
Align
with
RefAligner
Align
Datasets
Long
range
genome
maps
either
generated
by
the
Irys
Instrument
or
from
public
sources
(A)
and
genomic
datasets
(B)
are
aligned/mapped
using
the
appropriate
tools
against
the
assembly
and
loaded
into
to
the
browser
for
visualiza@on
(C).
A
B
C
1
Genome
Map
Con@g
and
BspQI
Insilico
Digest
track
Discordance
of
map
size
between
nickase/labels
and
digest
coloured
in
red.
2
Transcript(s)
track
Complete
mapping
in
green,
incomplete
in
orange.
3
Clone
end(s)
track
Concordant
paired
end
mappings
in
green,
insert
size/
orienta@on
issues
will
be
colored
orange/red.
1
2
3
Mouse
Genome
Project
Strain-­‐specific
Genome
Maps
129S1/SvImJ
A/J
AKR/J
BALB/cJ
C3H/HeJ
C57BL/6NJ
CAST/EiJ
CBA/J
DBA/2J
FVB/NJ
LP/J
NOD/ShiLtJ
NZO/HiLtJ
PWK/PhJ
SPRET/EiJ
WSB/EiJ
• Maps
Generated
by
the
Sanger
Ins[tute.
Mice Images courtesy of JAX creative division, The Jackson Laboratory
Genome
Reference
Consor[um
Species
Genome
Maps
Human
Ashkenazim
Trio
†
NA24149
(father)
NA24143
(mother)
NA24385
(son)
Southern
Han
Chinese
(CHS)
Trio
¤
HG00514
(daughter)
HG00512
(father)
HG00513
(mother)
Yoruba
(YRI)
Trio
¤
NA19240
(daughter)
NA19239
(father)
NA19238
(mother)
Yan
Huang
(YH)
§
PRJNA42199
† Zook,
J.,
et
al.
Extensive
sequencing
of
seven
human
genomes
to
characterize
benchmark
reference
materials.
BioRxiv
(2015)
‡ Mak
AC
et
al.
Genome-­‐Wide
Structural
Varia@on
Detec@on
by
Genome
Mapping
on
Nanochannel
Arrays
Gene@cs
(2015)
§ Cao,
H.,
et
al.
Rapid
Detec@on
of
Structural
Varia@on
in
a
Human
Genome
using
Nanochannel-­‐
based
Genome
Mapping
Technology.
Giga
Science
(2014);
3(December
2014):
34
¤
Human
Genome
Structural
Varia@on
Consor@um
(HGSV)
|1000
Genomes.
Currently
Under
Publica[on
Embargo.
^
Courtesy
of
T.Graves
(MGI),
E.Lam
(Bionano
Genomics).
(2014)
Central
Europe
Hapmap
(CEPH)
Trio
‡
NA12878
(daughter)
NA12891
(father)
NA12892
(mother)
Puerto
Rican
Trio
¤
HG00733
(daughter)
HG00731
(father)
HG00732
(mother)
Han
Chinese
Trio
†
NA24631
(son
only)
Haploid
Hyda[dform
mole
(CHM1)
^
PRJNA176729
Zebrafish
Sanger
AB
Tübingen
(SAT)
Generated
by
the
Sanger
Ins@tute
A
Trackhub
is
available:h,p://bit.ly/25b7Tqg
Genome Maps Available in gEVAL
To aid in this, we have incorporated long range
single molecule, genome mapping technology
datasets from both in-house (Sanger Institute)
and public repositories (Bionano Genomics,
Genome in a Bottle). Along with the wide range
of data already aligned to each genome, this
long range data can help identify structural
variation and confirm assembly irregularities
such as insertions, deletions and mis-
assemblies whilst providing suitable information
to resolve them.
In the image on the left, the genome maps (Ashkenazi, CHS
and CEPH Trio, Han Chinese son, YH and CHM1) are aligned
to GRCh38. The maps indicate two distinct patterns created
by the nickase labels providing evidence of an alternate locus
capturing ~6kb unique sequence compared to the primary
reference assembly.
A. Within some family trio, the maps were haplotype-aware
assembled creating two map contig per individual, this
can be used to illicit inheritance patterns in family.
B. When looking at all maps, the two patterns illustrate the
variation between two group, one consisting of
2 blocks (~11.8kb + 21kb = 32kb) and the other,
4 blocks (~9.8kb + 7kb + 3kb + 18kb = 38kb).
Note the former agrees with the BspQI digest of the
primary assembly (11.8kb +21kb).
C. When looking at the BspQI digest track in the primary
assembly (NC_00018) and the assembly representing the
alternate locus (NT_187618) versus the maps, the
concordance can be seen.
gEVAL
-­‐
A
web
based
browser
for
evalua[ng
genome
assemblies
Chow
W,
Brugger
K,
Caccamo
M,
Sealy
I,
Torrance
J,
Howe
K
Bioinforma@cs
2016
Apr
7.
pii:btw159:
PMID:
27153597
http://geval.sanger.ac.uk