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Comprehensive,Genome,and,Transcriptome,
Structural,Analysis,of,a,Breast,Cancer,Cell,
Line,using,PacBio,Long,Read,Sequencing,
Maria Nattestad
Schatz + McCombie + Hicks at Cold Spring Harbor Laboratory
McPherson + Beck at the Ontario Institute for Cancer Research
Pacific Biosciences
DNAnexus,
SK@BR@3,
Most,commonly,used,Her2@amplified,breast,cancer,cell,line,
80,chromosomes,instead,of,46,
OIen,used,for,pre@clinical,research,on,Her2@targeKng,therapeuKcs,such,as,
HercepKn,(Trastuzumab),and,resistance,to,these,therapies.,
(Davidson,et,al,,2000),
PacBio,long@read,DNA,sequencing,
,
,
,
,
,
,72X,coverage,
coverage
mean,read,length:,9,kb ,
max,read,length:,71,kb,
,
Genome@wide,coverage,averages,around,54X,,
Coverage,per,chromosome,varies,greatly,as,expected,from,previous,karyotyping,results,
Structural,variant,detecKon,
Assembly)based.
Assembly,with,
Falcon,on,
DNAnexus,
Assembly:,
Total:,2.97Gb,
Max:,19.9,Mb,
N50:,2.46,Mb,
Alignment,with,
MUMmer,
Call,variants,
between,
consecuKve,
alignments,with,
ABVC.
Call,variants,
within,
alignments,with,
ABVC.
~,11,000,local,variants,
50,bp,<,size,<,10,kbp,
Alignment)based.
Alignment,with,
BWA@MEM,
Copy,number,
analysis,
SV@calling,from,
split,reads,with,
Sniffles.
ValidaKons,
350,long@range,variants,
(>10kb,distance),
SplitThreader.
Detailed,
analysis,of,Her2,
amplificaKons,
Long@range,structural,variants,found,by,Sniffles,
(>,10kb),,
Threshold:,10,split,reads,broken,within,a,200,
bp,interval,on,both,sides,of,the,translocaKon,
Her2,
Chr,17:,,83,Mb,
8,Mb,
Her2,
Her2,
8,Mb,
Her2,
GSDMB,
RARA,
PKIA,
TATDN1,
SplitThreader:,
Graphical,threading,to,retrace,complex,history,
of,rearrangements,in,cancer,genomes,
CHR 1
20
ATCGCCTA
CHR 2
GTCCATAG
80
CHR 1
100
20
ATCG
CCGA
80
CHR 2
GTCC
100
ATAG
Her2,
GSDMB,
RARA,
Chr,17,
Chr,8,
1. 
2. 
3. 
4. 
5. 
Healthy,chromosome,17,
TranslocaKon,into,
chromosome,8,
TranslocaKon,within,
chromosome,8,
Complex,variant,and,
inverted,duplicaKon,within,
chromosome,8,
TranslocaKon,within,
chromosome,8,
PKIA,
TATDN1,
Transcriptome,analysis,with,IsoSeq,
IsoSeq,,
long@read,RNA@seq,
Gene,fusions,
DNA,+,RNA,evidence:,
•  13,fusions,in,previous,
literature,
•  4,novel,fusions,
•  CYTH1@MTBP,
•  SAMD12@EXT1,
•  PHF20@[email protected],
•  AMZ2@CASC8,
RNA,evidence,only:,
•  188,fusions,
Novel,isoforms,
~,45,000,novel,isoforms,(2+,reads),
,~,7,400,with,10+,reads,
,
279,putaKve,novel,genes,
•  10+,reads,of,the,same,isoform,
•  Not,overlapping,exisKng,annotaKon,
CYTH1@EIF3H,gene,fusion,
CYTH1,
Chr,17,
CYTH1, EIF3H,
36,
CYTH1, MTBP,
27,
3,IsoSeq,reads,
30,IsoSeq,reads,
3.7,Mb,
Chr,8,
MTBP,
EIF3H,
8,kb,,
The,genome,informs,the,transcriptome,
Explain,amplificaKons,
Trace,gene,fusions,
Data,and,addiKonal,results:,hkp://schatzlab.cshl.edu/data/skbr3/,
Acknowledgments,
Sara,Goodwin,
Timour,Baslan,
Fritz,Sedlazeck,
Tyler,Garvin,
Han,Fang,
James,Gurtowski,
Elizabeth,Hukon,
Marley,Alford,
Melissa,Kramer,
Eric,Antoniou,
James,Hicks,
Michael,Schatz,
W.,Richard,McCombie,
Karen,Ng,
Timothy,Beck,
Yogi,Sundaravadanam,
John,McPherson,
,
,
DNAnexus
Pacific Biosciences
Elizabeth,Tseng,
Jason,Chin,
Our.so<ware.in.development:.Sniffles,by,Fritz,,ABVC,and,SplitThreader,by,Maria,
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