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Introduction
The Hereditary Cancer Solution (HCS) by SOPHiA GENETICS is the first capture-based application, which has received the CE-IVD mark. The automation of the HCS by SOPHiA GENETICS protocol is frequently requested in the field, especially in the clinical environment where minimizing human intervention is a plus.
n Automation of library preparation workflow of SOPHiA GENETICS bundle solutions on Hamilton instruments
n Standardization of genomic testing in clinical settings
n Reduction of bias due to manual sample preparation
Next-Generation Sequencing (NGS) workflows require multiple sample manipulation steps. However, conventional manual rou-tines during library preparation and target enrichment are susceptible to human bias. Automating the process frees up the technicians’ time and also allows to standardize the workflow, thus reducing human errors. The HCS by SOPHiA GENETICS represents a comprehensive NGS application for the detection of genomic variants in 26 genes associated with breast and ovarian, as well as digestive cancers. It bundles the analytical power of SOPHiATM Artificial Intelligence (AI) with a capture-based target enrichment kit and full access to SOPHiA DDM® platform (Fig. 1). This application note describes the automation of two protocol steps, whole genome library preparation and target capture.
Method Description and Protocol
The HCS by SOPHiA GENETICS provides an integrated library preparation workflow that allows users to prepare ready-to-sequence target-enriched libraries in only two working days, starting with as little as 200 ng of genomic DNA (Fig. 2).
Pre and Post-PCR workflows are performed on the same deck layout. The Pre-PCR workflow is performed on day 1, starting from diluted genomic DNA at the proper working concentration, placed in an input plate. As a result, amplified genomic libraries
Authors: Enrico Tagliafico 1-2, Elena Tenedini 1-2, Iole Pezzuto 3, Anja Seffner 3, Fabio Celestini 4, and Federico Sebastiani 5
1 Center for Genome Research, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena Italy2 Clinical Genomics Laboratory, Modena University Hospital, Modena, Italy 3 SOPHiA GENETICS, Rue du Centre 172, 1025 Saint-Sulpice, Switzerland4 Hamilton Italia, Via Paracelso 22, 20864 Agrate Brianza, Italy5 Hamilton Bonaduz AG, Via Crusch 8, 7402 Bonaduz, Switzerland
Application Note Diagnostics
Figure 1: Starting from the left, a Hamilton STARlet platform, the HCS kit and SOPHiA DDM platform.
Automation of the Hereditary Cancer Solution by SOPHiA GENETICS on Hamilton STARlet
are obtained. These libraries are used to perform the target-enrichment workflow during the Post-PCR phase on day 2.
Extracted DNA is processed on the Hamilton STARlet through an input worklist. The automated workflow processes up to 48 samples per run in 2 days, including PCR amplification on the deck of the platform.
An evaluation study was performed on a total of 48 samples, 40 of which were unique samples. These samples contained a large array of distinct representative mutations and enabled estimates of sensitivity for variant calling. Replicates were included to estimate repeatability and reproducibility.
System Description
STARlet 8 channels, no autoload; clear cover with UV lamp for deck sterilization; 1x ODTC; 1x PCR plate cooling module; 1x vial cooling module; 2x32 vial carrier; 1x MFX carrier for troughs containing Ethanol; 1x shaker carrier with 2x plate modules, 1x Teleshaker and 1x Chemagic magnetic stand; 1x reagent carrier with 3x120 ml troughs as waste (Fig. 3).
Figure 3: The Hamilton STARlet deck layout.
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3
1
4
5
7
6
10
8
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12
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1. Lid Park Position
2. On-Deck Thermal Cycler
3. Tips
4. Reagent Carrier
5. Heating Cooling Module
6. Reagent Trough
7. Teleshaker
8. Magnet
9. Waste Reagent Trough
10. Plate Position
11. Waste
12. CO-RE Gripper
High quality dsDNAEnzymatic fragmentation,
End repair & A-tailing
Adapter ligation
Post-ligation clean up
Dual-size selection
Library amplification
Post amplification clean up
Pool libraries& lyophilization
Library quantification &quality control by capillaryelectrophoresis
LIBRARIES PREPARATIONWITH DNA LIBRARY PREP KIT BY SOPHIA GENETICS
CAPTUREEASY WORKFLOW- ONLY 1-4 TUBES TO HANDLE (MULITPLEX-POOLED LIBRARIES)- ONLY 3 HOURS HANDS ON TIME
Hybridize targetswith SG probes
Bind probe-target duplexes to streptavidin beads
Pull-down DNA-bead complexes
Wash DNA-bead complexes
Post capture amplification & clean up
Library quantification &quality control by capillaryelectrophoresis
DAY2
12pm
3pm
9am
12pm
3pm
9am
DAY1
4h of
hybridizationHigh quality dsDNAEnzymatic fragmentation,
End repair & A-tailing
Adapter ligation
Post-ligation clean up
Dual-size selection
Library amplification
Post amplification clean up
Pool libraries& lyophilization
Library quantification &quality control by capillaryelectrophoresis
LIBRARIES PREPARATIONWITH DNA LIBRARY PREP KIT BY SOPHIA GENETICS
CAPTUREEASY WORKFLOW- ONLY 1-4 TUBES TO HANDLE (MULITPLEX-POOLED LIBRARIES)- ONLY 3 HOURS HANDS ON TIME
Hybridize targetswith SG probes
Bind probe-target duplexes to streptavidin beads
Pull-down DNA-bead complexes
Wash DNA-bead complexes
Post capture amplification & clean up
Library quantification &quality control by capillaryelectrophoresis
DAY2
12pm
3pm
9am
12pm
3pm
9am
DAY1
4h of
hybridization
Figure 2: Workflow of the Hereditary Cancer Solution by SOPHiA GENETICS.
Analytical Technology
SOPHiA AI detects, annotates and pre-classifies genomic variants, such as SNVs, Indels, CNVs, ALU insertions and pseudo-gene conversion events, from raw NGS data. The results of the analysis are presented on the SOPHiA DDM platform. Thanks to its intuitive user interface and integrated features, variants visualization and interpretation are facilitated, while assuring the protection of clinical genomic data.
Kit Description
The HCS by SOPHiA GENETICS includes all reagents needed for library preparation and target capture workflow:
n DNA Library Prep Kit by SOPHiA GENETICS
n Individually-synthesized and quality-controlled target-capture probes
n Blocking oligos and Cot-DNA
n Streptavidin and clean-up beads
n All washing and hybridization buffers
n Dual Index Sequencing Adaptors
Automation Technology
The Hamilton STARlet is an ideal platform for the automation of the HCS by SOPHiA GENETICS protocol, as it is equipped with all the positions and devices required for this NGS workflow. In combination with proven Hamilton technologies like CO-RE, MAD, and cLLD, the process can be run with the high degree of robustness and process-safety required for diagnostic applications.
Results
The automation of the HCS by SOPHiA GE-NETICS resulted in a very uniform coverage, high on-target reads percentage and excep-tional coverage in GC-rich regions, even in the first exon. Moreover, all types of genomic variants have been accurately detected, in-cluding difficult variants like long Indels and gene conversion events.
Yield and Quality
Each sample yielded a sufficient number of reads (~2.3 M reads, data not shown) with very uniform coverage (Fig. 4). Moreover, the percentage of mapped on-target reads is very good with around 85% (Fig. 5), allowing 90% of target regions being covered with more than 1000x in all samples. All replicates se-quenced across different runs displayed ex-tremely high reproducibility (Fig. 6). A total of 29 samples carried Copy Number Variations (CNVs), as deletions and duplications. All of them were accurately detected by SOPHiA AI also in replicate samples as shown in the ex-ample in Fig. 7. Even gene conversion events have been reliably detected (Fig. 8).
Figure 4: Coverage uniformity plot of one exemplary sample. Each dot represents a 10 bp window. The whole target region (including AT- and GC-rich regions) is uniformly covered.
Figure 5: High on-target read percentage. On average 85% of all read base pairs mapped to the target regions (onTarget and flankTarget). Also, between sample variance is very low.
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50bp window:high ATneutral AThigh GC
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−10
−50
510
coverage uniformity in 3052−rep1 (1, medCov 1307)
log2
(cov
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ized
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APC
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Coverage Uniformity in 3052-rep1 (1, medCov 1307)
Sam
ple6
−310
1
Sam
ple4
−305
8
Sam
ple2
−304
6
Sam
ple1
−306
1−re
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Sam
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−306
1rep
2
Sam
ple3
−309
2
Sam
ple7
−298
8
Sam
ple9
−305
7−re
p1
SG01
9−re
p1
Sam
ple5
−309
0
Sam
ple8
−310
7
Sam
ple1
2−30
51
Sam
ple1
7−30
45
Sam
ple1
0−31
38
Sam
ple1
1−30
44
Sam
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6−30
87
Sam
ple1
3−30
56
Sam
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−305
7−re
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Sam
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4−18
48
Sam
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5−30
73−r
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Sam
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5−30
73−r
ep1
Sam
ple1
−305
4Read Base Mapping Distribution
Perc
enta
ge
offTarget_LowCovoffTarget_HighCovflankTargetonTarget
0102030405060708090
100
Mean onTarget mapping: 67.9% − Mean Flank mapping: 17%
Read Base Mapping DistributionMean onTarget mapping: 67.9% - Mean Flank mapping: 17%
Per
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Sam
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Sam
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Sam
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Sam
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Sam
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17-3
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SG
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Sam
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Sam
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10-3
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Sam
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5-30
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Sam
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15-3
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Sam
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11-3
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Sam
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8-31
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Sam
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16-3
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Sam
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Sam
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Sam
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1009080706050403020100
50bp window:high ATneutral AThigh GGC
Sam
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Sam
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−305
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Sam
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−304
6
Sam
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Sam
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−306
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Sam
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−309
2
Sam
ple7
−298
8
Sam
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−305
7−re
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SG01
9−re
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Sam
ple5
−309
0
Sam
ple8
−310
7
Sam
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2−30
51
Sam
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7−30
45
Sam
ple1
0−31
38
Sam
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1−30
44
Sam
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6−30
87
Sam
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3−30
56
Sam
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−305
7−re
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Sam
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4−18
48
Sam
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73−r
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Sam
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5−30
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Sam
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−305
4
Read Base Mapping Distribution
Perc
enta
ge
offTarget_LowCovoffTarget_HighCovflankTargetonTarget
0102030405060708090
100
Mean onTarget mapping: 67.9% − Mean Flank mapping: 17%
System and Labware Requirements
Description Part Number
HCS by SOPHiA GENETICS * BS.0242.0102-48
STARlet **, 8 channels, manual load 173000-003
TIP CARRIER 182085
ADAPTER PCR 96 188266
ADAPTER 24 188263
MULTIFLEX REAGENT MODULE 188047
MULTIFLEX CARRIER BASE 188039
MULTIFLEX COOLING MODULE 188046
CO-RE GRIPPER (1ml) set 184089
UV KIT STARlet ML 188129APE
* CE-IVD, 48rx, Illumina MiSeq® ** Dimensions (WxHxD): 1124x903x795 mm
Description Part Number
UV KIT STARlet ML 188129APE
REAGENT CARRIER 3X120ml 194058
PLT_CAR-L4_SHAKER 187001
DWP MODULE 187144
Teleshake Module 220v for DWP 187143
Multiflex Module Bracket 7T 188133APE
MULTIFLEX DWP MODULE 188042
KIT ODTC 96 TR (CLEAR) 819416
TUBE CARRIER 173410
SMP_INS_2ML_32 188102
Throughput and Capacity
The HCS by SOPHiA GENET-ICS allows to prepare maxi-mum 48 sample libraries that have been sequenced on the Illumina MiSeq® using v3 chemistry.
0.0 0.2 0.4 0.6 0.8 1.0
0.0
0.2
0.4
0.6
0.8
1.0
Variant fraction (replicate1)
Varia
nt fr
actio
n (re
plic
ate2
)
Reproducibility
SNP: 0.2
INDEL: 0.15
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Sample1−3061−rep1 vs. 3061 Sample1−3061rep2 vs. 3061 Sample15−3073−rep1 vs. 3073 Sample15−3073−rep2 vs. 3073 SG019−rep1 vs. SG019
Diagonal (R^2 = 0.989)Diagonal ± 10%
0.0 0.2 0.4 0.6 0.8 1.0
0.0
0.2
0.4
0.6
0.8
1.0
Variant fraction (replicate1)
Varia
nt fr
actio
n (re
plic
ate2
)
Reproducibility
SNP: 0.2
INDEL: 0.15
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Sample1−3061−rep1 vs. 3061 Sample1−3061rep2 vs. 3061 Sample15−3073−rep1 vs. 3073 Sample15−3073−rep2 vs. 3073 SG019−rep1 vs. SG019
Diagonal (R^2 = 0.989)Diagonal ± 10%
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
322732353240324432563259
SG019SG032−rep1SG032−rep2
bari1bari2bari3
MUT
YH_e
x16
MUT
YH_e
x15
MUT
YH_e
x03−
14M
UTYH
_ex0
2M
UTYH
_ex0
1
EPCA
M_5
UTR
EPCA
M_e
x01
EPCA
M_e
x02−
03EP
CAM
_ex0
4EP
CAM
_ex0
5EP
CAM
_ex0
6EP
CAM
_ex0
7EP
CAM
_ex0
8EP
CAM
_ex0
9
MSH
2_ex
01M
SH2_
ex02
MSH
2_ex
03M
SH2_
ex04
MSH
2_ex
05M
SH2_
ex06
MSH
2_ex
07M
SH2_
ex08
MSH
2_ex
09M
SH2_
ex10
MSH
2_ex
11M
SH2_
ex12
MSH
2_ex
13M
SH2_
ex14
MSH
2_ex
15M
SH2_
ex16
MSH
6_ex
01M
SH6_
ex02
MSH
6_ex
03M
SH6_
ex04
MSH
6_ex
05M
SH6_
ex06
MSH
6_ex
07M
SH6_
ex08−1
0
BARD
1_ex
11BA
RD1_
ex10
BARD
1_ex
09BA
RD1_
ex08
BARD
1_ex
07BA
RD1_
ex06
BARD
1_ex
05BA
RD1_
ex04
BARD
1_ex
03BA
RD1_
ex02
BARD
1_ex
01
MLH
1_ex
01−0
2M
LH1_
ex03
MLH
1_ex
04M
LH1_
ex05
MLH
1_ex
06M
LH1_
ex07
MLH
1_ex
08−0
9M
LH1_
ex10
MLH
1_ex
11M
LH1_
ex12
MLH
1_ex
13M
LH1_
ex14
MLH
1_ex
15M
LH1_
ex16
MLH
1_ex
17M
LH1_
ex18
MLH
1_ex
19M
LH1_
ex20
PIK3
CA_e
x01
PIK3
CA_e
x02
PIK3
CA_e
x03
PIK3
CA_e
x04
PIK3
CA_e
x05
PIK3
CA_e
x06
PIK3
CA_e
x07
PIK3
CA_e
x08−
09PI
K3CA
_ex1
0PI
K3CA
_ex1
1PI
K3CA
_ex1
2PI
K3CA
_ex1
3PI
K3CA
_ex1
4PI
K3CA
_ex1
5PI
K3CA
_ex1
6PI
K3CA
_ex1
7PI
K3CA
_ex1
8PI
K3CA
_ex1
9−20
PIK3
CA_e
x21
sam
ple
HCS_v1_1 (sample group 2 of 2)
●
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
322732353240324432563259
SG019SG032−rep1SG032−rep2
bari1bari2bari3
FAM
175A
_3UT
RFA
M17
5A_e
x09
FAM
175A
_ex0
8FA
M17
5A_e
x07
FAM
175A
_ex0
6FA
M17
5A_e
x05
FAM
175A
_ex0
4FA
M17
5A_e
x03
FAM
175A
_ex0
2FA
M17
5A_e
x01
APC_
ex01
APC_
ex02
APC_
ex03
APC_
ex04
APC_
ex05
APC_
ex06
APC_
ex07
APC_
ex08
APC_
ex09
APC_
ex10
APC_
ex11
APC_
ex12
APC_
ex13
APC_
ex14
APC_
ex15
APC_
ex16
RAD5
0_ex
01RA
D50_
ex02
RAD5
0_ex
03RA
D50_
ex04
RAD5
0_ex
05RA
D50_
ex06−0
7RA
D50_
ex08
RAD5
0_ex
09RA
D50_
ex10
RAD5
0_ex
11RA
D50_
ex12
RAD5
0_ex
13RA
D50_
ex14
RAD5
0_ex
15RA
D50_
ex16
RAD5
0_ex
17RA
D50_
ex18−1
9RA
D50_
ex20
RAD5
0_ex
21RA
D50_
ex22
RAD5
0_ex
23RA
D50_
ex24
RAD5
0_ex
25RA
D50_
3UTR
_1RA
D50_
3UTR
_2
PMS2
_ex1
1PM
S2_e
x10
PMS2
_ex0
9PM
S2_e
x08
PMS2
_ex0
7PM
S2_e
x06
PMS2
_ex0
5PM
S2_e
x04
PMS2
_ex0
3PM
S2_e
x02
PMS2
_ex0
1
XRCC
2_3U
TRXR
CC2_
ex03
XRCC
2_ex
02XR
CC2_
ex01
NBN_
3UTR
_2NB
N_3U
TR_1
NBN_
ex16
NBN_
ex15
NBN_
ex14
NBN_
ex13
NBN_
ex12
NBN_
ex11
NBN_
ex10
NBN_
ex09
NBN_
ex08
NBN_
ex07
NBN_
ex06
NBN_
ex05
NBN_
ex04
NBN_
ex03
NBN_
ex02
NBN_
ex01
sam
ple
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
322732353240324432563259
SG019SG032−rep1SG032−rep2
bari1bari2bari3
PTEN
_5UT
R_1
PTEN
_5UT
R_2
PTEN
_5UT
R_3
PTEN
_ex0
1PT
EN_e
x02
PTEN
_ex0
3PT
EN_e
x04
PTEN
_ex0
5PT
EN_e
x06
PTEN
_ex0
7PT
EN_e
x08
PTEN
_ex0
9
MRE
11A_
ex20
MRE
11A_
ex19
MRE
11A_
ex18
MRE
11A_
ex17
MRE
11A_
ex16
MRE
11A_
ex15
MRE
11A_
ex14
MRE
11A_
ex13
MRE
11A_
ex12
MRE
11A_
ex11
MRE
11A_
ex10
MRE
11A_
ex09
MRE
11A_
ex08
MRE
11A_
ex07
MRE
11A_
ex06
MRE
11A_
ex05
MRE
11A_
ex04
MRE
11A_
ex03
MRE
11A_
ex02
MRE
11A_
ex01
ATM
_ex0
1AT
M_e
x02−
03AT
M_e
x04
ATM
_ex0
5AT
M_e
x06
ATM
_ex0
7AT
M_e
x08
ATM
_ex0
9AT
M_e
x10
ATM
_ex1
1AT
M_e
x12
ATM
_ex1
3AT
M_e
x14
ATM
_ex1
5AT
M_e
x16
ATM
_ex1
7AT
M_e
x18
ATM
_ex1
9−20
ATM
_ex2
1−22
ATM
_ex2
3AT
M_e
x24
ATM
_ex2
5AT
M_e
x26
ATM
_ex2
7AT
M_e
x28
ATM
_ex2
9AT
M_e
x30
ATM
_ex3
1AT
M_e
x32
ATM
_ex3
3AT
M_e
x34
ATM
_ex3
5AT
M_e
x36
ATM
_ex3
7AT
M_e
x38
ATM
_ex3
9AT
M_e
x40
ATM
_ex4
1−42
ATM
_ex4
3AT
M_e
x44
ATM
_ex4
5AT
M_e
x46
ATM
_ex4
7AT
M_e
x48
ATM
_ex4
9AT
M_e
x50
ATM
_ex5
1AT
M_e
x52
ATM
_ex5
3AT
M_e
x54
ATM
_ex5
5AT
M_e
x56
ATM
_ex5
7AT
M_e
x58
ATM
_ex5
9AT
M_e
x60
ATM
_ex6
1AT
M_e
x62−
63AT
M_3
UTR_
1AT
M_3
UTR_
2AT
M_3
UTR_
3AT
M_3
UTR_
4AT
M_3
UTR_
5
sam
ple
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
322732353240324432563259
SG019SG032−rep1SG032−rep2
bari1bari2bari3
BRCA
2_ex
01BR
CA2_
ex02
BRCA
2_ex
03BR
CA2_
ex04
BRCA
2_ex
05−0
6BR
CA2_
ex07
BRCA
2_ex
08BR
CA2_
ex09
BRCA
2_ex
10BR
CA2_
ex11
BRCA
2_ex
12BR
CA2_
ex13
BRCA
2_ex
14BR
CA2_
ex15
BRCA
2_ex
16BR
CA2_
ex17
BRCA
2_ex
18BR
CA2_
ex19
BRCA
2_ex
20BR
CA2_
ex21
BRCA
2_ex
22BR
CA2_
ex23−2
4BR
CA2_
ex25
BRCA
2_ex
26BR
CA2_
ex27
BRCA
2_3U
TR
PALB
2_ex
13PA
LB2_
ex12
PALB
2_ex
11PA
LB2_
ex10
PALB
2_ex
09PA
LB2_
ex08
PALB
2_ex
07PA
LB2_
ex06
PALB
2_ex
05PA
LB2_
ex04
PALB
2_ex
02−0
3PA
LB2_
ex01
CDH1
_ex0
1CD
H1_e
x02
CDH1
_ex0
3CD
H1_e
x04−
05CD
H1_e
x06
CDH1
_ex0
7CD
H1_e
x08
CDH1
_ex0
9CD
H1_e
x10
CDH1
_ex1
1CD
H1_e
x12
CDH1
_ex1
3CD
H1_e
x14
CDH1
_ex1
5CD
H1_e
x16
CDH1
_3UT
R
TP53
_3UT
R_2
TP53
_3UT
R_1
TP53
_ex1
1TP
53_e
x10
TP53
_ex0
7−09
TP53
_ex0
6TP
53_e
x04−
05TP
53_e
x02−
03TP
53_e
x01
RAD5
1D_e
x10−
11RA
D51D
_ex0
8−09
RAD5
1D_e
x07
RAD5
1D_e
x06
RAD5
1D_e
x05
RAD5
1D_e
x04
RAD5
1D_e
x03
RAD5
1D_e
x02
RAD5
1D_e
x01
sam
ple
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
322732353240324432563259
SG019SG032−rep1SG032−rep2
bari1bari2bari3
BRCA
1_3U
TRBR
CA1_
ex24
BRCA
1_ex
23BR
CA1_
ex22
BRCA
1_ex
21BR
CA1_
ex20
BRCA
1_ex
19BR
CA1_
ex18
BRCA
1_ex
17BR
CA1_
ex16
BRCA
1_ex
15BR
CA1_
ex14
BRCA
1_in
13BR
CA1_
ex13
BRCA
1_ex
12BR
CA1_
ex11
BRCA
1_ex
10BR
CA1_
ex09
BRCA
1_ex
08BR
CA1_
ex07
BRCA
1_ex
06BR
CA1_
ex05
BRCA
1_ex
03BR
CA1_
ex02
BRCA
1_ex
01
RAD5
1C_e
x01
RAD5
1C_e
x02
RAD5
1C_e
x03
RAD5
1C_e
x04
RAD5
1C_e
x05
RAD5
1C_e
x06
RAD5
1C_e
x07
RAD5
1C_e
x08
RAD5
1C_e
x09
BRIP
1_3U
TR_5
BRIP
1_3U
TR_4
BRIP
1_3U
TR_3
BRIP
1_3U
TR_2
BRIP
1_3U
TR_1
BRIP
1_ex
20BR
IP1_
ex19
BRIP
1_ex
18BR
IP1_
ex17
BRIP
1_ex
16BR
IP1_
ex15
BRIP
1_ex
14BR
IP1_
ex13
BRIP
1_ex
12BR
IP1_
ex11
BRIP
1_ex
10BR
IP1_
ex09
BRIP
1_ex
08BR
IP1_
ex07
BRIP
1_ex
06BR
IP1_
ex05
BRIP
1_ex
04BR
IP1_
ex03
BRIP
1_ex
02BR
IP1_
ex01
STK1
1_5U
TRST
K11_
ex01
STK1
1_ex
02ST
K11_
ex03
STK1
1_ex
04−0
5ST
K11_
ex06
STK1
1_ex
07ST
K11_
ex08
STK1
1_ex
09ST
K11_
ex10
CHEK
2_ex
15CH
EK2_
ex14
CHEK
2_ex
13CH
EK2_
ex12
CHEK
2_ex
11CH
EK2_
ex10
CHEK
2_ex
09CH
EK2_
ex08
CHEK
2_ex
07CH
EK2_
ex06
CHEK
2_ex
05CH
EK2_
ex03−0
4CH
EK2_
ex02
CHEK
2_ex
01
sam
ple
Figure 6: Example of reproducibility between two runs. Each dot represents the variant fraction of one variant.
Figure 7: CNV detection. In this example an insertion in exon 13 of the BRCA gene was detected reliably in both replicate samples.
Figure 8: Example of gene conversion events in PMS2/PMS2CL.
Discussion and Summary
The automation of the library preparation of the Hereditary Cancer Solution by SOPHiA GENETICS on the Hamilton STARlet robot provided excellent results with top analytical performance. During this validation study, all confirmed variants (SNVs and Indels) were reliably called and all CNVs have been detected, including gene conversion events in PMS2/PMS2CL.
1 1 3 3 3 3 3 3 2 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 3 3 3 3 3 3 2 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
4 4 4 4 4 4 4 4 3 4 4 4 3 3 3 3 3 3 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
3 3 2 2 2 2 2 2 1 2 2 2 1 1 1 1 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 3
3 3 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2
2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 3
3 3 1 1 1 1 1 1 2 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 1 1 1 1 1 1 2 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 1 1 1 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
4 4 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
4 4 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
1 1 2 2 2 2 2 2 3 2 2 2 3 3 3 3 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 1
1 1 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 3 3 3 3 3 3 3 3 3 3 4 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2
2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 1
3052−rep1 : gene3052−rep1 : pseudo/other
3052−rep2 : gene3052−rep2 : pseudo/other
3061 : gene3061 : pseudo/other
3073 : gene3073 : pseudo/other
3078 : gene3078 : pseudo/other
3094 : gene3094 : pseudo/other
3167 : gene3167 : pseudo/other
3170 : gene3170 : pseudo/other
3194−rep1 : gene3194−rep1 : pseudo/other
3194−rep2 : gene3194−rep2 : pseudo/other
3204 : gene3204 : pseudo/other
3217 : gene3217 : pseudo/other
3227 : gene3227 : pseudo/other
3235 : gene3235 : pseudo/other
3240 : gene3240 : pseudo/other
3244 : gene3244 : pseudo/other
3256 : gene3256 : pseudo/other
3259 : gene3259 : pseudo/other
SG019 : geneSG019 : pseudo/other
SG032−rep1 : geneSG032−rep1 : pseudo/other
SG032−rep2 : geneSG032−rep2 : pseudo/other
bari1 : genebari1 : pseudo/other
bari2 : genebari2 : pseudo/other
bari3 : genebari3 : pseudo/other
PMS2
_ex1
5_do
wn_A
PMS2
_ex1
5_A
PMS2
_ex1
4_A
PMS2
_ex1
4_up
_A_2
PMS2
_ex1
4_up
_A_1
PMS2
_ex1
4_up
_B_5
PMS2
_ex1
4_up
_B_4
PMS2
_ex1
4_up
_B_3
PMS2
_ex1
4_up
_B_2
PMS2
_ex1
4_up
_B_1
PMS2
_ex1
3_do
wn_A
PMS2
_ex1
3_A
PMS2
_ex1
3_up
_APM
S2_e
x13_
up_B
_3PM
S2_e
x13_
up_B
_2PM
S2_e
x13_
up_B
_1
PMS2
_ex1
2_do
wn_B
PMS2
_ex1
2_do
wn_A
PMS2
_ex1
2_up
_A
PMS2
_ex1
1_V
PMS2
_ex1
1_U
PMS2
_ex1
1_T
PMS2
_ex1
1_S
PMS2
_ex1
1_R
PMS2
_ex1
1_Q
PMS2
_ex1
1_P
PMS2
_ex1
1_O
PMS2
_ex1
1_N
PMS2
_ex1
1_M
PMS2
_ex1
1_L
PMS2
_ex1
1_K
PMS2
_ex1
1_J
PMS2
_ex1
1_I
PMS2
_ex1
1_H
PMS2
_ex1
1_G
PMS2
_ex1
1_F
PMS2
_ex1
1_E
PMS2
_ex1
1_D
PMS2
_ex1
1_C
PMS2
_ex1
1_B
PMS2
_ex1
1_A
PMS2
_ex1
1_up
_A
sam
ple
HCS_v1_1 , PSV summary
1 1 3 3 3 3 3 3 2 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 3 3 3 3 3 3 2 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
4 4 4 4 4 4 4 4 3 4 4 4 3 3 3 3 3 3 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
3 3 2 2 2 2 2 2 1 2 2 2 1 1 1 1 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 3
3 3 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2
2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 3
3 3 1 1 1 1 1 1 2 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 1 1 1 1 1 1 2 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 1 1 1 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
4 4 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
4 4 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
1 1 2 2 2 2 2 2 3 2 2 2 3 3 3 3 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 1
1 1 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 3 3 3 3 3 3 3 3 3 3 4 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2
2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 1
3052−rep1 : gene3052−rep1 : pseudo/other
3052−rep2 : gene3052−rep2 : pseudo/other
3061 : gene3061 : pseudo/other
3073 : gene3073 : pseudo/other
3078 : gene3078 : pseudo/other
3094 : gene3094 : pseudo/other
3167 : gene3167 : pseudo/other
3170 : gene3170 : pseudo/other
3194−rep1 : gene3194−rep1 : pseudo/other
3194−rep2 : gene3194−rep2 : pseudo/other
3204 : gene3204 : pseudo/other
3217 : gene3217 : pseudo/other
3227 : gene3227 : pseudo/other
3235 : gene3235 : pseudo/other
3240 : gene3240 : pseudo/other
3244 : gene3244 : pseudo/other
3256 : gene3256 : pseudo/other
3259 : gene3259 : pseudo/other
SG019 : geneSG019 : pseudo/other
SG032−rep1 : geneSG032−rep1 : pseudo/other
SG032−rep2 : geneSG032−rep2 : pseudo/other
bari1 : genebari1 : pseudo/other
bari2 : genebari2 : pseudo/other
bari3 : genebari3 : pseudo/other
PMS2
_ex1
5_do
wn_A
PMS2
_ex1
5_A
PMS2
_ex1
4_A
PMS2
_ex1
4_up
_A_2
PMS2
_ex1
4_up
_A_1
PMS2
_ex1
4_up
_B_5
PMS2
_ex1
4_up
_B_4
PMS2
_ex1
4_up
_B_3
PMS2
_ex1
4_up
_B_2
PMS2
_ex1
4_up
_B_1
PMS2
_ex1
3_do
wn_A
PMS2
_ex1
3_A
PMS2
_ex1
3_up
_APM
S2_e
x13_
up_B
_3PM
S2_e
x13_
up_B
_2PM
S2_e
x13_
up_B
_1
PMS2
_ex1
2_do
wn_B
PMS2
_ex1
2_do
wn_A
PMS2
_ex1
2_up
_A
PMS2
_ex1
1_V
PMS2
_ex1
1_U
PMS2
_ex1
1_T
PMS2
_ex1
1_S
PMS2
_ex1
1_R
PMS2
_ex1
1_Q
PMS2
_ex1
1_P
PMS2
_ex1
1_O
PMS2
_ex1
1_N
PMS2
_ex1
1_M
PMS2
_ex1
1_L
PMS2
_ex1
1_K
PMS2
_ex1
1_J
PMS2
_ex1
1_I
PMS2
_ex1
1_H
PMS2
_ex1
1_G
PMS2
_ex1
1_F
PMS2
_ex1
1_E
PMS2
_ex1
1_D
PMS2
_ex1
1_C
PMS2
_ex1
1_B
PMS2
_ex1
1_A
PMS2
_ex1
1_up
_A
sam
ple
HCS_v1_1 , PSV summary
1 1 3 3 3 3 3 3 2 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 3 3 3 3 3 3 2 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
4 4 4 4 4 4 4 4 3 4 4 4 3 3 3 3 3 3 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
3 3 2 2 2 2 2 2 1 2 2 2 1 1 1 1 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 3
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 3
3 3 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2
2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 3
3 3 1 1 1 1 1 1 2 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 1 1 1 1 1 1 2 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 1 1 1 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
4 4 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
4 4 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
1 1 2 2 2 2 2 2 3 2 2 2 3 3 3 3 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 1
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 1
1 1 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 3 3 3 3 3 3 3 3 3 3 4 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 4 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2
2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 1
3052−rep1 : gene3052−rep1 : pseudo/other
3052−rep2 : gene3052−rep2 : pseudo/other
3061 : gene3061 : pseudo/other
3073 : gene3073 : pseudo/other
3078 : gene3078 : pseudo/other
3094 : gene3094 : pseudo/other
3167 : gene3167 : pseudo/other
3170 : gene3170 : pseudo/other
3194−rep1 : gene3194−rep1 : pseudo/other
3194−rep2 : gene3194−rep2 : pseudo/other
3204 : gene3204 : pseudo/other
3217 : gene3217 : pseudo/other
3227 : gene3227 : pseudo/other
3235 : gene3235 : pseudo/other
3240 : gene3240 : pseudo/other
3244 : gene3244 : pseudo/other
3256 : gene3256 : pseudo/other
3259 : gene3259 : pseudo/other
SG019 : geneSG019 : pseudo/other
SG032−rep1 : geneSG032−rep1 : pseudo/other
SG032−rep2 : geneSG032−rep2 : pseudo/other
bari1 : genebari1 : pseudo/other
bari2 : genebari2 : pseudo/other
bari3 : genebari3 : pseudo/other
PMS2
_ex1
5_do
wn_A
PMS2
_ex1
5_A
PMS2
_ex1
4_A
PMS2
_ex1
4_up
_A_2
PMS2
_ex1
4_up
_A_1
PMS2
_ex1
4_up
_B_5
PMS2
_ex1
4_up
_B_4
PMS2
_ex1
4_up
_B_3
PMS2
_ex1
4_up
_B_2
PMS2
_ex1
4_up
_B_1
PMS2
_ex1
3_do
wn_A
PMS2
_ex1
3_A
PMS2
_ex1
3_up
_APM
S2_e
x13_
up_B
_3PM
S2_e
x13_
up_B
_2PM
S2_e
x13_
up_B
_1
PMS2
_ex1
2_do
wn_B
PMS2
_ex1
2_do
wn_A
PMS2
_ex1
2_up
_A
PMS2
_ex1
1_V
PMS2
_ex1
1_U
PMS2
_ex1
1_T
PMS2
_ex1
1_S
PMS2
_ex1
1_R
PMS2
_ex1
1_Q
PMS2
_ex1
1_P
PMS2
_ex1
1_O
PMS2
_ex1
1_N
PMS2
_ex1
1_M
PMS2
_ex1
1_L
PMS2
_ex1
1_K
PMS2
_ex1
1_J
PMS2
_ex1
1_I
PMS2
_ex1
1_H
PMS2
_ex1
1_G
PMS2
_ex1
1_F
PMS2
_ex1
1_E
PMS2
_ex1
1_D
PMS2
_ex1
1_C
PMS2
_ex1
1_B
PMS2
_ex1
1_A
PMS2
_ex1
1_up
_A
sam
ple
HCS_v1_1 , PSV summary
Sample1−3061−rep1 vs. 3061Sample1−3061rep2 vs. 3061Sample15−3073−rep1 vs. 3073Sample15−3073−rep2 vs. 3073SG019−rep1 vs. SG019
Diagonal (R^2 = 0.989)Diagonal ± 10%
Variant fraction (replicate1)
Reproducibility
Sam
ple
s
Varia
nt fr
actio
n (re
plic
ate2
)
0.0
0.0
0.2
0.2
0.4
0.4
0.6
0.6
0.8
0.8
1.0
1.0
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© 2017 Hamilton Company. All rights reserved. Lit. No. AN-1710-01 — 10/2017The SOPHiA GENETICS’ solution is for In Vitro Diagnostic Use. Not available for diagnostic purposes in some countries and regions
