SDQB04-0

SDQB04-0
Working Instruction
CTS-SEQUENCE HLA-DQB1
For high-resolution typing of HLA-DQB1
Product No. 338
Lot No. SDQB04-0
For research use only
University Clinic Heidelberg
Department of Transplantation Immunology
Im Neuenheimer Feld 305
69120 Heidelberg
Germany
Phone: +49-6221-564013
Fax: +49-6221-564200
www.ctstransplant.org
Manual No. 38
Revision: March 8, 2012
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CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
Content
1
Introduction ................................................................................................................................................... 3
2
Materials and Equipment ............................................................................................................................. 3
Materials included in the CTS-SEQUENCE HLA-DQB1Kit .................................................................. 3
2.1
Storage and expiration ............................................................................................................................ 5
2.2
Materials and equipment not included .................................................................................................... 6
2.3
3
Preparation of buffers and agarose gel ....................................................................................................... 7
4
Isolation and concentration measurement of DNA .................................................................................... 7
5
Test procedure ............................................................................................................................................... 7
Amplification ........................................................................................................................................... 8
5.1
Gel control .............................................................................................................................................. 8
5.2
Purification of the amplification products .............................................................................................. 9
5.3
Sequencing reaction ................................................................................................................................ 9
5.4
Purification of the sequencing products ................................................................................................ 10
5.5
Sample preparation for sequencing runs .............................................................................................. 11
5.6
6
Start of a sequencing run on the sequencer .............................................................................................. 11
Instrument protocol for ABI Prism 3100 Genetic Analyzer .................................................................. 11
6.1
Run Sequencing ..................................................................................................................................... 11
6.2
7
Result evaluation ......................................................................................................................................... 12
8
Troubleshooting .......................................................................................................................................... 13
8.1
8.2
Amplification ......................................................................................................................................... 13
Sequencing ............................................................................................................................................ 13
Appendix
Worksheet Amplification Protocol………………………………………………………........
Worksheet Pipetting Scheme…………………………………………………………………..
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15
16
CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
The CTS-SEQUENCE HLA-DQB1 Kit is delivered at room temperature. Immediately upon receipt, store
PCR Buffer & sequencing primers at -20°C and PCR minitrays at 4°C.
1
Introduction
This working instruction describes the procedure for high-resolution genotyping of the human leukocyte antigens
HLA-DQB1 with the CTS-SEQUENCE HLA-DQB1 Kit. PCR-sequencing based typing (PCR-SBT) is an
accurate and reliable method, allowing high resolution of HLA alleles at least 4-digit level.
The strategy is based on two consecutive steps: first, group- and locus-specific amplification of exon 2 of HLADQB1 and additionally locus-specific amplification of exon 3; second, the amplification products are sequenced
in forward and reverse direction. Matching for exon 2 (antigen-recognition site) at allele-level is considered
relevant in hematopoietic stem cell transplantation. Sequencing of exon 3 helps to reduce ambiguities.
The SEQUENCE HLA-DQB1 Kit is validated and optimized with following reagents, instruments, softwares
and methods:
-
GeneAmp® PCR System 2700 Thermocycler (Applied Biosystems, Darmstadt, Germany).
Amplification with the MBI Taq polymerase (Fermentas, St. Leon-Rot, Germany).
Purification of amplification products with EXO-SAP-IT (USB, Staufen, Germany).
Sequencing reaction with BigDye terminator v1.1 Kits (Applied Biosystems, Darmstadt, Germany).
Purification of the sequencing products using ethanol precipitation.
Resuspension of sequencing products with HiDi formamide (Applied Biosystems, Darmstadt, Germany).
Separation of sequencing products with the ABI PRISM 3100 Genetic Analyzer (Applied Biosystems,
Darmstadt, Germany).
Sequence analysis and HLA allele assignment with Sequence PilotTM-HLA SBT (JSI Medical Systems,
Kippenheim, Germany).
Other reagents, instruments etc. may be used, but should be validated by the user. The CTS-SEQUENCE kits
have been validated to be performed with the GeneAmp® PCR System 2700 thermocycler. If other cyclers are
used, the ramp rate has to be set at 1°C/sec.
According to EFI standards for histocompatibility testing (Version 5.6.1; L3.2520) PCR-SBT typing of HLAclass II bases on amplification and sequencing primers which are located outside of exon 2. For many HLA-class
II variants only the sequence of the antigen recognition site (exon 2 ) are reported. Even though the PCR-SBT
HLA-SEQUENCING Kits have been extensively tested and validated, an allelic drop out of a rare or new allele
due to mutations in the priming sites cannot be categorically ruled out.
2
2.1
Materials and Equipment
Materials included in the CTS-SEQUENCE HLA-DQB1Kit
The SEQUENCE HLA-DQB1 Kit provides reagents sufficient for twenty four HLA-DQB1 high resolution
typings and contains:
1)
2)
3)
Twenty-four 8-well PCR stripes with prepipetted and dried primer mixes, each stripe for one HLADQB1 typing. Store at 4°C in pre-PCR area.
2 tubes of CTS-SEQUENCE PCR Buffer (1400 µl). Store at -20°C in pre-PCR area.
Sequencing primers (500 µl each):
DQB-E2F, DQB-E2R, DQB-E3F, DQB-E3R
Store at -20°C in post-PCR area.
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CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
a) PCR stripes and amplification mixes:
The amplification primers are prepipetted and dried in colorless PCR stripes composed of 8 cavities. For quality
reasons, we recommend to use only the caps included in the package.
Figure 1 shows the positions of the PCR mixes on the stripe and the allele group(s) and the exons amplified by
these mixes.
Mix DQB01 to DQB06 are for group-specific amplification of exon 2, mix DQB07 is for locus-specific
amplification of exon 2 and mix DQB08 is for locus-specific amplification of exon 3 .
08
Mix
07
06
05
04
DQB08
All HLA-DQB1 Alleles
Exon 3
DQB07
All HLA-DQB1 Alleles
Exon 2
DQB06
DQB1*06:01
Exon 2
DQB05
DQB1*06 (*06:01 not amplified)
Exon 2
DQB04
DQB1*05
Exon 2
DQB1*03, 04
Exon 2
DQB03
03
02
Amplified
Exon
Amplified Allels
(*03:01:01G, 03:04 not amplified)
DQB02
DQB1B*03:01:01G, 03:04
Exon 2
DQB01
DQB1B*02
Exon 2
01
Black marker line
Figure 1: Mix position on CTS-SEQUENCE HLA-DQB1stripe
b)
Sequencing primers:
The tubes containing the sequencing primers (500 µl) have colorless caps. Sequencing of exon 3 is only possible
with the locus-specific mix DQB08.
Table 1: Labeling of the sequencing primers
HLA-Locus
Tube label
HLA-DQB1
DQB-E2F
DQB-E2R
DQB-E3F
DQB-E3R
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Revision: March 8, 2012
Sequenced
Exon
2
2
3
3
Page 4 of 16
Applicable for
Mix
DQB01-DQB07
DQB01-DQB07
DQB08
DQB08
Direction of
sequencing
forward
reverse
forward
reverse
CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
2.2
Storage and expiration
All kit components are labeled with storage condition and date of expiration.
Frequent thawing and freezing can reduce the quality of the reagents and should be avoided. It is recommended
to make aliquots of appropriate volumes and store them as indicated.
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CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
2.3
Materials and equipment not included
Table 2: Pre-PCR area
Reagents/materials/softwares
Taq DNA Polymerase (5 U/µl)
Ultra Pure Agarose
Ethidium bromide (10 mg/ml)
Cave: potentially carcinogenic!
Magnetic stirring hotplate or a microwave oven for
gel preperation
Pipettes and filter tips for 0.5-10 µl, 10- 200 µl and 200-1000 µl
volumes
Sequence PilotTM-HLA SBT
Photometer for spectral measurememnt of DNA concentration
50x TAE buffer
Company/Catalogue number
Fermentas, St. Leon-Rot, Germany
Cat.No EP0401/ EP0402
Inno-Train, Kronberg/Taunus, Germany
Cat. No. GX04090
Sigma-Aldrich GmbH, Steinheim, Germany
Cat.No. E1510-10ML
Eppendorf, Wessing-Berzdorf, Germany
JSI Medical Systems GmbH, Kippenheim,
Germany
Inno-Train, Kronberg/Taunus, Germany
Cat.No. GX12765
Analytical balance
Table 3: Post-PCR area
ExoSAP-ITTM
Reagents/materials/softwares
BigDyeTM Terminator Cycle Sequencing Kit v1.1 (Sequencing
buffer (5x) included)
1x TAE electrophoresis buffer
HiDi Formamide
Loading buffer (bromophenol blue)
Sodium-Acetat 3M pH 5.2 for precipitation
Ethanol absolute GR for analysis
Ethanol 70%
10x EDTA running buffer for the sequencer
1x EDTA running buffer for the sequencer
Centrifuge for PCR plates
GeneAmp® PCR System 2700 thermocycler
Power supplier for electrophoresis
Gel Documentation System
Gel elektophoresis chamber
Capillary sequencer: ABI PRISM 3100 Genetic Analyzer
8-channel pipette and filter tips 0.5-10 µl
Pipettes and filter tips for 0.5-10 µl volume
Multipette and combitips (0.1, 0.2 ,0.5, 1.0, 2.5ml) Not
mandatory
Adhesive aluminium foils for 96-well PCR plate
Optical 96-well reaction plate and optical caps
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Company/Catalogue number
USB, Staufen, Germany
Cat.No. 78202
Applied Biosystems, Darmstadt, Germany
Cat.No.4336791
See section 3 below for instruction
Applied Biosystems, Darmstadt, Germany
Cat.No. 4311320
Fermentas, St. Leon-Rot, Germany
Sigma Aldrich, Germany
Cat.No. S7899
Merck, Darmstadt, Germany
Cat.No. 1.00983.1000
See section 3 below for instruction
Applied Biosystems, Darmstadt, Germany
Cat.No. 402824
Applied Biosystems, Darmstadt, Germany
Applied Biosystems, Darmstadt, Germany
Eppendorf, Wessing-Berzdorf, Germany
Cat.No. 0030.077.040
Eppendorf, Wessing-Berzdorf, Germany
Cat.No. 0030.077.040
Eppendorf, Wessing-Berzdorf, Germany
Kisker, Steinfurt, Germany
Cat.No. GO71
Applied Biosystems, Darmstadt, Germany
Cat.No. N801-0560, N801-0535
CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
Table 4: Pre-PCR and post-PCR area (two sets are needed!)
Reagents/materials/softwares
HPLC water (LiChrosolv® water)
Company/Catalogue number
Merck, Darmstadt, Germany
Cat.No. 1.15333.1000
Vortexer
Reaction tubes 1.5 ml
Eppendorf, Wessing-Berzdorf, Germany
Cat.No. 0030 120.086
Examination gloves
Nitril gloves
3
Preparation of buffers and agarose gel
1x TAE electrophoresis buffer:
49 volume parts of deionised water + 1 volume part of 50x TAE electrophoresis buffer
Ethanol 70%:
7 volume parts of absolute ethanol + 3 volume parts of HPLC water
2% agarose gel:
If you use CTS electrophoresis chamber and CTS combs (see www.ctstransplant.org for order information)
proceed as follows:
-
4
Add 7 g of agarose and 7 ml of 50x TAE buffer to 350 ml of ddH 2 0.
Boil to dissolve the agarose, using a magnetic stirring hot plate or a microwave oven.
Cool down to 60°C, add 17 µl of ethidium bromide (10 mg/ml), mix and pour the gel. Allow the gel to set
for 1 hour at room temperature. Cave: Ethidium bromide is potentially carcinogenic! Wear appropriate
protection, e.g. nitril gloves.
On a 20x25 cm gel, you can place up to six CTS combs. These combs have a tooth distance corresponding
to that of the channels of a standard 8-channel pipette. This allows the use of such a pipette for rapid
loading of the samples onto the gel.
Isolation and concentration measurement of DNA
Genomic DNA can be isolated from all nucleated cells. Starting material can be EDTA or citrate blood, buffy
coats, cell suspensions etc. Heparinized blood should not be used. DNA can be isolated by the salting out method
(Miller SA et al., Nucleic Acid Research 1999) or magnetic particle technology (e.g. GenoM-6/Qiagen EZ1
robot, Qiagen, Vienna, Austria). Magnetic beads should be separated from the DNA (e.g. by centrifugation). It is
likely that other commercial kits or automats for DNA isolation will also work, but they should be validated by
the users.
For optimal reaction, adjust the DNA concentration to approximately 25 ng/µl with HPLC water.
Cave: Human material should always considered to be potentially infectious and be handled with care. See your
own standard laboratory safety guidelines.
5
Test procedure
High resolution HLA-typing with the CTS-SEQUENCE HLA-DQB1 Kit is performed in 7 steps:
-
Amplification of the HLA locus by PCR (setup in pre-PCR area; thermal cycling in post-PCR area)
Electrophoresis to check for positive amplifications (“gel control”) (post-PCR area)
Purification of the (positive) amplification products for sequencing (post-PCR area)
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CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
-
Sequencing reaction (post-PCR area)
Purification of the sequencing products (post-PCR area)
Separation of the sequencing products in the capillary sequencer (post-PCR area)
Sequence analysis and allele assignment with the Sequence PilotTM-HLA SBT software
5.1
Amplification
Prepare PCR on ice.








Fill in your PCR protocol.
Label your PCR-minitray.
Thaw PCR Buffer.
Pre-mix 10.85 µl of PCR Buffer with 4 µl of 25 ng/µl genomic DNA and 0.15 µl of Taq polymerase for
each mix (each PCR). An excess volume to compensate loss during pipetting is recommended. For
example, if you want to perform one CTS-SEQUENCE HLA-DQB1 test (one stripe, 8 mixes), prepare
a pre-mix for 10 mixes (108.5 µl of PCR Buffer + 40 µl of 25 ng/µl DNA + 1.5 µl of Taq).
Vortex the pre-mix.
Pipette 15 µl of the pre-mix into each well of the minitray.
10.85 µl PCR Buffer
Close the tubes and spin them down.
+ 4 µl
DNA (25 ng/µl)
Put the stripe into the thermocycler and start the ampli+ 0.15 µl Taq Polymerase
fication program CTS-AMP (see below).
15 µl reaction volume
Cave: DNA resolved in buffers should always be diluted at least 1:1 with HPLC water prior to use in the
amplification (buffers often contain PCR inhibitors e.g. EDTA).
Cave: Do not use hot start polymerase (e.g. AmpliTaq Gold, Applied Biosystems) or a proofreading
polymerase!
Thermocycler program for amplification (CTS-AMP):
Step
1
2
3
4
Temperature
95 °C
95 °C
65 °C
95 °C
61 °C
72 °C
4 °C
Time
2 min
15 s
2 min
15 s
50 s
1 min 30 s
∞
Numbers of cycles
1
10
22
Cave: Do not forget to enter the reaction volume of 15 µl!
5.2
Gel control
The amplification products are separated on a 2% agarose gel by electrophoresis. This step is to check for
success of the amplification step and to identify the amplification mix(es) which will be subjected to sequencing.
A) Electrophoresis




Pre-pipette 5 µl of loading buffer for each amplification product into a PCR plate.
Add 5 µl of your amplification product. Use filter tips to avoid contamination.
Load the gel with 10 µl of the amplification/loading buffer mixture.
If you use CTS electrophoresis chamber, run the electrophoresis for 20 min at 170 Volts
(approx. 0.4 V/cm2).
Cave: Ethidium bromide is potentially carcinogenic! Wear appropriate protection, e.g. nitril gloves!
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CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
B) Documentation and interpretation
Place the gel on a UV light transilluminator (312 nm) and take a polaroid picture for interpretation and
documentation. Wear UV-protection goggles!
You can proceed with an amplification product if a band representing the specific amplicon is visible in the gel
picture. The length of the specific amplification products range from 340 to 660 bp.
Cave: Do not mistake primer dimers or primer clouds for specific amplification products! Primer dimers are
very small (15-50 bp). Use a size marker if you are not confident.
5.3
Purification of the amplification products
Before an amplification product is subjected to sequencing, it has to be purified e. g. with ExoSAP-ITTM (USB,
Staufen, Germany). ExoSAP-ITTM contains an exonuclease digesting single-stranded DNA (e.g. primers) and a
phosphatase inactivating the nucleotides. This enzymatic purification method is simple and appropriate to
perform large-scale testing. A further advantage compared with other methods is that the enzymatic digest is
performed in the same tube that will subsequently be used for the amplification step. This avoids contaminations
and a mix-up of samples.




Add 4 µl of ExoSAP-ITTM (2µl ExoSAP-ITTM per 5µl PCR products) to each well with a positive PCR
reaction (based on the gel control). For large-scale performances, a Multipette can be used.
Close the reaction tubes (avoid contaminations!).
Spin down the ExoSAP-ITTM in the reaction tubes.
Put the PCR reaction wells into the thermocycler and start the purification program CTS-PUR (see below).
Cave: ExoSAP-ITTM is a viscous fluid, vortex well before use and get rid of excessive enzyme hanging at the tip
of your pipette.
Thermocycler program for purification with ExoSAP-ITTM (CTS-PUR):
Step
1
2
3
Temperature
37 °C
80 °C
4 °C
Time
15 min
15 min
∞
Numbers of cycles
1
1
Cave: Do not forget to enter the reaction volume of 14 µl.
5.4
Sequencing reaction
General strategy
-
For high resolution typing of HLA class II, exon 2 must be completely sequenced.
If an allele is not separated by amplification (e. i. if only one of the group-specific mixes (DQB01 to
DQB06 + the locus-specific mixes (DQB07 and DQB08) are positive), we recommend to sequence the
group-specific mix in both directions (forward and reverse) to optimize base-calling.
In case of homozygouse results (single allele) mix DQB07 should be sequenced in both directions (DQBE2F and DQB-E2R) to reduce the risk of allelic drop out.
If the alleles are separated by amplification (e. i. if two group-specific mixes are positive), it is sufficient to
sequence the positive amplicons in only one direction (we recommend to use the reverse primers).
Sequencing of exon 3 (Mix DQB08) should be performed in forward and reverse direction.
Setting-up a sequencing reaction

Create a pipetting scheme determining which amplicon(s) and which sequencing primer(s) are pipetted into
which position(s) of the optical 96-well reaction plate. An example of a pipetting scheme can be seen in the
appendix.
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CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0


Place an optical 96-well reaction plate on ice.
Mix one volume of BigDye terminators (BDT) with one volume of 5x BigDye sequencing buffer (always
prepare freshly). Keep an excess volume to compensate loss during pipetting. Pipette 2 µl of the mixture
into the optical 96-well reaction plate.
Alternatively, pipette 1 µl of BigDye terminators + 1 µl of 5x BigDye sequencing buffer directly into the
optical 96-well reaction plate.
Close the wells with caps and spin down.
 Add 6 µl of sequencing primer.
 Add 2 µl of purified amplification product (DNA template).
1 µl BDT
 Spin down, close the plate with caps and place it into the thermocycler.
+ 1 µl 5x buffer
 Start the thermocycler program CTS-SEQ.
+ 6 µl Primer
+ 2 µl Template
Cave: Keep the BigDye terminators cool and minimize their exposure to light.
10 µl
Thermocycler program for sequencing reaction (CTS-SEQ):
Step
1
2
3
Temperature
96 °C
96 °C
60 °C
4 °C
Time
1 min
10 s
2 min
∞
Numbers of cycles
1
25
Cave: Do not forget to enter the reaction volume of 10 µl. Proceed with the purification of the sequencing
products immediately when the sequencing reaction has finished.
5.5
Purification of the sequencing products
Residual ddNTPs must be removed to avoid sequencing artifacts (e.g. dye blobs). This can be done e. g. by
ethanol precipitation which is a cheap method and can be used for high-throughput.
-
Pre-mix 1 µl of 3 M Sodium-Acetate (pH 5.2) with 25 µl of absolute ethanol for each sequencing reaction
to be purified. An excess volume to compensate loss during pipetting is recommended.
Add 25 µl of the pre-mix to each sequencing reaction.
Close the optical 96-well reaction plate with an adhesive aluminium foil and vortex well (30 sec).
Vortexing is crucial for a good precipitation!
Incubate the optical 96-well reaction plate at room temperature in a dark place for 15 min (keep light
exposure of ddNPTs low).
Centrifuge the optical 96-well reaction plate for 30 min at 2000 x g. Proceed immediately with the next
step. If you can not proceed immediately, centrifuge again for 3min at 2000 x g before the next step.
Remove the adhesive aluminium foil, flip the optical 96-well reaction plate and remove the supernatant.
Place the optical 96-well reaction plate upside down on paper towel into the centrifuge. Spin the plate for a
few seconds at 180 x g to dry.
Add 75 µl of 70% ethanol to the precipitated sequencing products and vortex briefly.
Centrifuge the optical 96-well reaction plate for 10 min at 2000 x g. Proceed immediately with the next
step. If you can not proceed immediately, centrifuge again for 3min at 2000 x g before the next step.
Remove the adhesive aluminium foil, flip the optical 96-well reaction plate and remove the supernatant.
Place the optical 96-well reaction plate upside down on paper towel into the centrifuge. Spin the plate for a
few seconds at 180 x g to dry.
Keep the plate in a dark place until all ethanol has evaporated (~ 20 min).
In dried form, the sequencing products are quite stable when kept in the dark.
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CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
5.6
Sample preparation for sequencing runs
-
Add 15µl of HiDi Formamide onto the dried sequencing products, close the wells with caps and spin down.
Put the plate into a thermocycler and denature for 2 min at 95 °C.
IMPORTANT: Vapours at high temperatures. Cool down the HiDi Formamide at 4 °C before opening the
caps.
6
Start of a sequencing run on the sequencer
6.1
Instrument protocol for ABI Prism 3100 Genetic Analyzer (Applied Biosystems, Darmstadt,
Germany)
POP medium
Capillary
Electrophoreses buffer
Instrument Protocol
Sequence File Format
Ending Base
Mixed Base
Clear Range Method
Mobility file
Sequencing Analysis Software
Run Module
(CTS2600)
Basecaller
Settings Sample Manager
Settings Plate Record
6.2
3100 POP-6
36 cm array
1x buffer with EDTA
Type
Regular
Run Module
CTS2600
Dye Set
E-Big-DyeV1
True Profile
At PCR Stop
Do not assign N’s to Basecalls
Use Mixed Base Identification
Call IUB if 2nd highest Peak is 25% of the highest peak
Use quality values, Remove bases from ends until viewer
then 10 bases out of 20 have QVs less then 15
3100_POP6_BDTv1
Vers. 5.1.1
Run Temperature
55°C
Leak Threshold
25 steps
Current tolerance
100 uAmps
Run current
100 uAmps
Voltage tolerance
0.6 kVolts
Pre Run Voltage
15 KVolts
Pre Run Time
180 sec
Injection Voltage
1,2 kVolts
Injection Time
10 sec
Run Voltage
15 kVolts
Number of Steps
10 steps
Voltage Step Interval
60 sec
Data delay Time
240 sec
Run Time
2600 sec
KB.bcp
Basecaller:KB.bcp
Dye set/primer file: KB_3100_POP6_BDTv1.mob
Dye Set: E
Mobility File: 3100_POP6_BDTv1.mob
Run Module: CTS2600
Run Sequencing
1) Transfer your sequencing pipetting scheme into the “Plate Record” of the ABI PRISM 3100 Genetic
Analyzer.
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CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
TM
(JSI Medical Systems
GmbH, Kippenheim, Germany) (see section 7), the sample naming conventions are:
(Sample name_Amplification mix_Sequencing primer)
Example: (Sample_DQB01_DQB-E2F) if amplification mix DQB01 was used in the sequencing
reaction with the DQB-E2F sequencing primer.
2) Place samples into the ABI PRISM 3100 Genetic Analyzer and run the instrument.
For details, refer to the User Guides of ABI PRISM 3100 Genetic Analyzer and its softwares.
7
Result evaluation
For allele assignment, the sequences are loaded into the Sequence PilotTM-HLA SBT Allele Identification
Software (JSI Medical Systems GmbH, Kippenheim, Germany). This software shows the electropherograms and
aligns them with HLA alleles as listed in the IMGT/HLA Sequence Database (http://www.ebi.ac.uk/imgt/hla/).
Mismatches to the proposed HLA alleles, if shown, can be edited. The sequencing results can be printed and
archived. For details, see User Manual of the Sequence Pilot TM-HLA SBT Allele Identification Software.
Add the sequencing primers with following names and parameters in the “Seq. Primer master file”:
HLA-DQB1
Name
Gene
Direction
SeqPrimer gene parts
RFName
Sorting
DQB-E2F
DQB1
fwd.
E2
DQB-E2F
0
DQB-E2R
DQB1
rev.
E2
DQB-E2R
0
DQB-E3F
DQB1
fwd.
E3
DQB-E3F
0
DQB-E3R
DQB1
rev.
E3
DQB-E3R
0
Adding the sequencing primer to the “Seq. Primer master file” is not mandatory. However, by doing so, one can
avoid a situation in which a forward sequence of exon 3 is shown, which has been sequenced by the forward
sequencing primer of exon 2; such a sequence will have bad quality and can be omitted.
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CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
8
8.1
Troubleshooting
Amplification
Observation
No, weak or non-specific
PCR-product(s).
Possible Cause(s)
Degraded DNA
DNA concentration to low
DNA contains PCR inhibitors
Thermocycler is defect.
→ Some primary checks:
Did you follow the
amplification protocol?
Did you vortex the solution
well?
Was the correct cycler
program used?
Was ethidium bromide
included in the gel?
8.2
Incorrect thermocycler program
Thermocycler program needs to be
adapted.
Taq Polymerase needs to be adapted.
Solution
New extraction of DNA
New extraction of DNA
Heparinized blood?
New extraction of DNA
Check cycler
(e.g. with the CTS Cycler Control
Kit)
Correct programm and repeat PCR
Our method was optimized for the
GeneAmp® PCR System 2700
Thermocycler. For other
thermocyclers, the cycling program
may have to be adjusted and
validated.
Our method was optimized for the
Taq DNA Polymerase purchased
from Fermentas, St. Leon-Rot,
Germany, Cat.No EP0401/ EP0402.
Repeat PCR with this polymerase.
Sequencing
Observation
No signal
Weak signals
Possible Cause(s)
No sample was in sequencing
reaction.
Not enough formamide or air bubble
at the bottom of the well.
Wrong “injection time” or “injection
voltage”.
Not enough sequencing products after
purification.
Not enough sequencing products
were loaded.
Signals are too strong
Wrong “injection time” or “injection
voltage”.
High concentration of sequencing
products.
Manual No. 38
Revision: March 8, 2012
Page 13 of 16
Solution
Repeat sequencing reaction.
Pipette enough formamide and spin
down well.
Differences between capillary
sequencer can occur. Adapt “injection
time” or “injection voltage” to get
fluorescent intensities between 400
and 9000 in raw data.
Cleaning-up by ethanol precipitation
requires very precise ethanol
concentrations. Ethanol concentration
can vary when tubes are frequently
opened. Aliquot ethanol solutions for
single use.
Increase “injection time” or “injection
voltage”.
Salt can reduce the amount of loaded
sequencing products. Reduce salt
contamination during ethanol
precipitation.
Differences between capillary
sequencer can occur. Adapt “injection
time” or “injection voltage” to reach
fluorescent intensities between 400 to
9000 in raw data.
Reduce the amount of PCR product
used in the sequencing reaction. The
CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
Electropherogram has high
background.
DyeBlobs
Very high, randomly
occurring peaks (spikes)
Two different peaks run at
nearly the same position in
the electropherogram
Manual No. 38
Revision: March 8, 2012
Purification of PCR amplification
products did not work well (primer
contamination).
Contamination with a second
sequencing primer.
Double sequence which starts in the
forward and reverse sequencing
reaction at the same base (in different
directions).
Purification of sequencing products
did not work well (leftover of dye).
Air bubbles or polymer crystals in
capillaries.
Secondary structures of sequencing
products (gel compression)
Page 14 of 16
reduced amount should be substituted
with HPLC water (e.g. dilute
amplicon with HPLC water)
Repeat PCR and purification of
amplification products.
Avoid contamination during pipetting
sequencing primers.
Double sequence due to inserts or
deletions within an HLA-Bllele.
Ethanol concentration during
precipitation to high.
Refill capillaries with new polymer.
This phenomenon is sequencedependent and occurs only in one
sequencing direction of a limited
region. Analyze this region with the
sequencing primer for the other
direction. The sequences obtained
with the forward primers tend to show
gel compressions more often than
reverse primers.
CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
CTS-SEQUENCE HLA-DQB1 Amplification Protocol
For Lot SDQB04-0
DNA-No.:
Date:
Thermocycler:
Lot
Volume
PCR Buffer
10,85 µl
TAQ
0,15 µl*
DNA (25ng/µl)
4 µl
*The exact amount of Taq-Polymerase needed may vary depending on brand and lot; it should therefore be established through your own
validation.
Photo
Mix
Positive/
purified
Length of
Amplificat
Amplified
Exon
Amplified Allels
DQB01
510 bp
*02
2
DQB02
500 bp
*03:01:01G, 03:04
2
DQB03
480 bp
*03, 04 (*03:01:01G, 03:04 not amplified)
2
DQB04
440 bp
*05
2
DQB05
480 bp
*06 (*06:01 not amplified)
2
DQB06
530 bp
*06:01
2
DQB07
660 bp
All HLA-DQB1 Alleles
2
DQB08
340 bp
All HLA-DQB1 Alleles
3
Cave: Use DQB-E2F and DQB-E2R for sequencing of Mix DQB01-07 and DQB-E3F and DQB-E3R for
sequencing of Mix DQB*08.
Comment:
Date, Signature Operator:
Date, Signature Reviewer:
Manual No. 38
Revision: March 8, 2012
Page 15 of 16
CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
Pipetting scheme
(Example)
Optical 96-well reaction plate
1
A
B
C
D
E
2
3
4
5
6
7
8
9
(Stan_DQB01
_DQB-E2R)
(Stan_DQB02
_DQB-E2R)
(Stan_DQB07
_DQB-E2F)
(Stan_DQB08
_DQB-E3F)
(Stan_DQB08
_DQB-E3R)
F
G
H
DNA sample ID: Name (e.g. Stan)
Amplification pattern of the DQB1 locus:
X
DQB08 positive
X
DQB07 positive
X
X
DQB02 positive
DQB01 positive
Manual No. 38
Revision: March 8, 2012
Position on
plate
A1
A2
A3
A4
A5
Page 16 of 16
Mix DQB01 was sequenced with the DQB-E2R sequencing primer
Mix DQB02 was sequenced with the DQB-E2R sequencing primer
Mix DQB07 was sequenced with the DQB-E2F sequencing primer
Mix DQB08 was sequenced with the DQB-E3F sequencing primer
Mix DQB08 was sequenced with the DQB-E3R sequencing primer
CTS-SEQUENCE HLA-DQB1
Lot No. SDQB04-0
10
11
12
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