MRC-Holland
®
Description version 07; 11-04-2008
MLPA
SALSA MLPA KIT P005-B1 Human chromosomal aberration-1
Lot 0308: As compared to 1005, 0503, 1203, two less reliable probes have been replaced and new reference
probes have been added. More information on page 3.
Many of the chromosomal aberrations present in human cell lines and cancer cells are numerical changes in
copy number of complete chromosomes or specific chromosomal regions.
This probemix contains probes for 41 different target sequences. Among these are many genes that are
often deleted or amplified in various tumors. For example this kit can be used for the detection of
chromosomal aberrations in small preneoplastic lesions and the determination of clonality in tumor samples.
In addition, the number of chromosomal rearrangements and numerical changes in various cell lines is often
very large. The SALSA MLPA kits P005, P006 and P007 can be used to prepare a fingerprint of DNA
extracted from cell lines, for instance for comparison of supposedly identical cell lines from different
laboratories.
This SALSA MLPA kit is designed to detect deletions/duplications of one or more exons of certain
chromosomal regions. Heterozygote deletions of probe recognition sequences should give a 35-50% reduced
relative peak area of the amplification product of that probe. However, mutations and/or polymorphisms
very close to the probe ligation site may also result in a reduced relative peak area. Therefore, apparent
deletions detected by a single probe always require confirmation by other methods. We have no information
on what percentage of defects in these genes is caused by deletions/duplications of complete exons. Please
note that most defects in these genes are expected to be small (point) mutations, most of which will not be
detected by this MLPA test.
SALSA® MLPA® kits are sold by MRC-Holland for research purposes and to demonstrate the
possibilities of the MLPA technique. This kit is not CE/FDA certified for use in diagnostic
procedures. SALSA MLPA kits are supplied with all necessary buffers and enzymes. Purchase of
the SALSA MLPA test kits includes a limited license to use these products for research
purposes.
The use of this MLPA kit requires a thermocycler with heated lid and sequence type electrophoresis
equipment. Different fluorescent PCR primers are available. The MLPA technique has been first described in
Nucleic Acid Research 30, e57 (2002).
References for SALSA MLPA kit P005
Tuhkananen H. et al. (2006). Frequent gene dosage alterations in stromal cells of epithelial ovarian
carcinomas. Int J Cancer. 2006 Sep 15;119(6):1345-53.
Bremmer JF et al (2005). A noninvasive genetic screening test to detect oral preneoplastic lesions. Lab
Invest. 2005 Dec;85(12):1481-8.
Takata M et al. (2005). Genome profiling of melanocytic tumors using multiplex ligation-dependent probe
amplification (MLPA): Its usefulness as an adjunctive diagnostic tool for melanocytic tumors. J Dermatol
Sci. 2005 Oct;40(1):51-7. .
Van Dijk MC et al. (2005). Multiplex ligation-dependent probe amplification for the detection of
chromosomal gains and losses in formalin-fixed tissue. Diagn Mol Pathol. 14(1):9-16.
Worsham MJ et al. (2003) Delineating genetic pathways of disease progression in head and neck
squamous cell carcinoma. Arch Otolaryngol Head Neck Surg. 129(7):702-8.
Related SALSA MLPA kits
P006 Human Chromosomal Aberrations-2
P007 Human Chromosomal Aberrations-3
More information
Website
E-mail
Mail
:http://www.mlpa.com
:info@mlpa.com; Fax :+31-20-6891149
:MRC-Holland bv; Willem Schoutenstraat 6, 1057 DN Amsterdam, the Netherlands
SALSA MLPA kit P005 H.C.A.-1
Page 1 of 5
MRC-Holland
®
Description version 07; 11-04-2008
MLPA
Data analysis
The P005-B1 probemix contains 41 different probes with amplification products between 130 and 472 nt. In
addition, it contains 7 control fragments generating an amplification product smaller than 120 nt: four DNA
Quantity fragments (Q-fragments) at 64-70-76-82 nt and three DNA denaturation control fragments (Dfragments) at 88-92-96 nt. More information on how to interpret observations on these control fragments
can be found in the MLPA protocol.
Data generated by this probemix should be normalized with a more robust method. The signals of all probes
should be intra-normalized against every single probe separately, thereby creating as many ratios as there
are probes. The median of all produced ratios gives an estimate of the final probe ratio, or ploidy status, of
the sample’s probes sequences in an MLPA mix. This way, the signal of each probe will be used as a
normalization constant (Population normalization). With the normalization constant, the ratio of each probe
between reference and patient sample is determined.
When only small numbers of samples are tested, visual comparison of peak profiles should be sufficient to
easily identify exon deletions. Comparison of results should preferably be performed within one experiment.
Only samples purified by the same method should be compared. Confirmation of most exons deletions and
amplifications can be done by e.g. Southern blots, long range PCR or FISH.
For a small number of genes, including TP53, CCND1, MYC and ERBB2, more than one probe is present in
the three SALSA MLPA human chromosomal aberration kits. The three different ERBB2 probes are identical
to the three probes in our SALSA MLPA kit P004 ERBB2.
The Mapview36 location is the distance in Mb towards the P-telomere according to the NCBI database
MapView Build 36, which was released in May 2006.
Info/remarks/suggestions for improvement: info@mlpa.com.
SALSA MLPA kit P005 H.C.A.-1
Page 2 of 5
MRC-Holland
®
MLPA
Description version 07; 11-04-2008
SALSA MLPA P005-B1 Human chromosomal aberration-1 probemix
Length (nt)
64-70-76-82
88-92-96
130**
136
142
148
154
160
166
175
184
193
202**
211
220
229
238
247
256
265*
274
283
292
301
310
319
328
337
346
355
364
373
382
391†
400
409
418
427
436
445
454**
463
472
SALSA
MLPA probe
Gene
Chromosomal
Position
Genbank
MAP-VIEW 36
Q-fragments: DNA quantity; only visible with less than 100 ng sample DNA
D-fragments: Low signal of 88 or 96 nt fragment indicates incomplete denaturation
00838-L12632
00981-L00566
00675-L00146
00798-L00316
00513-L00093
00845-L00378
00429-L00640
00477-L00060
00851-L00464
00612-L00050
00602-L09528
01036-L00609
00670-L00379
00434-L00020
00672-L00169
00841-L00359
00518-L00098
11499-L12634
00468-L00051
00438-L00003
00519-L00099
00348-L00174
00495-L00070
01017-L00322
00346-L00172
00442-L00380
01044-L00607
00452-L00360
01018-L00334
01046-L00624
00443-L00022
10372-L12633
00606-L00008
00820-L00338
00714-L00140
00585-L00150
00596-L00083
00678-L00124
00597-L06724
00979-L00568
01032-L00604
BCL2
CREM
ERBB2
ABCC4
IL4
RB1
ABCB1
RELA
UTY
IL10
CDKN2A
RECQL4
TANK
EMS1
MYC
MYB
IL1A
PIK3CA
IL13
BRCA1
MIF
BAX
LRMP
CDH2
F3
HRAS
PTP4A3
BRCA2
STCH
FGFR1
CDH1
CRK
STK15/STK6
PDCD8
BCAR3
CDKN1A
LMO2
TNFRSF7
TIMP2
RENT2
NRAS
18q21.33
10p12.1
17q12
13q32
5q31.1
13q14.2
7q21.1
11q13
Yq11.21
1q32.1
9p21
8q24.3
2q24.2
11q13
8q24.12
6q23
2q13
3q26.3
5q31.1
17q21.31
22q11.23
19q13.33
12p12.3
18q11.2
1p22.1
11p15.5
8q24.3
13q12.3
21q11.2
8p11.2
16q22.1
17p13.3
20q13.31
Xq25
1p22.1
6p21.2
11p13
12p13.31
17q25.3
10p14
1p13.2
M14745
NM_001881
X03363
NM_005845
M13982
L1487
AF016535
L19067
NM_007125
U16720
L27211
AB006532
U59863
M98343
X00364
U22376
X02851
Z29090
X69079
U14680
L10612
L22473
U10485
M34064
M16553
J00277
NM_007079
U43746
U04735
M34185
NM_004360
D10656
AF011468
NM_004208
U92715
L25610
X61118
NM_001242
M32304
NM_015542
X02751
18-058.9
10-035.5
17-035.1
13-094.5
05-132.0
13-047.9
07-087.1
11-065.2
Y-014.1
01-205.0
09-022.0
08-145.7 (0.5 Mb from telomere)
02-161.8
11-070.0
08-128.8
06-135.6
02-113.2
03-180.4
05-132.0
17-038.5
22-022.6
19-054.2
12-025.2
18-023.8
01-094.8
11-000.5
08-142.5
13-031.8
21-014.7
08-038.4
16-067.4
17-001.3
20-054.4
X-129.1
01-093.8
06-036.8
11-033.8
12-006.4
17-074.4
10-012.0
01-115.1
* New in lot 0803. Replaces the less reliable PIK3CA probe from previous lots.
** Small change in length or peak height, no change in sequence detected as compared to older lots.
† New in lot 0803. Replaces the less reliable CRK probe that was present in previous lots.
Note: Please notify us of any mistakes: info@mlpa.com.
SALSA MLPA kit P005 H.C.A.-1
Page 3 of 5
MRC-Holland
®
MLPA
Description version 07; 11-04-2008
SALSA MLPA P005-B1 probes in chromosomal order
Length (nt)
HUGO
Chromosomal
position
MAP-VIEW 36
418
328
472
193
256
220
265*
274
154
427
247
166
373
238
346
211
202
463
136
337
436
175
229
445
310
355
160
148
382
391*
142
283
454
319
130
301
400
364
292
409
184
BCAR3
F3
NRAS
IL10
IL1A
TANK
PIK3CA
IL13
IL4
CDKN1A
MYB
ABCB1
FGFR1
MYC
PTP4A3
RECQL4
CDKN2A
RENT2
CREM
HRAS
LMO2
RELA
EMS1
TNFRSF7
LRMP
BRCA2
RB1
ABCC4
CDH1
CRK
ERBB2
BRCA1
TIMP2
CDH2
BCL2
BAX
STK15/STK6
STCH
MIF
PDCD8
UTY
1p22.1
1p22
1p13.2
1q31
2q14
2q24
3q26.3
5q31
5q31.1
6p21.2
6q22
7q21
8p11.2
8q24.12
8q24.3
8q24.3
9p21
10p14
10p12.1
11p15.5
11p13
11q13
11q13
12p13
12p12.3
13q12.3
13q14.3
13q32
16q22.1
17p13.3
17q21.1
17q21
17q25
18q11.2
18q21.3
19q13.3
20q13.3
21q11
22q11.23
Xq25
Yq11.21
01-093.8
01-094.8
01-115.1
01-205.0
02-113.2
02-161.8
03-180.4
05-132.0
05-132.0
06-036.8
06-135.6
07-087.1
08-038.4
08-128.8
08-142.5
08-145.7 (0.5 Mb from telomere)
09-022.0
10-012.0
10-035.5
11-000.5
11-033.8
11-065.2
11-070.0
12-006.4
12-025.2
13-031.8
13-047.9
13-094.5
16-067.4
17-001.3
17-035.1
17-038.5
17-074.4
18-023.8
18-058.9
19-054.2
20-054.4
21-014.7
22-022.6
X-129.1
Y-014.1
* New as compared to previous lots.
Note: Please notify us of any mistakes: info@mlpa.com.
SALSA MLPA kit P005 H.C.A.-1
Page 4 of 5
MRC-Holland
®
Description version 07; 11-04-2008
MLPA
SALSA MLPA kit P005-B1 H.C.A.-1 sample pictures
Figure 1. Capillary electrophoresis pattern from a sample of approximately 50 ng human control male DNA
analyzed with SALSA MLPA kit P005-B1 H.C.A.-1 (lot 0308).
Figure 2. Capillary electrophoresis pattern from a sample of approximately 50 ng human control female
DNA analyzed with SALSA MLPA kit P005-B1 H.C.A.-1 (lot 0308).
SALSA MLPA kit P005 H.C.A.-1
Page 5 of 5