Examples illustrating data analysis of MLPA products of
SALSA MLPA KIT P245-A1 Microdeletion Syndromes

Tested on 41 samples with known abnormalities that were relevant for P245

Loss in 1p36 example no. 1
Loss in 1p36 example no. 2
Loss in 1p36 example no. 3

Loss in 4p16.3 example no. 1
Loss in 4p16.3 example no. 2
Gain in 4p16.3

Loss in 5p15pter

Loss in 5q35.3
Gain in 5q35.3

Loss in 7q11.23 example no. 1
Loss in 7q11.23 example no. 2
Loss in 7q11.23 example no. 3
Loss in 7q11.23 example no. 4
Loss in 7q11.23 example no. 5
Gain in 7q11.23

Loss in 15q12 example no. 1
Loss in 15q12 example no. 2
Loss in 15q12 example no. 3
Loss in 15q12 example no. 4
Gain in 15q12

Gain in 15q24 example no. 1
Gain in 15q24 example no. 2

Loss in 17p13.3
Gain in 17p13.3 example no. 1
Gain in 17p13.3 example no. 2

Loss in 17p11.2 example no. 1
Loss in 17p11.2 example no. 2
Gain in 17p11.2

Loss in 17q11.2

Loss in 17q21.31
Gain in 17q21.31

Loss in 22q11.21 example no. 1
Loss in 22q11.21 example no. 2
Loss in 22q11.21 example no. 3
Loss in 22q11.21 example no. 4
Loss in 22q11.21 example no. 5
Gain in 22q11.21 example no. 1
Gain in 22q11.21 example no. 2

Loss in 22q13.3qter (each probe doesn't clearly appear abnormal, but together they do)
Gain in 22q13.3qter

Gain in Xq28

Low DNA denaturation control fragments (D-fragments) reveal a characteristic probe pattern for the probes 465 nt, 253 nt, 382 nt and 184 nt for normal samples - this might be due to denaturation problems

Normal sample no. 1 with relativly low D-fragment probes
Normal sample no. 2 with relativly low D-fragment probes
Normal sample no. 3 with relativly low D-fragment probes
Normal sample no. 4 with relativly low D-fragment probes
Normal sample no. 5 with relativly low D-fragment probes
Normal sample no. 6 with relativly low D-fragment probes (worst example)

Currently RH-MLPA-Analysis.mdb checks how high the mean area of the two D-fragment CpG probes is compared to the mean area of the probes that are used for normalization in normalization group A**. When this mean ratio is small then the denaturation of the sample DNA may have been incomplete (or maybe these probes are just extra sensitive to procedure items like evaporation or polymerase activity). It looks as if the area of the 465 nt and 253 nt probes correlate to the area of the CpG D-fragment probes (especially regarding the 465 nt probe and the 96 nt CpG probe).
An example of corresponding high areas of the 465 nt and the 96 nt probes is illustrated here.
(** In RH-MLPA-Analysis group A is the probes that have the smallest fragment sizes in nt; often the first quarter of probes that come out by electrophoresis.)

The program currently also checks whether the D-fragment probe 2p14 likewise is low as this might indicate an incomplete hybridization. In case of a too low value this text will be added to the result sheet "The small 2q14 area indicates poor hybridization!".

Similar problems have been seen for P036-E1 and the main example page shows an example where a trisomy 21 cannot be detected due to low D-fragment areas of the P036-E1 probeset.