General information
The SALSA MLPA
Probemix P414 MDS is a
research use only (RUO) assay for the detection of deletions or duplications in different chromosomal regions described to be of potential diagnostic or prognostic relevance in myelodysplastic syndromes (MDS), and are used in the International Prognostic Scoring System-Revised (IPSS-R) and Molecular International Prognostic Scoring System for Myelodysplastic Syndromes (IPSS-M) (Bernard E et al. 2022): chromosome 3, 5q (
EGR1,
MIR145,
SPARC,
MIR146A), 7q (
EZH2), 8q (
MYC), 11q (
KMT2A), 12p (
ETV6), chromosome 17 (
TP53,
NF1,
SUZ12), chromosome 19, 20q (
ASXL1) and Y-chromosome. This probemix can also be used to detect the presence of the
JAK2 p.V617F (c.1849G>T) point mutation.
Myelodysplastic syndromes are a heterogeneous collection of hematologic disorders, which are characterized by dysplastic hematopoietic differentiation. In 30% of all cases, MDS progresses to acute myeloid leukemia (AML). There are several oncogenes and tumour suppressor genes, that have mutations or copy number alterations (CNAs) in MDS (Ogawa S. 2019), many of which can be detected with this P414 probemix.
This SALSA MLPA probemix is not CE/FDA registered for use in diagnostic procedures. Purchase of this product includes a limited license for research purposes.
Probemix content
The SALSA MLPA Probemix P414-C1 MDS contains 58 MLPA probes with amplification products between 118 and 496 nucleotides (nt). This includes 46 probes for the following chromosomal regions: chromosome 3 (
MLH1,
GATA2,
MECOM), 5q
(APC, EGR1, MIR145, RPS14,
SPARC, MIR146A) &
one flanking probe targeting
NIPBL at 5p, 7q (
CDK6,
SAMD9L,
EPO,
KMT2E,
MET,
EZH2)
& one flanking probe at 7p targeting
IKZF1, 8q
(FGFR1, NCOA2, RUNX1T1, MYC, PTK2) & one flanking probe targeting
FGFR1 at 8p, 11q
(KMT2A, TIRAP,
ETS1), 12p
(ETV6, CDKN1B), chromosome 17
(TP53, NF1, SUZ12, AATF), chromosome 19 (
SMARCA4,
PRPF31), 20q
(ASXL1, SRC, HNF4A, ZMYND8) and the Y-chromosome (
ZFY). Furthermore, this probemix also contains one probe specific for the
JAK2 p.V617F (c.1849G>T) mutation which will only generate a signal when the mutation is present. In addition, 12 reference probes are included that target relatively copy number stable regions in various cancer types including MDS. Complete probe sequences are available online (
www.mrcholland.com) and the identity of the genes detected by the reference probes is available in Table 3 of the Product Description.
This probemix contains nine quality control fragments generating amplification products between 64 and 105 nt: four DNA Quantity fragments (Q-fragments), two DNA Denaturation fragments (D-fragments), one Benchmark fragment, and one chromosome X and one chromosome Y-specific fragment. More information on how to interpret observations on these control fragments can be found in the MLPA General Protocol and online at
www.mrcholland.com.
SALSA Binning DNA SD029
The SD029 Binning DNA provided with this probemix can be used for binning of all probes including the
JAK2 p.V617F (c.1849G>T) mutation-specific probe (JAK2 probe 05672-L17742). SD029 Binning DNA is a mixture of genomic DNA from healthy individuals and plasmid DNA that contains the target sequence detected by the above mentioned probe. Inclusion of one reaction with 5 μl SD029 Binning DNA in initial MLPA experiments is essential as it can be used to aid in data binning of the peak pattern using Coffalyser.Net software. Furthermore, Binning DNA should be included in the experiment whenever changes have been applied to the set-up of the capillary electrophoresis device (e.g. when capillaries have been renewed). Binning DNA should never be used as a reference sample in the MLPA data analysis, neither should it be used in quantification of mutation signal(s). It is strongly advised that all samples tested are extracted with the same method and derived from the same source of tissue. For further details, please consult the SD029 Binning DNA product description, available online:
www.mrcholland.com.
This product is for research use only (RUO).
Sample DNA
Sample DNA developed for this product:
The product description of this Sample DNA can be found on this page under
Online available downloads >
Other product documentation.