Intended use: The SALSA MLPA probemix P335 ALL-IKZF1 is an in vitro diagnostic (IVD)¹ or research use only (RUO) assay for the detection of deletions in the IKZF1 gene in ALL (acute lymphoblastic leukemia) patients for patient stratification into prognostic subgroups, and a research use only (RUO) assay for the detection of deletions or duplications in B-cell differentiation and cell cycle control genes (EBF1, CDKN2A/B, PAX5, ETV6, BTG1 and RB1) and in the PAR1 region. This assay is for use on human DNA derived from peripheral blood and bone marrow, and not for use with DNA extracted from formalin-fixed paraffin embedded tumour materials.

Deletions or duplications detected by only a single probe always require validation. In the majority of patients, defects in the IKZF1 gene are deletions, but point mutations can occur which will not be detected by MLPA. It is therefore recommended to use this SALSA MLPA probemix in combination with sequence analysis of the IKZF1 gene. This assay is not intended to be used as a standalone assay for clinical decisions. The results of this test must be interpreted by a clinical molecular geneticist or equivalent.

Please note that this probemix is for In Vitro Diagnostic use (IVD) in the countries specified at the end of this product description. In all other countries, the product is for Research Use Only (RUO).

Note that the clinical relevance of some genes in the P335 ALL-IKZF1 probemix is not yet fully established. Therefore, the CE mark for diagnostic use only applies to the IKZF1 gene, and all other genes in the probemix are meant to be used in a research setting only.

Clinical background: The overall incidence rate of ALL amounts to 1.1/100,000 per year. The peak incidence lies in childhood at an age of less than 5 years (5.3/100,000). Thereafter the incidence rate declines. In patients over 50 years it rises a second time and reaches a peak at the age of over 80 years (2.3/100,000). There is a slight predominance of males (1.4:1). B-ALL accounts for 76% of all cases of ALL and T-ALL accounts for the remaining 24% of cases (https://www.onkopedia-guidelines.info/en/onkopedia/guidelines/acute-lymphoblastic-leukemia-all/@@view/html/index.html).

Partial or complete deletions of the IKZF1 (IKAROS family zinc finger 1) gene are frequently detected in ALL cases (Mullighan et al. 2008), especially in those patients who also carry the BCR-ABL1 gene fusion (Philadelphia chromosome). IKZF1 deletions can be identified in approximately 70% of the children with Philadelphia chromosome positive (Ph+) ALL (2%-4% of all paediatric ALL cases; Bernt and Hunger 2014), in 10-15% of Philadelphia chromosome negative (Ph−) paediatric ALL, and in ~40-75% of adult B-cell precursor ALL cases. Deletion of IKZF1 is associated with a poor prognosis in B-ALL patients (Mullighan et al. 2009) and a higher chance of relapse (Kuiper et al. 2010).

Several other (partial) gene deletions and duplications, such as in PAX5, ETV6, RB1, BTG1, EBF1 and CDKN2A/2B, have also been described in ALL patients. See Table 2 for more information on all genes and regions covered in this probemix.

Probemix content: This SALSA MLPA P335-C1 ALL-IKZF1 probemix contains 57 MLPA probes with amplification products between 120 and 504 nt. The probemix contains one probe for each of the eight exons in transcript variant 1 (NM_006060.6) of the IKZF1 gene (7p12.2). In addition, it contains seven probes for PAX5 (9p13.2), six probes for ETV6 (12p13.2), five probes for RB1 (13q14.2), four probes for BTG1 and the BTG1 downstream region (12q21.33), four probes for EBF1 (5q33.3), three probes for CDKN2A-CDKN2B (9p21.3) and five probes for the Xp22.33 region (PAR1 region; SHOX area, CRLF2, CSF2RA, IL3RA and P2RY8 genes). Additionally, one probe at Yp11.31 (ZFY) and one probe at 9p24.1 (JAK2) have been included to help determine the extent of a deletion/duplication detected in patient samples. See page 4 and 5 for more information about interpretation of results of the ZFY probe. Finally, 13 reference probes have been included targeting chromosomal regions that have relatively stable copy number in ALL. The identity of the genes detected by the reference probes is available online (www.mlpa.com) and in Table 2.

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.mlpa.com.