MRC-Holland MLPA. Description version 07; 26 November 2015

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1 SALSA MLPA probemix P266-B1 CLCNKB Lot B1-0415, B As compared to version A1 (lot A1-0908), one target probe for CLCNKB (exon 11) has been replaced. In addition, one reference probe has been replaced and four reference probes have been removed. Finally, QDX2 fragments have been added. Bartter syndrome refers to a group of disorders in which salt reabsorption in the thick ascending loop of Henle is impaired by approximately 70%. The phenotype of this syndrome is characterized by short stature, hyperactive renin-angiotensin system, lack of effect of angiotensin on blood pressure, renal potassium wasting, increased renal prostaglandin production, and occasionally hypomagnesemia. At present, four types of Bartter syndrome have been identified: Antenatal Bartter syndrome type 1 and 2 are caused by loss-of-function mutations in the SLC12A1 gene and KCNJ1 gene, respectively. Bartter syndrome type 3 is due to mutations in the kidney chloride channel B (CLCNKB) gene. Bartter syndrome type 4 (or infantile Bartter syndrome with sensorineural deafness) results from mutations of the BSND gene (type 4A) or by simultaneous mutations in both the CLCNKA and CLCNKB genes (type 4B). The CLCNKB gene encodes the ClC-Kb protein, which belongs to the CLC family of chloride channels. This protein consists of 687 amino acids and has 12 transmembrane domains. It shows 94% homology with ClC- Ka. In the kidney, ClC-Ka is located mainly in the thin ascending limb of the inner medulla and ClC-Kb in the thick ascending limb of Henle's loop and more distal nephron segments. Both associate with the beta subunit barttin to form functional, constitutively open chloride channels. Mutations in CLCNKB have been related to Bartter syndrome type 3. The CLCNKB gene (20 exons) spans ~14 kb of genomic DNA and is located at chromosome 1p36.13, 16 Mb from the p-telomere. The CLCNKA gene is located at only ~10 kb upstream of the CLCNKB gene. The P266-B1 CLCNKB probemix contains 14 probes for the CLCNKB gene. In addition, it contains 4 telomeric probes, including 2 probes for the CLCNKA gene. Also, 11 reference probes are included in this probemix, detecting several different autosomal chromosomal locations. This SALSA probemix is designed to detect deletions/duplications of one or more sequences in the aforementioned genes in a DNA sample. Heterozygous deletions of recognition sequences should give a 35-50% reduced relative peak height of the amplification product of that probe. Note that a mutation or polymorphism in the sequence detected by a probe can also cause a reduction in relative peak height, even when not located exactly on the ligation site! In addition, some probe signals are more sensitive to sample purity and small changes in experimental conditions. Therefore, deletions and duplications detected by MLPA should always be confirmed by other methods. Not all deletions and duplications detected by MLPA will be pathogenic; users should always verify the latest scientific literature when interpreting their findings. We have no information on what percentage of defects in these genes is caused by deletions/duplications of complete exons. Finally, note that most defects in this gene are expected to be small (point) mutations which will not be detected by this SALSA test. SALSA probemixes and reagents are sold by for research purposes and to demonstrate the possibilities of the MLPA technique. They are not CE/FDA certified for use in diagnostic procedures. Purchase of the SALSA test probemixes and reagents includes a limited license to use these products for research purposes. The use of a SALSA probemix and reagents 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). More information Website : info@mlpa.com (information & technical questions); order@mlpa.com (for orders) Mail : bv; Willem Schoutenstraat 1, 1057 DL Amsterdam, the Netherlands SALSA P266 CLCNKB probemix Page 1 of 5

2 Related SALSA probemixes P136 Gitelman: Contains probes for the SLC12A3 gene. References Okhubo et al., A novel mutation of CLCNKB in a Japanese patient of Gitelman-like phenotype with diuretic insensitivity to thiazide administration. Meta Gene. 2: Andrini et al., CLCNKB mutations causing mild Bartter syndrome profoundly alter the ph and Ca2+ dependence of ClC-Kb channels. Pflugers Arch. 466: Castano et al., Genetics of Type III Bartter Syndrome in Spain, Proposed Diagnostic Algorithm. PLoS One. 18:e Lee et al., Genetic basis of Bartter syndrome in Korea. Nephrol Dial Transplant. 27: Nozu et al., The pharmacological characteristics of molecular-based inherited salt-losing tubulopathies. J Clin Endocrinol Metab. 95:E Data analysis The P266-B1 CLCNKB probemix contains 29 MLPA probes with amplification products between 136 and 409 nt. In addition, it contains 9 control fragments generating an amplification product smaller than 120 nt: four DNA Quantity fragments (Q-fragments) at nt, three DNA Denaturation control fragments (Dfragments) at nt, one X-fragment at 100 nt and one Y-fragment at 105 nt. More information on how to interpret observations on these control fragments can be found in the MLPA protocol. Data generated by this probemix can first be normalised intra-sample by dividing the peak height of each probe s amplification product by the total peak height of only the reference probes in this probemix (block normalisation). Secondly, inter-sample normalisation can be achieved by dividing the intra-normalised probe ratio in a sample by the average intra-normalised probe ratio of all reference samples. Please note that this type of normalisation assumes no changes occurred in the genomic regions recognised by the reference probes. Data normalisation should 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 blotting, long range PCR, qpcr, FISH. Note that Coffalyser, the MLPA analysis tool developed at, can be downloaded free of charge from our website Many copy number alterations in healthy individuals are described in the database of genomic variants: For example, a duplication of a complete gene might not be pathogenic, while a partial duplication or a deletion may result in disease. For some genes, certain in-frame deletions may result in a very mild, or no disease. Copy number changes of reference probes are unlikely to be the cause of the condition tested for. Users should always verify the latest scientific literature when interpreting their findings. This probemix was developed at. Info/remarks/suggestions for improvement: info@mlpa.com. SALSA P266 CLCNKB probemix Page 2 of 5

3 Table 1. SALSA MLPA P266-B1 CLCNKB probemix Length Chromosomal position SALSA MLPA probe (nt) reference CLCNKB CLCNKA 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 92 Ligation-dependent control fragment at 2q X-fragment: Specific for the X chromosome 105 Y-fragment: Specific for the Y chromosome 136 Reference probe L q CLCNKB probe L12513 Exon CLCNKB probe L08560 Exon Reference probe L q CLCNKB probe L08564 Exon CLCNKB probe L08559 Exon Reference probe L q CASP9 probe L11959 Upstream 190 CLCNKA probe L21236 Exon CLCNKB probe L08567 Exon Reference probe L p Reference probe L p CLCNKB probe L11960 Exon CLCNKB probe L08554 Exon Reference probe L q Reference probe L q CLCNKB probe L11961 Exon CLCNKB probe L08565 Exon * Reference probe L p CLCNKB probe L11234 Exon * CLCNKB probe L16584 Exon Reference probe L p CLCNKA probe L08553 Exon Reference probe L p «PRDM2 probe L21354 Upstream 369 CLCNKB probe L08556 Exon CLCNKB probe L10728 Exon CLCNKB probe L11962 Exon Reference probe L q24 * New in version B1 (from lot B onwards). Flanking probe. Included to facilitate the determination of the extent of a deletion/duplication. Copy number alterations of flanking and reference probes are unlikely to be related to the condition tested. «This probe is located within, or close to, a very strong CpG island. A low signal of this probe can be due to incomplete sample DNA denaturation, e.g. due to the presence of salt in the sample DNA. Note: Exon numbering used here may differ from literature! Please notify us of any mistakes. The identity of the genes detected by the reference probes is available on request: info@mlpa.com. SALSA P266 CLCNKB probemix Page 3 of 5

4 Table 2. P266 probes arranged according to chromosomal location Length (nt) SALSA MLPA probe Gene exon Ligation site Partial sequence (24 nt adjacent to ligation site) Distance to next probe 360 «04702-L21354 PRDM2 Exon L11959 CASP9 Exon 7 NM_ ; NM_ ; TTGACCTTCCCT-CCACTCTTACAG GGTCGAGAAGAT-TGTGAACATCTT kb kb L21236 CLCNKA Exon L08553 CLCNKA Exon 10 NM_ ; reverse NM_ ; reverse TTGCCCAGGAAC-AGGGTGCTGCCG GACGCCGCAGAT-GCCACTGCGGGG 1.8 kb 15.9 kb NM_ start codon (ex 2) L08554 CLCNKB Exon 1 16 nt after exon 1 GGGGTCGCTGCA-AGATGCTGGGGC 0.6 kb L12513 CLCNKB Exon 2 28 nt before exon 2 AGCAGCTCACCG-CGGTCCCTCCCT 1.2 kb L08556 CLCNKB Exon CTTGGCTGTTGA-GAGTGTGGTCCG 2.3 kb L11234 CLCNKB Exon GAATCCCGGAGG-TGAAGACCATGT 0.4 kb L10728 CLCNKB Exon TCTGTGATGATG-GCTGCCTACCTG 0.8 kb L08559 CLCNKB Exon reverse CCAGTAATCCCA-GACAGAGAAGTG 0.7 kb L08560 CLCNKB Exon CTTCATCAGGAA-CAATAGGTTCAG 0.7 kb L16584 CLCNKB Exon CCTACCCACCCA-GCGCCGGCCGCT 1.0 kb L11961 CLCNKB Exon CATCTTTGTCTA-TGGTGAGTCTGG 0.2 kb L11960 CLCNKB Exon CTCTCTCTTTTA-TCTTCCCTGAGG 0.5 kb L08564 CLCNKB Exon reverse CTGGCCGGTCAC-CTCGAAGGCCAG 3.2 kb L08565 CLCNKB Exon CTGGTGGGCATA-GTGCGAAGGGCC 0.3 kb L11962 CLCNKB Exon AGTGACCCTGAA-GCTGTCCCCAGA 0.7 kb L08567 CLCNKB Exon reverse TCAAAGAGGTTG-TGTGCCTGGATG stop codon (ex 20) Flanking probe. Included to facilitate the determination of the extent of a deletion/duplication. Copy number alterations of flanking and reference probes are unlikely to be related to the condition tested. «This probe is located within, or close to, a very strong CpG island. A low signal of this probe can be due to incomplete sample DNA denaturation, e.g. due to the presence of salt in the sample DNA. The NM_ sequence is a reference standard in the NCBI RefSeqGene project. Note: Exon numbering used here may differ from literature! Complete probe sequences are available on request: info@mlpa.com. Please notify us of any mistakes: info@mlpa.com. SALSA P266 CLCNKB probemix Page 4 of 5

5 SALSA MLPA probemix P266-B1 CLCNKB sample picture Figure 1. Capillary electrophoresis pattern of a sample of approximately 50 ng human male control DNA analysed with SALSA MLPA probemix P266-B1 CLCNKB (lot B1-0415). Implemented Changes compared to the previous product description versions Version November 2015 (55) - Product description adapted to a new lot (lot number added, small changes in Table 1 and Table 2, new picture included). - Ligation sites of the CLCNKB probes adjusted to the NM_sequence. Version 06 (48) - Electropherogram picture of old buffer (introduced in Dec. 2012) removed. Version 05 (48) - Electropherogram pictures using the new MLPA buffer (introduced in December 2012) added. Version 04 (48) - Product description adapted to a new product version (version number changed, lot number added, small changes in Tables 1 and 2, new picture included). - Various minor textual changes. Version 03 (47) - Two new references added on page 1. - Various minor textual changes. - Small changes of probe lengths in Table 1 and 2 in order to better reflect the true lengths of the amplification products. - Remark on RefSeqGene standard and transcript variant added below Table 2. SALSA P266 CLCNKB probemix Page 5 of 5

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