Methylation-Specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences

Copy number changes and CpG methylation of various genes are hallmarks of tumor development but are not yet widely used in diagnostic settings. The recently developed multiplex ligation-dependent probe amplification (MLPA) method has increased the possibilities for multiplex detection of gene copy number aberrations in a routine laboratory. Here we describe a novel robust method: the methylation-specific MLPA (MS-MLPA) that can detect changes in both CpG methylation as well as copy number of up to 40 chromosomal sequences in a simple reaction. In MS-MLPA, the ligation of MLPA probe oligonucleotides is combined with digestion of the genomic DNA–probe hybrid complexes with methylation-sensitive endonucleases. Digestion of the genomic DNA–probe complex, rather than double-stranded genomic DNA, allowed the use of DNA derived from the formalin treated paraffin-embedded tissue samples, enabling retrospective studies. To validate this novel method, we used MS-MLPA to detect aberrant methylation in DNA samples of patients with Prader–Willy syndrome, Angelman syndrome or acute myeloid leukemia

Intragenic deletions and a deep intronic mutation affecting pre-mRNA splicing in the dihydropyrimidine dehydrogenase gene as novel mechanisms causing 5-fluorouracil toxicity

Dihydropyrimidine dehydrogenase (DPD) is the initial enzyme acting in the catabolism of the widely used antineoplastic agent 5-fluorouracil (5FU). DPD deficiency is known to cause a potentially lethal toxicity following administration of 5FU. Here, we report novel genetic mechanisms underlying DPD deficiency in patients presenting with grade III/IV 5FU-associated toxicity. In one patient a genomic DPYD deletion of exons 21–23 was observed. In five patients a deep intronic mutation c.1129–5923C>G was identified creating a cryptic splice donor site. As a consequence, a 44 bp fragment corresponding to nucleotides c.1129–5967 to c.1129–5924 of intron 10 was inserted in the mature DPD mRNA. The deleterious c.1129–5923C>G mutation proved to be in cis with three intronic polymorphisms (c.483 + 18G>A, c.959–51T>G, c.680 + 139G>A) and the synonymous mutation c.1236G>A of a previously identified haplotype. Retrospective analysis of 203 cancer patients showed that the c.1129–5923C>G mutation was significantly enriched in patients with severe 5FU-associated toxicity (9.1%) compared to patients without toxicity (2.2%). In addition, a high prevalence was observed for the c.1129–5923C>G mutation in the normal Dutch (2.6%) and German (3.3%) population. Our study demonstrates that a genomic deletion affecting DPYD and a deep intronic mutation affecting pre-mRNA splicing can cause severe 5FU-associated toxicity. We conclude that screening for DPD deficiency should include a search for genomic rearrangements and aberrant splicing

Analysis of severely affected patients with dihydropyrimidine dehydrogenase deficiency reveals large intragenic rearrangements of DPYD and a de novo interstitial deletion del(1)(p13.3p21.3)

Dihydropyrimidine dehydrogenase (DPD) deficiency is an infrequently described autosomal recessive disorder of the pyrimidine degradation pathway and can lead to mental and motor retardation and convulsions. DPD deficiency is also known to cause a potentially lethal toxicity following administration of the antineoplastic agent 5-fluorouracil. In an ongoing study of 72 DPD deficient patients, we analysed the molecular background of 5 patients in more detail in whom initial sequence analysis did not reveal pathogenic mutations. In three patients, a 13.8 kb deletion of exon 12 was found and in one patient a 122 kb deletion of exon 14-16 of DPYD. In the fifth patient, a c.299_302delTCAT mutation in exon 4 was found and also loss of heterozygosity of the entire DPD gene. Further analysis demonstrated a de novo deletion of approximately 14 Mb of chromosome 1p13.3-1p21.3, which includes DPYD. Haploinsufficiency of NTNG1, LPPR4, GPSM2, COL11A1 and VAV3 might have contributed to the severe psychomotor retardation and unusual craniofacial features in this patient. Our study showed for the first time the presence of genomic deletions affecting DPYD in 7% (5/72) of all DPD deficient patients. Therefore, screening of DPD deficient patients for genomic deletions should be considered

Genotype-Phenotype Analysis in Congenital Adrenal Hyperplasia due to P450 Oxidoreductase Deficiency

Context: P450 oxidoreductase deficiency (PORD) is a unique congenital adrenal hyperplasia variant that manifests with glucocorticoid deficiency, disordered sex development (DSD), and skeletal malformations. No comprehensive data on genotype-phenotype correlations in Caucasian patients are available. Objective: The objective of the study was to establish genotype-phenotype correlations in a large PORD cohort. Design: The design of the study was the clinical, biochemical, and genetic assessment including multiplex ligation-dependent probe amplification (MLPA) in 30 PORD patients from 11 countries. Results: We identified 23 P450 oxidoreductase (POR) mutations (14 novel) including an exonic deletion and a partial duplication detected by MLPA. Only 22% of unrelated patients carried homozygous POR mutations. p.A287P was the most common mutation (43% of unrelated alleles); no other hot spot was identified. Urinary steroid profiling showed characteristic PORD metabolomes with variable impairment of 17α-hydroxylase and 21-hydroxylase. Short cosyntropin testing revealed adrenal insufficiency in 89%. DSD was present in 15 of 18 46,XX and seven of 12 46,XY individuals. Homozygosity for p.A287P was invariably associated with 46,XX DSD but normal genitalia in 46,XY individuals. The majority of patients with mild to moderate skeletal malformations, assessed by a novel scoring system, were compound heterozygous for missense mutations, whereas nearly all patients with severe malformations carried a major loss-of-function defect on one of the affected alleles. Conclusions: We report clinical, biochemical, and genetic findings in a large PORD cohort and show that MLPA is a useful addition to POR mutation analysis. Homozygosity for the most frequent mutation in Caucasians, p.A287P, allows for prediction of genital phenotype and moderate malformations. Adrenal insufficiency is frequent, easily overlooked, but readily detected by cosyntropin testing

Sähkönlaadun ja energiankulutuksen tutkimus

Opinnäytetyössä tutkitaan sähkönlaadun ja energiankulutusta Raute Oyj:n rakentamissa vaneri- ja LVL-viilupalkkikoneissa. Opinnäytetyön tarkoituksena on selvittää esiintyykö Raute Oyj:n valmistamissa koneissa sähkönlaatua heikentäviä tekijöitä, kuten harmonisia yliaaltoja. Sähkönlaatua heikentävien tekijöiden lisäksi opinnäytetyössä selvitetään mahdollisuutta moottorikeskusten mitoituksessa käytettävän korjauskertoimen tarkentamiselle. Opinnäytetyön teoriaosassa esitellään sähkönlaatuun vaikuttavia tekijöitä, sekä niiden vaikutuksia sähköverkkoon ja verkonkäyttäjälle. Lisäksi teoriaosassa käydään läpi ratkaisuja, joilla esimerkiksi sähköverkossa esiintyvien yliaaltojen pitoisuutta voidaan vähentää tai poistaa kokonaan. Verkossa esiintyville häiriöille kuten harmonisille yliaalloille, taajuuden ja jännitteen vaihteluille on määritelty rajoituksia standardilla SFS-EN 50160, myös näitä rajoituksia ja niiden vaikutuksia sähkönlaatuun käydään läpi opinnäytetyön teoriaosassa. Sähkönlaatua ja energiankulutusta mitattiin kahdessa Raute Oyj:n koneessa, ja näiden mittaukseen käytettiin Fluken power quality analyzer mallia olevaa mittalaitetta. Mittaustuloksissa huomattiin sähkönlaadun olevan yleisesti hyvällä tasolla ja täyttävän standardissa SFS-EN 50160 sähkönlaadulle määritellyt raja-arvot. Tulosten perusteella huomattiin myös, että joissakin tapauksissa keskusten mitoituksessa käytettäviä korjauskertoimia pystyy tarkentamaan.The study researches the quality of electricity and the energy consumption on plywood and laminated veneer lumber (LVL) machines manufactured by Raute Plc. The Thesis aims to examine the potential existence of factors reducing the quality of electric, such as harmonic waves, on machines manufactured by Raute Plc. In addition to examine the electricity quality and consumption of energy, the thesis looks into the possibility of elaboration of motorcabin’s equalisation. The theory part of the Thesis presents factors that influence electric quality, as well as their influences on the electricity network and network’s users. Additionally, the theory part discusses solutions, which for instance reduce or eliminate harmonic waves in electric network. SFS-EN 50160 standard defines restrictions for disturbance in electric network such as harmonic waves, frequency and voltage variation, these restrictions are also presented in the theory part of the Thesis. In this study, electric quality and energy consumption were measured in two different machines manufactured by Raute Plc, and the measurements were conducted by Fluke power quality analyser measuring device. Electric quality was generally high according to the measurements, and it meets the electric quality standards defined in SFS-EN 50160. The measurements also indicated that in some cases the equalisation is possible to elaborate