DNA Analysis Laboratory

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DNA Analysis Laboratory

The DNA Analysis Laboratory renders services in the scope of comprehensive analysis of nucleic acids in the wide spectrum of biological samples, including human, microbiological, animal or plant material. Testing is performed using modern equipment and technologies used in the leading research centres in the world.

 

Isolation of the nucleic acids – we offer a high throughput automatic DNA and RNA isolation using the QIASymphony apparatus (min. 24 samples; 96 samples in approx. 7 hours). We isolate the nucleic acids from the following input materials:

  • blood
  • tissues (mechanical homogenizing or on a request cryo homogenizing)
  • cell cultures
  • human and animal egesta and secreta
  • bacteria (bacterial genome)
  • viruses (virus DNA isolation from cultures, blood)
  • bio traces (isolation minimum 96 samples) from cheek epithelial tissue smears, tissue paper (blood from infant screening) and other bio traces
  • Remark: Plasmid insulation (mini, midi, maxiprep) is possible manually only!
  • Protein purification – we carry on protein purification with histidine tag using the QIASymphony apparatus
  • Genotyping of single known mutations – the genotyping is performed with many molecular technologies, differing with costs, sensitivity and throughput:
  • Pyrosequencing – highly sensitive sequencing in search of definitive mutations (the length of the analysed sequence ~80 pz) using the Qiagen PyroMark Q24
  • NGS (next-generation sequencing) – next generation sequencing, allows for simultaneous sequencing of many amplicons in a very large number of samples in a single test glass using the Illumina MiSeq
  • The analysis of the genes involved in diseases using optimised sets of the Illumina (Illumina MiSeq)
  • TruSight Tumor 15 – a tumour panel of 15 genes
  • TruSight Tumor 26 – a tumour panel of 26 genes
  • TruSight Cancer – cancer panel >1700 exomes, 94 genes (gene lists are available on the manufacturer site and at the enquiry)
  • TruSight Cardio – 174 genes involved in 17 hereditary heart disorders
  • TruSight Inherited Disease – 552 genes, regions, in which mutations responsible for hereditary diseases occur
  • TruSight Myeloid – 54 genes involved in marrow cancers
  • TruSight Autism – 101 genes involved in autism spectrum
  • TruSight One – 4,813 genes related to the known clinical phenotypes
  • Sequencing of NGS RNA
  • assaying of microRNA form different organisms and tissue
  • targeted sequencing of transcripts form different organisms and tissues
  • Sequencing NGS of small genomes
  • bacteria
  • yeast
  • viruses
  • phage
  • mitochondria
  • Bacteria strain analysis – metagenomics 16S
    Identification of microorganisms in complex ecosystems:
  • food
  • sewage
  • human and animal egesta and secreta
  • DNA methylation analysis – the analysis of selected CpG spots using a pyro sequencer PyroMark Q24
  • Capillary electrophoresis – separation of amplicons/DNA and RNA fragments with the resolution up to 2 nucleotides (qualitative and quantitative analysis).

 

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Robot for DNA/RNA/protein isolation QIASymphony (Qiagen)

homogenisers

Homogenisers: TissueLyzerII (Qiagen) and CryoMill (Retsch)

nanodrops

Spectrophoto- and spectrofluorimeter NanoDrop 8000 and 3300 (ThermoFisher Scientific)

Labcycler_00012_engThermal Cycler LabCycler (SensoQuest)

rotor_gene_Q

Real-time PCR thermal cycler (CEIVD) Rotor Gene Q (Qiagen)

3.8.1.5.1.1-large

Real-time PCR HT thermal cycler Light Cycler 480 (Roche)

Laboratory pipetting robot

Pipetting robot Piro (DORNIER-LTF)

Instrument_fragment_analyzer

Capillary electrophoresis Fragment Analyzer (Advanced Analytical)

miseq-fgx-hero

Next generation sequencer MiSeq (Illumina)

pyromarkQ24

Pyrosequencer PyroMark Q24 (Qiagen)

Anna Tracewska PhD (Siemiątkowska) – Laboratory Manager

Milena Szafraniec MSc – senior process engineer

 

 

 

Grants

SONATA 10 (National Science Centre)
Grant No.: 2015/19/D/NZ2/031
Title: Towards the light: discovery of genetic causes of inherited retina disorders in Poland
Duration period: 01.12.2016 – 31.05.2019

 

PUBLISHINGS

  • van Huet RA, Siemiatkowska AM, Ozgül RK, Yücel D, Hoyng CB, Banin E, Blumenfeld A, Rotenstreich Y, Riemslag FC, den Hollander AI, Theelen T, Collin RW, van den Born LI, Klevering BJ. Retinitis pigmentosa caused by mutations in the ciliary MAK gene is relatively mild and is not associated with apparent extra-ocular features. Acta Ophthalmol. 2015;93:83-94.
  • Bujakowska KM, Zhang Q, Siemiatkowska AM, Liu Q, Place E, Falk MJ, Consugar M, Lancelot ME, Antonio A, Lonjou C, Carpentier W, Mohand-Saïd S, den Hollander AI, Cremers FP, Leroy BP, Gai X, Sahel JA, van den Born LI, Collin RW, Zeitz C, Audo I, Pierce EA. Mutations in IFT172 cause isolated retinal degeneration and Bardet-Biedl syndrome. Hum Mol Genet. 2015;24:230-42
  • Siemiatkowska AM, Schuurs-Hoeijmakers JH, Bosch DG, Boonstra FN, Riemslag FC, Ruiter M, de Vries BB, den Hollander AI, Collin RW, Cremers FP. Nonpenetrance of the most frequent autosomal recessive Leber congenital amaurosis mutation in NMNAT1. JAMA Ophthalmol. 2014;132:1002-4.
  • Siemiatkowska AM, Collin RW, den Hollander AI, Cremers FP. Genomic approaches for the discovery of genes mutated in inherited retinal degeneration. Cold Spring Harb Perspect Med. 2014;17;4. pii: a017137. (review)
  • van Huet RA, Collin RW, Siemiatkowska AM, Klaver CC, Hoyng CB, Simonelli F, Khan MI, Qamar R, Banin E, Cremers FP, Theelen T, den Hollander AI, van den Born LI, Klevering BJ. IMPG2-associated retinitis pigmentosa displays relatively early macular involvement. Invest Ophthalmol Vis Sci. 2014;55:3939-53.
  • Roosing S, Collin RW, den Hollander AI, Cremers FP#, Siemiatkowska AM#. Prenylation defects in inherited retinal diseases. J Med Genet. 2014;51:143-51. (review)
  • Siemiatkowska AM, van den Born LI, van Genderen MM, Bertelsen M, Zobor D, Rohrschneider K, van Huet RA, Nurohmah S, Klevering BJ, Kohl S, Faradz SM, Rosenberg T, den Hollander AI, Collin RW, Cremers FP. Novel compound heterozygous NMNAT1 variants associated with Leber congenital amaurosis. Mol Vis. 2014;20:753-9.
  • Siemiatkowska AM, van den Born LI, van Hagen PM, Stoffels M, Neveling K, Henkes A, Kipping-Geertsema M, Hoefsloot LH, Hoyng CB, Simon A, den Hollander AI,Cremers FP, Collin RW. Mutations in the mevalonate kinase (MVK) gene cause nonsyndromic retinitis pigmentosa. Ophthalmology. 2013;120:2697-705.
  • Neveling K, Collin RW, Gilissen C, van Huet RA, Visser L, Kwint MP, Gijsen SJ, Zonneveld MN, Wieskamp N, de Ligt J, Siemiatkowska AM, Hoefsloot LH, Buckley MF, Kellner U, Branham KE, den Hollander AI, Hoischen A, Hoyng C, Klevering BJ, van den Born LI, Veltman JA, Cremers FP, Scheffer H. Next-generation genetic testing for retinitis pigmentosa. Hum Mutat. 2012;33:963-72.
  • Paun CC, Pijl BJ, Siemiatkowska AM, Collin RW, Cremers FP, Hoyng CB, den Hollander AI. A novel crumbs homolog 1 mutation in a family with retinitis pigmentosa, nanophthalmos, and optic disc drusen. Mol Vis. 2012;18:2447-53.
  • Siemiatkowska AM*, Astuti GD*, Arimadyo K, den Hollander AI, Faradz SM, Cremers FP, Collin RW. Identification of a novel nonsense mutation in RP1 that causes autosomal recessive retinitis pigmentosa in an Indonesian family. Mol Vis. 2012;18:2411-9.
  • Ozgül RK*, Siemiatkowska AM*, Yücel D*, Myers CA, Collin RW, Zonneveld MN, Beryozkin A, Banin E, Hoyng CB, van den Born LI; European Retinal Disease Consortium, Bose R, Shen W, Sharon D, Cremers FP, Klevering BJ, den Hollander AI, Corbo JC. Exome sequencing and cis-regulatory mapping identify mutations in MAK, a gene encoding a regulator of ciliary length, as a cause of retinitis pigmentosa. Am J Hum Genet. 2011;89:253-64.
  • Collin RW, van den Born LI, Klevering BJ, de Castro-Miró M, Littink KW, Arimadyo K, Azam M, Yazar V, Zonneveld MN, Paun CC, Siemiatkowska AM, Strom TM, Hehir-Kwa JY, Kroes HY, de Faber JT, van Schooneveld MJ, Heckenlively JR, Hoyng CB, den Hollander AI, Cremers FP. High-resolution homozygosity mapping is a powerful tool to detect novel mutations causative of autosomal recessive RP in the Dutch population. Invest Ophthalmol Vis Sci. 2011;52:2227-39.
  • Siemiatkowska AM*, Arimadyo K*, Moruz LM, Astuti GD, de Castro-Miro M, Zonneveld MN, Strom TM, de Wijs IJ, Hoefsloot LH, Faradz SM, Cremers FP, den Hollander AI, Collin RW. Molecular genetic analysis of retinitis pigmentosa in Indonesia using genome-wide homozygosity mapping. Mol Vis. 2011;17:3013-24.
  • Bandah-Rozenfeld D, Collin RW, Banin E, van den Born LI, Coene KL, Siemiatkowska AM, Zelinger L, Khan MI, Lefeber DJ, Erdinest I, Testa F, Simonelli F, Voesenek K, Blokland EA, Strom TM, Klaver CC, Qamar R, Banfi S, Cremers FP, Sharon D, den Hollander AI. Mutations in IMPG2, encoding interphotoreceptor matrix proteoglycan 2, cause autosomal-recessive retinitis pigmentosa. Am J Hum Genet. 2010;87:199-208.
  • Siemiatkowska A, Bieniaszewska M, Hellmann A, Limon J. JAK2 and MPL gene mutations in V617F-negative myeloproliferative neoplasms. Leuk Res. 2010;34:387-9.
  • Duchnowska R, Siemiatkowska A, Grala B, Smoter M. [Long-term remission after erlotinib therapy in an elderly patient with advanced non-small-cell lung cancer. Case report and conclusions for clinical practice]. Pneumonol Alergol Pol. 2008;76:451-5.
  • Kanka C, Brozek I, Skalska B, Siemiatkowska A, Limon J. Germline NBS1 mutations in families with aggregation of breast and/or ovarian cancer from north-east Poland. Anticancer Res. 2007;27:3015-8.
  • Dziadziuszko R, Siemiatkowska A, Limon J, Rzyman W, Jassem J, Bunn PA Jr, Varella-Garcia M, Hirsch FR. Unusual chemosensitivity of advanced bronchioalveolar carcinoma after gefitinib response and progression: a case report. J Thorac Oncol. 2007;2:91-2.
  • Haack B, Kupka S, Ebauer M, Siemiatkowska A, Pfister M, Kwiatkowska J, Ereciński J, Limon J, Ochman K, Blin N. Analysis of candidate genes for genotypic diagnosis in the long QT syndrome. J Appl Genet. 2004;45:375-81.31.

* – equal contribution of the first authors

# – equal contribution of the last authors

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Posted by atracewska, Posted on 10.02.2016
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