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

  • Tracewska-Siemiątkowska AM, Haer-Wigman L, Bosch DGM, Nickerson D, Bamshad MJ, van de Vorst M, Rendtorff ND, Mӧller C., Kjellstrӧm U, Andréasson S, Cremers FPM, Tranebjærg L. An expanded multi-organ disease phenotype associated with mutations in YARS. Genes. 2017; 8, 381.
  • 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.
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Posted by atracewska, Posted on 10.02.2016
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