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Three multiplex snapshot assays for SNP genotyping in candidate innate immune genes

BMC Res Notes. 2013 Feb 7;6(1):54. [Epub ahead of print]
Esteves LM, Bulhões SM, Brilhante MJ, Mota-Vieira L.

Abstract

ABSTRACT:

BACKGROUND: Innate immune system is the first line of research when studying immune response to diverse infections and autoimmune/inflammatory diseases. This immune response has been reported to be genetically diverse, due to polymorphisms coded by different genes. For this reason, our purpose was to develop a multiplex assay that allows the genotyping of candidate single nucleotide polymorphisms (SNPs) in innate immune genes.

FINDINGS:

We developed three multiplex PCR panels coupled with the minisequencing (SNaPshot) technique (multiplex PCR, multiplex primer extension, and capillary electrophoresis). The panels were tested in a sample set composed of 100 anonymous DNAs from healthy blood donors living in Sao Miguel Island (Azores, Portugal). Sixteen relevant SNPs among nine genes of the innate immune system — IL1alpha, IL1beta, IL6, IL10, IL12RB1, TLR2, TLR4, TLR9 and CD14 — were genotyped and validated by direct sequencing, with the exception of one that was undetected by minisequencing. We suggest that these panels can be used in future studies for detection of risk gene variants in several populations and/or diseases.

CONCLUSIONS:

In summary, we propose a multiplex assay that is able to identify the most frequent candidate SNPs in innate immune genes, using a medium scale genotyping platform. The assays can be used to evaluate the risk gene variants in populations of various geographic origins.

[New Service] Mycoplasma Detection

Dear Facility Users,

The Mycoplasma Detection in the cell lines was transferred to the PCR-based detection in the Genotyping Core Facility.

In order to minimize the cost, please prepare your samples as following way,

  1. collect a 1mL sample off of the cells to be tested (do not change medium as it may be needed for retesting the next day)
  2. spin samples at 1500 rpm for 5 minutes and transfer supernatants to new microfuge tubes
  3. label tubes with your name and the name of the cell line
  4. bring samples to the Genotyping Core Facility

If you are interested in the service, please feel free to contact us.

 

From sample to PCR product in under 45 minutes: a polymeric integrated microdevice for clinical and forensic DNA analysis

Lab Chip. 2013 Feb 6. [Epub ahead of print]
Lounsbury JA, Karlsson A, Miranian DC, Cronk SM, Nelson DA, Li J, Haverstick DM, Kinnon P, Saul DJ, Landers JP.

Source

Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA, USA. jpl5e@virginia.edu.

Abstract

The extraction and amplification of DNA from biological samples is laborious and time-consuming, requiring numerous instruments and sample handling steps. An integrated, single-use, poly(methyl methacrylate) (PMMA) microdevice for DNA extraction and amplification would benefit clinical and forensic communities, providing a completely closed system with rapid sample-in-PCR-product-out capability. Here, we show the design and simple flow control required for enzyme-based DNA preparation and PCR from buccal swabs or liquid whole blood samples with an ∼5-fold reduction in time. A swab containing cells or DNA could be loaded into a novel receptacle together with the DNA liberation reagents, heated using an infrared heating system, mixed with PCR reagents for one of three different target sets under syringe-driven flow, and thermally-cycled in less than 45 min, an ∼6-fold reduction in analysis time as compared to conventional methods. The 4 : 1 PCR reagents : DNA ratio required to provide the correct final concentration of all PCR components for effective amplification was verified using image analysis of colored dyes in the PCR chamber. Novel single-actuation, ‘normally-open’ adhesive valves were shown to effectively seal the PCR chamber during thermal cycling, preventing air bubble expansion. The effectiveness of the device was demonstrated using three target sets: the sex-typing gene Amelogenin, co-amplification of the β-globin and gelsolin genes, and the amplification of 15 short tandem repeat (STR) loci plus Amelogenin. The use of the integrated microdevice was expanded to the analysis of liquid blood samples which, when incubated with the DNA liberation reagents, form a brown precipitate that inhibits PCR. A simple centrifugation of the integrated microchips (on a custom centrifuge), mobilized the precipitate away from the microchannel entrance, improving amplification of the β-globin and gelsolin gene fragments by ∼6-fold. This plastic integrated microdevice represents a microfluidic platform with potential for evolution into point-of-care prototypes for application to both clinical and forensic analyses, providing a 5-fold reduction from conventional analysis time.

New genotypes of Toxoplasma gondii obtained from farm animals in Northeast Brazil

Res Vet Sci. 2013 Feb 5. pii: S0034-5288(13)00008-8. doi: 10.1016/j.rvsc.2013.01.006. [Epub ahead of print]
Clementino Andrade MM, Pinheiro BV, Cunha MM, Carneiro AC, Andrade Neto VF, Vitor RW.

Source

Departamento de Parasitologia, Instituto de Ciências Biológicas, UFMG, Belo Horizonte 31270-901, Brazil; Departamento de Microbiologia e Parasitologia, Centro de Biociências, UFRN, Natal 59072-970, Brazil.

Abstract

Genotyping of Toxoplasma gondii in different regions of Brazil has shown high diversity and high frequency of virulent genotypes among Brazilian animals. The aim of the study was to characterize samples of T. gondii isolates obtained from naturally infected sheep, goats, pigs and free-range chickens slaughtered for human consumption in Rio Grande do Norte, Northeast Brazil. Nineteen T. gondii samples (isolated from 1 goat, 5 pigs and 13 free-range chickens) were genotyped. Six different genotypes were identified, including two novel genotypes. The archetype genotypes, i.e., types I, II and III, were not found. In mice, seventeen isolates (89.5%) were classified as virulent, and only two (10.5%) were classified as avirulent. This study displays the genotypic variability of the parasite in Northeast Brazil.

A microfluidic chip integrating DNA extraction and real-time PCR for the detection of bacteria in saliva

Lab Chip. 2013 Feb 1. [Epub ahead of print]
Oblath EA, Henley WH, Alarie JP, Ramsey JM.

Source

Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. jmramsey@unc.edu.

Abstract

A microfluidic chip integrating DNA extraction, amplification, and detection for the identification of bacteria in saliva is described. The chip design integrated a monolithic aluminum oxide membrane (AOM) for DNA extraction with seven parallel reaction wells for real-time polymerase chain reaction (rtPCR) amplification of the extracted DNA. Samples were first heated to lyse target organisms and then added to the chip and filtered through the nanoporous AOM to extract the DNA. PCR reagents were added to each of the wells and the chip was thermocycled. Identification of Streptococcus mutans in a saliva sample is demonstrated along with the detection of 300 fg (100-125 copies) of both methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) genomic DNA (gDNA) spiked into a saliva sample. Multiple target species and strains of bacteria can be simultaneously identified in the same sample by varying the primers and probes used in each of the seven reaction wells. In initial tests, as little as 30 fg (8-12 copies) of MSSA gDNA in buffer has been successfully amplified and detected with this device.

An HPV testing algorithm comprising a combination of the L1 broad-spectrum SPF10 PCR and a novel E6 high-risk Multiplex type-specific genotyping PCR

J Clin Microbiol. 2013 Jan 30. [Epub ahead of print]
van Alewijk D, Kleter B, Vent M, Delroisse JM, de Koning M, van Doorn LJ, Quint W, Colau B.

Source

DDL Diagnostic Laboratory, Visseringlaan 25, Rijswijk, The Netherlands.

Abstract

HPV epidemiological and vaccine studies require highly sensitive HPV detection and genotyping systems. To improve HPV detection by PCR, the broad-spectrum L1 based SPF(10) PCR DEIA LiPA system and a novel E6 based multiplex type-specific system (MPTS123) using Luminex xMAP technology were combined into a new testing algorithm. To evaluate this algorithm, cervical swabs (n=860) and cervical biopsies (n=355) were tested with a focus on HPV detected by the MPTS123 assay (HPV-16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, -68, -6 and -11). Among the HPV positive samples, identification of individual HPV genotypes was compared. When all MPTS123 targeted genotypes were taken together a good overall agreement was found (κ = 0.801, 95% CI: 0.784-0.818) with identification by SPF(10) LiPA, but significantly more genotypes (P<0.0001) were identified by the MPTS123 PCR Luminex assay, especially for HPV-16, -35, -39, -45, -58, and -59. An alternative type-specific assay was evaluated, based on detection of a limited number of HPV genotypes by type-specific PCR and a reverse hybridization assay (MPTS12 RHA). This assay showed similar results as the expanded MPTS123 Luminex assay.These results confirm the fact that broad-spectrum PCRs are hampered by type competition when multiple HPV genotypes are present in the same sample. Therefore, a testing algorithm combining the broad-spectrum PCR and a range of type-specific PCRs offers a highly accurate method for the analysis of HPV infections and diminishes the rate of false-negative results, which may be particularly useful for epidemiological and vaccine studies.

Fast and specific dermatophyte detection by automated DNA extraction and real-time PCR

Clin Microbiol Infect. 2013 Jan 24. doi: 10.1111/1469-0691.12153. [Epub ahead of print]
Bergman A, Heimer D, Kondori N, Enroth H.

Source

Department of Clinical Microbiology, Unilabs AB, Skövde, Sweden.

Abstract

The aim of this study was to develop and validate a rapid and sensitive real-time PCR method for detection of all known species of dermatophytes, including identification of Trichophyton rubrum and Trichophyton interdigitale. Fungal DNA was extracted directly from clinical samples by using a pre-lysis step, followed by automated DNA extraction on the MagNA Pure Compact. In total, 202 clinical samples were examined by both conventional culture and by the new PCR method. In 103 (51%) of the samples fungal nucleic acid was detected by PCR, while only 79 (39%) were found to be positive by culture. Out of 103 PCR-positive clinical samples, 94 (91%) were identified as T. rubrum and eight (8%) as T. interdigitale. This real-time PCR is far more sensitive and 2-4 weeks faster than conventional culture for detection of dermatophytes present in clinical samples.

Inquiry about the Copy Number Assay

We have received an inquiry about one of our services, the Copy Number Assay to distinguish “+/+” for “+/-” from a customer. And they have asked if we have a capability to perform that or not.

Yes, we are providing the service with the Copy Number Assay on the qPCR to see one copy or two copies in the target gene.

If you are also interested in the service, please feet free to ask us.

Use of PB-Cre4 Mice for Mosaic Gene Deletion

PLoS One. 2013;8(1):e53501. doi: 10.1371/journal.pone.0053501. Epub 2013 Jan 7.
Birbach A.

Source

Department of Vascular Biology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.

Abstract

Transgene expression from short promoters in transgenic animals can lead to unwanted transgene expression patterns, often as a byproduct of random integration of the expression cassette into the host genome. Here I demonstrate that the often used PB-Cre4 line (also referred to as “Probasin-Cre”), although expressing exclusively in the male prostate epithelium when transmitted through male mice, can lead to recombination of loxP-flanked alleles in a large variety of tissues when transmitted through female mice. This aberrant Cre activity due to Cre expression in the oocytes leads to different outcomes for maternally or paternally transmitted loxP-flanked alleles: Maternally inherited loxP-flanked alleles undergo recombination very efficiently, making female PB-Cre4 mice an efficient monoallelic “Cre deleter line”. However, paternally inherited loxP-flanked alleles are inefficiently recombined by maternal PB-Cre4, giving rise to mosaic expression patterns in the offspring. This mosaic recombination is difficult to detect with standard genotyping approaches of many mouse lines and should therefore caution researchers using PB-Cre4 to use additional approaches to exclude the presence of recombined alleles. However, mosaic recombination should also be useful in transgenic “knockout” approaches for mosaic gene deletion experiments.

A Multiplex PCR for the Simultaneous Detection and Genotyping of the Echinococcus granulosus Complex

PLoS Negl Trop Dis. 2013 Jan;7(1):e2017. doi: 10.1371/journal.pntd.0002017. Epub 2013 Jan 17.
Boubaker G, Macchiaroli N, Prada L, Cucher MA, Rosenzvit MC, Ziadinov I, Deplazes P, Saarma U, Babba H, Gottstein B, Spiliotis M.

Source

Institute of Parasitology, University of Bern, Bern, Switzerland ; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland ; University of Monastir, Faculty of Pharmacy, Department of Clinical Biology B, Laboratory of Parasitology and Mycology, Monastir, Tunisia.

Abstract

Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1-G10) and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1-G3), E. equinus (G4), E. ortleppi (G5), and E. canadensis (G6-G10). The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR) allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex in common, and (iii) the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20) and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13). The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (<40%). Thus, except for copro analysis, the mPCR described here has a high potential for a worldwide application in large-scale molecular epidemiological studies on the Echinococcus genus.