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PLos ONE 8, e62137. Genotyping-by-Sequencing (GBS): A novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing 2013

De Donato, M., Peters, S.O., Mitchell, S.E., Hussain, T. and Imumorin, I.G.

Notes: The authors of this study sought to apply a genotyping-by-sequencing approach to genotype cattle from the US and Africa. They collected blood samples from 47 unrelated animals slaughtered in the US and Nigeria. Genomic DNA was extracted and then quantitated using the QuantiFluor® dsDNA System on a SpectraFluor Plus plate-format fluorometer before being used for next-generation sequencing. (4508)

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Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 14, 125–36. Population structure in nontypeable Haemophilus influenzae. 2013

Lacross, N.C., Marrs, C.F. and Gilsdorf, J.R.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Haemophilus influenzae. (4336)

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Tree Genetics and Genomes 9, 1537–1544. Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform 2013

Chen, C., Mitchell, S.E., Elshire, R.J., Buckler, E.S., El-Kassably, Y.A.

Notes: In this study, the authors evaluated “genotyping-by-sequencing” for the economically important lodgepole pine and white spruce conifer species. DNA samples extracted from dormant vegetative buds and DNA was quantitated using Quantifluor® ds DNA System on a SpectraFluor Plus plate-format fluorometer. (4507)

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J. Wildl. Dis. 48, 416–24. Antibody prevalence and molecular identification of Babesia spp. in roe deer in France. 2012

Bastian, S. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Babesia spp. (4310)

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Veterinary Microbiology 161, 169–78. Genetic diversity of Flavobacterium psychrophilum isolated from rainbow trout in France: predominance of a clonal complex. 2012

Siekoula-Nguedia, C. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Flavobacterium psychrophilum. (4334)

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Antimicrob. Agents Chemother. 56, 5332–9. Identification of a novel genomic island conferring resistance to multiple aminoglycoside antibiotics in Campylobacter coli. 2012

Qin, S. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Campylobacter coli. (4316)

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Anaerobe 18, 566–75. Morphological, biochemical, physiological and molecular aspects of the response of Fusobacterium nucleatum exposed to subinhibitory concentrations of antimicrobials. 2012

de Souza Filho, J.A. et al.

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Fusobacterium nucleatum. (4335)

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Virol. J. 9, 144. Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch. 2012

Mitui, M.T., Chandrasena, T.N., Chan, P.K., Rajindrajith, S., Nelson, E.A., Leung, T.F., Nishizono, A. and Ahmed, K.

Notes: This study examined how well primers developed in 1990 and 2004 for type A rotavirus (RVA) were able to genotype (G type) currently circulating RVAs in Asia. The VP7 gene from RVA was amplified using 2µl of dsRNA template with the AccessQuick™ RT-PCR System in a total volume of 50µl. The G type was determined using hemi-nested multiplex PCR using 1µl of the VP7 cDNA and PCR Master Mix in a final volume of 50µl. The final products were sequenced. (4340)

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Nucl. Acids Res. 39, e81. A method for counting PCR template molecules with application to next-generation sequencing. 2011

Casbon, J.A., Osborne, R.J., Brenner, S. and Lichtenstein, C.P.

Notes: DNA templates are often amplified by PCR during library generation prior to next-generation sequencing, but amplification can introduce biases and duplications that are not easily corrected. In this paper, the authors developed a simple method to count the number of input template molecules to reduce these PCR-related problems: The ligation of a degenerate base region to all fragments during library creation. To evaluate their approach to correct for biases and duplications, the authors created a library using Human Genomic DNA, amplified the library by inverse PCR using the GoTaq® Hot Start Polymerase and 1X Colorless GoTaq® Flexi Buffer, sequenced the resulting DNA fragments and assessed the quality of the next-generation sequencing data. (4160)

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J. Exp. Bot. 60, 1409-25. A strong effect of growth medium and organ type on the identification of QTLs for phytate and mineral concentrations in three Arabidopsis thaliana RIL populations. 2009

Ghandilyan, A., Ilk, N., Hanhart, C., Mbengue, M., Barboza, L., Schat, H., Koornneef, M., El-Lithy, M., Vreugdenhil, D., Reymond, M. and Aarts, M.G.

Notes: Mineral accumulation was studied in Arabidopsis thaliana comparing loci involved with growing in soil versus hydroponics. An F2 population derived from a cross between Landsberg erecta (Ler; maternal parent) and Eringsboda-1 (Eri-1; paternal parent) was propagated by single seed descent for nine successive generations in soil.
The flower buds of three plants per line were collected, and the DNA extracted using the Wizard® Magnetic 96 DNA Plant System and used for genotyping with 90 amplified fragment length polymorphism PCR (AFLP) and 39 single sequence length polymorphisms (SSLP) markers to build a genetic map of quantitative trait loci (QTL). (4136)

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Drug Metab. Dispos. 37, 1726–1732. Characterizing the effects of common UDP glucuronosyltransferase (UGT) 1A6 and UGT1A1 polymorphisms on cis- and trans-resveratrol glucuronidation. 2009

Iwuchukwu, O.F., Ajetunmobi, J., Ung, D. and Nagar, S.

Notes: This study examined the genotype-phenotype correlation of the two major UGT isoforms, UGT1A1 and UGT1A6, involved in resveratrol metabolism. Genomic DNA was isolated from 30mg human liver tissue samples (normal and metastatic) using the Wizard® SV Genomic DNA Purification System. The purified DNA was eluted with 65°C water and 200–400ng of eluted DNA was used in a PCR-RFLP UGT1A6 genotyping assay. Amplification was carried out using PCR Master Mix in a final volume of 50µl, and the amplimers digested with appropriate restriction enzymes. (4018)

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Clin. Chem. 55, 748–56. Coamplification at lower denaturation temperature-PCR increases mutation-detection selectivity of TaqMan-based real-time PCR. 2009

Li, J., Wang, L., Jänne, P.A. and Makrigiorgos, GM.

Notes: The authors describe a new form of PCR, co-amplification at lower denaturation temperature PCR (COLD-PCR), to detect low-level somatic mutations. This technique is based on the facts that a) each DNA sequence has a critical denaturation temperature (Tc), which is lower than the melting temperature (Tm) and below which PCR efficiency decreases dramatically and b) Tc depends on DNA sequence. The authors used GoTaq® Flexi DNA Polymerase and mutation-specific TaqMan® probes for tumor protein 53 (TP53) and epidermal growth factor receptor (EGFR) to detect low-level somatic mutations in a mixture of wildtype and mutant DNAs. Conventional TaqMan® technology can detect mutant alleles at an abundance of 10–20% of that of the wildtype allele; using COLD-PCR the authors were able to increase selectivity 15- to 30-fold, detecting as little as 0.8% mutuant alleles. (4038)

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Proc. Natl. Acad. Sci. USA 106, 5258–63. Genomic identification in the historical case of the Nicholas II royal family. 2009

Rogaev, E.I., Grigorenko, A.P., Moliaka, Y.K., Faskhutdinova, G., Goltsov, A., Lahti, A., Hildebrandt, C., Kittler, E.L. and Morozova, I.

Notes: In 1991, the remains of murdered Emperor Nicholas II, Empress Alexandra and three of their five children were discovered. Until recently, the remains of the two other children were never found. In July of 2007 human bone fragments were discovered at a second grave site in the Ural region of Russia. The authors performed DNA typing to determine if these remains were those of the two missing children. Bone fragments and teeth were subjected to mitochondrial and nuclear DNA typing. DNA was quantitated using the Plexor® HY System. Nuclear DNA analysis was performed, in part, using the PowerPlex® S5 System. A comparison of mitochondrial DNA sequences from remains in the first and second graves and from maternal reference samples confirmed that the remains constituted a family with a "Queen Victoria" mitotype (Empress Alexandra was the granddaughter of Queen Victoria). Y-STR analysis of both sets of remains was performed, and the results confirmed that the Y-STR haplotypes of the two sets of male remains matched, and this haplotype matched that of several descendants from an unbroken paternal lineage of Nicholas I, father of Nichloas II. The mitochondrial and Y-STR haplotypes and autosomal STR profile also matched those obtained from a bloodstained shirt that Nicholas II was wearing during an assassination attempt. (3967)

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Malaria Journal Oct 29:7, 223. A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking. 2008

Daniels R, Volkman SK, Milner DA, Mahesh N, Neafsey DE, Park DJ, Rosen D, Angelino E, Sabeti PC, Wirth DF, Wiegand RC.

Notes: These authors used the Maxwell® 16 System to isolate DNA from frozen whole blood samples infected with Plasmodium falciparum. The isolated DNA was used in a qPCR-based SNP genotyping assay that sought to uniquely identify the parasites based on their SNP marker profile. (3962)

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Clin. Can. Res. 14(19), 6062–72. Androgen-regulated and highly tumorigenic human prostate cancer cell line established from a transplantable primary CWR22 tumor. 2008

Dagvadorj, A., Tan, S.H., Liao, Z., Cavalli, L.R., Haddad, B.R. and Nevalainen, M.T.

Notes: The authors developed a new human prostate cancer cell line, CWR22Pc, that is both androgen-dependent and able to produce tumors in dihydrotestosterone-supplemented nude mice. To confirm that CWR22Pc cells are derived from primary CWR22 human prostate xenograft tumors, the authors performed genotyping at 8 STR loci and amelogenin using the PowerPlex® 1.2 System. DNA purification from the cell line and original tumor samples was performed using the Wizard® Genomic DNA Purification Kit. (4041)

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Stem Cells 2008, 485-493. Development of human cloned blastocysts following somatic cell nuclear transfer with adult fibroblasts 2008

French, A.J., Adams, C.A., Anderson, L.S., Kitchen, J.R., Hughes, M.R. and Wood, S.H.

Notes: Somatic cell nuclear transfer technique was used to generate human blastocyst-stage embryos using nuclei from adult male fibroblasts cell lines and enucleated oocytes. Genomic DNA was analyzed using the PowerPlex® 16 system to confirm the genetic identity of the blastocyst cells. (3952)

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J. Clin. Microbiol. 46, 1741–1746. High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and and pathotypes within an urban District of Jakarta, Indonesia. 2008

Baker, S., Holt, K., van de Vosse, E., Roumagnac, P., Whitehead, S., King, E., Ewels, P., Keniry, A., Weill, F.X., Lightfoot, D., van Dissel, J.T., Sanderson, K.E., Farrar, J., Achtman, M., Deloukas, P. and Dougan, G.

Notes: The authors examined strains of Salmonella enterica serovar Typhi isolated from typhoid cases originating in or around Indonesia or from travelers returning from Indonesia to examine if serovar Typhi from this area has a greater level of genetic diversity compared to other countries. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit, diluted to 4 ng/µl and used in locus-specific PCR genotyping. (3980)

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J. Clin. Microbiol. 46, 652–64. Multilocus sequence typing reveals that the population structure of Candida dubliniensis is significantly less divergent than that of Candida albicans. 2008

McManus, B.A., Coleman, D.C., Moran, G., Pinjon, E., Diogo, D., Bougnoux, M.E., Borecká-Melkusova, S., Bujdákova, H., Murphy, P., d'Enfert, C. and Sullivan, D.J.

Notes: To determine the usefulness of multilocus sequence typing (MLST) in differentiating Candida species during epidemiological studies, the authors investigated the population structure of C. dubliniensis by amplifying the same 10 MLST loci found to be useful in differentiating isolates of C. albicans, a closely related species. PCRs were performed using 1.25 units of GoTaq® Flexi DNA Polymerase and 1ng of DNA template in a 50µl reaction. (3880)

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Clin. Chem. 54, 1080–4. Rapid determination of monozygous twinning with a microfabricated capillary array electrophoresis genetic-analysis device. 2008

Yeung, S.H., Medintz, I.L., Greenspoon, S.A. and Mathies, R.A.

Notes: The authors used a microfabricated capillary electrophoresis instrument to rapidly assess the genetic relationship between same-sex twins and their parents and siblings. STR typing was performed to determine if the twins were monozyotic or dizygotic and to confirm familial relationships. The authors used the PowerPlex® 16 System to examine 15 STR loci in this study. (4045)

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Forensic Sci. Int. Genet. 2, 301–309. Real-time forensic DNA analysis at a crime scene using a portable microchip analyzer. 2008

Liu, P. Yeung, S.H.I., Crenshaw, K.A., Crouse, C.A., Scherer, J.R. and Mathies, R.A.

Notes: This paper describes analysis of DNA samples at a mock crime scene using automated DNA purification followed by STR analysis on a portable microchip system. The mock crime scene was created using "victim" and "suspect" blood stains prepared by spotting 3µl of liquid blood onto paper towels and a cloth shirt. The samples were allowed to dry overnight before placement at the crime scene. Samples were processed at the scene using the Maxwell® 16 Instrument and DNA IQ™ Casework Sample Kit for DNA extraction, and a microchip analyzer to perform amplification and STR analysis. The 9-plex autosomal STR typing system used in the microchip system included primer sequences from the PowerPlex® 16 System (D3S1358, THO1, D21S11, D5S818, D13S317, D7S820, vWA and D8S1179) and amelogenin for sex identification. DNA purification from suspect samples was completed in 2 hours, and subsequent STR analysis and generation of a "suspect" DNA profile took a further 3 hours. The entire process from sample collection to generation of a CODIS "hit" took 6 hours. (3922)

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Hum. Reprod. 23, 2185–93. Similar biological characteristics of human embryonic stem cell lines with normal and abnormal karyotypes. 2008

Sun, X., Long, X., Yin, Y., Jiang, Y., Chen, X., Liu, W., Zhang, W., Du, H., Li, S., Zheng, Y., Kong, S., Pang, Q., Shi, Y., Huang, Y., Huang, S., Liao, B., Xiao, G. and Wang, W.

Notes: The authors developed seven new human embryonic stem cell (hESC) lines, five with normal karyotypes and two with abnormal karyotypes. They examined their biological characteristics, STR loci, HLA typing, differentiation capability, imprinted genes, DNA methylation and X chromosome inactivation status to determine if hESC lines with abnormal karyotypes are useful experimental tools. STR gemotyping was performed using the PowerPlex® 16 System and the ABI PRISM® 3100 Genetic Analyzer. (4040)

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Am. J. Pathol. 171, 19–31. A sertoli cell-specific knockout of connexin43 prevents initiation of spermatogenesis. 2007

Brehm, R., Zeiler, M., Rüttinger, C., Herde, K., Kibschull, M., Winterhager, E., Willecke, K., Guillou, F., Lécureuil, C., Steger, K., Konrad, L., Biermann, K., Failing, K. and Bergmann, M.

Notes: To study the role of connexin42 (cx43) in testis development, the authors generated a conditional cx43 knockout mouse, which lacked the cx43 gene in Sertoli cells. To confirm that the cx43 gene was deleted in these mice, PCR was performed using primers specific to cx43, 1X Colorless GoTaq® Flexi Reaction Buffer, 2mM MgCl2, dNTPs and 0.15µl of GoTaq® DNA Polymerase. Tissue-specific deletion of cx43 was confirmed by amplifying RNA isolated from mouse testis, heart and tail was also confirmed using the same PCR components. (3713)

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J. Forensic Sci. 52, 870–3. Concordance study between the AmpFlSTR MiniFiler PCR amplification kit and conventional STR typing kits. 2007

Hill, C.R., Kline, M.C., Mulero, J.J., Lagacé, R.E., Chang, C.W., Hennessy, L.K. and Butler, J.M.

Notes: The authors analyzed 1,308 samples for concordance between the Identifiler® kit, AmpFlSTR® Minifiler™ kit and PowerPlex® 16 System. DNA was isolated from liquid blood using the manual DNA IQ™ System protocol, and STR amplifications were performed as per the manufacturer's recommendations except that reaction volumes were decreased by half. Amplified products were analyzed using an Applied Biosystems 3130xl and POP™-4 or POP™-6 polymer. Twenty seven disconcordant phenotypes were identified between the Minifiler™ and Identifiler® kits, 14 between Minifiler™ and PowerPlex® 16 kits, and 4 between PowerPlex® 16 and Identifiler® kits. (3770)

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Croat. Med. J. 48, 513–519. DNA identification of skeletal remains from the World War II mass graves uncovered in Slovenia. 2007

Marjanovic, D., Durmic-Pasic, A., Bakal, N., Haveric, S., Kalamujic, B., Kovacevic, L., Ramic, J., Pojskic, N., Skaro, V., Projic, P., Bajrovic, K., Hadziselimovic, R., Drobnic, K., Huffine, E., Davoren, J. and Primorac, D.

Notes: The authors used the PowerPlex® 16 System to perform DNA typing of 27 sets of World War II skeletal remains found in two mass graves in Slovenia. Each bone sample was sanded to remove potential contaminants from exterior surfaces, then washed and air-dried. The same procedure was used to process teeth, except that the teeth were not sanded. DNA was isolated from the bone powder using organic extraction, then quantified. DNA was amplified using the PowerPlex® 16 System as per the manufacturer's recommendations; for samples with small amounts of DNA, the number of cycles was increased to 32 and the elongation time extended to 90 seconds. Fifteen sets of remains yielded full profiles, and 12 sets yielded partial profiles, with the least successful profile including 13 loci. DNA was also extracted and amplified from 69 reference buccal swab samples from potential relatives. (3817)

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J. Clin. Microbiol. 45, 3316-3322. Evaluation the Invader Assay with the BACTEC MGIT 960 System for prompt isolation and identification of Mycobacteria from clinical specimens. 2007

Ichimura, S., Nagano, M., Ito, N., Shimojima, M., Egashira, T., Miyamoto, C., Ohkusu, K., and Ezaki, T.

Notes: These authors compared standard culture conditions, DNA isolation and analysis (e.g, sequencing) with a liquid culture, DNA isolation and a homogeneous fluorescent detection system for identifying mycobacterial species. The standard DNA extraction began with a loopful (3–mm3 sphere) of bacterial colony grown on Ogawa slants that used glass beads to mechanically disrupt the cells. The resulting lysate was extracted using phenol/chloroform, and DNA purified from the aqueous phase using a robotic liquid handler AGE-96 (Biotec) and the MagneSil® Blood Genomic, Max Yield System. The DNA extractions were used in PCR and sequencing reactions. (3700)

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