Publications by authors named "Alan J Robertson"

7 Publications

  • Page 1 of 1

sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors.

Nucleic Acids Res 2017 03;45(5):e34

Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia.

Accurate identification of copy number alterations is an essential step in understanding the events driving tumor progression. While a variety of algorithms have been developed to use high-throughput sequencing data to profile copy number changes, no tool is able to reliably characterize ploidy and genotype absolute copy number from tumor samples that contain less than 40% tumor cells. To increase our power to resolve the copy number profile from low-cellularity tumor samples, we developed a novel approach that pre-phases heterozygote germline single nucleotide polymorphisms (SNPs) in order to replace the commonly used 'B-allele frequency' with a more powerful 'parental-haplotype frequency'. We apply our tool-sCNAphase-to characterize the copy number and loss-of-heterozygosity profiles of four publicly available breast cancer cell-lines. Comparisons to previous spectral karyotyping and microarray studies revealed that sCNAphase reliably identified overall ploidy as well as the individual copy number mutations from each cell-line. Analysis of artificial cell-line mixtures demonstrated the capacity of this method to determine the level of tumor cellularity, consistently identify sCNAs and characterize ploidy in samples with as little as 10% tumor cells. This novel methodology has the potential to bring sCNA profiling to low-cellularity tumors, a form of cancer unable to be accurately studied by current methods.
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http://dx.doi.org/10.1093/nar/gkw1086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389684PMC
March 2017

A Randomized Controlled Trial of Allopurinol in Patients With Peripheral Arterial Disease.

Can J Cardiol 2016 02 19;32(2):190-6. Epub 2015 May 19.

Division of Cardiovascular and Diabetes Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom.

Background: Patients with peripheral arterial disease (PAD) are limited by intermittent claudication in the distance they can walk. Allopurinol has been shown in coronary arterial disease to prolong exercise before angina occurs, likely by prevention of oxygen wastage in tissues and reduction of harmful oxidative stress.

Methods: In this study we evaluated whether allopurinol could prolong the time to development of leg pain in participants with PAD. In a double-blind, randomized controlled clinical trial participants were randomized to receive either allopurinol 300 mg twice daily or placebo for 6 months. The primary outcome was change in exercise capacity on treadmill testing at 6 months. Secondary outcomes were 6-minute walking distance, Walking Impairment Questionnaire, SF-36 questionnaire, flow-mediated dilatation, and oxidized low-density lipoprotein. Outcome measures were repeated midstudy and at the end of study. The mean age of the 50 participants was 68.4 ± 1.2 years with 39 of 50 (78%) male.

Results: Five participants withdrew during the study (2 active, 3 placebo). There was a significant reduction in uric acid levels in those who received active treatment of 52.1% (P < 0.001), but no significant change in either the pain-free or the maximum walking distance. Other measures of exercise capacity, blood vessel function, and the participants' own assessment of their health and walking ability also did not change during the course of the study.

Conclusions: Although allopurinol has been shown to be of benefit in a number of other diseases, in this study there was no evidence of any improvement after treatment in patients with PAD.
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http://dx.doi.org/10.1016/j.cjca.2015.05.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742517PMC
February 2016

Whole genomes redefine the mutational landscape of pancreatic cancer.

Nature 2015 Feb;518(7540):495-501

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded.
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http://dx.doi.org/10.1038/nature14169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4523082PMC
February 2015

An improved method for undertaking limiting dilution assays for in vitro cloning of Plasmodium falciparum parasites.

Malar J 2011 Apr 18;10:95. Epub 2011 Apr 18.

Clinical Tropical Medicine Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, 4006, Australia.

Background: Obtaining single parasite clones is required for many techniques in malaria research. Cloning by limiting dilution using microscopy-based assessment for parasite growth is an arduous and labor-intensive process. An alternative method for the detection of parasite growth in limiting dilution assays is using a commercial ELISA histidine-rich protein II (HRP2) detection kit.

Methods: Detection of parasite growth was undertaken using HRP2 ELISA and compared to thick film microscopy. An HRP2 protein standard was used to determine the detection threshold of the HRP2 ELISA assay, and a HRP2 release model was used to extrapolate the amount of parasite growth required for a positive result.

Results: The HRP2 ELISA was more sensitive than microscopy for detecting parasite growth. The minimum level of HRP2 protein detection of the ELISA was 0.11 ng/ml. Modeling of HRP2 release determined that 2,116 parasites are required to complete a full erythrocytic cycle to produce sufficient HRP2 to be detected by the ELISA. Under standard culture conditions this number of parasites is likely to be reached between 8 to 14 days of culture.

Conclusions: This method provides an accurate and simple way for the detection of parasite growth in limiting dilution assays, reducing time and resources required in traditional methods. Furthermore the method uses spent culture media instead of the parasite-infected red blood cells, enabling culture to continue.
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http://dx.doi.org/10.1186/1475-2875-10-95DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3089786PMC
April 2011

Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Nat Methods 2008 Jul 30;5(7):613-9. Epub 2008 May 30.

Expression Genomics Laboratory, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St. Lucia, Queensland, 4072, Australia.

We developed a massive-scale RNA sequencing protocol, short quantitative random RNA libraries or SQRL, to survey the complexity, dynamics and sequence content of transcriptomes in a near-complete fashion. This method generates directional, random-primed, linear cDNA libraries that are optimized for next-generation short-tag sequencing. We surveyed the poly(A)(+) transcriptomes of undifferentiated mouse embryonic stem cells (ESCs) and embryoid bodies (EBs) at an unprecedented depth (10 Gb), using the Applied Biosystems SOLiD technology. These libraries capture the genomic landscape of expression, state-specific expression, single-nucleotide polymorphisms (SNPs), the transcriptional activity of repeat elements, and both known and new alternative splicing events. We investigated the impact of transcriptional complexity on current models of key signaling pathways controlling ESC pluripotency and differentiation, highlighting how SQRL can be used to characterize transcriptome content and dynamics in a quantitative and reproducible manner, and suggesting that our understanding of transcriptional complexity is far from complete.
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http://dx.doi.org/10.1038/nmeth.1223DOI Listing
July 2008

Phosphorinanes as ligands for palladium-catalyzed cross-coupling chemistry.

Org Lett 2006 Jan;8(1):103-5

Department of Chemistry, McMaster University, Hamilton, Ontario, Canada.

[structure: see text] Phosphorinanes are presented as a class of phosphine ligand suitable for organopalladium cross-coupling chemistry. Prepared via a direct double Michael addition of a monoalkyl- or arylphosphine to phorone followed by a Wolf-Kishner reduction, phosphorinanes are relatively inexpensive to manufacture and allow modification of one of the alkyl moieties permitting steric and electronic fine-tuning of the ligands. Library screening and applications of these ligands in the Suzuki, Sonogashira, ketone arylation, and aryl amination reactions are presented.
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http://dx.doi.org/10.1021/ol052579hDOI Listing
January 2006

Phosphaadamantanes as ligands for palladium catalyzed cross-coupling chemistry: library synthesis, characterization, and screening in the Suzuki coupling of alkyl halides and tosylates containing beta-hydrogens with boronic acids and alkylboranes.

J Org Chem 2004 Oct;69(22):7635-9

Department of Chemistry, McMaster University, Hamilton, Ontario L8S 4M1, Canada.

A 15-member library of phosphaadamantane ligands has been prepared via P-arylation of 1,3,5,7-tetramethyl-2,4,8-trioxa-6-phosphaadamantane. Screening of this tertiary phosphine collection has allowed for the rapid determination of the most suitable ligand, specifically 1,3,5,7-tetramethyl-6-(2,4-dimethoxyphenyl)-2,4,8-trioxa-6-phosphaadamantane, for facilitating Suzuki-type couplings of alkyl halides or tosylates containing beta-hydrogens with either boronic acids or alkylboranes.
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http://dx.doi.org/10.1021/jo048875+DOI Listing
October 2004
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