488 research outputs found
Genomics of development and disease
No full textThe data will assist research in population genetic variation in health and disease genomics, cancer genomics and transcriptomics. They include data from the public domain which are frequently used by researchers in the research group, as well as data to be generated and analysis results during the progression of the project. Aim is to enable integration of the data collection to NecTAR which further facilitates genomic and medical research in Australia. Part of the data collection may be shared among researchers nationally, conditioning on ethics clearance
Bioinformatics: living on the edge
No full text08.05.14 KB. Ok to add published version to spiral, not an OA article but free report
cnvHiTSeq: Integrative models for high-resolution copy number variation detection and genotyping using population sequencing data
No full textRecent advances in sequencing technologies provide the means for identifying copy number variation (CNV) at an unprecedented resolution. A single next-generation sequencing experiment offers several features that can be used to detect CNV, yet current methods do not incorporate all available signatures into a unified model. cnvHiTSeq is an integrative probabilistic method for CNV discovery and genotyping that jointly analyzes multiple features at the population level. By combining evidence from complementary sources, cnvHiTSeq achieves high genotyping accuracy and a substantial improvement in CNV detection sensitivity over existing methods, while maintaining a low false discovery rate. cnvHiTSeq is available at http://sourceforge.net/projects/cnvhitseq
Too Tired, Uardrey Shed, Hay NSW, 21st February 2001 [picture] /
No full textTitle devised by photographer.; Also available in an electronic version via the Internet at: http://nla.gov.au/nla.pic-vn3563214; Purchased from the photographer, 2005. "'Too Tired', Uardrey Shed, Hay NSW, 21st Feb 2001. Shearers take a break at Uardrey shed. Shearing is one of the hardest jobs in Australia and when taking a break, exhaustion is apparent, whenever shearers take a break. A photograph of a Uardrey ram was used for the modelling of the rams head on the 1 shilling coin."--Notes supplied by photographer.Shearers take a break at "Uardrey", near Hay, NSW, 21st Feb. 200
SARS-COV-2.pptx
No full textPresentation given at Melbourne Integrative Genomics on 4/3/2020Abstract:Analysis of Sars-COV-2 direct RNA sequence dataAbstract SARS-Cov-2 (virus leading to COVID-19) transferred from an unknown animal host into humans in November 2019, and has since infected over 200,000 individuals globally and caused substantial mortality. SARS-Cov-2 is a single stranded RNA virus consisting of 29903 bases. While the majority of sequencing efforts of SARS-Cov-2 sequence cDNA utilizing a tiling amplicon approach, sequencing of native RNA is possible utilizing Oxford Nanopore Technologies GridION sequencer.In this talk, Lachlan will discuss analysis of SARS-Cov-2 direct RNA sequence data his team has recently acquired. In particular, he will demonstrate how direct RNA sequence data enables identification of subgenome-length mRNA, estimation of sub-genome relative expression, and also identification of non canonical recombination. He will also discuss analysis of SARS-COV-2 RNA methylation.</div
L208 Southeast Lachlan Seismic Survey 2018
No full textMaintenance and Update Frequency: asNeededStatement: No lineage availableSix hundred and twenty nine km of deep crustal reflection data were collected for the Southeast Lachlan 2D seismic survey along three transects: 18GA-SL1 (302 km), 18GA-SL2 (163 km) and 18GA-SL3 (164 km) during March to April 2018. The purpose of the survey was to image the Tabberabbera, Omeo, Deddick, Kuark and Mallacoota Zones (west to east) of the Lachlan Orogen at a high angle to their structural grain, as a key reference section for the study of the Palaeozoic geology, geodynamic evolution and mineral potential of Victoria and New South Wales with implications for eastern Australia mineral exploration as well as natural hazard mapping. The Project is a collaboration between Geoscience Australia (GA), the Geological Survey of Victoria (GSV), the Geological Survey of New South Wales (GSNSW), and AuScope. The data processing is being undertaken by a contractor on behalf of GA, GSV, GSNSW and AUScope and is expected to be released in early 2019. <br/><br/><b>Raw data are available on request from [email protected] - Quote eCat# 122684</b>
South East Lachlan Gravity (CSCBA 1VD grid)
No full textMaintenance and Update Frequency: notPlannedStatement: This South East Lachlan Gravity (CSCBA 1VD grid) is the first vertical derivative of the complete spherical cap Bouguer anomaly grid for the South East Lachlan Gravity Survey along Seismic Lines, P201930, Vic, NSW, 2019. This gravity survey was acquired under the project No. 201930 for the geological survey of NSW, VIC. The grid has a cell size of 0.0005 degrees (approximately 50m). A total of 3542 gravity stations at a spacing between 200m and 400m were acquired to produce this grid. Three processes are required to correct the gravity observations for the effects of the surrounding topography: (1) a Bouguer correction (Bullard A), which approximates the topography as an infinite horizontal slab; (2) a correction to that horizontal slab for the curvature of the Earth (Bullard B); and (3) a terrain correction (Bullard C), which accounts for the undulations of the surrounding topography. The complete spherical cap Bouguer gravity anomalies were calculated by applying terrain correction (Bullard C) to the spherical cap Bouguer anomaly point data of South East Lachlan Gravity Survey along Seismic Lines, P201930, Vic, NSW, 2019. These terrain corrections were calculated using software from INTREPID Geophysics. The Intrepid algorithm utilises concentric rings subdivided into cells (Direen, 2001) to calculate the terrain correction. The terrain corrected data were then gridded using a gridding technique provided by the INTREPID Geophysics software package. A first vertical derivative was calculated by applying a fast Fourier transform (FFT) process to the Bouguer gravity grid of the South East Lachlan Gravity Survey along Seismic Lines, P201930, Vic, NSW, 2019 survey to produce this grid. This grid was calculated using an algorithm from the INTREPID Geophysics software package. The processed data are checked by GA geophysicists using standard methods for assessing quality to ensure that the final data are fit-for-purpose. Details of the specifications of individual surveys held in the Australian National Gravity Database (ANGD) can be found in the Second Edition of the Index of Gravity Surveys (Wynne and Bacchin, 2009).
References:
Intrepid Geophysics, http://www.intrepid-geophysics.com;
Wynne, P. and Bacchin, M., 2009. Index of Gravity Surveys (Second Edition). Geoscience Australia, Record 2009/07.Gravity data measure small changes in gravity due to changes in the density of rocks beneath the Earth's surface. The data collected are processed via standard methods to ensure the response recorded is that due only to the rocks in the ground. The results produce datasets that can be interpreted to reveal the geological structure of the sub-surface. The processed data is checked for quality by GA geophysicists to ensure that the final data released by GA are fit-for-purpose.<br/>This South East Lachlan Gravity (CSCBA 1VD grid) is the first vertical derivative of the complete spherical cap Bouguer anomaly grid for the South East Lachlan Gravity Survey along Seismic Lines, P201930, Vic, NSW, 2019. This gravity survey was acquired under the project No. 201930 for the geological survey of NSW, VIC. The grid has a cell size of 0.0005 degrees (approximately 50m). A Fast Fourier Transform (FFT) process was applied to the original grid to calculate the first vertical derivative grid. A total of 3542 gravity stations at a spacing between 200m and 400m were acquired to produce this grid
Statistical approaches for copy number variation detection and association with complex human phenotypes
No full textCopy number variants (CNVs) play an important role in the disease pathogenesis, including epilepsy, diabetes and many others. CNVs, are also known to affect cellular phenotypes through several phenomenon such as gene dosage.
Next generation technologies for sequencing (DNA and RNA) and metabolite profiling (metabolomics) has led to the systematic discovery and evaluation of various genomic variants and their relationship to multiple phenotypes. Such approaches often involve application of several statistical and machine learning methods for unravelling new relationships between genomic variants and phenotypes i.e. disease outcomes or quantitative traits characterized at the molecular level.
This thesis explores and develops several statistical methods for CNV detection and association with complex human phenotypes, in particular for epilepsy drug-response, epilepsy susceptibility, metabolomics and gene expression.
In more detail, chapter 3, describes a genome wide CNV association analysis for two phenotypes including epilepsy susceptibility and epilepsy drug response. I have identified several important candidate genes for these two phenotypes, including the top most associated genes, SLC9A1 (p-value=6.69E-15) for epilepsy susceptibility and WWOX (p-value=1.93E-3) for epilepsy drug response. These associations were replicated in a separate Australian cohort and were further validated in lab and in-silico, leading to some positive and negative confirmation.
In chapter 4, I present CNV association with metabolomic data in the exonic regions of the TSPAN8 gene. A strong association signal was detected in the 6th exon and 7th exon of the TSPAN8 gene, where a large proportion of metabonomic lipid phenotypes were found to be associated with univariate (P-value=7.64E-4) and multivariate (P-value=1.33E-6) approaches. These CNVs were also found to be nominally associated with type 2 diabetes (P-value=3.32e-7). In addition, I also carried out advanced multivariate based association analysis to corroborate these results and further reported sequencing based validation results for TSPAN8 exonic CNVs in different human populations from the 1000 genomes project.
In chapter 5, I report a genome wide CNV association analysis with gene expression in ten different regions of the human brain. I identified a novel CNV near the DRD5 gene which was found to be strongly associated with gene expression. Further, I have reported on-going efforts to replicate and validate this finding.
Each of these different phenotype categories analysed posed its own unique challenges and required specific approaches for analysis and interpretation.Open Acces
Statistical methods for elucidating copy number variation in high-throughput sequencing studies
No full textCopy number variation (CNV) is pervasive in the human genome and has been shown to contribute significantly to phenotypic diversity and disease aetiology. High-throughput sequencing (HTS) technologies have allowed for the systematic investigation of CNV at an unprecedented resolution. HTS studies offer multiple distinct features that can provide evidence for the presence of CNV. We have developed an integrative statistical framework that jointly analyses multiple sequencing features at the population level to achieve sensitive and precise discovery of CNV. First, we applied our framework to low-coverage whole-genome sequencing experiments and used data from the 1000 Genomes Project to demonstrate a substantial improvement in CNV detection accuracy over existing methods. Next, we extended our approach to targeted HTS experiments, which offer improved cost-efficiency by focusing on a predetermined subset of the genome. Targeted HTS involves an enrichment step that introduces non-uniformity in sequencing coverage across target regions and thus hinders CNV identification. To that end, we designed a customized normalization procedure that counteracts the effects of enrichment bias and enhances the underlying CNV signal. Our extended framework was benchmarked on contiguous capture datasets, where it was shown to outperform competing strategies by a wide margin. Capture sequencing can also generate large amounts of data in untargeted genomic regions. Although these off-target results can be a valuable source of CNV evidence, they are subject to complex enrichment patterns that confound their interpretation. Therefore, we developed the first normalization strategy that can adapt to the highly heterogeneous nature of off-target capture and thus facilitate CNV investigation in untargeted regions. All in all, we present a generalized CNV detection toolset that has been shown to achieve robust performance across datasets and sequencing platforms and can therefore provide valuable insight into the prevalence and impact of CNV.Open Acces
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