Single molecule real-time sequencing with the PacBio RS

I attended a talk by Dr Stephen Turner, the founder and Chief Technology Officer of Pacific Biosciences, promoting PacBio’s SMRT (Single Molecule Real Time) sequencing platform. While I’d heard of the “next-next-generation” of sequencing technologies at least 18 months ago, this was the first time I’d paid much attention to them. What sets the “next-next-gen” from the “next-gen” platforms (why won’t this terminology die already!) is that rather than sequencing a cluster (Illumina) or a bead (SOLiD) of amplified and identical molecules we sequence a single molecule.

Detection of rare variants in massively parallel sequencing data and base quality recalibration

Rick Tankard, who is a research assistant in the Bahlo Lab at WEHI, gave a seminar discussing the quality scores produced by the Illumina sequencing machines. He also discussed the analysis pipeline he has built, in conjunction with other members of the Bahlo lab, for the detection of rare variants in MPS experiments The quality scores produced off the sequencer are meant to give an indication of the quality of the base-call (for SOLiD data the qualities measure the quality of the colour- or dinucleotide-call).

Variance models for RNA-seq

Update (21/02/2014) The voom method has now been published in Genome Biology Original post Gordon Smyth is well known for his development of the limma Bioconductor package for the analysis of differential gene expression using microarrays. More recently his group has led the way in the development of software for the statistical analysis of gene expression using RNA-seq with the edgeR Bioconductor package and the voom() method in limma. Today, Gordon spoke about modeling the variance in RNA-seq data for studying gene expression, in particular using the voom() method, and contrasted this approach with that taken by edgeR (and other Poisson/Negative binomial-like methods).

Understanding cancer neochromosome formation through integrated analysis of fusion and copy number data

Neochromosomes Neochromosomes (NCs) are “extra” chromosomes that are found in around 3% of tumour genomes. They are a hallmark of liposarcoma, which is a cancer of the fat cells studied by the Papenfuss lab at WEHI in conjunction with colleagues at the Peter MacCallum Cancer Centre. Circular chromosomes and giant rod chromosomes are both examples of NCs and are comprised of multiple donor segments from other regions of the region that are frequently highly amplified.

Analysing Illumina Infinium 450k methylation arrays

Dr Alicia Oshlack, head of Bioinformatics at the Murdoch Children’s Research Institute and formerly of WEHI Bioinformatics, gave today’s Bioinformatics seminar at WEHI. Her topic was “Analysing Human Infinium 450k Methylation Arrays”, in particular the normalisation and quality control issues associated with them. I’ve fleshed out the notes I made during the seminar, below. Alicia credited Jovana Maksimovic and Livinia Gordon (members of her lab) with most of the work she was to present today.