Daniel Swan

Also, this is a question and answer forum. Asking people to supply information to your inbox would mean that no-one else would get the answer to this question (not that it's going to be answered). The responsibility is on you to come back to the forum and check for answers, not wait for your problems be magically resolved by keeping an eye on your inbox. - Daniel Swan

Please don't append questions to other questions, I think your questions would stand quite well on their own as a separate topic. Please ask a separate question. - Daniel Swan

1000 Genomes regenerated alignments for some of their datasets I seem to recall, therefore they have different names. If you go to the FTP directory in a browser, it is still there, but the file is not. I think you want this file : ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20111114.bam - Daniel Swan

I think this is off topic and should be closed as this is a discussion on data security and outside the scope of this site. - Daniel Swan

Care to post an IGV screenshot of your BAM file for the position you're interested in? It's hard to do a diagnosis without seeing the region of interest. - Daniel Swan

Genome Medicine, Vol. 4, No. 1. (2012), 9. no abstract Charles Auffray, Timothy Caulfield, Muin Khoury, James Lupski, Matthias Schwab, Timothy Veenstra - Daniel Swan

Even if that is meant to read 'decoy' I'm not sure the question is answerable - Daniel Swan

Even if that is meant to read 'decoy' I'm not sure the question is answerable - Daniel Swan

Closed as offtopic. Perhaps oss.ly/licdif would be helpful. - Daniel Swan

You're describing a LIMS system. These are not trivial to develop, and not cheap to buy! - Daniel Swan

BMC Medical Genomics, Vol. 5, No. 1. (2012), 4. BACKGROUND:Companies are currently marketing personal genome tests directly-to-consumer that provide genetic susceptibility testing for a range of multifactorial diseases simultaneously. As these tests comprise multiple risk analyses for multiple diseases, they may be difficult to evaluate. Insight into morally relevant differences between diseases will assist researchers, healthcare professionals, policy-makers and other stakeholders in the ethical evaluation of personal genome tests.DISCUSSION:In this paper, we identify and discuss four disease characteristics - severity, actionability, age of onset, and the somatic/psychiatric nature of disease - and show how these lead to specific ethical issues. By way of illustration, we apply this framework to genetic susceptibility testing for three diseases: type 2 diabetes, age-related macular degeneration and clinical depression. For these three diseases, we point out the ethical issues that... - Daniel Swan

Programming and documentation questions are not bioinformatics. However you have an accepted answer and some good information. Question closed! - Daniel Swan

BMC Genomics, Vol. 13, No. 1. (18 January 2012), 28. BACKGROUND:Transcriptome analysis is of great interest in clinical research, where significant differences between individuals can be translated into biomarkers of disease. Although next generation sequencing provides robust, comparable and highly informative expression profiling data, with several million of tags per blood sample, reticulocyte globin transcripts can constitute up to 76% of total mRNA compromising the detection of low abundant transcripts. We have removed globin transcripts from 6 human whole blood RNA samples with a human globin reduction kit and compared them with the same non-reduced samples using deep Serial Analysis of Gene Expression.RESULTS:Globin tags comprised 52-76% of total tags in our samples. Out of 21,633 genes only 87 genes were detected at significantly lower levels in the globin reduced samples. In contrast, 11,338 genes were detected at significantly higher levels in the globin reduced samples.... - Daniel Swan

Nat Genet In Nat Genet, Vol. 40, No. 9. (17 September 2008), pp. 1068-1075. Uncertainty about the phase of strings of SNPs creates complications in genetic analysis, although methods have been developed for phasing population-based samples. However, these methods can only phase a small number of SNPs effectively and become unreliable when applied to SNPs spanning many linkage disequilibrium (LD) blocks. Here we show how to phase more than 1,000 SNPs simultaneously for a large fraction of the 35,528 Icelanders genotyped by Illumina chips. Moreover, haplotypes that are identical by descent (IBD) between close and distant relatives, for example, those separated by ten meioses or more, can often be reliably detected. This method is particularly powerful in studies of the inheritance of recurrent mutations and fine-scale recombinations in large sample sets. A further extension of the method allows us to impute long haplotypes for individuals who are not genotyped. Augustine Kong, Gisli... - Daniel Swan

From the website: "Note: Access is permitted for HMP funded researchers only. Please complete this form to request access to the HMP DACC archive and/or the project's Basecamp collaboration site." hmpdacc.org/internal/project_access.php - Daniel Swan

Answered here on SeqAnswers if there's no takers: seqanswers.com/forums/showthread.php?p=62059 - Daniel Swan

BMC Bioinformatics, Vol. 13, No. 1. (12 January 2012), 8. BACKGROUND:Whole exome capture sequencing allows researchers to cost-effectively sequence the coding regions of the genome. Although the exome capture sequencing methods have become routine and well established, there is currently a lack of tools specialized for variant calling in this type of data.RESULTS:Using statistical models trained on validated whole-exome capture sequencing data, the Atlas2 Suite is an integrative variant analysis pipeline optimized for variant discovery on all three of the widely used next generation sequencing platforms (SOLiD, Illumina, and Roche 454). The suite employs logistic regression models in conjunction with user-adjustable cutoffs to accurately separate true SNPs and INDELs from sequencing and mapping errors with high sensitivity (96.7%).CONCLUSION:We have implemented the Atlas2 Suite and applied it to 92 whole exome samples from the 1000 Genomes Project. The Atlas2 Suite is available for... - Daniel Swan

Nucleic Acids Research (12 January 2012) Miao-Xin Li, Hong-Sheng Gui, Johnny Kwan, Su-Ying Bao, Pak Sham - Daniel Swan

ProjectPier is worth considering, I have used that in projects before, or even something like RequestTracker. - Daniel Swan

Well we know where a centromere is without ever sequencing it.. Plenty of ways this could be done. FISH springs to mind. - Daniel Swan

It's not wrong, whilst it's debatable that this is a bioinformatics question, it's almost certainly a biological one, there are different audiences at each site and so you could have left it there as a legitimate question. - Daniel Swan

Absolutely, completely off topic, and answered as well as it's going to be be answered. So back to closed ;) - Daniel Swan

'More data!' :) - Daniel Swan

BMC medical genetics, Vol. 13, No. 1. (6 January 2012), 3. ABSTRACT: BACKGROUND: Mitochondrial diseases comprise a diverse set of clinical disorders that affect multiple organ systems with varying severity and age of onset. Due to their clinical and genetic heterogeneity, these diseases are difficult to diagnose. We have developed a targeted exome sequencing approach to improve our ability to properly diagnose mitochondrial diseases and apply it here to an individual patient. Our method targets mitochondrial DNA (mtDNA) and the exons of 1,600 nuclear genes involved in mitochondrial biology or Mendelian disorders with multi-system phenotypes, thereby allowing for simultaneous evaluation of multiple disease loci. Case Presentation: Targeted exome sequencing was performed on a patient initially suspected to have a mitochondrial disorder. The patient presented with diabetes mellitus, diffuse brain atrophy, autonomic neuropathy, optic nerve atrophy, and a severe amnestic syndrome. Further... - Daniel Swan

Nature Genetics, Vol. advance online publication (08 January 2012) Zamin Iqbal, Mario Caccamo, Isaac Turner, Paul Flicek, Gil McVean - Daniel Swan

PLoS ONE, Vol. 6, No. 12. (21 December 2011), e29500. Identification of gene variants plays an important role in research on and diagnosis of genetic diseases. A combination of enrichment of targeted genes and next-generation sequencing (targeted DNA-HiSeq) results in both high efficiency and low cost for targeted sequencing of genes of interest. To identify mutations associated with genetic diseases, we designed an array-based gene chip to capture all of the exons of 193 genes involved in 103 genetic diseases. To evaluate this technology, we selected 7 samples from seven patients with six different genetic diseases resulting from six disease-causing genes and 100 samples from normal human adults as controls. The data obtained showed that on average, 99.14% of 3,382 exons with more than 30-fold coverage were successfully detected using Targeted DNA-HiSeq technology, and we found six known variants in four disease-causing genes and two novel mutations in two other disease-causing genes... - Daniel Swan

Anecdotally.. I used to hold this view and would not separate out gene lists, until I was asked to try it for a researcher. Using the full list of perturbed genes, nothing of interest came out. Using up and down-regulated lists brought up relevant pathways to the phenotype, and this analysis was included in the subsequent publication. - Daniel Swan

PLoS ONE, Vol. 6, No. 12. (21 December 2011), e28879. Here we describe a virus discovery protocol for a range of different virus genera, that can be applied to biopsy-sized tissue samples. Our viral enrichment procedure, validated using canine and human liver samples, significantly improves viral read copy number and increases the length of viral contigs that can be generated by de novo assembly. This in turn enables the Illumina next generation sequencing (NGS) platform to be used as an effective tool for viral discovery from tissue samples. Gordon Daly, Nick Bexfield, Judith Heaney, Sam Stubbs, Antonia Mayer, Anne Palser, Paul Kellam, Nizar Drou, Mario Caccamo, Laurence Tiley, Graeme Alexander, William Bernal, Jonathan Heeney - Daniel Swan

PLoS ONE, Vol. 7, No. 1. (6 January 2012), e30080. The advent of next generation sequencing (NGS) technologies have revolutionised the way biologists produce, analyse and interpret data. Although NGS platforms provide a cost-effective way to discover genome-wide variants from a single experiment, variants discovered by NGS need follow up validation due to the high error rates associated with various sequencing chemistries. Recently, whole exome sequencing has been proposed as an affordable option compared to whole genome runs but it still requires follow up validation of all the novel exomic variants. Customarily, a consensus approach is used to overcome the systematic errors inherent to the sequencing technology, alignment and post alignment variant detection algorithms. However, the aforementioned approach warrants the use of multiple sequencing chemistry, multiple alignment tools, multiple variant callers which may not be viable in terms of time and money for individual... - Daniel Swan