Category Archives: News

Exome Chip Rare Caller Pipeline

A pipeline for running Zcall and Opticall on Illumina Exome Chip Datasets. This workflow will handle all the file parsing and run both callers and compare the output bed files.

Repository: https://github.com/KHP-Informatics/chip_gt

Author: Amos Folarin
Organisation: KCL/SLaM
Email: amosfolarin@gmail.com

 

REQUIREMENTS

1) Sun Grid Engine
2) Zcall
3) Opticall

RUNNING THE PIPELINE

1) Read notes (GenomeStudio.SOP.v1.2.docx – the most up-to-date SOP are on the confluence page http://confluence.brc.iop.kcl.ac.uk:8090/display/PUB/Production+Version%3A+Illumina+Exome+Chip+SOP+v1.4 ) on processing the data in GenomeStudio
2) Generate the GenomeStudio Report file (as required for by Zcall, parses this as input for both Zcall and Opticall rare callers):

i) In GenomeStudio select ‘Full Data Table’ tab.
ii) Click on ‘Column Chooser’ icon.
iii) In Displayed Columns select ‘Name’, ‘Chr’,’Position’, and all your samples.
iv) In Displayed Subcolumns select ‘GType’, ‘X’ and ‘Y’.
v) Hit OK then click on ‘Export displayed data to a file’ icon.

3) Copy the template.workflow.sh into a working directory
4) Edit the paths as indicated in this script for your installations of Zcall and Opticall etc.
5) Specify the datapath and basename variables for the GenomeStudio Report generated in step (2)
6) Execute the pipeline bash script (template.workflow.sh).

BRC Partners with Emerald Logic to Identify biomarkers for Alzheimer’s Disease

http://www.drugdiscoverynews.com/index.php?newsarticle=7135

Mining Electronic Health Records Symposium Slides

I hope everyone who came along to the BRC symposium on mining EHRs yesterday had an enjoyable and productive afternoon. Thanks to all of the speakers for some fantastic talks.

I will upload the presentations to the website over the next few days so please keep an eye on the event page if you would like copies.

Cheers,
Cass.

Mitochondrial Dysfunction and Immune Activation are Detectable in Early Alzheimer’s Disease Blood

Lunnon K, Ibrahim Z, Proitsi P, Lourdusamy A, Newhouse S, Sattlecker M, Furney S, Saleem M, Soininen H, Kłoszewska I, Mecocci P, Tsolaki M, Vellas B, Coppola G, Geschwind D, Simmons A, Lovestone S, Dobson R, Hodges A.

J Alzheimers Dis. 2012 Jan 1;30(3):685-710.

PMID: 22466004

Full Text

Abstract

Alzheimer’s disease (AD), like other dementias, is characterized by progressive neuronal loss and neuroinflammation in the brain. The peripheral leukocyte response occurring alongside these brain changes has not been extensively studied, but might inform therapeutic approaches and provide relevant disease biomarkers. Using microarrays, we assessed blood gene expression alterations occurring in people with AD and those with mild cognitive changes at increased risk of developing AD. Of the 2,908 differentially expressed probes identified between the three groups (p < 0.01), a quarter were altered in blood from mild cognitive impairment (MCI) and AD subjects, relative to controls, suggesting a peripheral response to pathology may occur very early. There was strong evidence for mitochondrial dysfunction with decreased expression of many of the respiratory complex I-V genes and subunits of the core mitochondrial ribosome complex. This mirrors changes previously observed in AD brain. A number of genes encoding cell adhesion molecules were increased, along with other immune-related genes. These changes are consistent with leukocyte activation and their increased the transition from circulation into the brain. In addition to expression changes, we also found increased numbers of basophils in people with MCI and AD, and increased monocytes in people with an AD diagnosis. Taken together this study provides both an insight into the functional response of circulating leukocytes during neurodegeneration and also identifies potential targets such as the respiratory chain for designing and monitoring future therapeutic interventions using blood.

BBGRE

The Brain & Body Genetic Resource Exchange (BB-GRE) provides a resource for investigating the genetic basis of neurodisability. It combines phenotype information from patients with neurodevelopmental and behavioural problems with clinical genetic data, and displays this information on the human genome map.