Bioinformatics and Genomics


Stanley Nelson, M.D.


The Muscle Genomics/Bioinformatics Core is designed to enable muscle researchers to access state of the art genomic tools and use sophisticated data processing tools within the Core. The Muscle Genomics/Bioinformatics Core is one component within our community of researchers at the Center for Duchenne Muscular Dystrophy at UCLA that is directed towards promoting translational research in the area of muscle disease, especially muscular dystrophy.  The Core is available to investigators to provide advice and guidance on the use of microarray and massively parallel sequencing tools for genomic assessment.  First, the core provides high density genome wide SNP analysis for genome-wide association studies on large datasets and linkage analysis within small families. Second, the core provides genome wide assessment of RNA abundance using both microarrays and sequencing based methods. Third the core provides genome –scale assessment of alternative splicing. Fourth, the core provides analytical support for the process of microarray gene expression data, microarray based SNP data, and massively parallel sequencing data.  Major technologies available through the Core include Agilent Commercial arrays, Agilent Custom arrays, Affymetrix commercial arrays for DNA and RNA analysis, Illumina GAII based massively parallel genome sequencing.  Sufficient capacity exists to meet the needs of the Center research community due to substantial investments from NIH, the University, and the Department of Human Genetics in the overall UCLA DNA Microarray Facility. However, even with the existence of critical technologies, critically important from the perspective of muscle researchers is the availability of analytical support and advice/guidance on genome-wide. 


a. RNA Preparation and Quality Assessment:

b. DNA Preparation and Quality Assessment  

c. Affymetrix GeneChip Service  

d. Affymetrix SNP array Service  

NSPI 250K SNP assay ($300 per array, array price included) 
Affy 6.0 SNP assay (approximately 1 million SNPs and 1 million copy number probes) ($480 per sample)    

e. Agilent Microarray Service  

f. Microarray hybridization and scanning service for Affymetrix, Agilent, and printed microarrays  

g. Illumina GAII Genomic Analysis  

This system generates 5-10 million 55 nt paired end reads from each of 8 channels in a 7 day run of the machine. Thus up to 5 billion bases of sequence can be generated for individual research projects each run. The CORE will train individuals on the generation of libraries appropriate for the below genomic analyses. The prepared libraries will be attached to the flow cell using a Cluster Generation Station housed within the CORE, and staff of the CORE will perform the sequencing experiment for CENTER investigators.  Types of experimentation already pursued with the facility include counting based gene expression, whole transcriptome alternative splicing analysis, copy number analysis, microRNA quantification genome wide, targeted region resequencing, whole genome methylation analysis, Chromatin-IP analysis by sequencing. 

Informatics support for Solexa based projects:  
The ~100,000 4mp images generated from the sequential sequencing are transferred to a secure server data storage system, and image analysis performed to read 35-55bases  of about 80 million reads per experiment. These data are transferred in the custom developed open source project SeqTools which is a LIMS system integrated with genomic analysis tools to permit the mapping of all 80 million short sequence reads to theappropriate genome and generate reports for the investigators. This process proceeds on 8 compute nodes of the computational cluster (64 processors). Due to the difficulty of handling these data on modern workstations, results are returned to investigators highly processed. Means for returning counting based gene expression data and genomic sequence data via custom tracks of the UCSC Genome Browser have been implemented thus far. 

Alignment with genomic DNA (newly implemented in house developed BFAST algorithm) 
Interpretation of sequence information 
To provide analytical advice and guidance.    

Services Offered: 

h. Experimental Design Guidance 
One-on-one advice is available through Dr. Zugen Chen, Dr. Stan Nelson, and staff(no charge) 

i. Pre-experiment advice and guidance 
Dr. Zugen Chen and Dr. S. Nelson are available to meet with individual researchers to plan genomic experimentation. 

j. Genome wide linkage analysis 
Muscle researchers/clinicians with family member DNA samples may perform genome wide linkage analysis using the Affymetrix 250K NSPI arrays. Dr. Merriman has implemented tools in Mathematica for genome-wide search of recessive and dominant loci which we term ‘pedigree free IBD mapping’ which can identify intervals of genomic sharing between individuals without known family relationships and permits more powerful genetic linkage mapping of mendelian traits. $50 per hour) 

k. Genome-wide gene expression analysis 
Muscle Center researchers will be guided through assessment of microarray data using the DCHIP software to identify differential gene expression. The core also housed a license for the GeneGo software and access the EASE software to determine enrichment of specific pathways. ($50 per hour) 

l. Microarray data analysis for gene expression, LOH, array CGH, and genetic linkage
Statistical support for data analysis for chromosome loss/gain experiments, gene expression including data visualization and expression reports, and linkage analysis using high density arrays are available through the Core. ($50 per hour) 

Training Sessions

The CORE holds practical training sessions for researchers at UCLA on RNA labeling techniques, both for the Affymetrix system and for the Agilent system.  Training sessions are arranged on an as needed basis at a cost of $300 per researcher.  On a daily basis, CORE staff guide users in the application of microarray software and assist users in optimizing probe labellings.  The CORE also sponsors workshops for the use of microarray software and provides ongoing practical feedback to researchers on campus.  Affymetrix Microarray Suite Software is provided free of charge to CORE users.  In additon, dCHIP and GeneSpring software are available at the shared resource.  The CORE staff use R scripts to programmatically access the data set available at UCLA (approximately 12,000 local experiments) and 150,000 experiments from other institutions. These data have been organized into the CELSIUS repository with programmatic access (Day et al 2007).  Users can be trained on how to access experimental database use R libraries and integrate these data into ongoing experiments.


The Core Center is dedicated to understanding processes in degenerative muscle disorders and to identifying therapeutic interventions. In order to most rapidly effect gains, the Center provides a host of interactive intellectual, administrative and research cores. The Center is comprised of four core facilities, all designed to facilitate discovery of therapeutics and test hypotheses related to muscle research. These cores include:

Highthroughput Screening and Cell Repository Muscle Phenotyping and Imaging Bioinformatics and Genomics Back

A primary goal for the Center in creating these Cores is to make available generically useful resources that can be distributed to other researchers in muscular dystrophy or to basic scientists interested in muscle research. The Center is structured to enrich existing muscle research programs on campus by providing its members with access to unique core facilities, pilot funding mechanisms, seminars and an annual retreat focused on muscle research.

Furthermore, the Core Center brings together investigators with a variety of specific interests, some of which are not directly muscle related, to benefit research in muscle disorders.