Genetics Core Laboratory

The objective of the genetic core facility is to provide genetic testing services and help investigators to refine the objectives for using genetic testing as part of your research study. The genetic core is located on the 5th floor of Children's Hospital. The laboratory provides access to a wide variety of "state of the art" molecular biology, genetics, genomics, and proteomics technologies. Staff is available to discuss how the genetic core lab can help you to achieve your research goals. Larger scope projects may need to be set up as a collaborative effort and should be discussed with the Center Director.

Standard services includes:

  • DNA and RNA extraction

  • DNA banking

  • DNA sequencing and mutation detection/ genotyping

  • DNA mutation or SNP screening

  • SNP Chip

  • Quantitative RT-PCR (Licor, TaqMan)

  • Western blot analysis

  • Expression profiling using Affymetrix GeneChips or cDNA microarray

  • Muscle biopsy protein analysis (to diagnose/ confirm diagnosis of muscular dystrophy)

  • Linkage analysis

  • Laser capture microdissection (LCM)

  • Proteomics and Mass Spectrometry analysis

  • Immunohistochemistry

  • Genetic counseling

These technologies can be used to help you explore the genetic and molecular aspects of your research. Following are descriptions of the most commonly used tools:

Sequencing of genomic DNA can be used to find mutations or polymorphisms in genes implicated in disease pathogenesis. This can be done fairly simply depending on the size of the gene involved and the number of samples. DNA can be obtained from almost any tissue or fluid. For example, in humans, DNA can be easily isolated from 3cc -5cc of blood; buccal (cheek) swabs, and mouthwash rinses.

Expression profiling is a tool that can be used to determine genetic patterns of disease. It is a very sensitive tool, which generates a high volume of data. Data reflects what genes are up or down regulated at any given time point in a given tissue. This tool is particularly well suited to investigate pathways involved in disease pathogenesis. These experiments are carried out on RNA from flash-frozen tissue samples. It is best to obtain the sample from the organ or tissue most implicated in the disease pathogenesis. Experimental design is extremely important in expression profiling in order to obtain meaningful information and to reduce experimental "noise" (variability among samples). Pooling RNA within the disease and control groups can help overcome the problems of variation from person to person, but it is important to control for variation in sex, age, race, and disease progression or severity. It is therefore very important to discuss the experimental design with the genetic core staff before designing your study.

Western blots and QMF-RT-PCR allow you to quantitate the amount of a particular protein or RNA expressed in cells. These techniques are often used to validate expression-profiling results.

Linkage analysis is used to find the chromosomal region, which is shared by affected family members but not their healthy relatives. Well-constructed, preferably large family pedigrees (10 family members) are needed for linkage analysis. Successful linkage analysis will lead to gene identification for the disease of interest.
SNP Chips can be used in a similar fashion as linkage analysis. SNP chips consist of 100,000 SNPs (normal variants). A comparison of SNPs shared between healthy family members and affected family members will lead to gene identification for the disease of interest. Well constructed large families consisting of affected and unaffected individuals are needed.

Proteomics (global analysis of proteins) promises to be a powerful tool to understand molecular mechanisms involved in human diseases and pathophysiology. One of the main goals of many proteomics studies is to measure protein abundances and/or modifications between samples representing different biological states (e.g. disease vs. healthy). Proteins can be extracted from tissue, cells and organelles and analyzed using different techniques such as two dimensional gel electrophoresis, liquid chromatography and mass spectrometry. Comprehensive protein analysis might help define new therapeutic targets for better treatment.

A genetic counselor is available to help with human subjects issues and to provide genetic counseling services for protocols that involve releasing genetic testing results to participants. Please note that all projects using the genetics core must have IRB approval prior to the submission of the first sample.

If you are interested in using the genetic core facilities, please contact us to set up a meeting with the core laboratory manager Susan Knoblach at 202-884-6094 or SKnoblach@cnmcresearch.org