GenePix Array List (GAL) files are text files with specific information about the location, size, and name of each DNA spot on a microarray. They are therefor of vital importance for the analysis of scanned microarray images. The format defines a specific header before the list of data columns follows:
ATF -> File conforms to Axon Text File
1 -> Version number of ATF
9 -> Number of header lines before the “Block, Column, Row, …” line
5 -> Number of data columns (Block, Column, Row, Name, ID)
Type=GenePix ArrayList V1.0 -> Type of file, same for all GAL files
Block Count=1 -> Number of blocks described in the file
Block Type=0 -> Type of block, 0 = rectangular Block
X=A, B, C, D, E, F, G -> The position and dimensions of each block.
A -> xOrigin
B -> yOrigin
C -> Feature diameter
D -> xFeatures
E -> xSpacing
F -> yFeatures
G -> ySpacing ScanResolution – Optional parameter to scale the position on higher-resolution images Block arrangement
Congress passed the Clinical Laboratory Improvement Amendments (CLIA) act in 1988 to establish quality standards for all non-research laboratory testing:
Performed on specimens derived from humans; and
For providing information for the diagnosis, prevention, and treatment of disease or impairment, or assessment of health.
The objective of the CLIA program is to ensure quality in laboratory testing procedures and specifically to establish quality standards to ensure the accuracy, reliability, and timeliness of the patient’s test results. The CLIA Quality System Regulations became effective on April 24, 2003. Now the laboratory is required to check (verify) the manufacturer’s performance specifications provided in the package insert for:
Accuracy: If test results for previously tested samples fall within the stated acceptable limits, accuracy is verified
Precision: Can the results be repeated mulitple times on the same day and on different days by different operators.
Reportable range: Use known samples to confirm the upper and lower limits of the test.
Also: Reference range or interval: Do the reference ranges provided by the test system’s manufacturer fit your patient population?
The number of samples needs to be established for every test, 20 samples are seen as a “rule of thumb”.
The FDA defines a Laboratory Developed Test (LDT) as an in vitro diagnostic test that is manufactured by and used within a single laboratory (i.e. a laboratory with a single CLIA certificate). LDTs are also sometimes called in-house developed tests, or “home brew” tests. Similar to other in vitro diagnostic tests, LDTs are considered “devices,” as defined by the FFDCA, and are therefore subject to regulatory oversight by FDA.
Sources:Centers for Medicare & Medicaid Services, Genohub
Medical Research Council scientists decipher the complete DNA sequence of the Epstein-Barr virus, 170 kb.
Kary Mullis and colleagues develop the polymerase chain reaction, a technique to replicate small fragments of DNA
Leroy E. Hood’s laboratory at the California Institute of Technology and Smith announce the first semi-automated DNA sequencing machine.
Applied Biosystems markets this first automated sequencing machine, the model ABI 370.
Walter Gilbert leaves the U.S. National Research Council genome panel to start Genome Corp., with the goal of sequencing and commercializing the data.
The U.S. National Institutes of Health (NIS) begins large-scale sequencing trials on Mycoplasma capricolum, Escherichia coli, Caenorhabditis elegans, and Saccharomyces cerevisiae (at 75 cents (US)/base).
BLAST algorithm for aligning sequences published (Lipman, Myers).
Capillary electrophoresis published (Barry Karger, Lloyd Smith, Norman Dovichi).
Official start of the Human Genome Project
Craig Venter develops strategy to find expressed genes with ESTs (Expressed Sequence Tags).
Uberbacher develops GRAIL, a gene-prediction program.
Craig Venter leaves NIH to set up The Institute for Genomic Research (TIGR).
William Haseltine heads Human Genome Sciences, to commercialize TIGR products.
Wellcome Trust begins participation in the Human Genome Project.
Simon et al. develop BACs (Bacterial Artificial Chromosomes) for cloning.
First chromosome physical maps published:
-Page et al. – Y chromosome;
-Cohen et al. chromosome 21.
-Lander – complete mouse genetic map;
-Weissenbach – complete human genetic map.
Wellcome Trust and MRC open Sanger Centre, near Cambridge, UK.
The GenBank database migrates from Los Alamos (DOE) to NCBI (NIH).
Venter, Fraser and Smith publish first sequence of free-living organism, Haemophilus influenzae (genome size of 1.8 Mb).
Richard Mathies et al. publish on sequencing dyes (PNAS, May).
Michael Reeve and Carl Fuller, thermostable polymerase for sequencing.
International HGP partners agree to release sequence data into public databases within 24 hours.
International consortium releases genome sequence of yeast S. cerevisiae (genome size of 12.1 Mb).
Yoshihide Hayashizaki’s at RIKEN completes the first set of full-length mouse cDNAs.
Blattner, Plunkett et al. publish the sequence of E. coli (genome size of 5 Mb)
The human DNA sequence has been read, now we know how the genome works and how to detect and cure genetic diseases, don’t we?
Unfortunately not – or fortunately if you are working in this area. While we know the sequence of bases for a number of reference and other genomes, not only are we far from knowing and understanding all the variations that can be found between different people and the consequences of the variations – but there are also other layers of information in the genome that we are only starting to understand. I am talking about the field of epigenetics here, which looks at molecular “tags” that are attached to the DNA at certain places and play a key role in activation or deactivation of the genes in these places. In contrast to the actual DNA sequence these markers are reversible and get altered during embryonic development and differentiation, i.e. when cells develop into a specific cell types, e.g. a skin cell. They also get modified in a less fortunate way as we get old and in certain disease conditions such as diabetes, inflammation or cancer. The study of these tags is called epigenetics, or epigenomics when applied to the entire human genome.
More specifically, these tags are molecular modifications, mostly methyl-groups that can be attached usually to the Cytosil DNA base and to histones, the proteins that the DNA is wrapped around to “get in shape”.