GAL file format

July 20th, 2017

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:

Example:

ATF	1			

9	5			

Type=GenePix ArrayList V1.0				

BlockCount=1				

BlockType=0				

"Block1=10000, 38780, 150, 20, 200, 18, 200"				

Supplier=BioRobotics				

ArrayerSoftwareName=TAS Application Suite (MicroGrid II)				

ArrayerSoftwareVersion=2.7.1.18					

ScanResolution=10	

Block	Column	Row	ID	Name

1	1	1	RP11-163J21	Clone 1

1	1	2	RP11-163J21	Clone 2

Explanantions:

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

1	2	3	4

5	6	7	8

9	10	11	12

13	14	15	16

The data columns are:

  • Block
  • Column
  • Row
  • Name
  • ID

Further reading and sources:

aCGH array QC measures

July 20th, 2017

The within-array quality for (genomic) microarrays is often measured using the following metrics:

  1. Standard Deviation Autosome / Robust (SD autosome) Measure of the dispersion of Log2 ratio of all clones on the array, giving an overall picture of the noise in the array. It is calculated on the normalised but unsmoothed data. The SD robust is the middle 58%/66% of the data. By excluding outliers large changes such as trisomies will not cause this number to change significantly. (The SD robust is the number we use when we say “3 SDs away from the noise” in the calling algorithm.) Both measures are given after all data processing but excluding any smoothing. For BlueFuse Multi processed data the values should be 0.07-0.15 and 0.05-0.11 for the autosome and robust measure respectively.
  2. Signal to Background Ratio (SBR) Brightness of the mean signal (after the background has been subtracted) divided by the raw background signal (global signal).
  3. Derivative Log2 Ratio / Fused (DLR) measure of the probe to probe variability. In an ideal world, probes within a region will have essentially the same ratio. In a noisy array adjacent probes can have a very large ratio difference. The DLR raw is before any data processing, DLR fused is after normalization and data correction BUT is always done on unsmoothed data so it is user setting independent and a cannot be adjusted by the user thereby giving a consistent array-to-array measure of noise. BlueFuse results should be < 0.2.
  4. % included clones Percentage of all clones that were not excluded on a BAC array due to inconsistencies between clone replicates. For BlueFuse results this should be > 95 %.
  5. Mean Spot Amplitude the mean fluorescent signal intensities for the two channels; channel 1 = sample (standardly Cy3; ex 550nm, emm 570nm) and channel 2 = reference (standardly Cy5; ex 650nm, emm 670nm). This metric is variable due to the differences between available scanners. The mean spot amplitude metric can give an indication of how well the DNA has labelled with fluorescent dyes, but more importantly, really high values can indicate over scanning of the microarray image OR can indicate poor washing so there is lots of non-specific signal left. The balance between channels can be assessed but the Cy5 signal tends to give a higher intensity than Cy3, major differences in the channels may indicate a labelling or a scanner problem.

Source: BlueGnome user docs

See also: Microarray Scanners and PGS consulting in the UK & Ireland

Vaccination of newborns

April 28th, 2017

Most of us take vaccinations for granten and rely on them from our very first days. The whooping cough as an example can be deadly, especially for young babies who are too young to be protected by their own vaccination. Since 2010, the Centers for Disease Control and Prevention (CDC) has recorded between 10,000 and 50,000 cases each year in the United States and up to 20 babies dying. One recent study showed that many whooping cough deaths among babies could be prevented if all babies received the first dose of vaccination on time at 2 months old, when they are old enough to get vaccinated (CDC). Still, some parents believe they know better and risk their childrens life by not vaccinating them at all. 

 

For the US the CDC recommends vaccination of newborns / babies against the following diseases:

For Germany the situation is almost the same and the following vacciantions are recommended for babies under 2 years:

  • Hib H. influenzae Typ b
  • Diphtherie
  • Hepatitis B
  • Masern
  • Mumps
  • Pertussis (Keuchhusten)
  • Pneumokokken
  • Poliomyelitis (Kinderlaehmung)
  • Röteln
  • Tetanus
  • Rotaviren
  • Varizellen (Windpocken)
  • Meningokokken C

Sources: CDC, Robert-Koch-Institut

Genetic Conditions Screened in Newborns

April 13th, 2017
Genetic Conditions Screened in Newborns

As part of the health assessment of newborn babys, a test for common genetic conditions is done by drawing a few drops of blood from the heel of the baby and sending this off for analysis. Any positive results will then be followed up by confirmatory test and a treatment can be initiated if required. The conditions are mostly life-threatening or disabeling for the child if undiagnosed or left untreated.

Below is a list of conditions that are screened as part of the current standard panel of core conditions and secondary conditions in the US-american health system. Secondary conditions are results that will be additionally (unintentinally) revealed when testing for the core conditions. If desired there are even more options for testing (supplemental screening). What test are offered or paid for depends on the state and the insurance. This information is taken from babysfirsttest.org.

 

1. Metabolic Disorders

ORGANIC ACID CONDITIONS

  • 2-Methyl-3-Hydroxybutyric Acidemia (2M3HBA)
  • 2-Methylbutyrylglycinuria (2MBG)
  • 3-Hydroxy-3-Methylglutaric Aciduria (HMG) *
  • 3-Methylcrotonyl-CoA Carboxylase Deficiency (3-MCC) *
  • 3-Methylglutaconic Aciduria (3MGA)
  • Beta-Ketothiolase Deficiency (BKT) *
  • Ethylmalonic Encephalopathy (EME)
  • Glutaric Acidemia, Type I (GA-1) *
  • Holocarboxylase Synthetase Deficiency (MCD)
  • Isobutyrylglycinuria (IBG)
  • Isovaleric Acidemia (IVA) *
  • Malonic Acidemia (MAL)
  • Methylmalonic Acidemia (Cobalamin Disorders) (Cbl A,B) *
  • Methylmalonic Acidemia (Methymalonyl-CoA Mutase Deficiency) (MUT) *
  • Methylmalonic Acidemia with Homocystinuria (Cbl C, D, F)
  • Propionic Acidemia (PROP) *

FATTY ACID OXIDATION DISORDERS

  • 2,4 Dienoyl-CoA Reductase Deficiency (DE RED)
  • Carnitine Acylcarnitine Translocase Deficiency (CACT)
  • Carnitine Palmitoyltransferase I Deficiency (CPT-IA)
  • Carnitine Palmitoyltransferase Type II Deficiency (CPT-II)
  • Carnitine Uptake Defect (CUD) *
  • Glutaric Acidemia, Type II (GA-2)
  • Long-Chain L-3 Hydroxyacyl-CoA Dehydrogenase Deficiency (LCHAD) *
  • Medium-Chain Acyl-CoA Dehydrogenase Deficiency (MCAD) *
  • Medium-Chain Ketoacyl-CoA Thiolase Deficiency (MCAT)
  • Medium/Short-Chain L-3 Hydroxyacyl-CoA Dehydrogenase Deficiency (M/SCHAD)
  • Short-Chain Acyl-CoA Dehydrogenase Deficiency (SCAD)
  • Trifunctional Protein Deficiency (TFP) *
  • Very Long-Chain Acyl-CoA Dehydrogenase Deficiency (VLCAD) *

AMINO ACID DISORDERS

  • Argininemia (ARG)
  • Argininosuccinic Aciduria (ASA) *
  • Benign Hyperphenylalaninemia (H-PHE)
  • Biopterin Defect in Cofactor Biosynthesis (BIOPT-BS)
  • Biopterin Defect in Cofactor Regeneration (BIOPT-REG)
  • Carbamoyl Phosphate Synthetase I Deficiency (CPS)
  • Citrullinemia, Type I (CIT) *
  • Citrullinemia, Type II (CIT II)
  • Classic Phenylketonuria (PKU) *
  • Homocystinuria (HCY) *
  • Hypermethioninemia (MET)
  • Hyperornithine with Gyrate Deficiency (Hyper ORN)
  • Maple Syrup Urine Disease (MSUD) *
  • Nonketotic Hyperglycinemia (NKH)
  • Ornithine Transcarbamylase Deficiency (OTC)
  • Prolinemia (PRO)
  • Tyrosinemia, Type I (TYR I) *
  • Tyrosinemia, Type II (TYR II)
  • Tyrosinemia, Type III (TYR III)

 

2. Endocrine Disorders

  • Congenital Adrenal Hyperplasia (CAH) *
  • Primary Congenital Hypothyroidism (CH) *

 

3. Hemoglobin Disorders

  • Glucose-6-Phosphate Dehydrogenase Deficiency (G6PD)
  • Hemoglobinopathies (Var Hb)
  • S, Beta-Thalassemia (Hb S/ßTh) *
  • S, C Disease (Hb S/C) *
  • Sickle Cell Anemia (Hb SS) *

 

4. Other Disorders

  • Adrenoleukodys-trophy (ALD)
  • Biotinidase Deficiency (BIOT) *
  • Classic Galactosemia (GALT) *
  • Congenital Toxoplasmosis (TOXO)
  • Critical Congenital Heart Disease (CCHD) *
  • Cystic Fibrosis (CF) *
  • Formiminoglutamic Acidemia (FIGLU)
  • Galactoepimerase Deficiency (GALE)
  • Galactokinase Deficiency (GALK)
  • Hearing loss (HEAR)
  • Human Immunodeficiency Virus (HIV)
  • Hyperornithinemia-Hyperammonemia-Homocitrullinuria Syndrome (HHH)
  • Pyroglutamic Acidemia (5-OXO)
  • Severe Combined Immunodeficiency (SCID) *
  • T-cell Related Lymphocyte Deficiencies

 

5. Lysosomal Storage Disorders

  • Fabry (FABRY)
  • Gaucher (GBA)
  • Krabbe
  • Mucopolysaccharidosis Type-I (MPS I)
  • Mucopolysaccharidosis Type-II (MPS II)
  • Niemann-Pick Disease (NPD)
  • Pompe (POMPE)

 

See more at: www.babysfirsttest.org

Comparing instance prices on the Amazon cloud

April 13th, 2017


As the largest cloud computing company Amazon Web Services (AWS) offers various options to use compute-power on a "as-needed" basis. You can choose what size and type of machine, what number of machines - and you can choose a price model where you are "bidding" for the resource. This means you might have to wait longer to get it, but you will get an impressive discount! You can choose your machines from the AWS dashboard.

 

Here is a comparison of the current prices for "General Purpose - Current Generation" AWS machines in the EU (Frankfurt) region (as of 13/04/2017):

vCPU ECU Memory (GiB) Instance Storage (GB) Linux / UNIX Usage On-Demand Price per Hour Spot Price per Hour Saving %
m4.large 2 6.5 8 EBS Only $0.129 $0.0336 74
m4.xlarge 4 13 16 EBS Only $0.257 $0.0375 85
m4.2xlarge 8 26 32 EBS Only $0.513 $0.1199 77
m4.4xlarge 16 53.5 64 EBS Only $1.026 $0.3536 66
m4.10xlarge 40 124.5 160 EBS Only $2.565 $1.1214 56
m4.16xlarge 64 188 256 EBS Only $4.104 $0.503 88
m3.medium 1 3 3.75 1x4 SSD $0.079 $0.0114 86
m3.large 2 6.5 7.5 1x32 SSD $0.158 $0.0227 86
m3.xlarge 4 13 15 2x40 SSD $0.315 $0.047 85
m3.2xlarge 8 26 30 2x80 SSD $0.632 $0.1504 76

 This only shows a selection of machine options and the prices obviously change over time - but the message should be clear...