study #: Study 1 (Somatic) trio #: NA twin #: NA twin info: NA gender: M phenotype: PD
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was extracted from leukocytes using the phenol chloroform method or Qiamp blood kits (Qiagen Pty Ltd, Doncaster, Vic, Australia), hair using the phenol chloroform method, and from sperm using Pure Sperm 100 kits (Nidacom, Gothenburg, Sweden).
Label
biotin
Label protocol
According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia), Affymetrix dsDNA terminal label.
Hybridization protocol
According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Scan protocol
According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Description
Affy 6.0 PD Brain (Brodmann area 46)
Data processing
Data processed using Affymetrix Command Console software and Affymetrix Genotyping Console 3.0.2 software using the Birdseed version 2 algorithm and default settings. Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
Affymetrix 6.0 study of sporadic motor neuron disease patients and controls.
Data table header descriptions
ID_REF
PROBE SET NAME
VALUE
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
CONFIDENCE
A value in the range [0,1] with lower values corresponding to greater confidence
FORCED CALL
This value is the genotyping call that would be made if the calling algorithm were tuned to the least stringency. Providing this value allows for determining what the calls would have been at a stringency different to that applied to the calls in the second field, without having to re-run the genotyping algorithm
