Biomedical Engineering Reference
In-Depth Information
— 17 inch LCD monitor (recommended)
— operating system Windows XP-SP2 (32 bits) or Windows XP-SP2 (64 bits)
Microsoft NET framework 1.1 (or above)
•
Illumina Beadstudio version 2 and Gencall version 6
•
Microsoft Access.
•
Method
1 Create a 'general' Access database to keep track of all samples.
p
2 Create a separate folder for every new Illumina experiment.
q
,
r
3 Create a specific Access database for each experiment in the 09_Database folder.
4 For each experiment, import the 'final Genotyping report' and the 'Locus-By-DNA' reports
into the database (New, Import Table function in Access).
s
5 Import the genome information table as provided by Illumina in this database.
t
6 Link the experiment database to the general sample sheet database (created in step 1)
by using the 'Link Table' wizard in Access.
7 Make an Access query (e.g. with the Simple Query Wizard) containing the 'final
Genotyping report' and add an extra colum n where the array (SentrixID) is defined
(SentrixID:Left$(tbl_LocusByDNA_final!DNA_Name;7). Save the query as
qryGenotypingfinal.
8 Make an Access query (e.g. with the Simple Query Wizard) containing the
qryGenotypingfinal, the 'Locus-By-DNA' report and the Samplesheet table.
9 To combine the qryGenotypingfinal and the 'Locus-By-DNA' table, join the Locus_Name
and SentrixID columns (use: view join properties). Link the samplesheet table to the
Locus-By-DNA table by joining the DNA_Name to the Sentrix_Position.
10 Select all columns for visualization in the query and add the following calculated
columns to the query:
(a) AB: [Allele1] and [Allele2] which combines the SNP calls into one column.
(b) ABnorm: IIf([AB]
=
'AB';'2';'1') which renames heterozygous SNPs to 2 and
homozygous SNPs to 1.
(c) Ratio: [GC_Score]/[Gentrain_Score] which calculates GCS/gene train score (GTS)
ratios for quality assignment and LOH analysis.
u
(d) ABnormRationorm: IIf([ABnorm]
=
'2'; (IIf([ratio]
>
0.8; [ABnorm];
'1.1'));[ABnorm]).
(e) This column sets each heterozygous SNP with a ratio
<
0.8 to 1.1 instead
of 2.
v
11 Save the query with a descriptive name; for example, qry_finalresults. This query
contains all results for all samples on the array.
