Download Genomic Data-Analysis

Genomic Data-Analysis
At GenomeScan, we use Next Generation Sequencing (NGS) to translate
patient samples into files with GigaBases of data. How are these analyzed?
In what time? What route leads to the right interpretation of the data?
Fast and accurate diagnosis
Our data-analysis workflow leads to identifying the disease-causing
mutation(s). After interpretation of the data, medical specialists will be
able to provide their patients with the diagnosis. Fast and accurate.
Quality
The Leiden University Medical Centre (LUMC) has
developed Magpie, an intricate software pipeline to
analyze diagnostic data. The pipeline is named after
this smart bird, because of its innovative tool-making
abilities. Its name reflects the innovative tools that are
necessary to go from Gigabases of data, to only
single disease-causing mutation(s).
All data-handling is fully automated. This ensures that
data-generation and processing proceed as fast as
possible. We deliver a constant and high data-quality,
thanks to thorough testing and validation. Magpie is
operated as part of multiple ISO 15189 accredited
services. Magpie is updated regularly, so the diagnostic
yield remains at the highest level possible.
We use Magpie for our genetic tests:
• Disease panels (MuscleScan, MODYScan etc.)
• ExomeScan (Whole Exome Sequencing, incl. FFPE)
• GenomeScan (Whole Genome Sequencing)
Magpie implements GATK best practices. The variant
calling pipeline is composed of the following programs:
Program
Used for
FastQC
Collection of raw and preprocessed
sequence metrics
Sickle
Base quality trimming
BWA
Sequence alignment
SAM tools Alignment indexing
Picard
Insert size and capture metrics,
alignment sorting and merging
BEDtools
Coverage calculation
GATK
Variant calling
VCF tools VCF concatenation and sorting
Python
Metrics collection, report generation
QC of raw data
by FastQC
Data cleaning
Sequence
alignment
by BWA
BAM file
Our workflow
We ask for samples of the index-patient and both p
­ arents
(trio-sequencing) to maximally increase the clinical
detection rate. This allows rapid detection of de novo
mutations. Per individual, we find thousands of variants.
Extensive processing leads to a shortlist of suspect
mutations. This is referenced to selected DNA variation
databases such as the Leiden Open Variation Database
(LOVD). These databases contain all published mutations
and their clinical features. Expert laboratory specialists
then identify the disease-causing mutation(s). You will
receive the results in a clear report letter.
Why GenomeScan?
• Large team of specialized Bioinformaticians build and maintain the analysis pipelines
• Skilled Laboratory Geneticists review the variant files and interpret the data
• All variants are stored anonymously in variation databases. This helps to review new variants
• Magpie is operated as part of multiple ISO 15189 accredited services, ensuring a reliable data-analysis procedure.
Variant Calling
by GATK
VCF file
QC filtering
and
annotation
Processed data
to Clinical
Laboratory
Geneticist
GenomeScan offers innovative NGS and microarray-based solutions for genetic research and diagnostics.
Our disease-oriented genetic tests consist of the most up-to-date gene panels.
www.genomescan.nl
T +31 71 568 1050 E [email protected]
Plesmanlaan 1d
2333 BZ Leiden
The Netherlands