Download Newsletter JUNE 2014

Newsletter JUNE 2014
Illumina iScan platform
Sequenom name change
Agena Bioscience, a portfolio company of Telegraph Hill Partners, has
acquired the Bioscience business of Sequenom, Inc. Agena Bioscience
aims to continue to advance the MassARRAY® MALDI-TOF System
through ongoing investment and key collaborations. The plans at
Agena Bioscience are to continue to enhance the MassARRAY System
with expanded automation, applications, software functionality, high
value assay content, and resources to support its growing use in basic,
agricultural, and clinical research.
ID panel
MAF has developed and validated a Sample Identification SNP Panel
for Exome, Transcriptome and Whole Genome Sequencing, together
with Science for Life Laboratory in Stockholm.
A panel consisting of 54 single nucleotide polymorphisms (SNPs) has
been developed to enable the unique identification of human samples.
The panel is meant to be used as a quality control step by high
throughput sequencing laboratories, ensuring that generated sequence
data is matched to the correct sample id. The panel can be used for
the identification of exome, transcriptome, and whole genome
sequenced samples.
FH panel
Familial hypercholesterolemia (FH) is an autosomal dominant disease
causing high levels of LDL cholesterol and high risk of premature
cardiovascular events and death. MAF has together with researchers at
Karolinska developed a panel consisting of 117 known mutations in the
LDLR, APO-B and PCSK-9 genes. Results of a pilot study including 37
Swedish individuals with probable FH were promising and indicate that
the panel may serve as a valuable diagnostic method. However, a
larger number of individuals will need to be investigated before its
efficacy can be fully concluded. Recruitment of additional individuals
with probable FH to the study is currently taking place.
To date, about 1300 samples have been analysed with Illumina
Infinium Methylation 450K arrays on the iScan platform, using the
Tecan Freedom Evo robot. Moreover, two gene expression projects
using Human HT-12 Expression arrays were recently completed.
MAF can perform any type of project that can be analysed using the
iScan platform. Illumina has a broad portfolio of Beadchips for the
iScan system which encompasses: genotyping, CNV analysis, DNA
methylation, and gene expression profiling. For more information:
http://www.illumina.com/applications/microarrays.ilmn?sciid=2014245
IBN1.
Throughout 2014, we are offering a 20% price-reduction on
Illumina 450K Methylation arrays.
Accreditation and quality assurance
MAF is a member of the European Molecular Genetics Quality Network
(EMQN) (http://www.emqn.org/emqn/Home). This network can be
used for proficiency testing by accredited laboratories such as MAF. We
recently participated in the Familial hypercholesterolemia - 2014 EQA
scheme which involved the comparison of data resulting from the
genetic analysis of the same samples, using different methods, at a
number of laboratories across Europe. MAF’s Sequenom genotyping
results were fully concordant.
Summer at MAF
MAF will be closed from 14th of July until 1st of August. If you need to
reach us during summer, please e‐mail [email protected] to reach
available staff.
MAF homepage
Please visit our homepage and find more information and current
news. www.maf.ki.se
HPV typing
The typing of Human Papilloma Virus (HPV) continues successfully. To
date, 20,000 samples have been analysed at MAF and we have
received a request for the analysis of almost 16,000 new samples.
For more information concerning the applications in the newsletter
please contact: Kristina Duvefelt +46 8 585 83693,
[email protected].
Sequenom panels
In our last newsletter, we announced that MAF was one of three
laboratories selected for beta testing the Hemo ID™ Blood Group
Genotyping Panel v1.0 for use on the MassARRAY® System. The
beta test was successfully completed early this year and an abstract
has been submitted to the 2014 British Blood Transfusion Society
(BBTS) Annual Conference. The Hemo ID panel was officially released
early this month. It consists of six independent modules each
containing a distinct set of assays which are used to interrogate 108
single nucleotide variations and indels in the human genome. The six
modules consist of: 1) Kell, Kidd, Duffy, 2) MNS, 3) Rare Blood
Groups, 4) RHD/CE Broad, 5) RHD Variant and 6) HPA & HNA.
Sequenom also has a number of other panels available :
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UltraSEEK Oncogene Panel
LungCarta Panel
OncoCarta Panel
iPLEX® Pro Sample ID Panel
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Karolinska University Hospital Huddinge, Mutation Analysis Facility MAF, KFC Novum plan 5, Hälsovägen 7-9, 14152 HUDDINGE
www.maf.ki.se