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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 : UltraSEEK Oncogene Panel LungCarta Panel OncoCarta Panel iPLEX® Pro Sample ID Panel __________________________________________________________________________________________________ Karolinska University Hospital Huddinge, Mutation Analysis Facility MAF, KFC Novum plan 5, Hälsovägen 7-9, 14152 HUDDINGE www.maf.ki.se