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OUR DNA LAB

Learn About Our State of the Art DNA Lab

Karmalife’s DNA Lab

The Karmalife’s DNA Lab was established 16 years ago as a core facility to support genomics research, and has since developed a unique composite of technology and analytic platforms that provide the research community with services in genotyping, sequencing, expression profiling and other functional genomics technologies and with consultative and computational support for design, analysis and interpretation of genomic datasets.

The Lab is distinguished from most other genomics technology providers by both the breadth of its technology services and the remarkable diversity of the individual technology platforms it supports, including a combination of sequencing and genotyping systems, array-based technologies and other systems for expression and other functional genomics analyses that enable exceptional service flexibility and customization so as to optimize project economy, throughput and scope.

The Lab is unique both locally and nationally in its ability to provide a “one-stop” genomics technology service spanning experimental design to data generation, analysis and mining as well as innovative technology development.

The Lab delivers the four consolidated research and technology platforms outlined below:

I. Genotyping: The Lab genotyping service accommodates all types (SNP, microsatellite, structural variant) and scale (single variant to whole-genome) of DNA variant analysis. SNP typing is the most highly-demanded genotyping service and is provided via multiple technology platforms (e.g. ABI7900, Sequenom MassArray, Illumina iSCAN, and Affymetrix GeneTitan) so as to optimize cost-efficiency and throughput for projects and meet ever-increasing demand with minimal wait times.

II. Sequencing: The Lab provides small to large sequencing service via its automated ABI capillary DNA sequencers, two Illumina HiSeq systems, and an Illumina MiSeq. In addition to targeted and whole exome sequencing, Lab next-generation sequencing (NGS)-related services include pre (i.e. target capture, library preparation) and post (sequence curation) sequencing service, RNA-Seq, ChIP-Seq and whole methylome analysis.

III. Expression and other functional genomics analyses: The Labs’s functional genomics service focuses on systematic analysis of gene expression in normal and diseased cells. By deploying multiple technologies (e.g. commercial arrays and NGS-based RNA-Seq), the Lab has unique flexibility to support all scales (global and focused) of expression studies with optimal timing and economy.

IV. Statistical/bioinformatics analysis service : The Lab provides extensive project design as well as statistical and bioinformatics support for all services. the Lab roles in front-end project design include: statistical guidance in study design, population/sample selection and power calculations; technology platform selection (to optimize sample selection, cost efficiency etc); and support for grant or ethics submissions. Lab also supports all aspects of data analysis and mining, including: guidance in statistical analysis of large-scale case/control or population genotyping; support for deep sequencing projects including variant calling and functional annotation of sequence variants and statistical tests for phenotypic associations; and an in-house developed computational pipeline of pathway analysis and other software to mine gene expression, GWAS and other high dimensional datasets.

In the spring of 2012, the Lab moved to Mount Sinai hospital where its 3,000 sq. ft., state-of-the-art facility operates under cGLP guidelines to meet the rigorous standards necessary for DNA analysis and generating quality genotyping data. Automated sample handling and processing is performed by advanced robotics that includes multiple Biomek and Caliper liquid handling systems, and RoboDesign plotting robot which allow for improved precision and massive throughput. The Lab has developed rigorous SOPs for each of its service platforms and have developed strong collaborative working relationships with various companies, including Affymetrix, Illumina, Agena (Sequenom), and Applied Biosystems. Instrumentation such as the BioRad Experion, and NanoDrop systems provide the sample (DNA, RNA, protein) processing and quality testing measures required to ensure rigorous control of sample quality pre-array loading. The facility can accommodate and process all sample formats and hosts an Oracle based database and advanced Laboratory Information Management Software (LIMS) which facilitates easy storage and retrieval of data.

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