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Broad Institute Genomics Services

Director: Wilkinson, Jane

Location: Broad Institute Genomics Services, 320 Charles St, Cambridge MA 02141

Summary:

For over twenty years, we've been pushing the boundaries of genomics by producing high quality data in a scalable environment. Broad Institute Genomic Services represents a new model for collaboration, offering the global community unprecedented access to capabilities.

Inquiry Form: http://genomics.broadinstitute.org/tell-us-about-your-project

Affiliations:

People:

Resources:

Instruments

Services

  • Clinical Research Sequencing ( Material processing service )

    Our CLIA licensed, CAP accredited Clinical Research Sequencing Platform (CRSP) laboratory provides physicians and physician-researchers with high quality molecular tests such as Whole Exome Sequencing with rapid turnaround times for use in a clinical setting. In addition, our CRSP lab provides clinical researchers with high quality sequencing services under a quality system for use in clinical trials. Supported by 8 HiSeq 2500 sequencers.

  • Custom Content ( Material processing service )

    Our Custom Content Products provide a wide range of solutions, ranging from highly focused genotyping panels to whole genome arrays, targeted to the specific needs of your research application. We have the experience and expertise to develop your custom content into fully validated assay performed in our CLIA licensed, CAP accredited laboratory, ensuring your data can be used to drive clinical discovery. By combining customizable content with other product offerings, we provide the comprehensive resources to extend and validate discovered variants across higher sample numbers.

  • Data Analysis ( Data analysis service )

    Finely-tuned and field-tested across hundreds of thousands of samples spanning flagship genomic initiatives, our tools are the industry-standard for genomic variant discovery. Coupled with the Broad-produced data used to train the tools, our outputs produce clean data with low false-positives and high sensitivity and specificity to discover causal variants. Sequence data analysis with the Picard Data Processing pipeline, VCF generation utilizing Genome Analysis Toolkit (GATK), Transcriptome analysis with TopHat & Star Aligner, GWAS array SNP and CNV analysis utilizing Birdsuite pipeline.

  • GWAS Arrays ( Material processing service )

    Our GWAS Arrays provide you with the greatest statistical power to detect trait and disease-associated variants available at a range of different scales. Optimized using data from the 1000 Genomes Project, Illumina Infinium arrays provide coverage of up to 5 million markers targeting genome-wide and functional exonic variants in cost-effective, high-throughput assays.

  • Nucleic Acid Extractions ( Material processing service )

    Our Nucleic Acid Extractions can be combined with sequencing, GWAS arrays, panels, or custom content products to provide you with an end-to-end solution for your study regardless of sample source. We offer extraction and qualification services for a wide range of sources and formats, including FFPE tissue.

  • Whole Exome Sequencing ( Material processing service )

    Our Human Whole Exome products provide you with the quality, reliability, and speed that come as a result of our experience sequencing more than 150,000 exomes. Optimized for depth and evenness of coverage, with high sensitivity to detect SNVs and indels, our exomes are available with guaranteed turnaround times of as little as 28 days.

  • Whole Genome Sequencing ( Material processing service )

    Our Human Whole Genome products offer the reliability and scalability to produce results you can trust for any size study. Combining the latest HiSeqX sequencing technology with the Broad industry-leading capabilities in process design, automation, and informatics produces the highest quality, most scalable whole genome sequencing available.

  • Whole Transcriptome Sequencing ( Material processing service )

    Our Whole Transcriptome Sequencing products offer a range of solutions tailored to your study's needs. Each product has been optimized to yield the highest quality, most reliable results for its given applications, from differential expression analysis to the discovery and identification of mutations and fusion transcripts, even in FFPE tissue.

Software

  • Genome Analysis Toolkit (GATK) ( Algorithmic software suite )

    The Genome Analysis Toolkit or GATK is a software package for analysis of high-throughput sequencing data, developed by the Data Science and Data Engineering group at the Broad Institute. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

    Used for VCF generation.

  • Picard Data Processing pipeline ( Software )

    - A set of tools for processing and analyzing next generation
    sequencing data
    - A set of pipelines that process all Illumina sequence data
    generated at Broad

  • Star Aligner ( Algorithmic software suite )

  • TopHat ( Algorithmic software suite )

    TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

    TopHat is a collaborative effort among Daehwan Kim and Steven Salzberg in the Center for Computational Biology at Johns Hopkins University, and Cole Trapnell in the Genome Sciences Department at the University of Washington. TopHat was originally developed by Cole Trapnell at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park.


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Last updated: 2016-01-06T10:21:12.642-06:00

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