TruSeq DNA Exome FAQs

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  • General


  • Nextera DNA Exome uses transposon-based fragmentation while TruSeq DNA Exome uses an alternate enrichment protocol that uses mechanical shearing. 

    The TruSeq DNA Exome method makes it suitable for DNA that does not respond well to Nextera tagmentation. The TruSeq DNA Exome protocol is a combination of the proven TruSeq Nano Library Prep and Enrichment kits. 

    The number of samples pooled pre-enrichment depends on the kit being used. The input amount of each library changes as plexity changes. Refer to the reference guide for the different plexities available and for detailed guidance.

    Library Prep Component

    Catalog #

    TruSeq DNA Library Prep for Enrichment (24 Samples)

    20020181

    TruSeq DNA Library Prep for Enrichment (96 Samples)

    20020182

     

     

    Index Adapter Component

    Catalog #

    TruSeq DNA Single Indexes (12 indexes, 24 samples) Set A

    20015960

    TruSeq DNA Single Indexes (12 indexes, 24 samples) Set B

    20015961

    TruSeq DNA Combinatorial Dual Indexes (96 indexes, 96 samples)

    20015949

     

    The following enrichment and panel components are available to order through IDT. From IDT, order two catalog numbers for the enrichment component (Blockers and Lockdown reagents) and one catalog number for the panel component depending on the number of samples for your experiment. More information can be found on the IDT website

    Enrichment Component

    Catalog #

    IDT xGen Universal Blockers- TS Mix (16 reactions)

    1075474

    IDT xGen Universal Blockers- TS Mix (96 reactions)

    1075475

    IDT xGen Lockdown Reagents (16 reactions)

    1072280

    IDT xGen Lockdown Reagents (96 reactions)

    1072281

     

     

    Panel Component

    Catalog #

    IDT xGen Exome Research Panel v1.0 (16 reactions)

    1056114

    IDT xGen Exome Research Panel v1.0 (96 reactions)

    1056115

    The following kits are available for performing the TruSeq DNA Exome workflow using Illumina reagents for library preparation and enrichment. These kits include index adapters and do not need to be ordered separately.

    Library Prep Kit

    Catalog #

    TruSeq Exome Kit (24 samples)

    20020614

    TruSeq Exome Kit (96 samples)

    20020615

    Single index adapters are provided in tubes.  Each i7 indexed adapter is paired in its tube with the same universal adapter that contains no (i5) barcode.

    Combinatorial Dual Indexed Adapters are plated pairs of adapters such that every i5 indexed adapter would be paired with each i7 indexed adapter in a arrayed matrix across the plate.

    Unique Dual Indexed Adapters are plated pairs of adapters such that every i5 indexed adapter and every i7 indexed adapter is only used once on a plate. With unique dual index adapters, identification and filtering of indexed hopped reads allow customers to confidently multiplex their samples.

    Illumina recommends using Unique Dual Indexed Adapters for library prep and sequencing on Illumina sequencers.

  • Sequencing


  • The insert fragments have a median size of ~150 bp. Therefore, a 2 x 76 sequencing run is recommended. Longer sequencing lengths show diminishing returns in terms of coverage.

  • Analysis


  • TruSeq Exome Enrichment data can be analyzed using the HiSeq Analysis Software enrichment workflow for HiSeq data or MiSeq Reporter Enrichment workflow for MiSeq data. For more information, see the HiSeq Analysis Software or MiSeq Reporter support pages.

    If the run is being uploaded to Basespace or BaseSpace Onsite, the samples can be analyzed with either the BWA Enrichment or ISAAC Enrichment apps. Make sure that the correct manifest is selected before running the app.

    Alternately, Illumina sequence base call output files (*.bcl) can be demultiplexed and converted to FASTQ format using the bcl2fastq converter software. The files can then be used for analysis with other third party software packages (eg, BWA and GATK).

    Datasets are available on the BaseSpace Public Data page.