Whole-exome sequencing of the tumor and leukocyte DNA samples from the patient and his mother were performed using the TargetSeq™ Exome Enrichment Kit (Life Technologies), followed by paired-end sequencing (75 × 50) in SOLiD 5500xl System (Life Technologies). Leukocyte DNA sample from his father was submitted for whole-exome sequencing using Ion Xpress™ Plus Fragment Library kit and Ion TargetSeq™ Exome Enrichment Kit (Life Technologies), followed by sequencing at Ion Proton™ platform (Ion Torrent™), according to the manufacturer’s instructions. Single-end sequencing was performed on an Ion PI™ Chip v2 with 200 pb sequencing kit (Ion Torrent™).
Targetseq exome enrichment kit
Manufactured by Thermo Fisher Scientific
Sourced in United States
The TargetSeq™ Exome Enrichment Kit is a laboratory tool designed for targeted enrichment of human exonic regions. It enables selective capture and sequencing of protein-coding regions of the genome.
Automatically generated - may contain errors
Lab products found in correlation
5500 solid fragment library core kit, by Thermo Fisher Scientific (2 mentions)
5500 solid fragment library barcodeadaptors 1 16, by Thermo Fisher Scientific (2 mentions)
Dneasy blood tissue kit, by Qiagen (2 mentions)
Ion proton platform, by Thermo Fisher Scientific (1 mentions)
Solid 5500xl system, by Thermo Fisher Scientific (1 mentions)
Ion xpress plus fragment library kit, by Thermo Fisher Scientific (1 mentions)
Solid5500, by Thermo Fisher Scientific (1 mentions)
Solid 5500 xl sequencing platform, by Thermo Fisher Scientific (1 mentions)
Sureselect qxt kit, by Agilent Technologies (1 mentions)
Hiseq platform, by Illumina (1 mentions)
High sensitivity dna kit, by Agilent Technologies (1 mentions)
5 protocols using targetseq exome enrichment kit
1
Whole-Exome Sequencing of Patient and Family
2
Whole Exome Sequencing of Multiple Cancers
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Serial samples of normal tissue, atypical adenomatous hyperplasia (AAH), and MPM tissue from the patient with multiple cancers including MPM were used for the exome sequencing library preparation. SOLiD 5500 (Life Technologies) was used for whole exome sequencing according to the manufacturer's protocol and our previous experiment [32 (link)]. Briefly, 3 ug of DNA was fragmented by Covaris S220 (Covaris), and the fragmented DNA was barcode ligated and amplified. After fragmented DNA was quantified, 500 ng of DNA was used for the TargetSeq Exome Enrichment kit (Life Technologies) to enrich the exome only. A diluted exome library was amplified by emulsion PCR and enriched. The prepared libraries were run onto the Flow Chip in SOLiD 5500.
3
Exome Sequencing for Mutation Analysis
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To analyse the mutation profile of clones, exome sequencing was performed after UVA irradiation. Libraries were prepared with 5 μg of genomic DNA using the Sure Select QXT kit (Agilent Technologies, Santa Clara, CA, USA). Sure Select QXT Human All Exon V6 baits were used for the exome capture procedure. Library preparation and the exon capture were carried out following the manufacturer's specifications. Quality control of libraries was performed with two kits: a High Sensitivity DNA kit (Agilent Technologies) and an Illumina library Quantification kit with primer premix and Light Cycler 480 qPCR mix (KAPA Biosystems, Wilmington, MA, USA). Libraries were sequenced in paired-end mode (2 × 125 bp) on the Illumina HiSeq platform (Illumina, San Diego, CA, USA). Similar but entirely independent experiments were performed using the SOLiD 5500xl sequencing platform (Applied Biosystems, Cleveland, Ohio, EUA) in paired-end mode (75 × 35 bp) with the TargetSeq Exome Enrichment Kit (Life Technologies, Carlsbad, CA, USA). The results are shown in detail in the Supplementary data (Supplementary Figures S2 and S3 ).
4
Exome Sequencing of HNSCC Cell Lines
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Genomic DNA from HNSCC lines and matched blood samples was
isolated from frozen cell pellets using the DNeasy Blood & Tissue
Kit (QIAGEN). Multiplexed libraries for exome capture sequencing were
constructed utilizing the 5500 SOLiD Fragment Library Core Kit,
TargetSeq Exome Enrichment Kits and 5500 SOLiD Fragment Library Barcode
Adaptors 1–16 (Life Technologies). The exome enriched genomic DNA
libraries were clonally amplified by emulsion PCR. Whole-exome
sequencing achieved an average of 87x coverage across targeted bases,
with 85% of target bases above 20x coverage.
isolated from frozen cell pellets using the DNeasy Blood & Tissue
Kit (QIAGEN). Multiplexed libraries for exome capture sequencing were
constructed utilizing the 5500 SOLiD Fragment Library Core Kit,
TargetSeq Exome Enrichment Kits and 5500 SOLiD Fragment Library Barcode
Adaptors 1–16 (Life Technologies). The exome enriched genomic DNA
libraries were clonally amplified by emulsion PCR. Whole-exome
sequencing achieved an average of 87x coverage across targeted bases,
with 85% of target bases above 20x coverage.
5
Exome Sequencing of HNSCC Cell Lines
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