Targeted NGS was performed on six recurrence patients with serial plasma samples. The KAPA LTP Library Preparation Kit was used to prepare DNA libraries for tumor and paired normal tissues. The Lotus DNA Library Prep Kit (Integrated DNA Technologies) was used to prepare plasma DNA libraries, with dual unique molecular identifiers to minimize false-positives. Subsequently, the xGen Pan-Cancer Panel v2.4 (Integrated DNA Technologies) targeting 532 cancer-related genes was used for target region enrichment, and the enriched libraries were then sequenced on the Illumina HiSeq X NGS platform according to the manufacturer’s instructions. Sequencing data analysis was performed with a combination of Fgbio, Burrows–Wheeler Aligner, Genome Analysis Toolkit, and MuTect2. All sequencing files are available from the National Center for Biotechnology Information’s BioProject database (accession no. PRJNA687345).
Hiseq x ngs platform
Manufactured by Illumina
The HiSeq X NGS platform is a high-throughput next-generation sequencing (NGS) system developed by Illumina. The core function of the HiSeq X is to perform large-scale, whole-genome sequencing with high efficiency and accuracy.
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2 protocols using hiseq x ngs platform
1
Serial Plasma NGS for Recurrence Monitoring
2
Molecular Profiling of Pancreatic Carcinosarcoma
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The carcinomatous and sarcomatous components of pancreatic carcinosarcoma were separately microdissected in one patient by laser capture microdissection. 14, 15 Approximately 7-mm-thick tissue was cut from frozen tissue and lightly stained with hematoxylin. Tumor epithelial cells were dissected manually using a 14-gauge needle under a dissecting microscope.
Targeted next-generation sequencing Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen, Germany). DNA from peripheral blood mononuclear cells was extracted using the DNeasy Blood & Tissue kit. Purified DNA was quantified using Qubit DNA Assay Kit in Qubit 2.0 Flurometer. Sequencing libraries were prepared using the Agilent SureSelect XT Custom kit with a protocol optimized by the manufacturer. To identify the target gene regions, probes were designed for exons of 560 cancer-relevant genes. The sequencing was performed on Illumina HiSeq X NGS platform. An average of 1000 × sequencing depth was intended to obtain. Reads from each sample were mapped to the reference sequence hg19. Somatic single nucleotide variant and small insertions and deletions were selected from paired tumornormal samples by muTect and Strelka, respectively.
Targeted next-generation sequencing Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen, Germany). DNA from peripheral blood mononuclear cells was extracted using the DNeasy Blood & Tissue kit. Purified DNA was quantified using Qubit DNA Assay Kit in Qubit 2.0 Flurometer. Sequencing libraries were prepared using the Agilent SureSelect XT Custom kit with a protocol optimized by the manufacturer. To identify the target gene regions, probes were designed for exons of 560 cancer-relevant genes. The sequencing was performed on Illumina HiSeq X NGS platform. An average of 1000 × sequencing depth was intended to obtain. Reads from each sample were mapped to the reference sequence hg19. Somatic single nucleotide variant and small insertions and deletions were selected from paired tumornormal samples by muTect and Strelka, respectively.
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