Genomic DNA was extracted from blood, whole genome amplified (74 familial UBC cases), exome captured with NimbleGen SeqCap EZ Human Exome Library, and sequenced on the Illumina HiSeq 2000 platform. The human reference genome and the known gene transcript annotation were downloaded from the UCSC database, hg19. Sequencing reads were trimmed (Trimmomatic), and only read pairs with both ends > 36 bp were used. Reads were aligned to the reference genome (NovoAlign). Duplicate reads were removed (MarkDuplicates), and only read pairs mapped in complementary directions at a fragment length of 200-400 bp were used. These alignments were further refined (RealignerTargetCreator and IndelRealigner). Variant discovery and genotype calling were performed on all individuals globally (UnifiedGenotyper, HaplotypeCaller from GATK, and FreeBayes). The three callers were used to call each sample in parallel, and the caller-specific results were generated independently. The ensemble variant calling pipeline was then implemented to integrate the results from the three callers.
Seqcap ez human exome library
Manufactured by Illumina
The SeqCap EZ Human Exome Library is a targeted enrichment system designed for sequencing the protein-coding regions of the human genome, known as the exome. It provides a comprehensive solution for capturing and sequencing the human exome, which represents approximately 1% of the total human genome but contains the majority of disease-associated genetic variations.
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2 protocols using seqcap ez human exome library
1
Ensemble Variant Calling Pipeline for Exome Sequencing
2
Exome Sequencing of Japanese Peripheral Blood Cells
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We sequenced libraries generated from genomic DNA derived from peripheral blood mononuclear cells of Japanese descent. Each exome captured sequencing library was produced from one of four different technologies: Roche/NimbleGen’s SeqCap EZ Human Exome Library v3.0, Illumina’s Nextera Rapid Capture Exome (v1.2), Agilent’s SureSelect XT Human All Exon v5 and Agilent’s SureSelect QXT. Each exome capture platform method was performed according to the manufacturer’s instructions except for Illumina platform. For the Illumina platform, we used 100 ng of total input genomic DNA. The captured DNA was sequenced using the Illumina HiSeq2500 platform with paired-end reads of 161bp for insert libraries according to the manufacturer’s instructions. We deposited all DNA sequence data used in this study to the National Bioscience Database Center (NBDC) Human Database (http://humandbs.biosciencedbc.jp/ ).
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