Project description:A technical comparison of Agilent SureSelect Focussed Exome and TruSight One Mendeliome sequencing kits, by triplicate sequencing of the cell line DNA of NA12878, NA12891, NA12892 and NIST RM8395
Project description:Targeted enrichment-based next-generation sequencing or whole exome sequencing were taken for patients with hypomyelinating leukodystrophies to reveal genetic aetiologies. All genomic DNA used in the experiments was extracted from the peripheral leukocytes. A complete kit was synthetized using the Agilent SureSelect Target Enrichment technique, capturing the coding regions from 104 candidate genes, including their exons and exon-intron boundaries (11,473 probes, 383.065 kbp in total). The following NGS which included equipment and reagents was performed on an Illumina NEXTSEQ500 platform manufactured by Illumina (San Diego, California, USA) using paired-end sequencing of 110 bp. The clean paired-end reads were aligned to the human reference genome build hg19, which was previously annotated using ANNOVAR, in addition to insertion-deletion (indel) and single-nucleotide polymorphism (SNP) calling.
Project description:Targeted enrichment-based next-generation sequencing or whole exome sequencing were taken for patients with hypomyelinating leukodystrophies to reveal genetic aetiologies. All genomic DNA used in the experiments was extracted from the peripheral leukocytes. A complete kit was synthetized using the Agilent SureSelect Target Enrichment technique, capturing the coding regions from 104 candidate genes, including their exons and exon-intron boundaries (11,473 probes, 383.065 kbp in total). The following NGS which included equipment and reagents was performed on an Illumina NEXTSEQ500 platform manufactured by Illumina (San Diego, California, USA) using paired-end sequencing of 110 bp. The clean paired-end reads were aligned to the human reference genome build hg19, which was previously annotated using ANNOVAR, in addition to insertion-deletion (indel) and single-nucleotide polymorphism (SNP) calling.
Project description:Accurate and comprehensive genomic annotation, including the full list of protein-coding genes, is vital for understanding the molecular mechanisms of human biology. We have previously shown that the genome contains a multitude of yet hidden functional exons and transcripts, some of which might represent novel mRNAs. These results resonate with those from other groups and strongly argue that two decades after the completion of the first draft of the human genome sequence, the current annotation of human genes and transcripts remains far from being complete. Using a targeted RNA enrichment technique, we showed that one of the novel functional exons previously discovered by us and currently annotated as part of a long non-coding RNA, is actually a part of a novel protein-coding gene, InSETG-4, which encodes a novel human protein with no known homologs or motifs. We found that InSETG-4 is induced by various DNA-damaging agents across multiple cell types and therefore might represent a novel component of DNA damage response. Despite its low abundance in bulk cell populations, InSETG-4 exhibited expression restricted to a small fraction of cells, as demonstrated by the amplification-based single-molecule fluorescence in situ hybridization (asmFISH) analysis. This study argues that yet undiscovered human protein-coding genes exist and provides an example of how targeted RNA enrichment techniques can help to fill this major gap in our knowledge of the information encoded in the human genome.
