ABSTRACT: Paired-end BAM files with associated index files of 15 AML samples were generated using Agilent SureSelect XT library capture system using a custom panel as described before Takahashi et al Blood 2018. Libraries were sequenced using Illumina HiSeq 2500.
Project description:Targeted capture massively parallel sequencing is increasingly being used in clinical settings, and as costs continue to decline, use of this technology may become routine in health care. However, a limited amount of tissue has often been a challenge in meeting quality requirements. To offer a practical guideline for the minimum amount of input DNA for targeted sequencing, we optimized and evaluated the performance of targeted sequencing depending on the input DNA amount. First, using various amounts of input DNA, we compared commercially available library construction kits and selected Agilent's SureSelect-XT and KAPA Biosystems' Hyper Prep kits as the kits most compatible with targeted deep sequencing using Agilent's SureSelect custom capture. Then, we optimized the adapter ligation conditions of the Hyper Prep kit to improve library construction efficiency and adapted multiplexed hybrid selection to reduce the cost of sequencing. In this study, we systematically evaluated the performance of the optimized protocol depending on the amount of input DNA, ranging from 6.25 to 200?ng, suggesting the minimal input DNA amounts based on coverage depths required for specific applications.
Project description:Whole exome sequencing (WXS) is widely used to identify causative genetic mutations of diseases. However, not only have several commercial human exome capture platforms been developed, but substantial updates have been released in the past few years. We report a performance comparison for the latest release of four commercial platforms, 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, using the same DNA samples. Agilent XT showed the highest target enrichment efficiency and the best SNV and short indel detection sensitivity in coding regions with the least amount of sequencing. Agilent QXT had slightly inferior target enrichment than Agilent XT. Illumina, with additional sequencing, detected SNVs and short indels at the same quality as Agilent XT, and showed the best performance in coverage of medically interesting mutations. NimbleGen detected more SNVs and indels in untranslated regions than the others. We also found that the platforms, which enzymatically fragment the genomic DNA (gDNA), detected more homozygous SNVs than those using sonicated gDNA. We believe that our analysis will help investigators when selecting a suitable exome capture platform for their particular research.
Project description:37 surgical samples were interrogated by WXS, and 50 formalin-fixed, paraffin-embedded samples were interrogated by target-seq. Agilent SureSelect XT kit and SureSelect Human Exon V6 were used to generate exome libraries. Agilent SureSelect XT low input kit and custom capture panel designed on SureDesign were used to generate target-seq libraries. All libraries were sequenced on Illumina HiSeq 2500 platform.
Project description:Whole exome sequencing of 5 HCLc tumor-germline pairs. Genomic DNA from HCLc tumor cells and T-cells for germline was used. Whole exome enrichment was performed with either Agilent SureSelect (50Mb, samples S3G/T, S5G/T, S9G/T) or Roche Nimblegen (44.1Mb, samples S4G/T and S6G/T). The resulting exome libraries were sequenced on the Illumina HiSeq platform with paired-end 100bp reads to an average depth of 120-134x. Bam files were generated using NovoalignMPI (v3.0) to align the raw fastq files to the reference genome sequence (hg19) and picard tools (v1.34) to flag duplicate reads (optical or pcr), unmapped reads, reads mapping to more than one location, and reads failing vendor QC.
Project description:Presented manuscript described data analysis on near infrared spectroscopy used as adopted and portable technology for cocoa farmers in Aceh Province, Indonesia. The near infrared spectroscopy (NIRS) assisted farmers in post-harvest handling especially for cocoa quality evaluation. This technology was used to determine moisture content (MC) and fat content (FC) of intact cocoa bean samples rapidly and simultaneously. Near infrared spectra data were acquired as absorbance spectrum in wavelength range from 1000 to 2500 nm with co-added of 32 scans for a total of 72 intact bulk cocoa bean samples. Spectra data can be used to predict MC and FC of intact cocoa beans by establishing prediction models and validate with actual MC and FC measured by means of standard laboratory procedures. Prediction performances were evaluated using several statistical indicators: coefficient correlation (r), coefficient of determination (R2), root mean square error (RMSE) and residual predictive deviation (RPD) index. Near infrared spectra data can be enhanced using spectra pre-treatment methods to improve prediction performances. Moreover, prediction models can be developed using principal component regression (PCR), partial least squares regression (PLSR) and other regression approaches. Ideal prediction models should have r and R2 above 0.75, RPD index above 2.0 and RMSE lower than its standard deviation (SD). Dataset were available as raw MS Excel format and The Unscrambler files as *.unsb extension.
Project description:Genomic DNA from IDH1 mutant and WT tumors were used to detect genome wide methylation using Agilent SureSelect XT Mouse Methyl-Seq Enrichment System capture kit following manufacturer’s recommendations. Overall design: Whole genome methylation analysis on IDH mutant and WT cell lines
Project description:Circular transcriptome sequencing of the middle silk gland (MSG) and posterior silk gland (PSG) in the Bombyx mori are presented. The middle silk gland and posterior silk gland were collected from the third day of fifth-instar B.mori larvae. The circular RNAs enriched by using RNase R to degrade the linear RNA molecules, and circular RNA sequencing (circRNA-seq) was performed using an Illumina Hiseq. 2500 sequencing platform. Samples are described in the SRA portal (SRP100385) and FASTQ files have been deposited in Sequence Read Archive (accession numbers: SRX2577343 and SRX2577342). The interpretation of these data is presented in the following research article: "Identification of circular RNA in the Bombyx mori silk gland"  (Gan et al., 2017).
Project description:The extreme genetic heterogeneity of nonsyndromic hearing loss (NSHL) makes genetic diagnosis expensive and time consuming using available methods. To assess the feasibility of target-enrichment and massively parallel sequencing technologies to interrogate all exons of all genes implicated in NSHL, we tested nine patients diagnosed with hearing loss. Solid-phase (NimbleGen) or solution-based (SureSelect) sequence capture, followed by 454 or Illumina sequencing, respectively, were compared. Sequencing reads were mapped using GSMAPPER, BFAST, and BOWTIE, and pathogenic variants were identified using a custom-variant calling and annotation pipeline (ASAP) that incorporates publicly available in silico pathogenicity prediction tools (SIFT, BLOSUM, Polyphen2, and Align-GVGD). Samples included one negative control, three positive controls (one biological replicate), and six unknowns (10 samples total), in which we genotyped 605 single nucleotide polymorphisms (SNPs) by Sanger sequencing to measure sensitivity and specificity for SureSelect-Illumina and NimbleGen-454 methods at saturating sequence coverage. Causative mutations were identified in the positive controls but not in the negative control. In five of six idiopathic hearing loss patients we identified the pathogenic mutation. Massively parallel sequencing technologies provide sensitivity, specificity, and reproducibility at levels sufficient to perform genetic diagnosis of hearing loss.
Project description:Huanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria 'Candidatus Liberibacter asiaticus' (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16?S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.
Project description:The objective of this study is to assess, in vitro, the shear bond strength of orthodontic brackets fixed with remineralizing adhesive systems submitted to thermomechanical cycling, simulating one year of orthodontic treatment. Sixty-four bovine incisor teeth were randomly divided into 4 experimental groups (n = 16): XT: Transbond XT, QC: Quick Cure, OL: Ortholite Color, and SEP: Transbond Plus Self-Etching Primer. The samples were submitted to thermomechanical cycling simulating one year of orthodontic treatment. Shear bond strength tests were carried out using a universal testing machine with a load cell of 50 KgF at 0.5 mm/minute. The samples were examined with a stereomicroscope and a scanning electron microscope (SEM) in order to analyze enamel surface and Adhesive Remnant Index (ARI). Kruskal-Wallis and Mann-Whitney (with Bonferroni correction) tests showed a significant difference between the studied groups (p < 0.05). Groups XT, QC, and SEP presented the highest values of adhesive resistance and no statistical differences were found between them. The highest frequency of failures between enamel and adhesive was observed in groups XT, QC, and OL. Quick Cure (QC) remineralizing adhesive system presented average adhesive resistance values similar to conventional (XT) and self-etching (SEP) adhesives, while remineralizing system (OL) provided the lowest values of adhesive resistance.