nFuse and defuse: Verification of the original <i>VTI1A-TCF7L2</i> fusion transcript and identification of a fusion transcript and genomic breakpoint involving <i>TCF7L2</i> and <i>RP11-57H14.3.</i>

<p><i>RP11-57H14.3</i> is located 44 kb upstream of <i>TCF7L2</i> on chromosome 10.</p><p>a)deFuse probability score,</p><p>b)nFuse path score. †) Split reads contain the fusion boundary in the read itself, while spanning reads are paired ends that harbor the fusion boundary within the insert sequence.</p

Matched tumor and normal colonic mucosa from series 1.

<p>For both fusion transcripts the tumor, or both the tumor and normal samples were frequently positive. In one pair the <i>VTI1A-TCF7L2</i> fusion transcript was positive only in the normal sample and not the matched tumor.</p

The number of positive fusion transcript PCRs for the samples, run in triplicates.

<p>a)Strong positives are defined as testing positive in all RT-PCR replicates.</p><p>b)Samples noted as positives have tested positive for the fusion transcript(s) in one or more of the three RT-PCR replicates.</p

The <i>TCF7L2-RP11-57H14.3</i> fusion transcript, identified in the HCT116 cell line, harbors a rearranged genomic locus.

<p>Three chimeric RNA sequence-reads spanned the fusion transcript breakpoint, passing from exon 4 of <i>TCF7L2</i> (ENST00000369395) to exon 3 of <i>RP11-57H14.3</i> (ENST00000428766), on chromosome 10. Dark colors indicate exons not part of the fusion transcript. RNA-seq expression and DNA-seq coverage levels are based on sequencing data of the HCT116 cell line. The two gene loci are marked in blue and red boxes. The genomic breakpoint sequence as identified by nFUSE in the CRC cell line HCT116 is given; spanning from the intronic region of <i>TCF7L2</i> to upstream of <i>RP11-57H14.3</i>. The coordinates of the breakpoint (chr10∶114,850,371-114,640,318 (GRCh37)) are marked on the chromosome position axis. The location of the breakpoint correlates well with the increased genomic coverage seen from the genome sequencing data.</p

Confirmation of the original <i>VTI1A-TCF7L2</i> fusion transcript breakpoint in the cell line NCI-H508.

<p>Sanger sequencing confirmed the original fusion transcript discovered in NCI-H508, showing the breakpoint sequence spanning exon-exon junctions between exon 2 in <i>VTI1A</i> and exon 6 in <i>TCF7L2</i>. Bass et al. also discovered three other fusion transcripts by nested-PCR. However, as transcript annotation was not sufficiently described, we are not able to say if these fusions are identical to some of the transcripts we have identified.</p

Schematic presentation of the genomic location of <i>VTI1A, RP11-57H14.3</i> and <i>TCF7L2</i>.

<p>All three genes are located within 720<i>VTI1A,</i> ENST00000428766 in <i>RP11-57H14.3</i> and ENST00000369395 in <i>TCF7L2</i>. Also, the nested PCR assays used for detection of both fusion transcripts are shown. The red and black arrows represent the first round and second round primers used, respectively.</p

Data_Sheet_2_A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing.XLSX

<p>Single-nucleotide polymorphisms (SNPs) are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout (Oncorhynchus mykiss), SNP discovery has been previously done through sequencing of restriction-site associated DNA (RAD) libraries, reduced representation libraries (RRL) and RNA sequencing. Recently we have performed high coverage whole genome resequencing with 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples added to 12 aquaculture samples from AquaGen (Norway) that we previously used for SNP discovery. Of the 49 new samples, 11 were double-haploid lines from Washington State University (WSU) and 38 represented wild and hatchery populations from a wide range of geographic distribution and with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout reference genome assembly (GCA_002163495.1) which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMtools mpileup, followed by filtering of SNPs based on quality score, sequence complexity, read depth on the locus, and number of genotyped samples. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used for detecting and filtering putative paralogous sequence variants (PSVs) and multi-sequence variants (MSVs). Overall, 30,302,087 SNPs were identified on the rainbow trout genome 29 chromosomes and 1,139,018 on unplaced scaffolds, with 4,042,723 SNPs having high minor allele frequency (MAF > 0.25). The average SNP density on the chromosomes was one SNP per 64 bp, or 15.6 SNPs per 1 kb. Results from the phylogenetic analysis that we conducted indicate that the SNP markers contain enough population-specific polymorphisms for recovering population relationships despite the small sample size used. Intra-Population polymorphism assessment revealed high level of polymorphism and heterozygosity within each population. We also provide functional annotation based on the genome position of each SNP and evaluate the use of clonal lines for filtering of PSVs and MSVs. These SNPs form a new database, which provides an important resource for a new high density SNP array design and for other SNP genotyping platforms used for genetic and genomics studies of this iconic salmonid fish species.</p

Additional file 9: Figure S3. of CRABP1, C1QL1 and LCN2 are biomarkers of differentiated thyroid carcinoma, and predict extrathyroidal extension

Differential gene expression of C1QL1, LCN2, CRABP1 and CILP in thyroid tumours and normal tissues. Gene expression of C1QL1 (a), LCN2 (b), CRABP1 (c) and CILP (d) genes was measured by real-time quantitative PCR in normal thyroid (NT) tissues, follicular thyroid adenoma (FTA) and differentiated thyroid cancer (DTC). Each dot represents the mean of gene expression of each sample. The lines represent the averages. Statistical significance values: *, P = 0.002; **, P = 0.005; ***, P = 0.013; ****, P < 0.001; *****, P = 0.022; ******, P = 0.018. (JPEG 417 kb

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MOESM5 of Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13

Additional file 5: Table S5. Results from single-marker association analyses on SNPs in the candidate gene region