Journal: Physiological Genomics

Article Title: Human gene copy number spectra analysis in congenital heart malformations

doi: 10.1152/physiolgenomics.00013.2012

Figure Lengend Snippet: Known CHD risk genes

Article Snippet: ACP6 , ACID PHOSPHATASE 6, LYSOPHOSPHATIDE , 1q21.1 , 145585791 , 23467 , Hs00320736_cn , , 611471 , 15117819, 19597493.

Techniques: Retroviral, Sequencing, Virus, Reverse Transcription

Journal: Physiological Genomics

Article Title: Human gene copy number spectra analysis in congenital heart malformations

doi: 10.1152/physiolgenomics.00013.2012

Figure Lengend Snippet: Case reports of likely causal CNVs

Article Snippet: ACP6 , ACID PHOSPHATASE 6, LYSOPHOSPHATIDE , 1q21.1 , 145585791 , 23467 , Hs00320736_cn , , 611471 , 15117819, 19597493.

Techniques:

Journal: Physiological Genomics

Article Title: Human gene copy number spectra analysis in congenital heart malformations

doi: 10.1152/physiolgenomics.00013.2012

Figure Lengend Snippet: CHD-associated gene regions significantly enriched with large, rare CNVs

Article Snippet: ACP6 , ACID PHOSPHATASE 6, LYSOPHOSPHATIDE , 1q21.1 , 145585791 , 23467 , Hs00320736_cn , , 611471 , 15117819, 19597493.

Techniques:

Journal: Physiological Genomics

Article Title: Human gene copy number spectra analysis in congenital heart malformations

doi: 10.1152/physiolgenomics.00013.2012

Figure Lengend Snippet: Enriched syndrome genes

Article Snippet: ACP6 , ACID PHOSPHATASE 6, LYSOPHOSPHATIDE , 1q21.1 , 145585791 , 23467 , Hs00320736_cn , , 611471 , 15117819, 19597493.

Techniques:

Journal: Physiological Genomics

Article Title: Human gene copy number spectra analysis in congenital heart malformations

doi: 10.1152/physiolgenomics.00013.2012

Figure Lengend Snippet: Known CHD risk genes

Article Snippet: TFAP2B , TRANSCRIPTION FACTOR AP2-BETA , 6p12.3 , 50894397 , 28888 , Hs01355864_cn , NS, S , 601601 , 10802654.

Techniques: Retroviral, Sequencing, Virus, Reverse Transcription

Journal: BMC Cancer

Article Title: Case report: long-term survival of an infant syndromic patient affected by atypical teratoid-rhabdoid tumor

doi: 10.1186/1471-2407-13-100

Figure Lengend Snippet: A , Schematic representation of the family tree of index case. Karyotype and SMARCB1/INI1 molecular evaluation ( E ) is reported (wt= wild type; Arg40X denotes the constitutional mutation found in index case). Present age and age of onset of clinical symptoms is given in years (y). B , Brain MRI of primary ATRT lesion. C , MRI of metastatic lesion. D , Hematoxylin eosin staining and E , SMARCB1/INI1 staining of ATRT tumor from index case, showing absence of SMARCB1/INI1 protein expression in cancer cells.

Article Snippet: Analysis of SMARCB1/INI1 copy number by real-time quantitative PCR was performed by means of relative quantification using standard curve method [ ], using TaqMan assays 4401631 (Applera) for RPPH1 endogenous control gene and Hs01497967_cn (Applera) for SMARCB1/INI1 .

Techniques: Mutagenesis, Staining, Expressing

Journal: BMC Cancer

Article Title: Case report: long-term survival of an infant syndromic patient affected by atypical teratoid-rhabdoid tumor

doi: 10.1186/1471-2407-13-100

Figure Lengend Snippet: A-C , Electropherogram of normal and tumor DNA-derived sequences showing the presence of heterozygous exon 2 c. 118C>T (Arg40X) in ( A ) patient’s constitutional DNA and the same homozygous mutation ( B ) in tumor samples. C , Parental sample, displaying normal DNA sequence. D-E , Fragment analysis ( D ) and histogram ( E ) of MLPA results for SMARCB1/INI1 gene dosage analysis in primary tumor tissue and in control samples. Red dots indicate peaks corresponding to SMARCB1/INI1 fragments.

Article Snippet: Analysis of SMARCB1/INI1 copy number by real-time quantitative PCR was performed by means of relative quantification using standard curve method [ ], using TaqMan assays 4401631 (Applera) for RPPH1 endogenous control gene and Hs01497967_cn (Applera) for SMARCB1/INI1 .

Techniques: Derivative Assay, Mutagenesis, Sequencing, Control

Journal: Cell

Article Title: Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

doi: 10.1016/j.cell.2013.02.032

Figure Lengend Snippet: PHGDH , EFHD1 , and SLC2A1 Are Expressed in Liver and Downregulated by Intragenic, Tumor-Specific L1 Insertions, Related to Figure 6 qRT-PCR revealed significantly reduced transcription in tumor versus nontumor in all three genes. P values were calculated using a two-tailed t test (df = 4). Three other genes contained intronic, tumor-specific L1 insertions: SLC5A8 , STXBP5L and ST18 . Of these, SLC5A8 and STXBP5L were not expressed in liver according to our qRT-PCR results and ST18 was upregulated in tumor ( Figure 6 D). Values were normalized to TBP . Data are mean +/− SD.

Article Snippet: ST18 copy number was assessed by quantitative real-time PCR using a TaqMan copy number assay (gene probe: Mm00040629_cn) on a 7900HT Fast Real-Time PCR System (Applied Biosystems) with sequence detection systems software 2.2.2.

Techniques: Quantitative RT-PCR, Two Tailed Test

Journal: Cell

Article Title: Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

doi: 10.1016/j.cell.2013.02.032

Figure Lengend Snippet: A Tumor-Specific L1 Insertion Causes Induction of ST18 (A) ST18 mutant allele: a 0.4 kb L1-Ta insertion antisense to ST18 . Primers used for PCR validation (1,2) are indicated above the gene. (B) L1 insertion, magnified view: RC-seq detected the L1 5′ and 3′ termini, indicating a 17 nt TSD and a 5′ inversion. (C) Insertion-site PCR validation: the L1 was detected only in 47T, whereas the empty site was found in both 47T and 47NT. (D) qRT-PCR: ST18 was upregulated 4-fold in 47T versus 47NT ( ∗ p < 0.005, two-tailed t test, df = 4). Data are presented as mean ± SD. (E) ST18 immunoblot: ST18 (115 kDa) was enriched in 47T versus 47NT and normal liver controls. (F) ST18 immunohistochemistry: accumulation of ST18 (brown) was observed in tumor nodules compared to surrounding nontumor regions. Nuclei were stained with hematoxylin (blue). (G) A palindromic sequence motif was bisected by the L1. Each 8 nt unit (α and β, light green) contained a subsequence 1 nt different to a PIT1 -enhancer motif known to bind MYT1 ( Rhodes et al., 1993 ). A second motif −58 bp from the L1 integration site matched the consensus CEBPA binding motif (orange). (H) ChIP followed by quantitative real-time PCR in Huh7 cells confirmed enrichment for ST18 bound to the putative ST18 -enhancer element illustrated in (G), compared to GAPDH. Data from antibodies targeting both the N termini and C termini of ST18 are shown. Significance values were calculated using two-tailed t tests (df = 4). Data are presented as mean ± SD. Please see and and and for further information regarding tumor-specific L1 insertions and additional ST18 characterization.

Article Snippet: ST18 copy number was assessed by quantitative real-time PCR using a TaqMan copy number assay (gene probe: Mm00040629_cn) on a 7900HT Fast Real-Time PCR System (Applied Biosystems) with sequence detection systems software 2.2.2.

Techniques: Mutagenesis, Biomarker Discovery, Quantitative RT-PCR, Two Tailed Test, Western Blot, Immunohistochemistry, Staining, Sequencing, Binding Assay, Real-time Polymerase Chain Reaction

Journal: Cell

Article Title: Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

doi: 10.1016/j.cell.2013.02.032

Figure Lengend Snippet: Pronounced ST18 Expression in HCC Model Systems, Related to Figure 6 (A) An immunoblot for ST18 (115kDa) found enrichment in 4 analyzed human HCC cell lines compared to normal liver controls. (B) qRT-PCR indicated ST18 transcription was strongly upregulated in four Mdr2 −/− mouse nodules with amplified ST18 versus wild-type liver (p < 0.0001, two-tailed t test, df = 19). Values were normalized to TBP . Data are mean +/− SD.

Article Snippet: ST18 copy number was assessed by quantitative real-time PCR using a TaqMan copy number assay (gene probe: Mm00040629_cn) on a 7900HT Fast Real-Time PCR System (Applied Biosystems) with sequence detection systems software 2.2.2.

Techniques: Expressing, Western Blot, Quantitative RT-PCR, Amplification, Two Tailed Test