Journal: Journal of Clinical Oncology

Article Title: Identification of Clinical and Biologic Correlates Associated With Outcome in Children With Adrenocortical Tumors Without Germline TP53 Mutations: A St Jude Adrenocortical Tumor Registry and Children’s Oncology Group Study

doi: 10.1200/JCO.2017.74.2460

Figure Lengend Snippet: Somatic TP53 mutations in patients with adrenocortical tumors (ACTs) without TP53 mutations. (A) Schematic diagram of acquired TP53 mutations. (B) Kaplan-Meier estimates for progression-free survival (B) in pediatric patients with ACTs with or without acquired TP53 mutations and (C) by TP53 status and disease stage. After discriminating for disease stage and including stage IV disease in the Cox regression model, presence of somatic TP53 mutations was no longer associated with outcome (P = .21). hom, homozygous.

Article Snippet: Large deletions of TP53 and ATRX were assessed using commercial multiplex ligation-dependent probe amplification (MLPA) kits (PO56 TP53 probemix and P013 ATRX probemix; MRC-Holland, Amsterdam, the Netherlands) as per manufacturer instructions.

Techniques:

Journal: Journal of Clinical Oncology

Article Title: Identification of Clinical and Biologic Correlates Associated With Outcome in Children With Adrenocortical Tumors Without Germline TP53 Mutations: A St Jude Adrenocortical Tumor Registry and Children’s Oncology Group Study

doi: 10.1200/JCO.2017.74.2460

Figure Lengend Snippet: Somatic CTNNB1 mutations in patients with adrenocortical tumors (ACTs) without TP53 mutations. (A) Schematic diagram of activating CTNNB1 mutations. (B) Immunohistochemical analysis of β-catenin and yes-associated protein 1 (YAP1) in pediatric ACTs. YAP serves as a surrogate marker for β-catenin expression. Moderate nuclear immunostaining of (i) β-catenin and (ii) YAP in a tumor with the S45P mutation in CTNNB1. Strong nuclear immunoreactivity for (iii) β-catenin and (iv) YAP in a pediatric patient with unknown CTNNB1 molecular status. These results are indicative of Wnt signaling pathway activation. Size bars represent 50 μm. (C) Kaplan-Meier estimates for progression-free survival by CTNNB1 status (P = .80).

Article Snippet: Large deletions of TP53 and ATRX were assessed using commercial multiplex ligation-dependent probe amplification (MLPA) kits (PO56 TP53 probemix and P013 ATRX probemix; MRC-Holland, Amsterdam, the Netherlands) as per manufacturer instructions.

Techniques: Immunohistochemical staining, Marker, Expressing, Immunostaining, Mutagenesis, Activation Assay

Journal: Journal of Clinical Oncology

Article Title: Identification of Clinical and Biologic Correlates Associated With Outcome in Children With Adrenocortical Tumors Without Germline TP53 Mutations: A St Jude Adrenocortical Tumor Registry and Children’s Oncology Group Study

doi: 10.1200/JCO.2017.74.2460

Figure Lengend Snippet: (A) Hematoxylin and eosin staining and Ki-67 labeling index (LI) in pediatric adrenocortical tumors without TP53 mutations: (i, ii) tumor with a high (≥ 15%) Ki-67 labeling index (LI; red arrows indicate mitotic figures), (iii, iv) tumor with a low (< 5%) LI. Size bars represent 50 μm. (B) Kaplan-Meier estimates for progression-free survival (PFS) according to Ki-67 LI showing that Ki-67 LI < 15% was significantly associated with longer PFS (P = .002). (C) Kaplan-Meier estimates for PFS according to Ki-67 LI and disease stage. Ki-67 LI remained significantly associated with outcome after adjusting for disease stage (P = .0048).

Article Snippet: Large deletions of TP53 and ATRX were assessed using commercial multiplex ligation-dependent probe amplification (MLPA) kits (PO56 TP53 probemix and P013 ATRX probemix; MRC-Holland, Amsterdam, the Netherlands) as per manufacturer instructions.

Techniques: Staining, Labeling

Journal: Journal of Clinical Oncology

Article Title: Identification of Clinical and Biologic Correlates Associated With Outcome in Children With Adrenocortical Tumors Without Germline TP53 Mutations: A St Jude Adrenocortical Tumor Registry and Children’s Oncology Group Study

doi: 10.1200/JCO.2017.74.2460

Figure Lengend Snippet: Characteristics of Patients With ACTs Harboring Mutations or No Mutations in TP53

Article Snippet: Large deletions of TP53 and ATRX were assessed using commercial multiplex ligation-dependent probe amplification (MLPA) kits (PO56 TP53 probemix and P013 ATRX probemix; MRC-Holland, Amsterdam, the Netherlands) as per manufacturer instructions.

Techniques:

Journal: Genes

Article Title: Prevalent Pathogenic Variants of ATP7B in Chinese Patients with Wilson’s Disease: Geographical Distribution and Founder Effect

doi: 10.3390/genes12030336

Figure Lengend Snippet: Geographical distribution of three ATP7B prevalent pathogenic variants (p.R778L, p.P992L, p.T935M) in Chinese mainland: ( a ) the geographical distribution of 709 Wilson’s disease (WD) patients. Various colors in different regions indicate the corresponding number range of patients; ( b – d ) the frequency of p.R778L, p.P992L and p.T935M in five regions (Fujian, Zhejiang, Jiangsu, Shanghai and Jiangxi). Five regions are represented by different colors. Asterisks indicate that there existed significant differences between the corresponding two provinces (** p < 0.01).

Article Snippet: For patients who were detected with only one heterozygous pathogenic variant, we performed multiplex ligation-dependent probe amplification assay (MLPA) with the ATP7B MLPA kit (SALSA P098-D1, MRC-Holland, the Netherlands) [ ].

Techniques:

Journal: European Journal of Human Genetics

Article Title: Expanding the clinical and molecular findings in RASA1 capillary malformation-arteriovenous malformation

doi: 10.1038/s41431-018-0196-1

Figure Lengend Snippet: Clinical and molecular findings of 69 unrelated cases with a RASA1 variant

Article Snippet: Structural variation analysis Large exonic deletions and duplications of RASA1 were identified using the P409 RASA1 multiplex ligation-dependent probe amplification (MLPA) kit (MRC-Holland, Amsterdam, Netherlands).

Techniques: Variant Assay, Staining

Journal: European Journal of Human Genetics

Article Title: Expanding the clinical and molecular findings in RASA1 capillary malformation-arteriovenous malformation

doi: 10.1038/s41431-018-0196-1

Figure Lengend Snippet: 14-gene vascular malformation panel

Article Snippet: Structural variation analysis Large exonic deletions and duplications of RASA1 were identified using the P409 RASA1 multiplex ligation-dependent probe amplification (MLPA) kit (MRC-Holland, Amsterdam, Netherlands).

Techniques: Sequencing

Journal: European Journal of Human Genetics

Article Title: Expanding the clinical and molecular findings in RASA1 capillary malformation-arteriovenous malformation

doi: 10.1038/s41431-018-0196-1

Figure Lengend Snippet: Large RASA1 deletions. a, b Two large RASA1 deletions detected by MLPA. c Large RASA1 deletion of the 5’UTR and exon 1 detected by aCGH

Article Snippet: Structural variation analysis Large exonic deletions and duplications of RASA1 were identified using the P409 RASA1 multiplex ligation-dependent probe amplification (MLPA) kit (MRC-Holland, Amsterdam, Netherlands).

Techniques:

Journal: European Journal of Human Genetics

Article Title: Expanding the clinical and molecular findings in RASA1 capillary malformation-arteriovenous malformation

doi: 10.1038/s41431-018-0196-1

Figure Lengend Snippet: Case photographs and pedigrees. a Cutaneous AVM of the ear (left panel) and large birthmark covering the right face, ear, and scalp (left and right panels) of case 60. b Pedigree of family suspicious for HHT in which exome sequencing of the proband (case 1) showed a RASA1 frameshift. c Family pedigree of case 48 with a novel RASA1 splice site variant in which the affected infant was diagnosed prenatally with cerebral AVFs. d Fetal color Doppler ultrasound demonstrates a high-flow arteriovenous shunt in the posterior fossa (affected sibling of case 48). e MRI demonstrates a signal void (arrow) representing a high flow with arteriovenous shunting along the surface of the left cerebellar hemisphere (affected sibling of case 48). f Frontal early and latter images of the left vertebral artery shows the multiple AVFs in the posterior fossa draining to a markedly dilated tributary to the left transverse sinus (affected sibling of case 48). g The thigh of case 69 had innumerable, diffuse tiny telangiectases (arrows, left panel) with significant surrounding halos giving the skin a mottled effect (left panel). Pale pink capillary malformation (~1 cm) on the left arm of case 69 (right panel)

Article Snippet: Structural variation analysis Large exonic deletions and duplications of RASA1 were identified using the P409 RASA1 multiplex ligation-dependent probe amplification (MLPA) kit (MRC-Holland, Amsterdam, Netherlands).

Techniques: Sequencing, Variant Assay

Journal: European Journal of Human Genetics

Article Title: Expanding the clinical and molecular findings in RASA1 capillary malformation-arteriovenous malformation

doi: 10.1038/s41431-018-0196-1

Figure Lengend Snippet: Complex RASA1/PTEN case identified by NGS panel testing. a Pedigree depicts which genetic variants (RASA1, PTEN, and/or SMAD4) the proband and family members carry. b NGS panel data and c Sanger sequencing data from for each variant

Article Snippet: Structural variation analysis Large exonic deletions and duplications of RASA1 were identified using the P409 RASA1 multiplex ligation-dependent probe amplification (MLPA) kit (MRC-Holland, Amsterdam, Netherlands).

Techniques: Sequencing, Variant Assay

Journal: Molecular Biotechnology

Article Title: Development of a Flow-Trough Microarray based Reverse Transcriptase Multiplex Ligation-Dependent Probe Amplification Assay for the Detection of European Bunyaviruses

doi: 10.1007/s12033-011-9389-3

Figure Lengend Snippet: Outline of Flow-through microarray-based MLPA assay. MLPA probes consist of two oligonucleotides: the left probe oligonucleotide ( LPO) and the right probe oligonucleotide (RPO), respectively, containing left- and right-hybridisation sequences (LHS and RHS) specific for the sequence of interest marked in blue . They also contain universal hybridisation sequences for the SALSA primers (in brown ) which drive the MLPA PCR reaction. In addition, the LPO includes a unique artificial sequence (Zip-code or Cpam marked in green ) which is complementary to the Pam4U sequence immobilized on the PamChip ® 4U (marked in pink ) for the signal detection. The fluorescent signal of the hybridized FAM tagged amplicon is read out by a CCD camera (Color figure online)

Article Snippet: The authors have developed an approach that combines Multiplex ligation-dependent probe amplification (MLPA) with a flow-through chip hybridisation system (PamGene, Netherlands).

Techniques: Microarray, Hybridization, Sequencing, Amplification

Journal: Molecular Biotechnology

Article Title: Development of a Flow-Trough Microarray based Reverse Transcriptase Multiplex Ligation-Dependent Probe Amplification Assay for the Detection of European Bunyaviruses

doi: 10.1007/s12033-011-9389-3

Figure Lengend Snippet: Analysis of MLPA amplicons. Gel electrophoresis of MLPA PCR products generated by amplification of ligated MLPA probes for seven European Bunyaviruses. Two-three S-segment-based MLPA probe sets for each virus were used. L . Ladder, Lanes : 1 . SFSV, 2 . SFNV, 3 . UUKV, 4 . TAHV, 5 . BATV, 6 . INKV, 7 . TOSV

Article Snippet: The authors have developed an approach that combines Multiplex ligation-dependent probe amplification (MLPA) with a flow-through chip hybridisation system (PamGene, Netherlands).

Techniques: Nucleic Acid Electrophoresis, Generated, Amplification

Journal: Molecular Biotechnology

Article Title: Development of a Flow-Trough Microarray based Reverse Transcriptase Multiplex Ligation-Dependent Probe Amplification Assay for the Detection of European Bunyaviruses

doi: 10.1007/s12033-011-9389-3

Figure Lengend Snippet: MLPA hybridisation pattern on the flow-through chip . Representative images of MLPA amplicon hybridisation on flow-trough microarray for the detection of seven the European arboviruses, TOSV, SFSV, SFNV, TAHV, INKV, BATV and UUKV

Article Snippet: The authors have developed an approach that combines Multiplex ligation-dependent probe amplification (MLPA) with a flow-through chip hybridisation system (PamGene, Netherlands).

Techniques: Hybridization, Amplification, Microarray

Journal: Molecular Biotechnology

Article Title: Development of a Flow-Trough Microarray based Reverse Transcriptase Multiplex Ligation-Dependent Probe Amplification Assay for the Detection of European Bunyaviruses

doi: 10.1007/s12033-011-9389-3

Figure Lengend Snippet: Sensitivity of RT-MLPA hybridisation patterns on the flow-through chip. Representative microarray images of RT-MLPA PCR products for the detection of seven European Arboviruses, showing detection limits for TOSV, SFSV, SFNV, TAHV, INKV, BATV and UUKV

Article Snippet: The authors have developed an approach that combines Multiplex ligation-dependent probe amplification (MLPA) with a flow-through chip hybridisation system (PamGene, Netherlands).

Techniques: Hybridization, Microarray