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IFACT: Incidental Findings in Advanced Cancer Therapy

ABSTRACT: The proposed study, IFACT - Incidental Findings in Advanced Cancer Therapy, will address this research gap by examining MSK patients’ attitudes, preferences, and information needs regarding incidental findings arising from tumor genomic profiling.

DISEASE(S): Lung Cancer,Colorectal Cancer,Colorectal Neoplasms,Urinary Bladder Neoplasms,Bladder Cancer,Breast Cancer

PROVIDER: 2172681 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

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An Interactive Preventive Health Record to Increase Colorectal Cancer Screening

Project description:This study involves 3 phases that modifies current Interactive Preventative Health Record-Colorectal Cancer Screening (IPHR-CRCS) modules to address each patient’s individual colorectal cancer screening (CRCS) knowledge, attitudes, preferences, and test-specific barriers. The study will engage patients, ages 50-75 years who are non-adherent to CRCS, to assess their CRCS test preferences and corresponding test-specific barriers in "real time". Based on patient characteristics (e.g. age, personal and family history, physician CRCS recommendation, CRCS test preferences, top test-specific barriers), tailored messages/videos will appear in the pop-up screens to address/reduce the top patient-reported, test-specific CRCS barriers while incorporating an action plan for CRCS adherence. The investigators hypothesize that modifying the IPHR-CRCS module to address each patient’s individual CRCS knowledge, attitudes, preferences, and test-specific barriers will further increase CRCS.

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Genomic and Clinical Findings in Myeloid Neoplasms with PDGFRB Rearrangement

Project description:Genomic and Clinical Findings in Myeloid Neoplasms with PDGFRB Rearrangement

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Genomic and Clinical Findings in Myeloid Neoplasms with PDGFRB Rearrangement [seq]

Project description:Genomic and Clinical Findings in Myeloid Neoplasms with PDGFRB Rearrangement [seq]

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Synthetic genetic circuit reveals overlapping binding sites underlie TF genomic occupancy

Project description:Sequence-specific DNA binding by transcription factors (TFs) is required for accurately regulating target gene expression. However, rules governing TF-DNA interactions remain elusive because current high-throughput approaches to map them fail to identify lower-affinity interactions. To address this gap, we have developed PADIT-seq, a novel technology to detect TF-DNA interactions across the entire spectrum of affinities. By profiling the binding preferences of Egr1 and Hoxd13 to all possible 10-mers, we found that nucleotides flanking high-affinity binding sites create additional, overlapping lower-affinity sites that together modulate TF genomic occupancy. The formation of these extended recognition sequences is enabled by an inherent property of TF binding sites to interweave together. Highlighting the importance of lower-affinity binding sites, we provide mechanistic insights into their role in fine-tuning gene regulation.

2024-03-06 | GSE250601 | GEO

Posttransplant diffuse large B-cell lymphoma: new genetic findings

Project description:Molecular pathogenesis of posttransplant (PT) lymphoproliferative disorder, including the most prevalent diffuse large B cell lymphoma (DLBCL), is largely unknown. We have recently showed that Epstein-Barr Virus (EBV)+ and EBV- PT-DLBCL are biologically different, but gene expression profile of the latter lymphoma is similar to that of immunocompetent (IC) DLBCL. To validate these findings on a genomic level, we performed array CGH analysis of 21 EBV+ and 6 EBV- PT-DLBCL, and 11 control IC-DLBCL. Genomic and transcriptomic data were subsequently integrated. Notably, EBV+ and EBV- PT-DLBCL revealed only one shared recurrent imbalance, while EBV- PT-DLBCL displayed at least 10 aberrations recurrent in IC-DLBCL, among others gain of 3/3q and 18q, and loss of 6q23/TNFAIP3 and 9p21/CDKN2A. EBV+ PT-DLBCL showed distinct aberrations, including the most prevalent gain/amplification of 9p24.1 targeting PDCD1LG2/PDL2. Significant differential representation/expression of 3p13/FOXP1 and 9p21/CDKNA2 in EBV+ PT-DLBCL when compared with EBV- PT-/IC-DLBCL, suggests that the oncogene FOXP1 and the tumor suppressor gene CDKNA2 are not implicated in pathogenesis of EBV+ PT-DLBCL. In summary, genomic profiling of PT-/IC-DLBCL confirmed biological distinctness of EBV+ and EBV- PT-DLBCL, and relationship between EBV- PT-DLBCL and IC-DLBCL. These findings support the hypothesis that EBV- PT-DLBCL are coincidental lymphomas in transplant recipients

2015-06-02 | GSE69440 | GEO

Epigenetic findings in periodontitis in UK twins: a cross sectional study

Project description:Epigenetic findings in periodontitis in UK twins: a cross sectional study

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Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells

Project description:We were interested in how the complex mammalian transcriptomes were established. Using spermatogenesis as a model system, we address this question first by profiling the mRNAs, lncRNAs and circRNAs and examining their relative abundances in 4 types of SPCs (priSG-A, plpSC, pacSC, rST).

2016-08-28 | GSE75826 | GEO

Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder - implications of a copy number variation involving dpp10 (CGX-12)

Project description:Background: Array-Comparative-Genomic-Hybridization (aCGH) is recommended as first-tier genetic test for children with autism spectrum disorder (ASD). However, result interpretation can be challenging as copy number variants (CNVs) in non-European ASD patients is not well studied. To address this literature gap, we report the CNV findings in a cohort of Chinese children with ASD. Methods DNA samples were obtained from 258 Chinese ASD patients recruited from a child assessment center between January 2011 and August 2014. aCGH was performed using NimbleGen-CGX-135k or Agilent-CGX 60k oligonucleotide array. Results were classified based on existing guidelines and literature. Results: Ten pathogenic and one likely-pathogenic CNVs were found in nine patients, with an overall diagnostic yield of 3.5%. A 138kb duplication involving 3â exons of DPP10 (hg[19]chr2:116534689-116672358), reported to be associated with ASD, was identified in one patient (0.39%). The same CNV was reported as variant of unknown significance (VUS) in DECIPHER database. Multiple individuals of typical development carrying a similar duplication were identified amongst our ancestry-matched control with frequency of 6/653 (0.92%) as well as from literature and genomic databases. Conclusions: DPP10 duplication is likely a benign CNV polymorphism enriched in Southern Chinese with population frequency of ~1%. This highlights the importance of using ancestry-matched controls in interpretation of aCGH findings.

2017-04-07 | E-MTAB-5665 | biostudies-arrayexpress

Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder - implications of a copy number variation involving dpp10 (Perkin Elmer CGX)

Project description:Background Array-Comparative-Genomic-Hybridization (aCGH) is recommended as first-tier genetic test for children with autism spectrum disorder (ASD). However, result interpretation can be challenging as copy number variants (CNVs) in non-European ASD patients is not well studied. To address this literature gap, we report the CNV findings in a cohort of Chinese children with ASD. Methods DNA samples were obtained from 258 Chinese ASD patients recruited from a child assessment center between January 2011 and August 2014. aCGH was performed using NimbleGen-CGX-135k or Agilent-CGX 60k oligonucleotide array. Results were classified based on existing guidelines and literature. Results Ten pathogenic and one likely-pathogenic CNVs were found in nine patients, with an overall diagnostic yield of 3.5%. A 138kb duplication involving 3â exons of DPP10 (hg[19]chr2:116534689-116672358), reported to be associated with ASD, was identified in one patient (0.39%). The same CNV was reported as variant of unknown significance (VUS) in DECIPHER database. Multiple individuals of typical development carrying a similar duplication were identified amongst our ancestry-matched control with frequency of 6/653 (0.92%) as well as from literature and genomic databases. Conclusions DPP10 duplication is likely a benign CNV polymorphism enriched in Southern Chinese with population frequency of ~1%. This highlights the importance of using ancestry-matched controls in interpretation of aCGH findings.

2017-04-07 | E-MTAB-5672 | biostudies-arrayexpress

Virus infection of the CNS disrupts the immune-neural-synaptic axis via induction of pleiotropic gene regulation of host responses

Project description:Treatment for many viral infections of the central nervous system (CNS) remains only supportive. Here we address a remaining gap in our knowledge regarding how the CNS and immune systems interact during viral infection. By examining the regulation of the immune and nervous system processes in a nonhuman primate model of West Nile virus neurological disease, we show that virus infection disrupts the homeostasis of the immune-neural-synaptic axis via induction of pleiotropic genes with distinct functions in each component of the axis. This pleiotropic gene regulation suggests an unintended off-target negative impact of virus-induced host immune responses on the neurotransmission, which may be a common feature of various viral infections of the CNS.

2021-02-18 | GSE122798 | GEO

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