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Artikel ; Online: Probabilistic association of differentially expressed genes with

Roberts, Brian S / Anderson, Ashlyn G / Partridge, E Christopher / Cooper, Gregory M / Myers, Richard M

2024 Band 34, Heft 4, Seite(n) 620–632

Abstract: Differential gene expression in response to perturbations is mediated at least in part by changes in binding of transcription factors (TFs) and other proteins at specific genomic regions. Association of ... ...

Abstract	Differential gene expression in response to perturbations is mediated at least in part by changes in binding of transcription factors (TFs) and other proteins at specific genomic regions. Association of these
Mesh-Begriff(e)	Humans ; Transcription Factors/metabolism ; Transcription Factors/genetics ; Chromatin/metabolism ; Chromatin/genetics ; Gene Expression Regulation ; Regulatory Sequences, Nucleic Acid ; Regulatory Elements, Transcriptional
Sprache	Englisch
Erscheinungsdatum	2024-05-15
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.278598.123
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Parlez-vous VUS?

Cooper, Gregory M

Genome research

2015 Band 25, Heft 10, Seite(n) 1423–1426

Abstract: Human genome sequencing is routine and will soon be a staple in research and clinical genetics. However, the promise of sequencing is often just that, with genome data routinely failing to reveal useful insights about disease in general or a person's ... ...

Abstract	Human genome sequencing is routine and will soon be a staple in research and clinical genetics. However, the promise of sequencing is often just that, with genome data routinely failing to reveal useful insights about disease in general or a person's health in particular. Nowhere is this chasm between promise and progress more evident than in the designation, "variant of uncertain significance" (VUS). Although it serves an important role, careful consideration of VUS reveals it to be a nebulous description of genomic information and its relationship to disease, symptomatic of our inability to make even crude quantitative assertions about the disease risks conferred by many genetic variants. In this perspective, I discuss the challenge of "variant interpretation" and the value of comparative and functional genomic information in meeting that challenge. Although already essential, genomic annotations will become even more important as our analytical focus widens beyond coding exons. Combined with more genotype and phenotype data, they will help facilitate more quantitative and insightful assessments of the contributions of genetic variants to disease.
Mesh-Begriff(e)	Animals ; Data Curation ; Genetic Research ; Genetic Variation ; Genomics/trends ; Humans ; Terminology as Topic ; Uncertainty
Sprache	Englisch
Erscheinungsdatum	2015-09-30
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.190116.115
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Combined Bioinformatic and Splicing Analysis of Likely Benign Intronic and Synonymous Variants Reveals Evidence for Pathogenicity.

Hirschi, Owen R / Felker, Stephanie A / Rednam, Surya P / Vallance, Kelly L / Parsons, D Williams / Roy, Angshumoy / Cooper, Gregory M / Plon, Sharon E

medRxiv : the preprint server for health sciences

2023

Abstract: Background: Current clinical variant analysis pipelines focus on coding variants and intronic variants within 10-20 bases of an exon-intron boundary that may affect splicing. The impact of newer splicing prediction algorithms combined with : Methods: ...

Abstract	Background: Current clinical variant analysis pipelines focus on coding variants and intronic variants within 10-20 bases of an exon-intron boundary that may affect splicing. The impact of newer splicing prediction algorithms combined with Methods: Exome sequencing data from 576 pediatric cancer patients enrolled in the Texas KidsCanSeq study were filtered for intronic or synonymous variants absent from population databases, predicted to alter splicing via SpliceAI (>0.20), and scored as potentially deleterious by CADD (>10.0). Total cellular RNA was extracted from monocytes and RT-PCR products analyzed. Subsequently, rare synonymous or intronic B/LB variants in a subset of genes submitted to ClinVar were similarly evaluated. Variants predicted to lead to a frameshifted splicing product were functionally assessed using an Results: KidsCanSeq exome data analysis revealed a rare, heterozygous, intronic variant (NM_177438.3( Conclusions: Our results demonstrate the power of newer predictive splicing algorithms to highlight rare variants previously considered B/LB in patients with features of hereditary conditions. Incorporation of SpliceAI annotation of existing variant data combined with either direct RNA analysis or
Sprache	Englisch
Erscheinungsdatum	2023-11-01
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.1101/2023.10.30.23297632
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Clinical utility of genomic sequencing.

Neu, Matthew B / Bowling, Kevin M / Cooper, Gregory M

Current opinion in pediatrics

2019 Band 31, Heft 6, Seite(n) 732–738

Abstract: Purpose of review: Identifying pathogenic variation underlying pediatric developmental disease is critical for medical management, therapeutic development, and family planning. This review summarizes current genetic testing options along with their ... ...

Abstract	Purpose of review: Identifying pathogenic variation underlying pediatric developmental disease is critical for medical management, therapeutic development, and family planning. This review summarizes current genetic testing options along with their potential benefits and limitations. We also describe results from large-scale genomic sequencing projects in pediatric and neonatal populations with a focus on clinical utility. Recent findings: Recent advances in DNA sequencing technology have made genomic sequencing a feasible and effective testing option in a variety of clinical settings. These cutting-edge tests offer much promise to both medical providers and patients as it has been demonstrated to detect causal genetic variation in ∼25% or more of previously unresolved cases. Efforts aimed at promoting data sharing across clinical genetics laboratories and systematic reanalysis of existing genomic sequencing data have further improved diagnostic rates and reduced the number of unsolved cases. Summary: Genomic sequencing is a powerful and increasingly cost-effective alternative to current genetic tests and will continue to grow in clinical utility as more of the genome is understood and as analytical methods are improved. The evolution of genomic sequencing is changing the landscape of clinical testing and requires medical professionals who are adept at understanding and returning genomic results to patients.
Mesh-Begriff(e)	Child ; DNA Mutational Analysis ; Developmental Disabilities ; Genetic Testing ; Genomics ; Humans ; Pediatrics ; Rare Diseases/diagnosis ; Rare Diseases/genetics ; Sequence Analysis, DNA ; Whole Genome Sequencing
Sprache	Englisch
Erscheinungsdatum	2019-12-12
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1049374-8
ISSN	1531-698X ; 1040-8703
ISSN (online)	1531-698X
ISSN	1040-8703
DOI	10.1097/MOP.0000000000000815
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Multiomic profiling of transcription factor binding and function in human brain.

Loupe, Jacob M / Anderson, Ashlyn G / Rizzardi, Lindsay F / Rodriguez-Nunez, Ivan / Moyers, Belle / Trausch-Lowther, Katie / Jain, Rashmi / Bunney, William E / Bunney, Blynn G / Cartagena, Preston / Sequeira, Adolfo / Watson, Stanley J / Akil, Huda / Cooper, Gregory M / Myers, Richard M

Nature neuroscience

2024

Abstract: Transcription factors (TFs) orchestrate gene expression programs crucial for brain function, but we lack detailed information about TF binding in human brain tissue. We generated a multiomic resource (ChIP-seq, ATAC-seq, RNA-seq, DNA methylation) on bulk ...

Abstract	Transcription factors (TFs) orchestrate gene expression programs crucial for brain function, but we lack detailed information about TF binding in human brain tissue. We generated a multiomic resource (ChIP-seq, ATAC-seq, RNA-seq, DNA methylation) on bulk tissues and sorted nuclei from several postmortem brain regions, including binding maps for more than 100 TFs. We demonstrate improved measurements of TF activity, including motif recognition and gene expression modeling, upon identification and removal of high TF occupancy regions. Further, predictive TF binding models demonstrate a bias for these high-occupancy sites. Neuronal TFs SATB2 and TBR1 bind unique regions depleted for such sites and promote neuronal gene expression. Binding sites for TFs, including TBR1 and PKNOX1, are enriched for risk variants associated with neuropsychiatric disorders, predominantly in neurons. This work, titled BrainTF, is a powerful resource for future studies seeking to understand the roles of specific TFs in regulating gene expression in the human brain.
Sprache	Englisch
Erscheinungsdatum	2024-06-03
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	1420596-8
ISSN	1546-1726 ; 1097-6256
ISSN (online)	1546-1726
ISSN	1097-6256
DOI	10.1038/s41593-024-01658-8
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Regression modeling to inform cell incorporation into therapies for craniosynostosis.

Cray, James / Cooper, Gregory M

The Journal of craniofacial surgery

2013 Band 24, Heft 1, Seite(n) 226–231

Abstract: Designing an appropriate tissue engineering solution for craniosynostosis (CS) necessitates determination of whether CS-derived cells differ from normal (wild-type, WT) cells and what assays are appropriate to test for differences. Traditional ... ...

Abstract	Designing an appropriate tissue engineering solution for craniosynostosis (CS) necessitates determination of whether CS-derived cells differ from normal (wild-type, WT) cells and what assays are appropriate to test for differences. Traditional methodologies to statistically compare cellular behavior may not accurately reflect biologically relevant differences because they poorly address variation. Here, logistic regression was used to determine which assays could identify a biological difference between WT and CS progenitor cells. Quantitative alkaline phosphatase and MTS proliferation assays were performed on adipose, muscle, and bone marrow-derived cells from WT and CS rabbits. Data were stratified by assay, cell type, and days in culture. Coefficients of variation were calculated and assay results coded as predictive variables. Phenotype (WT or CS) was coded as the dependent variable. Sensitivity-specificity curves, classification tables, and receiver operating characteristic curves were plotted for discriminating models. Two data sets were utilized for subsequent analyses; one was used to develop the logistic regression models for prediction, and the other independent data set was used to determine the ability to predict group membership based on the predictive equation. The resulting coefficients of variation were high for all differentiation measures. Upon model implementation, bone marrow assays were observed to result in 72%-100% predictability for phenotype. We found predictive differences in our muscle-derived and bone marrow-derived cells suggesting biologically relevant differences. This data analysis methodology could help identify homogenous cells that do not differ between pathologic and normal individuals or cells that differ in their osteogenic potential, depending on the type of cell-based therapy being developed.
Mesh-Begriff(e)	Animals ; Cell Differentiation ; Cells, Cultured ; Craniosynostoses/pathology ; Craniosynostoses/therapy ; Logistic Models ; Osteogenesis/physiology ; Phenotype ; Predictive Value of Tests ; Rabbits ; Sensitivity and Specificity ; Stem Cells/cytology ; Tissue Engineering/methods
Sprache	Englisch
Erscheinungsdatum	2013-01-21
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1159501-2
ISSN	1536-3732 ; 1049-2275
ISSN (online)	1536-3732
ISSN	1049-2275
DOI	10.1097/SCS.0b013e31826cfe09
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders.

Hiatt, Susan M / Lawlor, James M J / Handley, Lori H / Latner, Donald R / Bonnstetter, Zachary T / Finnila, Candice R / Thompson, Michelle L / Boston, Lori Beth / Williams, Melissa / Nunez, Ivan Rodriguez / Jenkins, Jerry / Kelley, Whitley V / Bebin, E Martina / Lopez, Michael A / Hurst, Anna C E / Korf, Bruce R / Schmutz, Jeremy / Grimwood, Jane / Cooper, Gregory M

medRxiv : the preprint server for health sciences

2024

Abstract: Variant detection from long-read genome sequencing (lrGS) has proven to be considerably more accurate and comprehensive than variant detection from short-read genome sequencing (srGS). However, the rate at which lrGS can increase molecular diagnostic ... ...

Abstract	Variant detection from long-read genome sequencing (lrGS) has proven to be considerably more accurate and comprehensive than variant detection from short-read genome sequencing (srGS). However, the rate at which lrGS can increase molecular diagnostic yield for rare disease is not yet precisely characterized. We performed lrGS using Pacific Biosciences "HiFi" technology on 96 short-read-negative probands with rare disease that were suspected to be genetic. We generated hg38-aligned variants and
Sprache	Englisch
Erscheinungsdatum	2024-03-26
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.1101/2024.03.22.24304633
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Evaluating the strength of genetic results: Risks and responsibilities.

Barsh, Gregory S / Cooper, Gregory M / Copenhaver, Gregory P / Sirugo, Giorgio / Tang, Hua / Williams, Scott M

PLoS genetics

2019 Band 15, Heft 10, Seite(n) e1008437

Mesh-Begriff(e)	Exome ; Humans ; Multiple Sclerosis ; Social Behavior ; Surveys and Questionnaires ; Whole Exome Sequencing
Sprache	Englisch
Erscheinungsdatum	2019-10-11
Erscheinungsland	United States
Dokumenttyp	Editorial ; Comment
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1008437
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Calvarial Versus Long Bone: Implications for Tailoring Skeletal Tissue Engineering.

Wang, Dan / Gilbert, James R / Zhang, Xu / Zhao, Bingkun / Ker, Dai Fei Elmer / Cooper, Gregory M

Tissue engineering. Part B, Reviews

2019 Band 26, Heft 1, Seite(n) 46–63

Abstract: Tissue-engineered graft substitutes have shown great potential to treat large bone defects. While we usually assume that therapeutic approaches developed for appendicular bone healing could be similarly translated for application in craniofacial ... ...

Abstract	Tissue-engineered graft substitutes have shown great potential to treat large bone defects. While we usually assume that therapeutic approaches developed for appendicular bone healing could be similarly translated for application in craniofacial reconstruction and
Mesh-Begriff(e)	Animals ; Bone Diseases/therapy ; Bone and Bones/cytology ; Fracture Healing ; Humans ; Osteogenesis ; Skull/cytology ; Tissue Engineering/methods
Sprache	Englisch
Erscheinungsdatum	2019-12-18
Erscheinungsland	United States
Dokumenttyp	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2420584-9
ISSN	1937-3376 ; 1937-3368
ISSN (online)	1937-3376
ISSN	1937-3368
DOI	10.1089/ten.TEB.2018.0353
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs.

Moyers, Belle A / Loupe, Jacob M / Felker, Stephanie A / Lawlor, James M J / Anderson, Ashlyn G / Rodriguez-Nunez, Ivan / Bunney, William E / Bunney, Blynn G / Cartagena, Preston M / Sequeira, Adolfo / Watson, Stanley J / Akil, Huda / Mendenhall, Eric M / Cooper, Gregory M / Myers, Richard M

bioRxiv : the preprint server for biology

2023

Abstract: Transcription Factors (TFs) influence gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because genomic localization of TFs is in part driven by TF recognition of DNA sequence, ... ...

Abstract	Transcription Factors (TFs) influence gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because genomic localization of TFs is in part driven by TF recognition of DNA sequence, variation in TF binding sites can disrupt TF-DNA associations and affect gene regulation. To identify variants that impact TF binding in human brain tissues, we quantified allele bias for 93 TFs analyzed with ChIP-seq experiments of multiple structural brain regions from two donors. Using graph genomes constructed from phased genomic sequence data, we compared ChIP-seq signal between alleles at heterozygous variants within each tissue sample from each donor. Comparison of results from different brain regions within donors and the same regions between donors provided measures of allele bias reproducibility. We identified thousands of DNA variants that show reproducible bias in ChIP-seq for at least one TF. We found that alleles that are rarer in the general population were more likely than common alleles to exhibit large biases, and more frequently led to reduced TF binding. Combining ChIP-seq with RNA-seq, we identified TF-allele interaction biases with RNA bias in a phased allele linked to 6,709 eQTL variants identified in GTEx data, 3,309 of which were found in neural contexts. Our results provide insights into the effects of both common and rare variation on gene regulation in the brain. These findings can facilitate mechanistic understanding of cis-regulatory variation associated with biological traits, including disease.
Sprache	Englisch
Erscheinungsdatum	2023-10-09
Erscheinungsland	United States
Dokumenttyp	Preprint
DOI	10.1101/2023.10.06.561245
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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