Publications by authors named "Carol Scott"

38 Publications

Psychometric Properties of the Assessment of Recovery Capital (ARC) Instrument in a Diverse Low-Income Sample.

Subst Use Misuse 2020 13;55(1):108-118. Epub 2019 Sep 13.

School of Social Work, University at Buffalo, State University of New York, Buffalo, New York, USA.

Recovery capital is a theoretical construct elucidating the resources that support recovery from addiction. The 50-item Assessment of Recovery Capital (ARC) instrument and related brief-format versions are the predominant measures of this construct. However, some of the ARC's psychometric properties are not well-established, particularly in racially and economically diverse populations. We aimed to determine if the ARC is a valid and reliable measure of recovery capital in a diverse sample. Paper-and-pencil survey data were collected between March 2017 and May 2018 from a low-income, racially diverse sample of adults in recovery ( = 273). Participants were recruited from nontreatment community settings throughout a mid-sized northeastern U.S. city. They completed the ARC and sociodemographic questions. To determine the ARC's reliability and factor structure, we used item-level analyses and Cronbach's alpha, followed by confirmatory and exploratory factor analyses. Several items performed poorly, having means close to response extremes and problematically small variances. Cronbach's alpha for the full measure was = .92; however, alphas for the majority of subscales were below .70. The a priori 10-factor model solution failed, preventing interpretation of the confirmatory factor analysis results. Exploratory factor analysis revealed that although the 10-factor model marginally fit the data, items did not load together as proposed. Not once did all five subscale items load highly on the same factor. The ARC has substantial weaknesses in its theoretical alignment, item performance, and psychometric properties with diverse populations. We recommend the development of a new multidimensional, theory-aligned measure, following a rigorous measurement development protocol.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/10826084.2019.1657148DOI Listing
October 2020

RRAD mutation causes electrical and cytoskeletal defects in cardiomyocytes derived from a familial case of Brugada syndrome.

Eur Heart J 2019 10;40(37):3081-3094

Division of Cardiovascular Medicine, Department of Medicine, Stanford Cardiovascular Institute, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.

Aims: The Brugada syndrome (BrS) is an inherited cardiac disorder predisposing to ventricular arrhythmias. Despite considerable efforts, its genetic basis and cellular mechanisms remain largely unknown. The objective of this study was to identify a new susceptibility gene for BrS through familial investigation.

Methods And Results: Whole-exome sequencing performed in a three-generation pedigree with five affected members allowed the identification of one rare non-synonymous substitution (p.R211H) in RRAD, the gene encoding the RAD GTPase, carried by all affected members of the family. Three additional rare missense variants were found in 3/186 unrelated index cases. We detected higher levels of RRAD transcripts in subepicardium than in subendocardium in human heart, and in the right ventricle outflow tract compared to the other cardiac compartments in mice. The p.R211H variant was then subjected to electrophysiological and structural investigations in human cardiomyocytes derived from induced pluripotent stem cells (iPSC-CMs). Cardiomyocytes derived from induced pluripotent stem cells from two affected family members exhibited reduced action potential upstroke velocity, prolonged action potentials and increased incidence of early afterdepolarizations, with decreased Na+ peak current amplitude and increased Na+ persistent current amplitude, as well as abnormal distribution of actin and less focal adhesions, compared with intra-familial control iPSC-CMs Insertion of p.R211H-RRAD variant in control iPSCs by genome editing confirmed these results. In addition, iPSC-CMs from affected patients exhibited a decreased L-type Ca2+ current amplitude.

Conclusion: This study identified a potential new BrS-susceptibility gene, RRAD. Cardiomyocytes derived from induced pluripotent stem cells expressing RRAD variant recapitulated single-cell electrophysiological features of BrS, including altered Na+ current, as well as cytoskeleton disturbances.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/eurheartj/ehz308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769825PMC
October 2019

Time spent online: Latent profile analyses of emerging adults' social media use.

Comput Human Behav 2017 Oct 18;75:311-319. Epub 2017 May 18.

University at Buffalo, Buffalo, NY 14260-1660, USA.

Studies of youth social media use (SMU) often focus on its frequency, measuring time they spend online. While informative, this perspective is only one way of viewing SMU. Consistent with uses and gratification theory, another is to consider youth spend their time online (i.e., degree of engagement). We conducted latent profile analyses of survey data from 249 U.S. emerging adults (ages 18-26) to explore their SMU in terms of frequency and engagement. We derived separate 3-profile solutions for both frequency and engagement. High frequency social media users tended to be women and to have more Facebook friends. Highly engaged users (i.e., those most interactive online) tended to be White and more highly educated. Findings from this exploratory study indicate that youth SMU frequency and SMU engagement warrant separate consideration. As SMU becomes more ingrained into the fabric of daily life, it is conceivable that engagement may be a more meaningful way to assess youth SMU, especially in relation to the digital divide, since it can be used to meet important needs, including social interaction, information exchange, and self-expression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.chb.2017.05.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8319841PMC
October 2017

Dysfunction of the Voltage-Gated K+ Channel β2 Subunit in a Familial Case of Brugada Syndrome.

J Am Heart Assoc 2016 06 10;5(6). Epub 2016 Jun 10.

INSERM, UMR 1087, l'Institut du Thorax, Nantes, France CNRS, UMR 6291, Nantes, France Université de Nantes, Nantes, France CHU Nantes, l'Institut du Thorax, Service de Cardiologie, Nantes, France

Background: The Brugada syndrome is an inherited cardiac arrhythmia associated with high risk of sudden death. Although 20% of patients with Brugada syndrome carry mutations in SCN5A, the molecular mechanisms underlying this condition are still largely unknown.

Methods And Results: We combined whole-exome sequencing and linkage analysis to identify the genetic variant likely causing Brugada syndrome in a pedigree for which SCN5A mutations had been excluded. This approach identified 6 genetic variants cosegregating with the Brugada electrocardiographic pattern within the pedigree. In silico gene prioritization pointed to 1 variant residing in KCNAB2, which encodes the voltage-gated K(+) channel β2-subunit (Kvβ2-R12Q). Kvβ2 is widely expressed in the human heart and has been shown to interact with the fast transient outward K(+) channel subunit Kv4.3, increasing its current density. By targeted sequencing of the KCNAB2 gene in 167 unrelated patients with Brugada syndrome, we found 2 additional rare missense variants (L13F and V114I). We then investigated the physiological effects of the 3 KCNAB2 variants by using cellular electrophysiology and biochemistry. Patch-clamp experiments performed in COS-7 cells expressing both Kv4.3 and Kvβ2 revealed a significant increase in the current density in presence of the R12Q and L13F Kvβ2 mutants. Although biotinylation assays showed no differences in the expression of Kv4.3, the total and submembrane expression of Kvβ2-R12Q were significantly increased in comparison with wild-type Kvβ2.

Conclusions: Altogether, our results indicate that Kvβ2 dysfunction can contribute to the Brugada electrocardiographic pattern.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1161/JAHA.115.003122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937261PMC
June 2016

Five-Year Experience with Screening Electrocardiograms in National Collegiate Athletic Association Division I Athletes.

Clin J Sport Med 2016 Sep;26(5):369-75

*Northern Nevada Medical Center, University of Nevada School of Medicine; †University of Nevada School of Medicine; ‡University of Nevada, Reno, School of Community Health Sciences; and §Silver Sage Sports and Fitness Lab, University of Nevada School of Medicine.

Objective: (1) Compare rates of abnormal screening electrocardiograms (ECGs) using updated criteria compared with older criteria. (2) Compare rates of abnormal ECGs by ethnicity. (3) Evaluate ability of ECG criteria to detect the predicted number of athletes with previously undetected cardiovascular abnormalities.

Design: Prospective and retrospective review of ECGs. During the prospective portion of the study, the 2005 European Society of Cardiology criteria were used from 2008 to July 2011 and the 2011 Stanford criteria were used from August 2011 to 2013. Retrospectively, all ECGs were reevaluated using the 2011 Stanford criteria, 2013 Seattle criteria, and 2014 Sharma Refined criteria.

Setting: Division I National Collegiate Athletic Association University.

Participants: 874 incoming athletes over a 5-year period.

Interventions: ECG screening program.

Main Outcome Measures: Number of abnormal ECGs and number of athletes with newly discovered cardiac abnormalities.

Results: Abnormal ECG rates were the 2005 European criteria 10.7%, 2011 Stanford criteria 6.6%, 2013 Seattle criteria 2.8%, and 2014 Sharma Refined criteria 2.8%. In black athletes, the Stanford criteria resulted in more abnormal ECGs compared with Seattle or Sharma Refined. Three athletes were found to have a previously undetected cardiac abnormality (2 with hypertrophic cardiomyopathy and 1 with preexcitation).

Conclusions: More recent ECG screening criteria substantially reduce the abnormal ECG rate and thus the number of athletes requiring additional testing. ECG screening criteria identified the predicted number (1/300) of young athletes with serious underlying cardiovascular disease. These criteria prompt not only additional cardiovascular testing but also a more thorough cardiovascular history.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/JSM.0000000000000318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5228614PMC
September 2016

Timeliness of interfacility transfer for ED patients with ST-elevation myocardial infarction.

Am J Emerg Med 2015 Mar 6;33(3):423-9. Epub 2015 Jan 6.

Department of Medicine, Institute for Medicine and Public Health, Vanderbilt University School of Medicine, Nashville, TN; Geriatric Research, Education, and Clinical Center, Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN.

Objectives: Most US hospitals lack primary percutaneous coronary intervention (PCI) capabilities to treat patients with ST-elevation myocardial infarction (STEMI) necessitating transfer to PCI-capable centers. Transferred patients rarely meet the 120-minute benchmark for timely reperfusion, and referring emergency departments (EDs) are a major source of preventable delays. We sought to use more granular data at transferring EDs to describe the variability in length of stay at referring EDs.

Methods: We retrospectively analyzed a secondary data set used for quality improvement for patients with STEMI transferred to a single PCI center between 2008 and 2012. We conducted a descriptive analysis of the total time spent at each referring ED (door-in-door-out [DIDO] interval), periods that comprised DIDO (door to electrocardiogram [EKG], EKG-to-PCI activation, and PCI activation to exit), and the relationship of each period with overall time to reperfusion (medical contact-to-balloon [MCTB] interval).

Results: We identified 41 EDs that transferred 620 patients between 2008 and 2012. Median MCTB was 135 minutes (interquartile range [IQR] 114,172). Median overall ED DIDO was 74 minutes (IQR 56,103) and was composed of door to EKG, 5 minutes (IQR 2,11); EKG-to-PCI activation, 18 minutes (IQR 7,37); and PCI activation to exit, 44 minutes (IQR 34,56). Door-in door-out accounted for the largest proportion (60%) of overall MCTB and had the largest variability (coefficient of variability, 1.37) of these intervals.

Conclusions: In this cohort of transferring EDs, we found high variability and substantial delays after EKG performance for patients with STEMI. Factors influencing ED decision making and transportation coordination after PCI activation are a potential target for intervention to improve the timeliness of reperfusion in patients with STEMI.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ajem.2014.12.067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385487PMC
March 2015

New toolkit to measure quality of person-centered care: development and pilot evaluation with nursing home communities.

J Am Med Dir Assoc 2014 Sep 8;15(9):671-80. Epub 2014 Apr 8.

Polisher Research Institute, Madlyn and Leonard Abramson Center for Jewish Life, North Wales, PA.

Background: Increasingly, nursing home (NH) providers are adopting a person-centered care (PCC) philosophy; yet, they currently lack methods to measure their progress toward this goal. Few PCC tools meet criteria for ease of use and feasibility in NHs. The purpose of this article is to report on the development of the concept and measurement of preference congruence among NH residents (phase 1), its refinement into a set of quality indicators by Advancing Excellence in America's Nursing Homes (phase 2), and its pilot evaluation in a sample of 12 early adopting NHs prior to national rollout (phase 3). The recommended toolkit for providers to use to measure PCC consists of (1) interview materials for 16 personal care and activity preferences from Minimum Data Set 3.0, plus follow-up questions that ask residents how satisfied they are with fulfillment of important preferences; and (2) an easy to use Excel spreadsheet that calculates graphic displays of quality measures of preference congruence and care conference attendance for an individual, household or NH. Twelve NHs interviewed residents (N = 146) using the toolkit; 10 also completed a follow-up survey and 9 took part in an interview evaluating their experience.

Results: NH staff gave strong positive ratings to the toolkit. All would recommend it to other NHs. Staff reported that the toolkit helped them identify opportunities to improve PCC (100%), and found that the Excel tool was comprehensive (100%), easy to use (90%), and provided high quality information (100%). Providers anticipated using the toolkit to strengthen staff training as well as to enhance care planning, programming and quality improvement.

Conclusions: The no-cost PCC toolkit provides a new means to measure the quality of PCC delivery. As of February 2014, over 700 nursing homes have selected the Advancing Excellence in America's Nursing Homes PCC goal as a focus for quality improvement. The toolkit enables providers to incorporate quality improvement by moving beyond anecdote, and advancing more systematically toward honoring resident preferences.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jamda.2014.02.004DOI Listing
September 2014

Massively parallel sequencing reveals the complex structure of an irradiated human chromosome on a mouse background in the Tc1 model of Down syndrome.

PLoS One 2013 15;8(4):e60482. Epub 2013 Apr 15.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

Down syndrome (DS) is caused by trisomy of chromosome 21 (Hsa21) and presents a complex phenotype that arises from abnormal dosage of genes on this chromosome. However, the individual dosage-sensitive genes underlying each phenotype remain largely unknown. To help dissect genotype--phenotype correlations in this complex syndrome, the first fully transchromosomic mouse model, the Tc1 mouse, which carries a copy of human chromosome 21 was produced in 2005. The Tc1 strain is trisomic for the majority of genes that cause phenotypes associated with DS, and this freely available mouse strain has become used widely to study DS, the effects of gene dosage abnormalities, and the effect on the basic biology of cells when a mouse carries a freely segregating human chromosome. Tc1 mice were created by a process that included irradiation microcell-mediated chromosome transfer of Hsa21 into recipient mouse embryonic stem cells. Here, the combination of next generation sequencing, array-CGH and fluorescence in situ hybridization technologies has enabled us to identify unsuspected rearrangements of Hsa21 in this mouse model; revealing one deletion, six duplications and more than 25 de novo structural rearrangements. Our study is not only essential for informing functional studies of the Tc1 mouse but also (1) presents for the first time a detailed sequence analysis of the effects of gamma radiation on an entire human chromosome, which gives some mechanistic insight into the effects of radiation damage on DNA, and (2) overcomes specific technical difficulties of assaying a human chromosome on a mouse background where highly conserved sequences may confound the analysis. Sequence data generated in this study is deposited in the ENA database, Study Accession number: ERP000439.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0060482PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626651PMC
October 2013

The zebrafish reference genome sequence and its relationship to the human genome.

Nature 2013 Apr 17;496(7446):498-503. Epub 2013 Apr 17.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature12111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703927PMC
April 2013

A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling.

PLoS One 2012 29;7(11):e50233. Epub 2012 Nov 29.

Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

DNA methylation is one of the most studied epigenetic marks in the human genome, with the result that the desire to map the human methylome has driven the development of several methods to map DNA methylation on a genomic scale. Our study presents the first comparison of two of these techniques - the targeted approach of the Infinium HumanMethylation450 BeadChip® with the immunoprecipitation and sequencing-based method, MeDIP-seq. Both methods were initially validated with respect to bisulfite sequencing as the gold standard and then assessed in terms of coverage, resolution and accuracy. The regions of the methylome that can be assayed by both methods and those that can only be assayed by one method were determined and the discovery of differentially methylated regions (DMRs) by both techniques was examined. Our results show that the Infinium HumanMethylation450 BeadChip® and MeDIP-seq show a good positive correlation (Spearman correlation of 0.68) on a genome-wide scale and can both be used successfully to determine differentially methylated loci in RefSeq genes, CpG islands, shores and shelves. MeDIP-seq however, allows a wider interrogation of methylated regions of the human genome, including thousands of non-RefSeq genes and repetitive elements, all of which may be of importance in disease. In our study MeDIP-seq allowed the detection of 15,709 differentially methylated regions, nearly twice as many as the array-based method (8070), which may result in a more comprehensive study of the methylome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050233PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510246PMC
June 2013

Analyses of pig genomes provide insight into porcine demography and evolution.

Nature 2012 Nov;491(7424):393-8

Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature11622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564PMC
November 2012

Clinical pathway: helicopter scene STEMI protocol to facilitate long-distance transfer for primary PCI.

Crit Pathw Cardiol 2012 Dec;11(4):193-8

Vanderbilt Heart and Vascular Institute, 1215 21st Avenue South, Nashville, TN 37232, USA.

Background: The latest American College of Cardiology/American Heart Association guidelines recommend primary percutaneous coronary intervention (PCI) in acute ST-elevation myocardial infarction (STEMI) patients within 90 minutes from presentation to the emergency room. For interhospital transfers, the most recent PCI guidelines recommend first medical contact-to-device times ≤120 minutes. Although PCI-capable hospitals have improved door-to-balloon times, many patients present to non-PCI-capable facilities and have been excluded from national quality measures.

Methods: In our acute myocardial infarction network, not only do we enable non-PCI hospitals to transfer STEMI patients but empower outside emergency medical services (EMS) to activate the catheterization laboratory team with a burst page and transfer STEMI patients directly from the scene. Data on patient characteristics, outcomes, and time elements were collected for "scene STEMI" patients who circumvented outlying rural non-PCI hospitals and are presented in this case series.

Results: From December 2007 to November 2010, 22 STEMI patients with higher than average acuity were transported by helicopter directly to our medical center for primary PCI. Median distance from the scene to our medical center was 47 miles [25th to 75th interquartile range (IQR) = 39-71 miles]. Median EMS-to-balloon time was 120 minutes (IQR = 111-134 minutes). There were no false activations by EMS. In comparison, our median time for interhospital STEMI transfers (N = 335) was 145 minutes (IQR = 121-186 minutes) from 2007 to 2009.

Conclusions: In our single-center experience, 22 scene STEMI patients were diagnosed and appropriately triaged by EMS to our center for primary PCI. Our data show feasibility of an EMS-activated STEMI network over long distances with good reperfusion times.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/HPC.0b013e318261c995DOI Listing
December 2012

Implementation of a standardized pathway for the treatment of cardiac arrest patients using therapeutic hypothermia: "CODE ICE".

Crit Pathw Cardiol 2012 Sep;11(3):91-8

Vanderbilt University Medical Center, Nashville, TN 37232, USA.

Out-of-hospital cardiac arrest is common and is associated with high mortality. The majority of in-hospital deaths from resuscitated victims of cardiac arrest are due to neurologic injury. Therapeutic hypothermia (TH) is now recommended for the management of comatose survivors of cardiac arrest. The rapid triage and standardized treatment of cardiac arrest patients can be challenging, and implementation of a TH program requires a multidisciplinary team approach. In 2010, we revised our institution's TH protocol, creating a "CODE ICE" pathway to improve the timely and coordinated care of cardiac arrest patients. As part of CODE ICE, we implemented comprehensive care pathways including measures such as a burst paging system and computerized physician support tools. "STEMI on ICE" integrates TH with our regional ST-elevation myocardial infarction network. Retrospective data were collected on 150 consecutive comatose cardiac arrest victims treated with TH (n = 82 pre-CODE ICE and n = 68 post-CODE ICE) from 2007 to 2011. After implementation of CODE ICE, the mean time to initiation of TH decreased from 306 ± 165 minutes to 196 ± 144 minutes (P < 0.001), and the time to target temperature decreased from 532 ± 214 minutes to 392 ± 215 minutes (P < 0.001). There was no significant change in survival or neurologic outcome at hospital discharge. Through the implementation of CODE ICE, we were able to reduce the time to initiation of TH and time to reach target temperature. Additional studies are needed to determine the effect of CODE ICE and similar pathways on clinical outcomes after cardiac arrest.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/HPC.0b013e31825b7bc3DOI Listing
September 2012

Mosaic overgrowth with fibroadipose hyperplasia is caused by somatic activating mutations in PIK3CA.

Nat Genet 2012 Jun 24;44(8):928-33. Epub 2012 Jun 24.

The National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA.

The phosphatidylinositol 3-kinase (PI3K)-AKT signaling pathway is critical for cellular growth and metabolism. Correspondingly, loss of function of PTEN, a negative regulator of PI3K, or activating mutations in AKT1, AKT2 or AKT3 have been found in distinct disorders featuring overgrowth or hypoglycemia. We performed exome sequencing of DNA from unaffected and affected cells from an individual with an unclassified syndrome of congenital progressive segmental overgrowth of fibrous and adipose tissue and bone and identified the cancer-associated mutation encoding p.His1047Leu in PIK3CA, the gene that encodes the p110α catalytic subunit of PI3K, only in affected cells. Sequencing of PIK3CA in ten additional individuals with overlapping syndromes identified either the p.His1047Leu alteration or a second cancer-associated alteration, p.His1047Arg, in nine cases. Affected dermal fibroblasts showed enhanced basal and epidermal growth factor (EGF)-stimulated phosphatidylinositol 3,4,5-trisphosphate (PIP(3)) generation and concomitant activation of downstream signaling relative to their unaffected counterparts. Our findings characterize a distinct overgrowth syndrome, biochemically demonstrate activation of PI3K signaling and thereby identify a rational therapeutic target.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng.2332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3461408PMC
June 2012

The GENCODE exome: sequencing the complete human exome.

Eur J Hum Genet 2011 Jul 2;19(7):827-31. Epub 2011 Mar 2.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.

Sequencing the coding regions, the exome, of the human genome is one of the major current strategies to identify low frequency and rare variants associated with human disease traits. So far, the most widely used commercial exome capture reagents have mainly targeted the consensus coding sequence (CCDS) database. We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an additional 5594 genes and 10.3 Mb compared with the current CCDS-based sets. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed here covers 47.9 Mb and performed well in sequence capture experiments. In the sample set used in this study, we identified over 5000 SNP variants more in the GENCODE exome target (24%) than in the CCDS-based exome sequencing.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ejhg.2011.28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137498PMC
July 2011

Early Diagnosis of Werner's Syndrome Using Exome-Wide Sequencing in a Single, Atypical Patient.

Front Endocrinol (Lausanne) 2011 29;2. Epub 2011 Mar 29.

Institute of Metabolic Science, University of Cambridge Metabolic Research Laboratories Cambridge, UK.

Genetic diagnosis of inherited metabolic disease is conventionally achieved through syndrome recognition and targeted gene sequencing, but many patients receive no specific diagnosis. Next-generation sequencing allied to capture of expressed sequences from genomic DNA now offers a powerful new diagnostic approach. Barriers to routine diagnostic use include cost, and the complexity of interpreting results arising from simultaneous identification of large numbers of variants. We applied exome-wide sequencing to an individual, 16-year-old daughter of consanguineous parents with a novel syndrome of short stature, severe insulin resistance, ptosis, and microcephaly. Pulldown of expressed sequences from genomic DNA followed by massively parallel sequencing was undertaken. Single nucleotide variants were called using SAMtools prior to filtering based on sequence quality and existence in control genomes and exomes. Of 485 genetic variants predicted to alter protein sequence and absent from control data, 24 were homozygous in the patient. One mutation - the p.Arg732X mutation in the WRN gene - has previously been reported in Werner's syndrome (WS). On re-evaluation of the patient several early features of WS were detected including loss of fat from the extremities and frontal hair thinning. Lymphoblastoid cells from the proband exhibited a defective decatenation checkpoint, consistent with loss of WRN activity. We have thus diagnosed WS some 15 years earlier than average, permitting aggressive prophylactic therapy and screening for WS complications, illustrating the potential of exome-wide sequencing to achieve early diagnosis and change management of rare autosomal recessive disease, even in individual patients of consanguineous parentage with apparently novel syndromes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fendo.2011.00008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356119PMC
August 2012

CEP152 is a genome maintenance protein disrupted in Seckel syndrome.

Nat Genet 2011 Jan 5;43(1):23-6. Epub 2010 Dec 5.

Department of Medical Biology, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey.

Functional impairment of DNA damage response pathways leads to increased genomic instability. Here we describe the centrosomal protein CEP152 as a new regulator of genomic integrity and cellular response to DNA damage. Using homozygosity mapping and exome sequencing, we identified CEP152 mutations in Seckel syndrome and showed that impaired CEP152 function leads to accumulation of genomic defects resulting from replicative stress through enhanced activation of ATM signaling and increased H2AX phosphorylation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng.725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430850PMC
January 2011

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.

Nature 2010 Apr;464(7289):713-20

Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed approximately 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated approximately 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature08979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892339PMC
April 2010

Target-enrichment strategies for next-generation sequencing.

Nat Methods 2010 Feb;7(2):111-8

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

We have not yet reached a point at which routine sequencing of large numbers of whole eukaryotic genomes is feasible, and so it is often necessary to select genomic regions of interest and to enrich these regions before sequencing. There are several enrichment approaches, each with unique advantages and disadvantages. Here we describe our experiences with the leading target-enrichment technologies, the optimizations that we have performed and typical results that can be obtained using each. We also provide detailed protocols for each technology so that end users can find the best compromise between sensitivity, specificity and uniformity for their particular project.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.1419DOI Listing
February 2010

Keeping a watchful eye on retinopathy of prematurity.

Neonatal Netw 2008 Sep-Oct;27(5):355-7

Moravian College, Bethlehem, Pennsylvania, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1891/0730-0832.27.5.355DOI Listing
December 2008

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21.

Genome Res 2007 Nov 25;17(11):1690-6. Epub 2007 Sep 25.

Department of Genetic Medicine and Development, University of Geneva Medical School, and University Hospitals, 1211 Geneva, Switzerland.

The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. This region contains extensive euchromatic-like sequence and includes on average one transcript every 100 kb. These transcripts show multiple inter- and intrachromosomal copies, and extensive copy number and sequence variability. The sequencing of the "heterochromatic" regions of the human genome is likely to reveal many additional functional elements and provide important evolutionary information.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.6675307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045151PMC
November 2007

A high utility integrated map of the pig genome.

Genome Biol 2007 ;8(7):R139

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK.

Background: The domestic pig is being increasingly exploited as a system for modeling human disease. It also has substantial economic importance for meat-based protein production. Physical clone maps have underpinned large-scale genomic sequencing and enabled focused cloning efforts for many genomes. Comparative genetic maps indicate that there is more structural similarity between pig and human than, for example, mouse and human, and we have used this close relationship between human and pig as a way of facilitating map construction.

Results: Here we report the construction of the most highly continuous bacterial artificial chromosome (BAC) map of any mammalian genome, for the pig (Sus scrofa domestica) genome. The map provides a template for the generation and assembly of high-quality anchored sequence across the genome. The physical map integrates previous landmark maps with restriction fingerprints and BAC end sequences from over 260,000 BACs derived from 4 BAC libraries and takes advantage of alignments to the human genome to improve the continuity and local ordering of the clone contigs. We estimate that over 98% of the euchromatin of the 18 pig autosomes and the X chromosome along with localized coverage on Y is represented in 172 contigs, with chromosome 13 (218 Mb) represented by a single contig. The map is accessible through pre-Ensembl, where links to marker and sequence data can be found.

Conclusion: The map will enable immediate electronic positional cloning of genes, benefiting the pig research community and further facilitating use of the pig as an alternative animal model for human disease. The clone map and BAC end sequence data can also help to support the assembly of maps and genome sequences of other artiodactyls.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2007-8-7-r139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323232PMC
February 2008

Definition of the zebrafish genome using flow cytometry and cytogenetic mapping.

BMC Genomics 2007 Jun 27;8:195. Epub 2007 Jun 27.

Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.

Background: The zebrafish (Danio rerio) is an important vertebrate model organism system for biomedical research. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of human genes using the zebrafish model. To facilitate analysis of the zebrafish genome, genetic maps have been constructed and sequence annotation of a reference zebrafish genome is ongoing. However, the duplicative nature of teleost genomes, including the zebrafish, complicates accurate assembly and annotation of a representative genome sequence. Cytogenetic approaches provide "anchors" that can be integrated with accumulating genomic data.

Results: Here, we cytogenetically define the zebrafish genome by first estimating the size of each linkage group (LG) chromosome using flow cytometry, followed by the cytogenetic mapping of 575 bacterial artificial chromosome (BAC) clones onto metaphase chromosomes. Of the 575 BAC clones, 544 clones localized to apparently unique chromosomal locations. 93.8% of these clones were assigned to a specific LG chromosome location using fluorescence in situ hybridization (FISH) and compared to the LG chromosome assignment reported in the zebrafish genome databases. Thirty-one BAC clones localized to multiple chromosomal locations in several different hybridization patterns. From these data, a refined second generation probe panel for each LG chromosome was also constructed.

Conclusion: The chromosomal mapping of the 575 large-insert DNA clones allows for these clones to be integrated into existing zebrafish mapping data. An accurately annotated zebrafish reference genome serves as a valuable resource for investigating the molecular basis of human diseases using zebrafish mutant models.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-8-195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1925092PMC
June 2007

A high-resolution map of synteny disruptions in gibbon and human genomes.

PLoS Genet 2006 Dec 13;2(12):e223. Epub 2006 Nov 13.

BACPAC Resources, Children's Hospital of Oakland Research Institute, Oakland, California, United States of America.

Gibbons are part of the same superfamily (Hominoidea) as humans and great apes, but their karyotype has diverged faster from the common hominoid ancestor. At least 24 major chromosome rearrangements are required to convert the presumed ancestral karyotype of gibbons into that of the hominoid ancestor. Up to 28 additional rearrangements distinguish the various living species from the common gibbon ancestor. Using the northern white-cheeked gibbon (2n = 52) (Nomascus leucogenys leucogenys) as a model, we created a high-resolution map of the homologous regions between the gibbon and human. The positions of 100 synteny breakpoints relative to the assembled human genome were determined at a resolution of about 200 kb. Interestingly, 46% of the gibbon-human synteny breakpoints occur in regions that correspond to segmental duplications in the human lineage, indicating a common source of plasticity leading to a different outcome in the two species. Additionally, the full sequences of 11 gibbon BACs spanning evolutionary breakpoints reveal either segmental duplications or interspersed repeats at the exact breakpoint locations. No specific sequence element appears to be common among independent rearrangements. We speculate that the extraordinarily high level of rearrangements seen in gibbons may be due to factors that increase the incidence of chromosome breakage or fixation of the derivative chromosomes in a homozygous state.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.0020223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1756914PMC
December 2006

Accurate and reliable high-throughput detection of copy number variation in the human genome.

Genome Res 2006 Dec 22;16(12):1566-74. Epub 2006 Nov 22.

The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.

This study describes a new tool for accurate and reliable high-throughput detection of copy number variation in the human genome. We have constructed a large-insert clone DNA microarray covering the entire human genome in tiling path resolution that we have used to identify copy number variation in human populations. Crucial to this study has been the development of a robust array platform and analytic process for the automated identification of copy number variants (CNVs). The array consists of 26,574 clones covering 93.7% of euchromatic regions. Clones were selected primarily from the published "Golden Path," and mapping was confirmed by fingerprinting and BAC-end sequencing. Array performance was extensively tested by a series of validation assays. These included determining the hybridization characteristics of each individual clone on the array by chromosome-specific add-in experiments. Estimation of data reproducibility and false-positive/negative rates was carried out using self-self hybridizations, replicate experiments, and independent validations of CNVs. Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.5630906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665640PMC
December 2006

HIV and pregnancy: considerations for nursing practice.

MCN Am J Matern Child Nurs 2006 Jul-Aug;31(4):233-40; quiz 241-2

Department of Professional Nursing, Georgetown University, School of Nursing and Health Studies, Washington, DC, USA.

This article describes current nursing practice for pregnant women with HIV. In the United States, the number of new cases of HIV continues to rise in women of childbearing age. Women often learn of their HIV status when a pregnancy involves them in the healthcare delivery system. Since the manifestation of the disease in 1981, there have been significant advances in treatment, and now, among pregnant women testing positive for HIV, the risk of perinatal transmission can be decreased to 1% with pharmacologic intervention. Yet, HIV disease poses many new challenges to the woman testing positive who is considering pregnancy or who is already pregnant. The progression of the symptoms of AIDS is similar to the common symptoms of pregnancy; the HIV medications may also cause these symptoms. Adherence to the HIV medication regime is necessary for ongoing viral suppression, for missed doses can initiate drug resistance and the whole categories of antiretroviral drugs may become ineffective. Additionally, the HIV stigma continues to impact those infected and interferes with the access to healthcare. HIV poses a major challenge for the nurse caring for the childbearing woman.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/00005721-200607000-00007DOI Listing
January 2007

Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping.

Nat Rev Genet 2005 08;6(8):643-8

CNRS, UMR 6061, Génétique et développement, Faculte de Médecine, Rennes, France.

Accurate and comprehensive sequence coverage for large genomes has been restricted to only a few species of specific interest. Lower sequence coverage (survey sequencing) of related species can yield a wealth of information about gene content and putative regulatory elements. But survey sequences lack long-range continuity and provide only a fragmented view of a genome. Here we show the usefulness of combining survey sequencing with dense radiation-hybrid (RH) maps for extracting maximum comparative genome information from model organisms. Based on results from the canine system, we propose that from now on all low-pass sequencing projects should be accompanied by a dense, gene-based RH map-construction effort to extract maximum information from the genome with a marginal extra cost.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrg1658DOI Listing
August 2005

Comprehensive DNA copy number profiling of meningioma using a chromosome 1 tiling path microarray identifies novel candidate tumor suppressor loci.

Cancer Res 2005 Apr;65(7):2653-61

Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden.

Meningiomas are common neoplasms of the meninges lining of the central nervous system. Deletions of 1p have been established as important for the initiation and/or progression of meningioma. The rationale of this array-CGH study was to characterize copy number imbalances of chromosome 1 in meningioma, using a full-coverage genomic microarray containing 2,118 distinct measurement points. In total, 82 meningiomas were analyzed, making this the most detailed analysis of chromosome 1 in a comprehensive series of tumors. We detected a broad range of aberrations, such as deletions and/or gains of various sizes. Deletions were the predominant finding and ranged from monosomy to a 3.5-Mb terminal 1p homozygous deletion. Although multiple aberrations were observed across chromosome 1, every meningioma in which imbalances were detected harbored 1p deletions. Tumor heterogeneity was also observed in three recurrent meningiomas, which most likely reflects a progressive loss of chromosomal segments at different stages of tumor development. The distribution of aberrations supports the existence of at least four candidate loci on chromosome 1, which are important for meningioma tumorigenesis. In one of these regions, our results already allow the analysis of a number of candidate genes. In a large series of cases, we observed an association between the presence of segmental duplications and deletion breakpoints, which suggests their role in the generation of these tumor-specific aberrations. As 1p is the site of the genome most frequently affected by tumor-specific aberrations, our results indicate loci of general importance for cancer development and progression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1158/0008-5472.CAN-04-3651DOI Listing
April 2005

The DNA sequence of the human X chromosome.

Nature 2005 Mar;434(7031):325-37

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature03440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665286PMC
March 2005
-->