Publications by authors named "Colin Farrell"

22 Publications

  • Page 1 of 1

Survey of spiking in the mouse visual system reveals functional hierarchy.

Nature 2021 04 20;592(7852):86-92. Epub 2021 Jan 20.

Allen Institute for Brain Science, Seattle, WA, USA.

The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically. However, direct observation of cellular-level functional interactions across this hierarchy is lacking due to the challenge of simultaneously recording activity across numerous regions. Here we describe a large, open dataset-part of the Allen Brain Observatory-that surveys spiking from tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli. Using cross-correlation analysis, we reveal that the organization of inter-area functional connectivity during visual stimulation mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas. We find that four classical hierarchical measures-response latency, receptive-field size, phase-locking to drifting gratings and response decay timescale-are all correlated with the hierarchy. Moreover, recordings obtained during a visual task reveal that the correlation between neural activity and behavioural choice also increases along the hierarchy. Our study provides a foundation for understanding coding and signal propagation across hierarchically organized cortical and thalamic visual areas.
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http://dx.doi.org/10.1038/s41586-020-03171-xDOI Listing
April 2021

Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2-induced systemic toxicity.

JCI Insight 2021 01 25;6(2). Epub 2021 Jan 25.

Division of Cardiology, Department of Medicine, David Geffen School of Medicine.

Extrapulmonary manifestations of COVID-19 are associated with a much higher mortality rate than pulmonary manifestations. However, little is known about the pathogenesis of systemic complications of COVID-19. Here, we create a murine model of SARS-CoV-2-induced severe systemic toxicity and multiorgan involvement by expressing the human ACE2 transgene in multiple tissues via viral delivery, followed by systemic administration of SARS-CoV-2. The animals develop a profound phenotype within 7 days with severe weight loss, morbidity, and failure to thrive. We demonstrate that there is metabolic suppression of oxidative phosphorylation and the tricarboxylic acid (TCA) cycle in multiple organs with neutrophilia, lymphopenia, and splenic atrophy, mirroring human COVID-19 phenotypes. Animals had a significantly lower heart rate, and electron microscopy demonstrated myofibrillar disarray and myocardial edema, a common pathogenic cardiac phenotype in human COVID-19. We performed metabolomic profiling of peripheral blood and identified a panel of TCA cycle metabolites that served as biomarkers of depressed oxidative phosphorylation. Finally, we observed that SARS-CoV-2 induces epigenetic changes of DNA methylation, which affects expression of immune response genes and could, in part, contribute to COVID-19 pathogenesis. Our model suggests that SARS-CoV-2-induced metabolic reprogramming and epigenetic changes in internal organs could contribute to systemic toxicity and lethality in COVID-19.
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http://dx.doi.org/10.1172/jci.insight.145027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934846PMC
January 2021

Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells.

Cell 2020 Nov;183(4):935-953.e19

Allen Institute for Brain Science, Seattle, WA 98109, USA.

Neurons are frequently classified into distinct types on the basis of structural, physiological, or genetic attributes. To better constrain the definition of neuronal cell types, we characterized the transcriptomes and intrinsic physiological properties of over 4,200 mouse visual cortical GABAergic interneurons and reconstructed the local morphologies of 517 of those neurons. We find that most transcriptomic types (t-types) occupy specific laminar positions within visual cortex, and, for most types, the cells mapping to a t-type exhibit consistent electrophysiological and morphological properties. These properties display both discrete and continuous variation among t-types. Through multimodal integrated analysis, we define 28 met-types that have congruent morphological, electrophysiological, and transcriptomic properties and robust mutual predictability. We identify layer-specific axon innervation pattern as a defining feature distinguishing different met-types. These met-types represent a unified definition of cortical GABAergic interneuron types, providing a systematic framework to capture existing knowledge and bridge future analyses across different modalities.
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http://dx.doi.org/10.1016/j.cell.2020.09.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781065PMC
November 2020

Cardiac fibroblast proliferation rates and collagen expression mature early and are unaltered with advancing age.

JCI Insight 2020 12 17;5(24). Epub 2020 Dec 17.

Division of Cardiology, Department of Medicine, David Geffen School of Medicine.

Cardiac fibrosis is a pathophysiologic hallmark of the aging heart, but little is known about how fibroblast proliferation and transcriptional programs change throughout the life span of the organism. Using EdU pulse labeling, we demonstrated that more than 50% of cardiac fibroblasts were actively proliferating in the first day of postnatal life. However, by 4 weeks, only 10% of cardiac fibroblasts were proliferating. By early adulthood, the fraction of proliferating cardiac fibroblasts further decreased to approximately 2%, where it remained throughout the rest of the organism's life. We observed that maximal changes in cardiac fibroblast transcriptional programs and, in particular, collagen and ECM gene expression both in the heart and cardiac fibroblast were maximal in the newly born and juvenile animal and decreased with organismal aging. Examination of DNA methylation changes both in the heart and in cardiac fibroblasts did not demonstrate significant changes in differentially methylated regions between young and old mice. Our observations demonstrate that cardiac fibroblasts attain a stable proliferation rate and transcriptional program early in the life span of the organism and suggest that phenotypic changes in the aging heart are not directly attributable to changes in proliferation rate or altered collagen expression in cardiac fibroblasts.
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http://dx.doi.org/10.1172/jci.insight.140628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7819745PMC
December 2020

A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin.

Elife 2020 11 12;9. Epub 2020 Nov 12.

Translational Gerontology Branch, Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, United States.

Robust biomarkers of aging have been developed from DNA methylation in humans and more recently, in mice. This study aimed to generate a novel epigenetic clock in rats-a model with unique physical, physiological, and biochemical advantages-by incorporating behavioral data, unsupervised machine learning, and network analysis to identify epigenetic signals that not only track with age, but also relates to phenotypic aging. Reduced representation bisulfite sequencing (RRBS) data was used to train an epigenetic age (DNAmAge) measure in Fischer 344 CDF (F344) rats. This measure correlated with age at (r = 0.93) in an independent sample, and related to physical functioning (p=5.9e-3), after adjusting for age and cell counts. DNAmAge was also found to correlate with age in male C57BL/6 mice (r = 0.79), and was decreased in response to caloric restriction. Our signatures driven by CpGs in intergenic regions that showed substantial overlap with H3K9me3, H3K27me3, and E2F1 transcriptional factor binding.
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http://dx.doi.org/10.7554/eLife.59201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7661040PMC
November 2020

A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy.

Nat Commun 2020 10 2;11(1):4949. Epub 2020 Oct 2.

Allen Institute, Seattle, WA, USA.

Electron microscopy (EM) is widely used for studying cellular structure and network connectivity in the brain. We have built a parallel imaging pipeline using transmission electron microscopes that scales this technology, implements 24/7 continuous autonomous imaging, and enables the acquisition of petascale datasets. The suitability of this architecture for large-scale imaging was demonstrated by acquiring a volume of more than 1 mm of mouse neocortex, spanning four different visual areas at synaptic resolution, in less than 6 months. Over 26,500 ultrathin tissue sections from the same block were imaged, yielding a dataset of more than 2 petabytes. The combined burst acquisition rate of the pipeline is 3 Gpixel per sec and the net rate is 600 Mpixel per sec with six microscopes running in parallel. This work demonstrates the feasibility of acquiring EM datasets at the scale of cortical microcircuits in multiple brain regions and species.
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http://dx.doi.org/10.1038/s41467-020-18659-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7532165PMC
October 2020

Targeted bisulfite sequencing for biomarker discovery.

Methods 2021 03 2;187:13-27. Epub 2020 Aug 2.

Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, United States; UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, United States; Institute for Quantitative and Computational Biosciences - The Collaboratory, University of California Los Angeles, Los Angeles, CA 90095, United States. Electronic address:

Cytosine methylation is one of the best studied epigenetic modifications. In mammals, DNA methylation patterns vary among cells and is mainly found in the CpG context. DNA methylation is involved in important processes during development and differentiation and its dysregulation can lead to or is associated with diseases, such as cancer, loss-of-imprinting syndromes and neurological disorders. It has been also shown that DNA methylation at the cellular, tissue and organism level varies with age. To overcome the costs of Whole-Genome Bisulfite Sequencing, the gold standard method to detect 5-methylcytosines at a single base resolution, DNA methylation arrays have been developed and extensively used. This method allows one to assess the status of a fraction of the CpG sites present in the genome of an organism. In order to combine the relatively low cost of Methylation Arrays and digital signals of bisulfite sequencing, we developed a Targeted Bisulfite Sequencing method that can be applied to biomarker discovery for virtually any phenotype. Here we describe a comprehensive step-by-step protocol to build a DNA methylation-based epigenetic clock.
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http://dx.doi.org/10.1016/j.ymeth.2020.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7855209PMC
March 2021

Epigenetic Suppression of Transgenic T-cell Receptor Expression via Gamma-Retroviral Vector Methylation in Adoptive Cell Transfer Therapy.

Cancer Discov 2020 Nov 22;10(11):1645-1653. Epub 2020 Jul 22.

Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California.

Transgenic T-cell receptor (TCR) adoptive cell therapies recognizing tumor antigens are associated with robust initial response rates, but frequent disease relapse. This usually occurs in the setting of poor long-term persistence of cells expressing the transgenic TCR, generated using murine stem cell virus (MSCV) γ-retroviral vectors. Analysis of clinical transgenic adoptive cell therapy products revealed that despite strong persistence of the transgenic TCR DNA sequence over time, its expression was profoundly decreased over time at the RNA and protein levels. Patients with the greatest degrees of expression suppression displayed significant increases in DNA methylation over time within the MSCV promoter region, as well as progressive increases in DNA methylation within the entire MSCV vector over time. These increases in vector methylation occurred independently of its integration site within the host genomes. These results have significant implications for the design of future viral vector gene-engineered adoptive cell transfer therapies. SIGNIFICANCE: Cellular immunotherapies' reliance on retroviral vectors encoding foreign genetic material can be vulnerable to progressive acquisition of DNA methylation and subsequent epigenetic suppression of the transgenic product in TCR adoptive cell therapy. This must be considered in the design of future generations of cellular immunotherapies for cancer..
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http://dx.doi.org/10.1158/2159-8290.CD-20-0300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641915PMC
November 2020

The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework.

Bioinformatics 2020 11;36(17):4662-4663

Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.

Summary: Epigenetic rates of change, much as evolutionary mutation rate along a lineage, vary during lifetime. Accurate estimation of the epigenetic state has vast medical and biological implications. To account for these non-linear epigenetic changes with age, we recently developed a formalism inspired by the Pacemaker model of evolution that accounts for varying rates of mutations with time. Here, we present a python implementation of the Epigenetic Pacemaker (EPM), a conditional expectation maximization algorithm that estimates epigenetic landscapes and the state of individuals and may be used to study non-linear epigenetic aging.

Availability And Implementation: The EPM is available at https://pypi.org/project/EpigeneticPacemaker/ under the MIT license. The EPM is compatible with python version 3.6 and above.
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http://dx.doi.org/10.1093/bioinformatics/btaa585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7750963PMC
November 2020

Genome-wide CRISPR-Cas9 screening reveals ubiquitous T cell cancer targeting via the monomorphic MHC class I-related protein MR1.

Nat Immunol 2020 02 20;21(2):178-185. Epub 2020 Jan 20.

Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.

Human leukocyte antigen (HLA)-independent, T cell-mediated targeting of cancer cells would allow immune destruction of malignancies in all individuals. Here, we use genome-wide CRISPR-Cas9 screening to establish that a T cell receptor (TCR) recognized and killed most human cancer types via the monomorphic MHC class I-related protein, MR1, while remaining inert to noncancerous cells. Unlike mucosal-associated invariant T cells, recognition of target cells by the TCR was independent of bacterial loading. Furthermore, concentration-dependent addition of vitamin B-related metabolite ligands of MR1 reduced TCR recognition of cancer cells, suggesting that recognition occurred via sensing of the cancer metabolome. An MR1-restricted T cell clone mediated in vivo regression of leukemia and conferred enhanced survival of NSG mice. TCR transfer to T cells of patients enabled killing of autologous and nonautologous melanoma. These findings offer opportunities for HLA-independent, pan-cancer, pan-population immunotherapies.
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http://dx.doi.org/10.1038/s41590-019-0578-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6983325PMC
February 2020

A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex.

Nat Neurosci 2020 01 16;23(1):138-151. Epub 2019 Dec 16.

Allen Institute for Brain Science, Seattle, WA, USA.

To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes the cortical activity of nearly 60,000 neurons from six visual areas, four layers, and 12 transgenic mouse lines in a total of 243 adult mice, in response to a systematic set of visual stimuli. We classify neurons on the basis of joint reliabilities to multiple stimuli and validate this functional classification with models of visual responses. While most classes are characterized by responses to specific subsets of the stimuli, the largest class is not reliably responsive to any of the stimuli and becomes progressively larger in higher visual areas. These classes reveal a functional organization wherein putative dorsal areas show specialization for visual motion signals.
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http://dx.doi.org/10.1038/s41593-019-0550-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6948932PMC
January 2020

Aberration-free multi-plane imaging of neural activity from the mammalian brain using a fast-switching liquid crystal spatial light modulator.

Biomed Opt Express 2019 Oct 12;10(10):5059-5080. Epub 2019 Sep 12.

Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA.

We report a novel two-photon fluorescence microscope based on a fast-switching liquid crystal spatial light modulator and a pair of galvo-resonant scanners for large-scale recording of neural activity from the mammalian brain. The spatial light modulator is used to achieve fast switching between different imaging planes in multi-plane imaging and correct for intrinsic optical aberrations associated with this imaging scheme. The utilized imaging technique is capable of monitoring the neural activity from large populations of neurons with known coordinates spread across different layers of the neocortex in awake and behaving mice, regardless of the fluorescent labeling strategy. During each imaging session, all visual stimulus driven somatic activity could be recorded in the same behavior state. We observed heterogeneous response to different types of visual stimuli from 3,300 excitatory neurons reaching from layer II/III to V of the striate cortex.
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http://dx.doi.org/10.1364/BOE.10.005059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6788611PMC
October 2019

Classification of electrophysiological and morphological neuron types in the mouse visual cortex.

Nat Neurosci 2019 07 17;22(7):1182-1195. Epub 2019 Jun 17.

Allen Institute for Brain Science, Seattle, Washington, USA.

Understanding the diversity of cell types in the brain has been an enduring challenge and requires detailed characterization of individual neurons in multiple dimensions. To systematically profile morpho-electric properties of mammalian neurons, we established a single-cell characterization pipeline using standardized patch-clamp recordings in brain slices and biocytin-based neuronal reconstructions. We built a publicly accessible online database, the Allen Cell Types Database, to display these datasets. Intrinsic physiological properties were measured from 1,938 neurons from the adult laboratory mouse visual cortex, morphological properties were measured from 461 reconstructed neurons, and 452 neurons had both measurements available. Quantitative features were used to classify neurons into distinct types using unsupervised methods. We established a taxonomy of morphologically and electrophysiologically defined cell types for this region of the cortex, with 17 electrophysiological types, 38 morphological types and 46 morpho-electric types. There was good correspondence with previously defined transcriptomic cell types and subclasses using the same transgenic mouse lines.
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http://dx.doi.org/10.1038/s41593-019-0417-0DOI Listing
July 2019

Human epigenetic ageing is logarithmic with time across the entire lifespan.

Epigenetics 2019 09 6;14(9):912-926. Epub 2019 Jun 6.

b Department of Molecular, Cell and Developmental Biology, University of California , Los Angeles , CA , USA.

Epigenetic changes during ageing have been characterized by multiple epigenetic clocks that allow the prediction of chronological age based on methylation status. Despite their accuracy and utility, epigenetic age biomarkers leave many questions about epigenetic ageing unanswered. Specifically, they do not permit the unbiased characterization of non-linear epigenetic ageing trends across entire life spans, a critical question underlying this field of research. Here we provide an integrated framework to address this question. Our model, inspired from evolutionary models, is able to account for acceleration/deceleration in epigenetic changes by fitting an individual's model age, the epigenetic age, which is related to chronological age in a non-linear fashion. Application of this model to DNA methylation data measured across broad age ranges, from before birth to old age, and from two tissue types, suggests a universal logarithmic trend characterizes epigenetic ageing across entire lifespans.
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http://dx.doi.org/10.1080/15592294.2019.1623634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691990PMC
September 2019

Biological variation in the sizes, shapes and locations of visual cortical areas in the mouse.

PLoS One 2019 1;14(5):e0213924. Epub 2019 May 1.

Allen Institute for Brain Science, Seattle, WA, United States of America.

Visual cortex is organized into discrete sub-regions or areas that are arranged into a hierarchy and serves different functions in the processing of visual information. In retinotopic maps of mouse cortex, there appear to be substantial mouse-to-mouse differences in visual area location, size and shape. Here we quantify the biological variation in the size, shape and locations of 11 visual areas in the mouse, after separating biological variation and measurement noise. We find that there is biological variation in the locations and sizes of visual areas.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213924PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6493719PMC
January 2020

Epigenome-wide association in adipose tissue from the METSIM cohort.

Hum Mol Genet 2018 05;27(10):1830-1846

Department of Molecular, Cell and Developmental Biology, University of California Los Angeles.

Most epigenome-wide association studies to date have been conducted in blood. However, metabolic syndrome is mediated by a dysregulation of adiposity and therefore it is critical to study adipose tissue in order to understand the effects of this syndrome on epigenomes. To determine if natural variation in DNA methylation was associated with metabolic syndrome traits, we profiled global methylation levels in subcutaneous abdominal adipose tissue. We measured association between 32 clinical traits related to diabetes and obesity in 201 people from the Metabolic Syndrome in Men cohort. We performed epigenome-wide association studies between DNA methylation levels and traits, and identified associations for 13 clinical traits in 21 loci. We prioritized candidate genes in these loci using expression quantitative trait loci, and identified 18 high confidence candidate genes, including known and novel genes associated with diabetes and obesity traits. Using methylation deconvolution, we examined which cell types may be mediating the associations, and concluded that most of the loci we identified were specific to adipocytes. We determined whether the abundance of cell types varies with metabolic traits, and found that macrophages increased in abundance with the severity of metabolic syndrome traits. Finally, we developed a DNA methylation-based biomarker to assess type 2 diabetes risk in adipose tissue. In conclusion, our results demonstrate that profiling DNA methylation in adipose tissue is a powerful tool for understanding the molecular effects of metabolic syndrome on adipose tissue, and can be used in conjunction with traditional genetic analyses to further characterize this disorder.
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http://dx.doi.org/10.1093/hmg/ddy093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932563PMC
May 2018

Two novel mutations in TMPRSS6 associated with iron-refractory iron deficiency anemia in a mother and child.

Blood Cells Mol Dis 2017 06 9;65:38-40. Epub 2017 Apr 9.

Center for Iron and Heme Disorders, University of Utah, and Division of Hematology/Oncology, Department of Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA; Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.

In an iron deficient child, oral iron repeatedly failed to improve the condition. Whole exome sequencing identified one previously reported plus two novel mutation in the TMPRSS6 gene, with no mutations in other iron-associated genes. We propose that these mutations result in a novel variety of iron-refractory iron deficiency anemia.
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http://dx.doi.org/10.1016/j.bcmd.2017.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5656052PMC
June 2017

The D519G Polymorphism of Glyceronephosphate O-Acyltransferase Is a Risk Factor for Familial Porphyria Cutanea Tarda.

PLoS One 2016;11(9):e0163322. Epub 2016 Sep 23.

Department of Medicine, Hematology Division, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.

Both familial and sporadic porphyria cutanea tarda (PCT) are iron dependent diseases. Symptoms of PCT resolve when iron stores are depleted by phlebotomy, and a sequence variant of HFE (C282Y, c.843G>A, rs1800562) that enhances iron aborption by reducing hepcidin expression is a risk factor for PCT. Recently, a polymorphic variant (D519G, c.1556A>G, rs11558492) of glyceronephosphate O-acyltransferase (GNPAT) was shown to be enriched in male patients with type I hereditary hemochromatosis (HFE C282Y homozygotes) who presented with a high iron phenotype, suggesting that GNPAT D519G, like HFE C282Y, is a modifier of iron homeostasis that favors iron absorption. To challenge this hypothesis, we investigated the frequency of GNPAT D519G in patients with both familial and sporadic PCT. Patients were screened for GNPAT D519G and allelic variants of HFE (both C282Y and H63D). Nucleotide sequencing of uroporphyrinogen decarboxylase (URO-D) identified mutant alleles. Patients with low erythrocyte URO-D activity or a damaging URO-D variant were classified as familial PCT (fPCT) and those with wild-type URO-D were classified as sporadic PCT (sPCT). GNPAT D519G was significantly enriched in the fPCT patient population (p = 0.0014) but not in the sPCT population (p = 0.4477). Both HFE C282Y and H63D (c.187C>G, rs1799945) were enriched in both PCT patient populations (p<0.0001) but showed no greater association with fPCT than with sPCT.

Conclusion: GNPAT D519G is a risk factor for fPCT, but not for sPCT.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5035022PMC
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163322PLOS
September 2016

Exome sequencing for molecular characterization of non-HFE hereditary hemochromatosis.

Blood Cells Mol Dis 2015 Aug 1;55(2):101-3. Epub 2015 May 1.

University of Utah School of Medicine, Hematology Division, 30North 1900 East, Salt Lake City, UT 84132, United States. Electronic address:

Diagnostic genetic testing for hereditary hemochromatosis is readily available for clinically relevant HFE variants (i.e., those that generate the C282Y, H63D and S65C HFE polymorphisms); however, genetic testing for other known causes of iron overload, including mutations affecting genes encoding hemojuvelin, transferrin receptor 2, HAMP, and ferroportin is not. As an alternative to conventional genetic testing we propose diagnostic use of whole exome sequencing for characterization of non-HFE hemochromatosis. To illustrate the effectiveness of whole exome sequencing as a diagnostic tool, we present the case of an 18-year-old female with a probable case of juvenile hemochromatosis, who was referred for specialty care after testing negative for commonly occurring HFE variants. Whole exome sequencing offered complete coverage of target genes and is a fast, cost effective diagnostic tool for characterization of non-HFE hemochromatosis.
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http://dx.doi.org/10.1016/j.bcmd.2015.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491409PMC
August 2015

8th GCC: consolidated feedback to US FDA on the 2013 draft FDA guidance on bioanalytical method validation.

Bioanalysis 2014 ;6(22):2957-63

Covance Laboratories, Chantilly, VA, USA.

The 8th GCC Closed Forum for Bioanalysis was held in Baltimore, MD, USA on 5 December 2013, immediately following the 2013 AAPS Workshop (Crystal City V): Quantitative Bioanalytical Methods Validation and Implementation--The 2013 Revised FDA Guidance. This GCC meeting was organized to discuss the contents of the draft revised FDA Guidance on bioanalytical method validation that was published in September 2013 and consolidate the feedback of the GCC members. In attendance were 63 senior-level participants, from seven countries, representing 46 bioanalytical CRO companies/sites. This event represented a unique opportunity for CRO bioanalytical experts to share their opinions and concerns regarding the draft FDA Guidance, and to build unified comments to be provided to the FDA.
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http://dx.doi.org/10.4155/bio.14.287DOI Listing
July 2015