Papers by Christopher Mason
The panoply of microorganisms and other species present in our environment influence human health... more The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harm- less genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent
a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
Abstract By the end of 2011 we will likely know the DNA sequences for 30,000 human genomes. Howev... more Abstract By the end of 2011 we will likely know the DNA sequences for 30,000 human genomes. However, to truly understand how the variation between these genomes affect phenotype at a molecular level, future research projects need to analyze these genomes in conjunction with data from multiple ultra-high throughput assays obtained from large sample populations.
Abstract The ability to determine the gene expression pattern in low quantities of cells or singl... more Abstract The ability to determine the gene expression pattern in low quantities of cells or single cells is important for resolving a variety of problems in many biological disciplines. A robust description of the expression signature of a single cell requires determination of the full-length sequence of the expressed mRNAs in the cell, yet existing methods have either 3′ biased or variable transcript representation.
Abstract Disease gene discovery has been transformed by affordable sequencing of exomes and genom... more Abstract Disease gene discovery has been transformed by affordable sequencing of exomes and genomes. Identification of disease-causing mutations requires sifting through a large number of sequence variants.
Paired box gene 6 (PAX6) is the causative gene of aniridia. It is a dominantly inherited eye abno... more Paired box gene 6 (PAX6) is the causative gene of aniridia. It is a dominantly inherited eye abnormality characterized by partial or complete absence of the iris. The PAX6 gene is located on chromosome 11p13 and contains 14 exons. It is expressed mainly in the developing eye and central nervous system. Submicroscopic copy number variations are common in the human genome.
Aging is characterized by clonal expansion of myeloid-biased hematopoietic stem cells and by incr... more Aging is characterized by clonal expansion of myeloid-biased hematopoietic stem cells and by increased risk of myeloid malignancies. Exome sequencing of three elderly females with clonal hematopoiesis, demonstrated by X-inactivation analysis, identified somatic TET2 mutations. Recurrence testing identified TET2 mutations in 10 out of 182 individuals with X-inactivation skewing.
Abstract Hereditary sensory and autonomic neuropathy type IV (HSAN IV), or congenital insensitivi... more Abstract Hereditary sensory and autonomic neuropathy type IV (HSAN IV), or congenital insensitivity to pain with anhidrosis, is an autosomal recessive disorder characterized by insensitivity to noxious stimuli, anhidrosis from deinnervated sweat glands, and delayed mental and motor development. Mutations in the neurotrophic tyrosine kinase receptor type 1 (NTRK1), a receptor in the neurotrophin signaling pathway phosphorylated in response to nerve growth factor, are associated with this disorder.
Abstract Recent studies have found methyl-6-adenosine in thousands of mammalian genes, and this m... more Abstract Recent studies have found methyl-6-adenosine in thousands of mammalian genes, and this modification is most pronounced near the beginning of the 3'UTR. We present a perspective on current work and new single-molecule sequencing methods for detecting RNA base modifications.
Abstract 3p deletion syndrome is a rare disorder involving developmental delay, dysmorphic physic... more Abstract 3p deletion syndrome is a rare disorder involving developmental delay, dysmorphic physical features, and growth retardation. Molecular mapping of several cases in the literature have identified a critical region on chromosome 3p26. We present a child patient with characteristic features of 3p deletion syndrome and a de novo unbalanced translocation involving chromosomes 3 and 13.
Recently, we delineated a syndrome of pachygyria, mental impairment, seizures, and arachnoid cyst... more Recently, we delineated a syndrome of pachygyria, mental impairment, seizures, and arachnoid cysts [Guzel et al., 2007]. This syndrome was found in a consanguineous family from Southeastern Turkey. The three affected sibs in this family were the first generation to present with this condition, strongly suggesting autosomal recessive inheritance (Fig. 1).
Abstract SNP and comparative genome hybridization arrays (aCGH) are powerful techniques for ident... more Abstract SNP and comparative genome hybridization arrays (aCGH) are powerful techniques for identifying genome rearrangements, deletions, and duplications. We hypothesized that current array-based detection of copy number variation (CNV) could complement parametric linkage analysis and allow the rapid identification of functional mutations in families with inherited disorders.
Abstract Genome-wide mutagenesis was performed in mice to identify candidate genes for male infer... more Abstract Genome-wide mutagenesis was performed in mice to identify candidate genes for male infertility, for which the predominant causes remain idiopathic. Mice were mutagenized using N-ethyl-N-nitrosourea (ENU), bred, and screened for phenotypes associated with the male urogenital system. Fifteen heritable lines were isolated and chromosomal loci were assigned using low-density genome-wide SNP arrays. Ten of the 15 lines were pursued further using higher-resolution SNP analysis to narrow the candidate gene regions.
Abstract RNA-based next-generation sequencing (RNA-Seq) provides a tremendous amount of new infor... more Abstract RNA-based next-generation sequencing (RNA-Seq) provides a tremendous amount of new information regarding gene and transcript structure, expression and regulation. This is particularly true for non-coding RNAs where whole transcriptome analyses have revealed that the much of the genome is transcribed and that many non-coding transcripts have widespread functionality.
The human genome is a three billion-letter recipe for the genesis of a human being, directing dev... more The human genome is a three billion-letter recipe for the genesis of a human being, directing development from a single-celled embryo to the trillions of adult cells. Since the sequencing of the human genome was announced in 2001, researchers have an increased ability to discern the genetic basis for diseases. This reference genome has opened the door to genomic medicine, aimed at detecting and understanding all genetic variations of the human genome that contribute to the manifestation and progression of disease.
We have developed an enhanced form of reduced representation bisulfite sequencing with extended g... more We have developed an enhanced form of reduced representation bisulfite sequencing with extended genomic coverage, which resulted in greater capture of DNA methylation information of regions lying outside of traditional CpG islands. Applying this method to primary human bone marrow specimens from patients with Acute Myelogeneous Leukemia (AML), we demonstrated that genetically distinct AML subtypes display diametrically opposed DNA methylation patterns.
The human genome reference sequence is well characterized, highly annotated, and its development ... more The human genome reference sequence is well characterized, highly annotated, and its development represents a considerable investment of time and money. This sequence is the foundation for genotyping microarrays and DNA sequencing analysis. Yet, in several critical aspects the reference sequence remains incomplete as are the many research tools that are based on it.
Synopsis One promise of the Human Genome Project was to stimulate the translation of large-scale ... more Synopsis One promise of the Human Genome Project was to stimulate the translation of large-scale functional analyses of the human genome to produce novel targets useful in the diagnosis or treatment of complex diseases. Here, we demonstrate an integrated approach to the study of a transcriptional regulatory cascade involved in the progression of breast cancer and we identify a protein associated with disease progression.
Abstract We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascari... more Abstract We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals∼ 3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of∼ 2.6 million scaffolds (N50 scaffold size= 13,597 bp) based on short paired-end sequencing reads.
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Papers by Christopher Mason
a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.