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1.  Gene-Based Sequencing Identifies Lipid-Influencing Variants with Ethnicity-Specific Effects in African Americans 
PLoS Genetics  2014;10(3):e1004190.
Although a considerable proportion of serum lipids loci identified in European ancestry individuals (EA) replicate in African Americans (AA), interethnic differences in the distribution of serum lipids suggest that some genetic determinants differ by ethnicity. We conducted a comprehensive evaluation of five lipid candidate genes to identify variants with ethnicity-specific effects. We sequenced ABCA1, LCAT, LPL, PON1, and SERPINE1 in 48 AA individuals with extreme serum lipid concentrations (high HDLC/low TG or low HDLC/high TG). Identified variants were genotyped in the full population-based sample of AA (n = 1694) and tested for an association with serum lipids. rs328 (LPL) and correlated variants were associated with higher HDLC and lower TG. Interestingly, a stronger effect was observed on a “European” vs. “African” genetic background at this locus. To investigate this effect, we evaluated the region among West Africans (WA). For TG, the effect size among WA was the same in AA with only African local ancestry (2–3% lower TG), while the larger association among AA with local European ancestry matched previous reports in EA (10%). For HDLC, there was no association with rs328 in AA with only African local ancestry or in WA, while the association among AA with European local ancestry was much greater than what has been observed for EA (15 vs. ∼5 mg/dl), suggesting an interaction with an environmental or genetic factor that differs by ethnicity. Beyond this ancestry effect, the importance of African ancestry-focused, sequence-based work was also highlighted by serum lipid associations of variants that were in higher frequency (or present only) among those of African ancestry. By beginning our study with the sequence variation present in AA individuals, investigating local ancestry effects, and seeking replication in WA, we were able to comprehensively evaluate the role of a set of candidate genes in serum lipids in AA.
Author Summary
Most of the work on the genetic epidemiology of serum lipids in African Americans (AA) has focused on replicating findings that were identified in European ancestry individuals. While this can be very informative about the generalizability of lipids loci across populations, African ancestry-specific variation will be missed using this approach. Our aim was to comprehensively evaluate five lipid candidate genes in an AA population, from the identification of variants of interest to population-level analysis of high-density lipoprotein cholesterol (HDLC) and triglycerides (TG). We sequenced five genes in individuals with extreme lipids (n = 48) drawn from a population-based study of AA. The variants identified were genotyped in 1,694 AA and analyzed. Notable among the findings were the observation of ancestry specific effect for several variants in the LPL gene among these admixed individuals, with a greater effect observed among those with European ancestry in this region. These associations were further elucidated by replication in West Africans. By beginning with the sequence variation present among AA, investigating ancestry effects, and seeking replication in West Africans, we were able to comprehensively evaluate these candidate genes with a focus on African ancestry individuals.
doi:10.1371/journal.pgen.1004190
PMCID: PMC3945436  PMID: 24603370
3.  Topographical and Temporal Diversity of the Human Skin Microbiome 
Science (New York, N.Y.)  2009;324(5931):1190-1192.
Human skin is a large, heterogeneous organ that protects the body from pathogens while sustaining microorganisms that influence human health and disease. Our analysis of 16S ribosomal RNA gene sequences obtained from 20 distinct skin sites of healthy humans revealed that physiologically comparable sites harbor similar bacterial communities. The complexity and stability of the microbial community are dependent on the specific characteristics of the skin site. This topographical and temporal survey provides a baseline for studies that examine the role of bacterial communities in disease states and the microbial interdependencies required to maintain healthy skin.
doi:10.1126/science.1171700
PMCID: PMC2805064  PMID: 19478181
4.  Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates 
BMC Genomics  2010;11:21.
Background
The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing') remains tedious, labor-intensive, and expensive. As a result, the vast majority of vertebrate genome sequences generated to date remain at a draft stage.
Results
To date, our genome sequencing efforts have focused on comparative studies of targeted genomic regions, requiring sequence finishing of large blocks of orthologous sequence (average size 0.5-2 Mb) from various subsets of 75 vertebrates. This experience has provided a unique opportunity to compare the relative effort required to finish shotgun-generated genome sequence assemblies from different species, which we report here. Importantly, we found that the sequence assemblies generated for the same orthologous regions from various vertebrates show substantial variation with respect to misassemblies and, in particular, the frequency and characteristics of sequence gaps. As a consequence, the work required to finish different species' sequences varied greatly. Application of the same standardized methods for finishing provided a novel opportunity to "assay" characteristics of genome sequences among many vertebrate species. It is important to note that many of the problems we have encountered during sequence finishing reflect unique architectural features of a particular vertebrate's genome, which in some cases may have important functional and/or evolutionary implications. Finally, based on our analyses, we have been able to improve our procedures to overcome some of these problems and to increase the overall efficiency of the sequence-finishing process, although significant challenges still remain.
Conclusion
Our findings have important implications for the eventual finishing of the draft whole-genome sequences that have now been generated for a large number of vertebrates.
doi:10.1186/1471-2164-11-21
PMCID: PMC2827409  PMID: 20064230
5.  Systematic sequencing of cDNA clones using the transposon Tn5 
Nucleic Acids Research  2002;30(11):2469-2477.
In parallel with the production of genomic sequence data, attention is being focused on the generation of comprehensive cDNA-sequence resources. Such efforts are increasingly emphasizing the production of high-accuracy sequence corresponding to the entire insert of cDNA clones, especially those presumed to reflect the full-length mRNA. The complete sequencing of cDNA clones on a large scale presents unique challenges because of the generally small, yet heterogeneous, sizes of the cloned inserts. We have developed a strategy for high-throughput sequencing of cDNA clones using the transposon Tn5. This approach has been tailored for implementation within an existing large-scale ‘shotgun-style’ sequencing program, although it could be readily adapted for use in virtually any sequencing environment. In addition, we have developed a modified version of our strategy that can be applied to cDNA clones with large cloning vectors, thereby overcoming a potential limitation of transposon-based approaches. Here we describe the details of our cDNA-sequencing pipeline, including a summary of the experience in sequencing more than 4200 cDNA clones to produce more than 8 million base pairs of high-accuracy cDNA sequence. These data provide both convincing evidence that the insertion of Tn5 into cDNA clones is sufficiently random for its effective use in large-scale cDNA sequencing as well as interesting insight about the sequence context preferred for insertion by Tn5.
PMCID: PMC117195  PMID: 12034835
6.  Marek's Disease Herpesvirus-Induced DNA Polymerase 
Journal of Virology  1974;14(5):1209-1219.
Infection of duck embryo fibroblasts by Marek's disease herpesvirus (MDHV), strain GA, led to the induction of a novel DNA polymerase. This novel DNA polymerase, designated MDHV-induced DNA polymerase, could be distinguished from the DNA polymerase activities of uninfected duck embryo fibroblasts by its chromatographic behavior on phosphocellulose, by its sedimentation coefficient, and by its catalytic properties. The characteristics of MDHV-induced DNA polymerase which had been purified by phosphocellulose chromatography were investigated. The sedimentation coefficient of the enzyme, as determined by sucrose density gradient centrifugation in the presence of 0.25 M KCl, was 5.9S. From this sedimentation coefficient, the molecular weight of MDHV-induced DNA polymerase was estimated to be 100,000. MDHV-induced DNA polymerase could not effectively use either poly(dA)·oligo(dT)12-18 or poly(dC)·oligo(dG)12-18 as a template-primer. The DNA polymerases from uninfected duck embryo fibroblasts could use these synthetic template-primers. MDHV-induced DNA polymerase also could not use poly(rA)·oligo(dT)12-18 or poly(rC)·oligo(dG)12-18 as template-primers or oligo(dT)12-18 as a primer, indicating that it was not a polymerase of the type R-DNA polymerase, reverse transcriptase, or a terminal nucleotidyl transferase. In vitro synthesis of DNA by MDHV-induced DNA polymerase was markedly inhibited by the addition of (NH4)2SO4 to the reaction mixture.
PMCID: PMC355637  PMID: 4473569
7.  Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes 
BMC Biology  2012;10:107.
Background
Calcium-activated photoproteins are luciferase variants found in photocyte cells of bioluminescent jellyfish (Phylum Cnidaria) and comb jellies (Phylum Ctenophora). The complete genomic sequence from the ctenophore Mnemiopsis leidyi, a representative of the earliest branch of animals that emit light, provided an opportunity to examine the genome of an organism that uses this class of luciferase for bioluminescence and to look for genes involved in light reception. To determine when photoprotein genes first arose, we examined the genomic sequence from other early-branching taxa. We combined our genomic survey with gene trees, developmental expression patterns, and functional protein assays of photoproteins and opsins to provide a comprehensive view of light production and light reception in Mnemiopsis.
Results
The Mnemiopsis genome has 10 full-length photoprotein genes situated within two genomic clusters with high sequence conservation that are maintained due to strong purifying selection and concerted evolution. Photoprotein-like genes were also identified in the genomes of the non-luminescent sponge Amphimedon queenslandica and the non-luminescent cnidarian Nematostella vectensis, and phylogenomic analysis demonstrated that photoprotein genes arose at the base of all animals. Photoprotein gene expression in Mnemiopsis embryos begins during gastrulation in migrating precursors to photocytes and persists throughout development in the canals where photocytes reside. We identified three putative opsin genes in the Mnemiopsis genome and show that they do not group with well-known bilaterian opsin subfamilies. Interestingly, photoprotein transcripts are co-expressed with two of the putative opsins in developing photocytes. Opsin expression is also seen in the apical sensory organ. We present evidence that one opsin functions as a photopigment in vitro, absorbing light at wavelengths that overlap with peak photoprotein light emission, raising the hypothesis that light production and light reception may be functionally connected in ctenophore photocytes. We also present genomic evidence of a complete ciliary phototransduction cascade in Mnemiopsis.
Conclusions
This study elucidates the genomic organization, evolutionary history, and developmental expression of photoprotein and opsin genes in the ctenophore Mnemiopsis leidyi, introduces a novel dual role for ctenophore photocytes in both bioluminescence and phototransduction, and raises the possibility that light production and light reception are linked in this early-branching non-bilaterian animal.
doi:10.1186/1741-7007-10-107
PMCID: PMC3570280  PMID: 23259493
Bioluminescence; ctenophore; Mnemiopsis leidyi; opsin; photocyte; photoprotein; photoreception; phototransduction
8.  Personalized Genomic Medicine: Lessons from the Exome 
Molecular genetics and metabolism  2011;104(1-2):189-191.
While genomic sequencing methods are powerful tools in the discovery of the genetic underpinnings of human disease, incidentally-revealed novel genomic risk factors may be equally important, both scientifically, and as relates to direct patient care. We performed whole-exome sequencing on a child with VACTERL association who suffered severe post-surgical neonatal pulmonary hypertension, and identified a potential novel genetic risk factor for this complication: a heterozygous mutation in CPSI. Newborn screening results from this patient’s monozygotic twin provided evidence that this mutation, in combination with an environmental trigger (in this case, surgery), may have resulted in pulmonary artery hypertension due to inadequate nitric oxide production. Identification of this genetic risk factor allows for targeted medical preventative measures in this patient as well as relatives with the same mutation, and illustrates the power of incidental medical information unearthed by whole-exome sequencing.
doi:10.1016/j.ymgme.2011.06.022
PMCID: PMC3171610  PMID: 21767969
Whole-exome sequencing; CPSI; pulmonary artery hypertension; VACTERL
9.  Whole-Exome Sequencing Identifies Homozygous AFG3L2 Mutations in a Spastic Ataxia-Neuropathy Syndrome Linked to Mitochondrial m-AAA Proteases 
PLoS Genetics  2011;7(10):e1002325.
We report an early onset spastic ataxia-neuropathy syndrome in two brothers of a consanguineous family characterized clinically by lower extremity spasticity, peripheral neuropathy, ptosis, oculomotor apraxia, dystonia, cerebellar atrophy, and progressive myoclonic epilepsy. Whole-exome sequencing identified a homozygous missense mutation (c.1847G>A; p.Y616C) in AFG3L2, encoding a subunit of an m-AAA protease. m-AAA proteases reside in the mitochondrial inner membrane and are responsible for removal of damaged or misfolded proteins and proteolytic activation of essential mitochondrial proteins. AFG3L2 forms either a homo-oligomeric isoenzyme or a hetero-oligomeric complex with paraplegin, a homologous protein mutated in hereditary spastic paraplegia type 7 (SPG7). Heterozygous loss-of-function mutations in AFG3L2 cause autosomal-dominant spinocerebellar ataxia type 28 (SCA28), a disorder whose phenotype is strikingly different from that of our patients. As defined in yeast complementation assays, the AFG3L2Y616C gene product is a hypomorphic variant that exhibited oligomerization defects in yeast as well as in patient fibroblasts. Specifically, the formation of AFG3L2Y616C complexes was impaired, both with itself and to a greater extent with paraplegin. This produced an early-onset clinical syndrome that combines the severe phenotypes of SPG7 and SCA28, in additional to other “mitochondrial” features such as oculomotor apraxia, extrapyramidal dysfunction, and myoclonic epilepsy. These findings expand the phenotype associated with AFG3L2 mutations and suggest that AFG3L2-related disease should be considered in the differential diagnosis of spastic ataxias.
Author Summary
Mitochondria are cellular organelles important for converting sugar or fats into energy that cells can use for their functions and survival. Many neurological diseases are the result of mitochondrial dysfunction as affected cells are unable to cope with lowered energy supplies and increased oxidative stress. These deficiencies cause accumulation of cellular damage and eventually cell death. Spastic ataxias are neurological disorders involving cells with large energy requirements, the cerebellar Purkinje cells and the cerebral upper motor neurons. When these cells function improperly or die, individuals develop symptoms of incoordination (ataxia) and abnormal muscle tone in their legs (spastic paraplegia). Using emerging techniques of whole-exome sequencing we discovered that homozygous mutations in the AFG3L2 gene caused spastic ataxia in two brothers of a consanguineous family. AFG3L2 encodes a subunit of mitochondrial matrix proteases (m-AAA proteases) that regulate the functional integrity of mitochondria. Heterozygous mutations in AFG3L2 were previously found to cause a disorder involving the Purkinje cells of the cerebellum resulting in ataxia. Interestingly, another isoform of m-AAA proteases consists of AFG3L2 complexing with paraplegin, a similar protein associated with a hereditary spastic paraplegia. Our analysis provides insight into why different mutations in m-AAA protease subunits cause different neurological disorders.
doi:10.1371/journal.pgen.1002325
PMCID: PMC3192828  PMID: 22022284
10.  TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum 
Nature genetics  2011;43(3):189-196.
Ciliary dysfunction leads to a broad range of overlapping phenotypes, termed collectively as ciliopathies. This grouping is underscored by genetic overlap, where causal genes can also contribute modifying alleles to clinically distinct disorders. Here we show that mutations in TTC21B/IFT139, encoding a retrograde intraflagellar transport (IFT) protein, cause both isolated nephronophthisis (NPHP) and syndromic Jeune Asphyxiating Thoracic Dystrophy (JATD). Moreover, although systematic medical resequencing of a large, clinically diverse ciliopathy cohort and matched controls showed a similar frequency of rare changes, in vivo and in vitro evaluations unmasked a significant enrichment of pathogenic alleles in cases, suggesting that TTC21B contributes pathogenic alleles to ∼5% of ciliopathy patients. Our data illustrate how genetic lesions can be both causally associated with diverse ciliopathies, as well as interact in trans with other disease-causing genes, and highlight how saturated resequencing followed by functional analysis of all variants informs the genetic architecture of disorders.
doi:10.1038/ng.756
PMCID: PMC3071301  PMID: 21258341

Results 1-10 (10)