Publications by authors named "David Mittelman"

38 Publications

FEVR findings in patients with Loeys-Dietz syndrome type II.

Ophthalmic Genet 2018 12 8;39(6):754-758. Epub 2018 Nov 8.

a Retinal Consultants , Des Plaines , IL , USA.

Background: Loeys-Dietz syndrome (LDS) is a connective tissue disorder that has phenotypic overlap with Marfan syndrome. In LDS, the aortic root dissections can be more aggressive and occur at a younger age than Marfan syndrome.

Materials And Methods: Review of two cases.

Results: A 7-year old boy with history of LDS was found to have a vitreous hemorrhage in the right eye. Further examination showed findings of Familial Exudative Vitreoretinopathy (FEVR). Both eyes were found to have peripheral non-perfusion and neovascularization. A non-related 25-month-old boy with no molecularly confirmed connective tissue disorder was found to have bilateral peripheral non-perfusion and bilateral tractional retinal detachments. The boy was clinically diagnosed with Larsen syndrome, Ehlers-Danlos syndrome kyphoscoliotic form, and Marfan syndrome before presentation. The FEVR lead to consideration of LDS that was molecularly confirmed. Consequently, he was monitored for aortic root dilation.

Conclusion: FEVR findings may lead to diagnosis of LDS and patients with LDS may present with proliferative retinopathy.
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http://dx.doi.org/10.1080/13816810.2018.1532526DOI Listing
December 2018

Consumer genomics will change your life, whether you get tested or not.

Genome Biol 2018 08 20;19(1):120. Epub 2018 Aug 20.

Department of Biology, Texas A&M University, College Station, TX, 77843, USA.

With more than 10 million genotyped customers, the consumer genomics industry is maturing and becoming a mainstream phenomenon. At last, innovations and applications, some unforeseen, are being brought to the masses.
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http://dx.doi.org/10.1186/s13059-018-1506-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6100720PMC
August 2018

Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine.

BMC Med Genomics 2017 02 23;10(1):10. Epub 2017 Feb 23.

Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.

Background: Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, there have been relatively few reports combining whole genome sequencing (WGS) and HPO, especially in the context of structural variants.

Methods: We illustrate an integrative analysis of WGS and HPO using an extended pedigree, which involves Prader-Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms. A comprehensive WGS pipeline was used to ensure reliable detection of genomic variants. Beyond variant filtering, we pursued phenotypic prioritization of candidate genes using Phenolyzer.

Results: Regarding PWS, WGS confirmed a 5.5 Mb de novo deletion of the parental allele at 15q11.2 to 15q13.1. Phenolyzer successfully returned the diagnosis of PWS, and pinpointed clinically relevant genes in the deletion. Further, Phenolyzer revealed how each of the genes is linked with the phenotypes represented by HPO terms. For HH, WGS identified a known disease variant (p.C282Y) in HFE of an affected female. Analysis of HPO terms alone fails to provide a correct diagnosis, but Phenolyzer successfully revealed the phenotype-genotype relationship using a disease-centric approach. Finally, Phenolyzer also revealed the complexity behind dysautonomia-like symptoms, and seven variants that might be associated with the phenotypes were identified by manual filtering based on a dominant inheritance model.

Conclusions: The integration of WGS and HPO can inform comprehensive molecular diagnosis for patients, eliminate false positives and reveal novel insights into undiagnosed diseases. Due to extreme heterogeneity and insufficient knowledge of human diseases, it is also important that phenotypic and genomic data are standardized and shared simultaneously.
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http://dx.doi.org/10.1186/s12920-017-0246-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322674PMC
February 2017

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.

Nat Genet 2016 06 25;48(6):593-9. Epub 2016 Apr 25.

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

We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.
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http://dx.doi.org/10.1038/ng.3559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4884158PMC
June 2016

Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.

Nucleic Acids Res 2016 05 7;44(8):3750-62. Epub 2016 Apr 7.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA

Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) quantitative trait loci. To test this we analyzed the effect of variation at 4849 promoter-associated TRs, genotyped in 120 individuals, on neighboring gene expression and DNA methylation. Polymorphic promoter TRs were associated with increased variance in local gene expression and DNA methylation, suggesting functional consequences related to TR variation. We identified >100 TRs associated with expression/methylation levels of adjacent genes. These potential eQTL/mQTL TRs were enriched for overlaps with transcription factor binding and DNaseI hypersensitivity sites, providing a rationale for their effects. Moreover, we showed that most TR variants are poorly tagged by nearby single nucleotide polymorphisms (SNPs) markers, indicating that many functional TR variants are not effectively assayed by SNP-based approaches. Our study assigns biological significance to TR variations in the human genome, and suggests that a significant fraction of TR variations exert functional effects via alterations of local gene expression or epigenetics. We conclude that targeted studies that focus on genotyping TR variants are required to fully ascertain functional variation in the genome.
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http://dx.doi.org/10.1093/nar/gkw219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857002PMC
May 2016

TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations.

Am J Hum Genet 2015 Dec;97(6):922-32

Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA; Utah Foundation for Biomedical Research, Salt Lake City, UT 84107, USA. Electronic address:

We describe an X-linked genetic syndrome associated with mutations in TAF1 and manifesting with global developmental delay, intellectual disability (ID), characteristic facial dysmorphology, generalized hypotonia, and variable neurologic features, all in male individuals. Simultaneous studies using diverse strategies led to the identification of nine families with overlapping clinical presentations and affected by de novo or maternally inherited single-nucleotide changes. Two additional families harboring large duplications involving TAF1 were also found to share phenotypic overlap with the probands harboring single-nucleotide changes, but they also demonstrated a severe neurodegeneration phenotype. Functional analysis with RNA-seq for one of the families suggested that the phenotype is associated with downregulation of a set of genes notably enriched with genes regulated by E-box proteins. In addition, knockdown and mutant studies of this gene in zebrafish have shown a quantifiable, albeit small, effect on a neuronal phenotype. Our results suggest that mutations in TAF1 play a critical role in the development of this X-linked ID syndrome.
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http://dx.doi.org/10.1016/j.ajhg.2015.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678794PMC
December 2015

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence.

Genome Res 2015 Nov 19;25(11):1591-9. Epub 2015 Aug 19.

Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-805 Zurich, Switzerland; The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; The Santa Fe Institute, Santa Fe, New Mexico 87501, USA.

Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1-5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2-50 bp). Genes that contained TRs in the promoters, in their 3' untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1-5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation.
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http://dx.doi.org/10.1101/gr.190868.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617956PMC
November 2015

Focusing of mammalian cells under an ultrahigh pH gradient created by unidirectional electropulsation in a confined microchamber†Electronic supplementary information (ESI) available: Figures S1-S5 and videos S1-S2. See DOI: 10.1039/c4sc00319eClick here for additional data file.Click here for additional data file.Click here for additional data file.

Chem Sci 2014 Aug 20;5(8):3331-3337. Epub 2014 Jun 20.

Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , USA . Email: ; ; Tel: +1 540 231 8681 ; School of Biomedical Engineering and Sciences , Virginia Tech-Wake Forest University , Blacksburg , Virginia 24061 , USA.

The transport and manipulation of cells in microfluidic structures are often critically required in cellular analysis. Cells typically make consistent movement in a dc electric field in a single direction, due to their electrophoretic mobility or electroosmotic flow or the combination of the two. Here we demonstrate that mammalian cells focus to the middle of a closed microfluidic chamber under the application of unidirectional direct current pulses. With experimental and computational data, we show that under the pulses electrochemical reactions take place in the confined microscale space and create an ultrahigh and nonlinear pH gradient (∼2 orders of magnitude higher than the ones in protein isoelectric focusing) at the middle of the chamber. The varying local pH affects the cell surface charge and the electrophoretic mobility, leading to focusing in free solution. Our approach provides a new and simple method for focusing and concentrating mammalian cells at the microscale.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4348711PMC
http://dx.doi.org/10.1039/c4sc00319eDOI Listing
August 2014

An analytical framework for optimizing variant discovery from personal genomes.

Nat Commun 2015 Feb 25;6:6275. Epub 2015 Feb 25.

1] Gene by Gene Ltd, Houston, Texas 77008, USA [2] Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA.

The standardization and performance testing of analysis tools is a prerequisite to widespread adoption of genome-wide sequencing, particularly in the clinic. However, performance testing is currently complicated by the paucity of standards and comparison metrics, as well as by the heterogeneity in sequencing platforms, applications and protocols. Here we present the genome comparison and analytic testing (GCAT) platform to facilitate development of performance metrics and comparisons of analysis tools across these metrics. Performance is reported through interactive visualizations of benchmark and performance testing data, with support for data slicing and filtering. The platform is freely accessible at http://www.bioplanet.com/gcat.
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http://dx.doi.org/10.1038/ncomms7275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351570PMC
February 2015

Dragging scientific publishing into the 21st century.

Genome Biol 2014 Dec 11;15(12):556. Epub 2014 Dec 11.

Scientific publishers must shake off three centuries of publishing on paper and embrace 21st century technology to make scientific communication more intelligible, reproducible, engaging and rapidly available.
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http://dx.doi.org/10.1186/s13059-014-0556-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288552PMC
December 2014

GFP-based fluorescence assay for CAG repeat instability in cultured human cells.

PLoS One 2014 25;9(11):e113952. Epub 2014 Nov 25.

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

Trinucleotide repeats can be highly unstable, mutating far more frequently than point mutations. Repeats typically mutate by addition or loss of units of the repeat. CAG repeat expansions in humans trigger neurological diseases that include myotonic dystrophy, Huntington disease, and several spinocerebellar ataxias. In human cells, diverse mechanisms promote CAG repeat instability, and in mice, the mechanisms of instability are varied and tissue-dependent. Dissection of mechanistic complexity and discovery of potential therapeutics necessitates quantitative and scalable screens for repeat mutation. We describe a GFP-based assay for screening modifiers of CAG repeat instability in human cells. The assay exploits an engineered intronic CAG repeat tract that interferes with expression of an inducible GFP minigene. Like the phenotypes of many trinucleotide repeat disorders, we find that GFP function is impaired by repeat expansion, in a length-dependent manner. The intensity of fluorescence varies inversely with repeat length, allowing estimates of repeat tract changes in live cells. We validate the assay using transcription through the repeat and engineered CAG-specific nucleases, which have previously been reported to induce CAG repeat instability. The assay is relatively fast and should be adaptable to large-scale screens of chemical and shRNA libraries.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113952PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244167PMC
January 2016

The landscape of human STR variation.

Genome Res 2014 Nov 18;24(11):1894-904. Epub 2014 Aug 18.

Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;

Short tandem repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across more than 1000 individuals in Phase 1 of the 1000 Genomes Project. Extensive quality controls show that reliable allelic spectra can be obtained for close to 90% of the STR loci in the genome. We utilize this call set to analyze determinants of STR variation, assess the human reference genome's representation of STR alleles, find STR loci with common loss-of-function alleles, and obtain initial estimates of the linkage disequilibrium between STRs and common SNPs. Overall, these analyses further elucidate the scale of genetic variation beyond classical point mutations.
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http://dx.doi.org/10.1101/gr.177774.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216929PMC
November 2014

Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo.

Genome Biol 2014 May 30;15(5):R75. Epub 2014 May 30.

Background: Cell lines are often regarded as clonal, even though this simplifies what is known about mutagenesis, transformation and other processes that destabilize them over time. Monitoring these clonal dynamics is important for multiple areas of biomedical research, including stem cell and cancer biology. Tracking the contributions of individual cells to large populations, however, has been constrained by limitations in sensitivity and complexity.

Results: We utilize cellular barcoding methods to simultaneously track the clonal contributions of tens of thousands of cells. We demonstrate that even with optimal culturing conditions, common cell lines including HeLa, K562 and HEK-293 T exhibit ongoing clonal dynamics. Starting a population with a single clone diminishes but does not eradicate this phenomenon. Next, we compare lentiviral and zinc-finger nuclease barcode insertion approaches, finding that the zinc-finger nuclease protocol surprisingly results in reduced clonal diversity. We also document the expected reduction in clonal complexity when cells are challenged with genotoxic stress. Finally, we demonstrate that xenografts maintain clonal diversity to a greater extent than in vitro culturing of the human non-small-cell lung cancer cell line HCC827.

Conclusions: We demonstrate the feasibility of tracking and quantifying the clonal dynamics of entire cell populations within multiple cultured cell lines. Our results suggest that cell heterogeneity should be considered in the design and interpretation of in vitro culture experiments. Aside from clonal cell lines, we propose that cellular barcoding could prove valuable in modeling the clonal behavior of heterogeneous cell populations over time, including tumor populations treated with chemotherapeutic agents.
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http://dx.doi.org/10.1186/gb-2014-15-5-r75DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073073PMC
May 2014

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines.

Genome Res 2014 Jul 8;24(7):1193-208. Epub 2014 Apr 8.

Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27595, USA;

The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.
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http://dx.doi.org/10.1101/gr.171546.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079974PMC
July 2014

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.

Nat Biotechnol 2014 Mar 16;32(3):246-51. Epub 2014 Feb 16.

Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA.

Clinical adoption of human genome sequencing requires methods that output genotypes with known accuracy at millions or billions of positions across a genome. Because of substantial discordance among calls made by existing sequencing methods and algorithms, there is a need for a highly accurate set of genotypes across a genome that can be used as a benchmark. Here we present methods to make high-confidence, single-nucleotide polymorphism (SNP), indel and homozygous reference genotype calls for NA12878, the pilot genome for the Genome in a Bottle Consortium. We minimize bias toward any method by integrating and arbitrating between 14 data sets from five sequencing technologies, seven read mappers and three variant callers. We identify regions for which no confident genotype call could be made, and classify them into different categories based on reasons for uncertainty. Our genotype calls are publicly available on the Genome Comparison and Analytic Testing website to enable real-time benchmarking of any method.
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http://dx.doi.org/10.1038/nbt.2835DOI Listing
March 2014

Rapid multiplexed genotyping of simple tandem repeats using capture and high-throughput sequencing.

Hum Mutat 2013 Sep 17;34(9):1304-11. Epub 2013 Jun 17.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.

Although simple tandem repeats (STRs) comprise ~2% of the human genome and represent an important source of polymorphism, this class of variation remains understudied. We have developed a cost-effective strategy for performing targeted enrichment of STR regions that utilizes capture probes targeting the flanking sequences of STR loci, enabling specific capture of DNA fragments containing STRs for subsequent high-throughput sequencing. Utilizing a capture design targeting 6,243 STR loci <94 bp and multiplexing eight individuals in a single Illumina HiSeq2000 sequencing lane we were able to call genotypes in at least one individual for 67.5% of the targeted STRs. We observed a strong relationship between (G+C) content and genotyping rate. STRs with moderate (G+C) content were recovered with >90% success rate, whereas only 12% of STRs with ≥ 80% (G+C) were genotyped in our assay. Analysis of a parent-offspring trio, complete hydatidiform mole samples, repeat analyses of the same individual, and Sanger sequencing-based validation indicated genotyping error rates between 7.6% and 12.4%. The majority of such errors were a single repeat unit at mono- or dinucleotide repeats. Altogether, our STR capture assay represents a cost-effective method that enables multiplexed genotyping of thousands of STR loci suitable for large-scale population studies.
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http://dx.doi.org/10.1002/humu.22359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3745529PMC
September 2013

The fractured genome of HeLa cells.

Genome Biol 2013 Apr 17;14(4):111. Epub 2013 Apr 17.

Whole-genome sequencing of the widely used HeLa cell line provides a nucleotide-resolution view of a greatly mutated and in some places shattered genome.
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http://dx.doi.org/10.1186/gb-2013-14-4-111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663084PMC
April 2013

Divergence insufficiency esotropia is a misnomer.

Authors:
David Mittelman

JAMA Ophthalmol 2013 Apr;131(4):547

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http://dx.doi.org/10.1001/jamaophthalmol.2013.1584DOI Listing
April 2013

Personal genomes and precision medicine.

Genome Biol 2012 Dec 19;13(12):324. Epub 2012 Dec 19.

A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012.
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http://dx.doi.org/10.1186/gb-2012-13-12-324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580409PMC
December 2012

Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.

Nucleic Acids Res 2013 Jan 22;41(1):e32. Epub 2012 Oct 22.

Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA.

Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping microsatellite repeats called RepeatSeq, which uses Bayesian model selection guided by an empirically derived error model that incorporates sequence and read properties. Next, we apply RepeatSeq to high-coverage genomes from the 1000 Genomes Project to evaluate performance and accuracy. The software uses common formats, such as VCF, for compatibility with existing genome analysis pipelines. Source code and binaries are available at http://github.com/adaptivegenome/repeatseq.
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http://dx.doi.org/10.1093/nar/gks981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3592458PMC
January 2013

Analysis of microsatellite variation in Drosophila melanogaster with population-scale genome sequencing.

PLoS One 2012 12;7(3):e33036. Epub 2012 Mar 12.

Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America.

Genome sequencing technologies promise to revolutionize our understanding of genetics, evolution, and disease by making it feasible to survey a broad spectrum of sequence variation on a population scale. However, this potential can only be realized to the extent that methods for extracting and interpreting distinct forms of variation can be established. The error profiles and read length limitations of early versions of next-generation sequencing technologies rendered them ineffective for some sequence variant types, particularly microsatellites and other tandem repeats, and fostered the general misconception that such variants are inherently inaccessible to these platforms. At the same time, tandem repeats have emerged as important sources of functional variation. Tandem repeats are often located in and around genes, and frequent mutations in their lengths exert quantitative effects on gene function and phenotype, rapidly degrading linkage disequilibrium between markers and traits. Sensitive identification of these variants in large-scale next-gen sequencing efforts will enable more comprehensive association studies capable of revealing previously invisible associations. We present a population-scale analysis of microsatellite repeats using whole-genome data from 158 inbred isolates from the Drosophila Genetics Reference Panel, a collection of over 200 extensively phenotypically characterized isolates from a single natural population, to uncover processes underlying repeat mutation and to enable associations with behavioral, morphological, and life-history traits. Analysis of repeat variation from next-generation sequence data will also enhance studies of genome stability and neurodegenerative diseases.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033036PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299726PMC
August 2012

SEQanswers: an open access community for collaboratively decoding genomes.

Bioinformatics 2012 May 13;28(9):1272-3. Epub 2012 Mar 13.

School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR.

Summary: The affordability of high-throughput sequencing has created an unprecedented surge in the use of genomic data in basic, translational and clinical research. The rapid evolution of sequencing technology, coupled with its broad adoption across biology and medicine, necessitates fast, collaborative interdisciplinary discussion. SEQanswers provides a real-time knowledge-sharing resource to address this need, covering experimental and computational aspects of sequencing and sequence analysis. Developers of popular analysis tools are among the >4000 active members, and ~40 peer-reviewed publications have referenced SEQanswers.

Availability: The SEQanswers community is freely accessible at http://SEQanswers.com/
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http://dx.doi.org/10.1093/bioinformatics/bts128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338018PMC
May 2012

The Drosophila melanogaster Genetic Reference Panel.

Nature 2012 Feb 8;482(7384):173-8. Epub 2012 Feb 8.

Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA.

A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.
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http://dx.doi.org/10.1038/nature10811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683990PMC
February 2012

Stress-induced modulators of repeat instability and genome evolution.

J Mol Microbiol Biotechnol 2011 13;21(1-2):36-44. Epub 2012 Jan 13.

Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA.

Evolution hinges on the ability of organisms to adapt to their environment. A key regulator of adaptability is mutation rate, which must be balanced to maintain genome fidelity while permitting sufficient plasticity to cope with environmental changes. Multiple mechanisms govern an organism's mutation rate. Constitutive mechanisms include mutator alleles that drive global, permanent increases in mutation rates, but these changes are confined to the subpopulation that carries the mutator allele. Other mechanisms focus mutagenesis in time and space to improve the chances that adaptive mutations can spread through the population. For example, environmental stress can induce mechanisms that transiently relax the fidelity of DNA repair to bring about a temporary increase in mutation rates during times when an organism experiences a reduced fitness for its surroundings, as has been demonstrated for double-strand break repair in Escherichia coli. Still, other mechanisms control the spatial distribution of mutations by directing changes to especially mutable sequences in the genome. In eukaryotic cells, for example, the stress-sensitive chaperone Hsp90 can regulate the length of trinucleotide repeats to fine-tune gene function and can regulate the mobility of transposable elements to enable larger functional changes. Here, we review the regulation of mutation rate, with special emphasis on the roles of tandem repeats and environmental stress in genome evolution.
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http://dx.doi.org/10.1159/000332748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697269PMC
May 2012

Surgical management of adult onset age-related distance esotropia.

Authors:
David Mittelman

J Pediatr Ophthalmol Strabismus 2011 Jul-Aug;48(4):214-6; quiz 217. Epub 2010 Aug 23.

Department of Ophthalmology, Rush University Medical Center and Advocate Lutheran General Children’s Hospital, Chicago, Illinois, USA.

Purpose: To study the effects of bilateral medial rectus recession for the management of adult onset age-related distance esotropia.

Methods: Ten patients with adult onset age-related distance esotropia measuring 14 prism diopters or greater underwent bilateral medial rectus recession to eliminate the need for prism glasses.

Results: In all but one case, the diplopia completely resolved postoperatively, with a median residual deviation of 1 prism diopter esophoria for distance and 2 prism diopters exophoria at near.

Conclusion: Bilateral medial rectus recession is a useful technique for the management of adult onset age-related distance esotropia.
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http://dx.doi.org/10.3928/01913913-20100818-04DOI Listing
April 2016

Stress, genomes, and evolution.

Cell Stress Chaperones 2010 Sep 4;15(5):463-6. Epub 2010 Jun 4.

Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

Evolutionary change, whether in populations of organisms or malignant tumor cells, is contingent on the availability of inherited variation for natural selection to act upon. It is becoming clear that the Hsp90 chaperone, which normally functions to buffer client proteins against the effects of genetic variation, plays a central role in this process. Severe environmental stress can overwhelm the chaperone's buffering capacity, causing previously cryptic genetic variation to be expressed. Recent studies now indicate that in addition to exposing existing variation, Hsp90 can induce novel epigenetic and genetic changes. We discuss key findings that suggest a rich set of pathways by which Hsp90 can mediate the influences of the environment on the genome.
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http://dx.doi.org/10.1007/s12192-010-0205-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006615PMC
September 2010

Hsp90 modulates CAG repeat instability in human cells.

Cell Stress Chaperones 2010 Sep 8;15(5):753-9. Epub 2010 Apr 8.

Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

The Hsp90 molecular chaperone has been implicated as a contributor to evolution in several organisms by revealing cryptic variation that can yield dramatic phenotypes when the chaperone is diverted from its normal functions by environmental stress. In addition, as a cancer drug target, Hsp90 inhibition has been documented to sensitize cells to DNA-damaging agents, suggesting a function for Hsp90 in DNA repair. Here we explore the potential role of Hsp90 in modulating the stability of nucleotide repeats, which in a number of species, including humans, exert subtle and quantitative consequences for protein function, morphological and behavioral traits, and disease. We report that impairment of Hsp90 in human cells induces contractions of CAG repeat tracks by tenfold. Inhibition of the recombinase Rad51, a downstream target of Hsp90, induces a comparable increase in repeat instability, suggesting that Hsp90-enabled homologous recombination normally functions to stabilize CAG repeat tracts. By contrast, Hsp90 inhibition does not increase the rate of gene-inactivating point mutations. The capacity of Hsp90 to modulate repeat-tract lengths suggests that the chaperone, in addition to exposing cryptic variation, might facilitate the expression of new phenotypes through induction of novel genetic variation.
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http://dx.doi.org/10.1007/s12192-010-0191-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006633PMC
September 2010

Zinc-finger directed double-strand breaks within CAG repeat tracts promote repeat instability in human cells.

Proc Natl Acad Sci U S A 2009 Jun 29;106(24):9607-12. Epub 2009 May 29.

Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.

Expanded triplet repeats have been identified as the genetic basis for a growing number of neurological and skeletal disorders. To examine the contribution of double-strand break repair to CAG x CTG repeat instability in mammalian systems, we developed zinc finger nucleases (ZFNs) that recognize and cleave CAG repeat sequences. Engineered ZFNs use a tandem array of zinc fingers, fused to the FokI DNA cleavage domain, to direct double-strand breaks (DSBs) in a site-specific manner. We first determined that the ZFNs cleave CAG repeats in vitro. Then, using our previously described tissue culture assay for identifying modifiers of CAG repeat instability, we found that transfection of ZFN-expression vectors induced up to a 15-fold increase in changes to the CAG repeat in human and rodent cell lines, and that longer repeats were much more sensitive to cleavage than shorter ones. Analysis of individual colonies arising after treatment revealed a spectrum of events consistent with ZFN-induced DSBs and dominated by repeat contractions. We also found that expressing a dominant-negative form of RAD51 in combination with a ZFN, dramatically reduced the effect of the nuclease, suggesting that DSB-induced repeat instability is mediated, in part, through homology directed repair. These studies identify a ZFN as a useful reagent for characterizing the effects of DSBs on CAG repeats in cells.
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http://dx.doi.org/10.1073/pnas.0902420106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701052PMC
June 2009

Age-related distance esotropia.

Authors:
David Mittelman

J AAPOS 2006 Jun;10(3):212-3

Advocate Lutheran General Hospital/Advocate Lutheran General Children's Hospital, Park Ridge, Illinois, USA.

Purpose: To describe a form of acquired esotropia occurring in older adults, which here is termed age-related distance esotropia.

Methods: A retrospective consecutive case series of 26 patients with this condition was reviewed.

Results: The patients ranged in age from 62 to 91 years old with a median age of 77 years. The distance deviation varied from 4 prism diopters (PD) ET (esotropia) to 20 PD ET, with a median angle of 9 PD ET. At near fixation, the measurements ranged from 9 PD ET' to 10 PD X' (exophoria), with a median deviation of 3 PD ET'. Ductions and versions were full, with no evidence of lateral rectus paresis. None of these patients had an obvious underlying neurologic disorder, such as tumor or stroke. Treatment consisted of prescribing the minimum prismatic correction that eliminated distance diplopia, which was then incorporated into the patients' current spectacles. This treatment successfully eliminated the symptoms in all patients. No patient in this study required surgery.

Conclusion: A distinctive form of strabismus occurs in older adults that is characterized by esotropia greater at distance than near fixation. The etiology of this disorder is unknown, but it is likely secondary to anatomical changes in the orbit and/or muscles associated with aging. Most patients are readily corrected by prisms but, surgical correction might be required in some cases.
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http://dx.doi.org/10.1016/j.jaapos.2006.01.217DOI Listing
June 2006