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Targeted capture and massively parallel sequencing of 12 human exomes (2009)

S. B. Ng ; E. H. Turner ; P. D. Robertson ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 461(7261): 272-6. doi: 10.1038/nature08250.

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Publication Date: 2009-08-18

Description: Genome-wide association studies suggest that common genetic variants explain only a modest fraction of heritable risk for common diseases, raising the question of whether rare variants account for a significant fraction of unexplained heritability. Although DNA sequencing costs have fallen markedly, they remain far from what is necessary for rare and novel variants to be routinely identified at a genome-wide scale in large cohorts. We have therefore sought to develop second-generation methods for targeted sequencing of all protein-coding regions ('exomes'), to reduce costs while enriching for discovery of highly penetrant variants. Here we report on the targeted capture and massively parallel sequencing of the exomes of 12 humans. These include eight HapMap individuals representing three populations, and four unrelated individuals with a rare dominantly inherited disorder, Freeman-Sheldon syndrome (FSS). We demonstrate the sensitive and specific identification of rare and common variants in over 300 megabases of coding sequence. Using FSS as a proof-of-concept, we show that candidate genes for Mendelian disorders can be identified by exome sequencing of a small number of unrelated, affected individuals. This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844771/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844771/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ng, Sarah B -- Turner, Emily H -- Robertson, Peggy D -- Flygare, Steven D -- Bigham, Abigail W -- Lee, Choli -- Shaffer, Tristan -- Wong, Michelle -- Bhattacharjee, Arindam -- Eichler, Evan E -- Bamshad, Michael -- Nickerson, Deborah A -- Shendure, Jay -- R01 HL094976/HL/NHLBI NIH HHS/ -- R01 HL094976-01/HL/NHLBI NIH HHS/ -- R21 HG004749/HG/NHGRI NIH HHS/ -- R21 HG004749-01/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Sep 10;461(7261):272-6. doi: 10.1038/nature08250. Epub 2009 Aug 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. sarahng@u.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19684571" target="_blank"〉PubMed〈/a〉

Keywords: Exons/*genetics ; Gene Frequency/genetics ; Gene Library ; Genes, Dominant/genetics ; Genetic Predisposition to Disease/*genetics ; Genetic Testing/*methods ; Genetic Variation/*genetics ; Genome, Human/*genetics ; Haplotypes/genetics ; Humans ; INDEL Mutation/genetics ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; RNA Splice Sites/genetics ; Sample Size ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Syndrome

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Closing a loophole in the FDA Amendments Act (2008)

E. H. Turner

American Association for the Advancement of Science (AAAS)

In: Science. 322(5898): 44-6. doi: 10.1126/science.322.5898.44c.

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Publication Date: 2008-10-04

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Turner, Erick H -- New York, N.Y. -- Science. 2008 Oct 3;322(5898):44-6. doi: 10.1126/science.322.5898.44c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18832629" target="_blank"〉PubMed〈/a〉

Keywords: Clinical Trials as Topic/*legislation & jurisprudence ; Databases, Factual ; Disclosure ; Drug Approval ; Humans ; Registries ; United States ; United States Food and Drug Administration/*legislation & jurisprudence

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders (2012)

B. J. O'Roak ; L. Vives ; W. Fu ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 338(6114): 1619-22. doi: 10.1126/science.1227764.

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Publication Date: 2012-11-20

Description: Exome sequencing studies of autism spectrum disorders (ASDs) have identified many de novo mutations but few recurrently disrupted genes. We therefore developed a modified molecular inversion probe method enabling ultra-low-cost candidate gene resequencing in very large cohorts. To demonstrate the power of this approach, we captured and sequenced 44 candidate genes in 2446 ASD probands. We discovered 27 de novo events in 16 genes, 59% of which are predicted to truncate proteins or disrupt splicing. We estimate that recurrent disruptive mutations in six genes-CHD8, DYRK1A, GRIN2B, TBR1, PTEN, and TBL1XR1-may contribute to 1% of sporadic ASDs. Our data support associations between specific genes and reciprocal subphenotypes (CHD8-macrocephaly and DYRK1A-microcephaly) and replicate the importance of a beta-catenin-chromatin-remodeling network to ASD etiology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528801/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528801/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Roak, Brian J -- Vives, Laura -- Fu, Wenqing -- Egertson, Jarrett D -- Stanaway, Ian B -- Phelps, Ian G -- Carvill, Gemma -- Kumar, Akash -- Lee, Choli -- Ankenman, Katy -- Munson, Jeff -- Hiatt, Joseph B -- Turner, Emily H -- Levy, Roie -- O'Day, Diana R -- Krumm, Niklas -- Coe, Bradley P -- Martin, Beth K -- Borenstein, Elhanan -- Nickerson, Deborah A -- Mefford, Heather C -- Doherty, Dan -- Akey, Joshua M -- Bernier, Raphael -- Eichler, Evan E -- Shendure, Jay -- HD065285/HD/NICHD NIH HHS/ -- HL-102923/HL/NHLBI NIH HHS/ -- HL-102924/HL/NHLBI NIH HHS/ -- HL-102925/HL/NHLBI NIH HHS/ -- HL-102926/HL/NHLBI NIH HHS/ -- HL-103010/HL/NHLBI NIH HHS/ -- NS069605/NS/NINDS NIH HHS/ -- R01 HD065285/HD/NICHD NIH HHS/ -- R01 NS064077/NS/NINDS NIH HHS/ -- R01 NS069605/NS/NINDS NIH HHS/ -- RC2 HL102926/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Dec 21;338(6114):1619-22. doi: 10.1126/science.1227764. Epub 2012 Nov 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23160955" target="_blank"〉PubMed〈/a〉

Keywords: Cephalometry ; Child ; Child Development Disorders, Pervasive/*genetics ; Child, Preschool ; Chromatin Assembly and Disassembly ; Cohort Studies ; DNA Probes ; DNA-Binding Proteins/genetics ; Exome ; Female ; *Genetic Association Studies ; Genetic Predisposition to Disease ; Humans ; Male ; Megalencephaly/genetics ; Microcephaly/genetics ; *Mutation ; Nuclear Proteins/genetics ; PTEN Phosphohydrolase/genetics ; Protein-Serine-Threonine Kinases/genetics ; Protein-Tyrosine Kinases/genetics ; Receptors, Cytoplasmic and Nuclear/genetics ; Receptors, N-Methyl-D-Aspartate/genetics ; Repressor Proteins/genetics ; Sequence Analysis, DNA/*methods ; T-Box Domain Proteins/genetics ; Transcription Factors/genetics ; beta Catenin/genetics/metabolism

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Crystal/melt partitioning of water and other volatiles during the near-solidus melting of mantle peridotite: Comparisons with non-volatile incompatible elements and implications for the generation of intraplate magmatism (2016)

Adam, J., Turner, M., Hauri, E. H., Turner, S.

Mineralogical Society of America

In: American Mineralogist

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Publication Date: 2016-04-02

Description: Concentrations of H 2 O, F, Cl, C, P, and S have been measured by secondary ion mass spectrometry (SIMS) in experimentally produced peridotite phases (including clinopyroxene, orthopyroxene, olivine, garnet, amphibole, and mica) and coexisting basanitic glasses. Because only two experiments produced glasses on quenching (with the melt phase in others reverting to felt-like crystallite masses) H 2 O concentrations in melts were also separately determined from mass-balance relationships and by assuming constant H 2 O/La in melts and starting materials. The resulting values were used to calculate mineral/melt partition coefficients ( D values) for H 2 O [where D H 2 O crystal/melt = (mass fraction of H 2 O in crystal)/(mass fraction of H 2 O in melt)] for conditions of 1025–1190 °C and 1.0–3.5 GPa. These gave 0.0064–0.0164 for clinopyroxene, 0.0046–0.0142 for orthopyroxene, 0.0015–0.0016 for olivine, and 0.0016–0.0022 for garnet. Although less information was obtained for the other volatiles, F was found to be significantly more compatible than H 2 O during peridotite melting, whereas Cl is significantly less compatible. S also has small but appreciable solubilities in amphiboles and micas, but not in pyroxenes or olivine. The solubility of C in silicate minerals appears to be negligible, although C was present in coexisting melts (~0.5 wt% as CO 2 ) and as residual graphite during experiments. The D values for H 2 O in clinopyroxene and orthopyroxene are positively correlated with iv Al but negatively correlated with the H 2 O concentrations of melts (when considered as wt%). These relationships are consistent with the broad trends of previously published partitioning data. Although some of the concentration dependence can be related to cross-correlation between iv Al in pyroxenes and H 2 O concentrations in melts (via the latter’s control of liquidus temperatures) this relationship is too inconsistent to be a complete explanation. A concentration dependence for D H 2 O mineral/melt can also be independently predicted from speciation models for H 2 O in silicate melts. Thus it is likely that D H 2 O pyx/melt is influenced by both iv Al and the absolute concentration of H 2 O in melts. D H 2 O / D Ce for clinopyroxene is inversely correlated with M2 site radii. Because the latter decrease with increasing pressure and temperature, relatively hot and/or deeply derived melts should be enriched in Ce relative to H 2 O when compared to melts from cooler and shallower mantle sources. Conversely, melts from H 2 O-rich settings (e.g., subduction zones) should have higher H 2 O/Ce than their source rocks. When combined with previously obtained partitioning data for non-volatile elements (from the same experiments), our data are consistent with the enrichment of intraplate basalt sources in both volatile and non-volatile incompatible elements by small-degree melts derived from local mid-ocean ridge basalt sources. In this way, volatiles can be seen to play an active role (via their promotion of partial-melting and metasomatic processes) in the auto-regulation of incompatible element concentrations in the depleted upper mantle.

Print ISSN: 0003-004X

Electronic ISSN: 1945-3027

Topics: Geosciences

Published by Mineralogical Society of America

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Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations (2012)

B. J. O'Roak ; L. Vives ; S. Girirajan ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 485(7397): 246-50. doi: 10.1038/nature10989.

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Publication Date: 2012-04-13

Description: It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes--so-called sporadic or simplex families--we sequenced all coding regions of the genome (the exome) for parent-child trios exhibiting sporadic ASD, including 189 new trios and 20 that were previously reported. Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19), for a total of 677 individual exomes from 209 families. Here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD. Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected beta-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. In proband exomes, recurrent protein-altering mutations were observed in two genes: CHD8 and NTNG1. Mutation screening of six candidate genes in 1,703 ASD probands identified additional de novo, protein-altering mutations in GRIN2B, LAMC3 and SCN1A. Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350576/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350576/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Roak, Brian J -- Vives, Laura -- Girirajan, Santhosh -- Karakoc, Emre -- Krumm, Niklas -- Coe, Bradley P -- Levy, Roie -- Ko, Arthur -- Lee, Choli -- Smith, Joshua D -- Turner, Emily H -- Stanaway, Ian B -- Vernot, Benjamin -- Malig, Maika -- Baker, Carl -- Reilly, Beau -- Akey, Joshua M -- Borenstein, Elhanan -- Rieder, Mark J -- Nickerson, Deborah A -- Bernier, Raphael -- Shendure, Jay -- Eichler, Evan E -- HD065285/HD/NICHD NIH HHS/ -- HHSN273200800010C/PHS HHS/ -- HL 094976/HL/NHLBI NIH HHS/ -- HL 1029230/HL/NHLBI NIH HHS/ -- HL 102924/HL/NHLBI NIH HHS/ -- HL102926/HL/NHLBI NIH HHS/ -- R01 HD065285/HD/NICHD NIH HHS/ -- R01 HD065285-02/HD/NICHD NIH HHS/ -- R01 HL094976/HL/NHLBI NIH HHS/ -- RC2 HL102923/HL/NHLBI NIH HHS/ -- RC2 HL102926/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Apr 4;485(7397):246-50. doi: 10.1038/nature10989.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22495309" target="_blank"〉PubMed〈/a〉

Keywords: Autistic Disorder/*genetics ; DNA-Binding Proteins/genetics ; Exome/*genetics ; Exons/*genetics ; GPI-Linked Proteins/genetics ; Genetic Predisposition to Disease/genetics ; Humans ; Laminin/genetics ; NAV1.1 Voltage-Gated Sodium Channel ; Nerve Tissue Proteins/genetics ; Parents ; Point Mutation/*genetics ; Protein Interaction Maps/*genetics ; Receptors, N-Methyl-D-Aspartate/genetics ; Reproducibility of Results ; Siblings ; Signal Transduction ; Sodium Channels/genetics ; Stochastic Processes ; Transcription Factors/genetics ; Tumor Suppressor Protein p53/metabolism ; beta Catenin/metabolism

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Electronic Resource

Photoelastic and electrooptic properties of crystals by T. S. Narasimhamurty (1982)

Turner, E. H.

[S.l.] : International Union of Crystallography (IUCr)

Acta crystallographica 38 (1982), S. 399-400

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ISSN: 1600-5724

Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001

Topics: Chemistry and Pharmacology , Geosciences , Physics

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1107/S0567739482000916

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Electronic Resource

Pyroelectric sign of LiIO3 (1976)

Turner, E. H.

Copenhagen : International Union of Crystallography (IUCr)

Applied crystallography online 9 (1976), S. 52-52

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ISSN: 1600-5767

Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001

Topics: Geosciences , Physics

Notes: The sign of the total pyroelectric coefficient, p3, of LiIO3 has been related to the known [Morosin, 1972. Private communication quoted as Ref. 25 of Bergman, J. G. & Crane, G. R. (1974). J. Chem. Phys. 60, 2470–2474] absolute configuration by use of a model of Liminga & Abrahams [J. Appl. Cryst. (1976). 9, 42–47]. It has been experimentally verified to be positive (piezoelectric convention) as predicted.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1107/S0021889876010509

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8

Electronic Resource

Novel treatment for joint inflammation (1978)

DINGLE, J. T. ; GORDON, J. L. ; HAZLEMAN, B. L. ; [et al.]

[s.l.] : Nature Publishing Group

Nature 271 (1978), S. 372-373

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ISSN: 1476-4687

Source: Nature Archives 1869 - 2009

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Notes: [Auszug] Old English rabbits (body weight 1.5-2.0 kg) were used throughout the study. A bilateral inflammation of the knee joints was induced by the intra-articular injection of a complex formed from 7.5 mg poly-D-lysine (molecular weight 150,000) and 7.5 mg hyaluronic acid7 (both Miles). The initial ...

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1038/271372a0

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