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1. High incidence of clinical fragility fractures in postmenopausal women with rheumatoid arthritis. A case-control study

Author

Gómez-Vaquero, Carmen, Hernández, José Luis, Olmos, José Manuel, Cerdà, Dacia, Calleja, Cristina Hidalgo, López, Juan Antonio Martínez, Arboleya, Luis, del Rey, Francisco Javier Aguilar, Pardo, Silvia Martinez, Vilamajó, Inmaculada Ros, Armangué, Xavier Surís, Grados, Dolors, Audera, Chesús Beltrán, Suero-Rosario, Evelyn, Gracia, Inmaculada Gómez, Chamizo, Asunción Salmoral, Martín-Esteve, Irene, Florez, Helena, Naranjo, Antonio, Castañeda, Santos, Bruno, Soledad Ojeda, Carazo, Sara García, Garcia-Vadillo, Alberto, Vives, Laura López, Martínez-Ferrer, Àngels, Paños, Helena Borrell, Acín, Pilar Aguado, Castellanos-Moreira, Raul, Satorra, Pau, Tebé, Cristian, and Guañabens, Núria

Published
2023
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2. Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases

Author

Stessman, Holly AF, Xiong, Bo, Coe, Bradley P, Wang, Tianyun, Hoekzema, Kendra, Fenckova, Michaela, Kvarnung, Malin, Gerdts, Jennifer, Trinh, Sandy, Cosemans, Nele, Vives, Laura, Lin, Janice, Turner, Tychele N, Santen, Gijs, Ruivenkamp, Claudia, Kriek, Marjolein, van Haeringen, Arie, Aten, Emmelien, Friend, Kathryn, Liebelt, Jan, Barnett, Christopher, Haan, Eric, Shaw, Marie, Gecz, Jozef, Anderlid, Britt-Marie, Nordgren, Ann, Lindstrand, Anna, Schwartz, Charles, Kooy, R Frank, Vandeweyer, Geert, Helsmoortel, Celine, Romano, Corrado, Alberti, Antonino, Vinci, Mirella, Avola, Emanuela, Giusto, Stefania, Courchesne, Eric, Pramparo, Tiziano, Pierce, Karen, Nalabolu, Srinivasa, Amaral, David G, Scheffer, Ingrid E, Delatycki, Martin B, Lockhart, Paul J, Hormozdiari, Fereydoun, Harich, Benjamin, Castells-Nobau, Anna, Xia, Kun, Peeters, Hilde, Nordenskjöld, Magnus, Schenck, Annette, Bernier, Raphael A, and Eichler, Evan E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Brain Disorders, Behavioral and Social Science, Genetic Testing, Intellectual and Developmental Disabilities (IDD), Mental Health, Neurosciences, Pediatric, Autism, Aetiology, 2.1 Biological and endogenous factors, Mental health, Autistic Disorder, Developmental Disabilities, Female, Humans, Intellectual Disability, Male, Mutation, Phenotype, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Gene-disruptive mutations contribute to the biology of neurodevelopmental disorders (NDDs), but most of the related pathogenic genes are not known. We sequenced 208 candidate genes from >11,730 cases and >2,867 controls. We identified 91 genes, including 38 new NDD genes, with an excess of de novo mutations or private disruptive mutations in 5.7% of cases. Drosophila functional assays revealed a subset with increased involvement in NDDs. We identified 25 genes showing a bias for autism versus intellectual disability and highlighted a network associated with high-functioning autism (full-scale IQ >100). Clinical follow-up for NAA15, KMT5B, and ASH1L highlighted new syndromic and nonsyndromic forms of disease.

Published
2017

3. Extreme selective sweeps independently targeted the X chromosomes of the great apes

Author

Nam, Kiwoong, Munch, Kasper, Hobolth, Asger, Dutheil, Julien Yann, Veeramah, Krishna R, Woerner, August E, Hammer, Michael F, Mailund, Thomas, Schierup, Mikkel Heide, Prado-Martinez, Javier, Sudmant, Peter H, Kidd, Jeffrey M, Li, Heng, Kelley, Joanna L, Lorente-Galdos, Belen, O’Connor, Timothy D, Santpere, Gabriel, Cagan, Alexander, Theunert, Christoph, Casals, Ferran, Laayouni, Hafid, Halager, Anders E, Malig, Maika, Hernandez-Rodriguez, Jessica, Hernando-Herraez, Irene, Prüfer, Kay, Pybus, Marc, Johnstone, Laurel, Lachmann, Michael, Alkan, Can, Twigg, Dorina, Petit, Natalia, Baker, Carl, Hormozdiari, Fereydoun, Fernandez-Callejo, Marcos, Dabad, Marc, Wilson, Michael L, Stevison, Laurie, Camprubí, Cristina, Carvalho, Tiago, Ruiz-Herrera, Aurora, Vives, Laura, Mele, Marta, Abello, Teresa, Kondova, Ivanela, Bontrop, Ronald E, Pusey, Anne, Lankester, Felix, Kiyang, John A, Bergl, Richard A, Lonsdorf, Elizabeth, Myers, Simon, Ventura, Mario, Gagneux, Pascal, Comas, David, Siegismund, Hans, Blanc, Julie, Agueda-Calpena, Lidia, Gut, Marta, Fulton, Lucinda, Tishkoff, Sarah A, Mullikin, James C, Wilson, Richard K, Gut, Ivo G, Gonder, Mary Katherine, Ryder, Oliver A, Hahn, Beatrice H, Navarro, Arcadi, Akey, Joshua M, Bertranpetit, Jaume, Reich, David, Schierup, Mikkel H, Hvilsom, Christina, Andrés, Aida M, Wall, Jeffrey D, Bustamante, Carlos D, Eichler, Evan E, and Marques-Bonet, Tomas

Subjects
Human Genome, Genetics, Animals, Computational Biology, Databases, Genetic, Genetic Variation, Genetics, Population, Hominidae, Models, Genetic, Polymorphism, Genetic, Selection, Genetic, Species Specificity, X Chromosome, Great Ape Genome Diversity Project, X-chromosome evolution, ampliconic genes, great apes, meiotic drive, selective sweeps
Abstract

The unique inheritance pattern of the X chromosome exposes it to natural selection in a way that is different from that of the autosomes, potentially resulting in accelerated evolution. We perform a comparative analysis of X chromosome polymorphism in 10 great ape species, including humans. In most species, we identify striking megabase-wide regions, where nucleotide diversity is less than 20% of the chromosomal average. Such regions are found exclusively on the X chromosome. The regions overlap partially among species, suggesting that the underlying targets are partly shared among species. The regions have higher proportions of singleton SNPs, higher levels of population differentiation, and a higher nonsynonymous-to-synonymous substitution ratio than the rest of the X chromosome. We show that the extent to which diversity is reduced is incompatible with direct selection or the action of background selection and soft selective sweeps alone, and therefore, we suggest that very strong selective sweeps have independently targeted these specific regions in several species. The only genomic feature that we can identify as strongly associated with loss of diversity is the location of testis-expressed ampliconic genes, which also have reduced diversity around them. We hypothesize that these genes may be responsible for selective sweeps in the form of meiotic drive caused by an intragenomic conflict in male meiosis.

Published
2015

4. Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability.

Author

Antonacci, Francesca, Dennis, Megan Y, Huddleston, John, Sudmant, Peter H, Steinberg, Karyn Meltz, Rosenfeld, Jill A, Miroballo, Mattia, Graves, Tina A, Vives, Laura, Malig, Maika, Denman, Laura, Raja, Archana, Stuart, Andrew, Tang, Joyce, Munson, Brenton, Shaffer, Lisa G, Amemiya, Chris T, Wilson, Richard K, and Eichler, Evan E

Subjects
Chromosomes, Artificial, Bacterial, Chromosomes, Human, Pair 15, Animals, Primates, Humans, Seizures, Chromosome Disorders, Chromosome Deletion, In Situ Hybridization, Fluorescence, Cluster Analysis, Sequence Analysis, DNA, Repetitive Sequences, Nucleic Acid, Gene Dosage, Polymorphism, Genetic, Genome, Human, Models, Genetic, Comparative Genomic Hybridization, Segmental Duplications, Genomic, Biological Evolution, Intellectual Disability, Genetics, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Recurrent deletions of chromosome 15q13.3 associate with intellectual disability, schizophrenia, autism and epilepsy. To gain insight into the instability of this region, we sequenced it in affected individuals, normal individuals and nonhuman primates. We discovered five structural configurations of the human chromosome 15q13.3 region ranging in size from 2 to 3 Mb. These configurations arose recently (∼0.5-0.9 million years ago) as a result of human-specific expansions of segmental duplications and two independent inversion events. All inversion breakpoints map near GOLGA8 core duplicons-a ∼14-kb primate-specific chromosome 15 repeat that became organized into larger palindromic structures. GOLGA8-flanked palindromes also demarcate the breakpoints of recurrent 15q13.3 microdeletions, the expansion of chromosome 15 segmental duplications in the human lineage and independent structural changes in apes. The significant clustering (P = 0.002) of breakpoints provides mechanistic evidence for the role of this core duplicon and its palindromic architecture in promoting the evolutionary and disease-related instability of chromosome 15.

Published
2014

5. The contribution of de novo coding mutations to autism spectrum disorder.

Author

Ronemus, Michael, Krumm, Niklas, Levy, Dan, Stessman, Holly, Witherspoon, Kali, Vives, Laura, Patterson, Karynne, Smith, Joshua, Paeper, Bryan, Nickerson, Deborah, Dea, Jeanselle, Dong, Shan, Gonzalez, Luis, Mandell, Jeffrey, Mane, Shrikant, Murtha, Michael, Sullivan, Catherine, Wigler, Michael, Yamrom, Boris, Lee, Yoon-ha, Grabowska, Ewa, Dalkic, Ertugrul, Wang, Zihua, Marks, Steven, Andrews, Peter, Leotta, Anthony, Kendall, Jude, Hakker, Inessa, Rosenbaum, Julie, Ma, Beicong, Rodgers, Linda, Troge, Jennifer, Narzisi, Giuseppe, Yoon, Seungtai, Schatz, Michael, Ye, Kenny, McCombie, W, Shendure, Jay, Eichler, Evan, Iossifov, Ivan, ORoak, Brian, Waqar, Zainulabedin, Wei, Liping, State, Matthew, Sanders, Stephan, Willsey, Arthur, and Walker, Michael

Subjects
Child, Child Development Disorders, Pervasive, Cluster Analysis, Exome, Female, Genes, Genetic Predisposition to Disease, Humans, Intelligence Tests, Male, Mutation, Open Reading Frames, Reproducibility of Results
Abstract

Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females.

Published
2014

6. Great ape genetic diversity and population history.

Author

Prado-Martinez, Javier, Sudmant, Peter H, Kidd, Jeffrey M, Li, Heng, Kelley, Joanna L, Lorente-Galdos, Belen, Veeramah, Krishna R, Woerner, August E, O'Connor, Timothy D, Santpere, Gabriel, Cagan, Alexander, Theunert, Christoph, Casals, Ferran, Laayouni, Hafid, Munch, Kasper, Hobolth, Asger, Halager, Anders E, Malig, Maika, Hernandez-Rodriguez, Jessica, Hernando-Herraez, Irene, Prüfer, Kay, Pybus, Marc, Johnstone, Laurel, Lachmann, Michael, Alkan, Can, Twigg, Dorina, Petit, Natalia, Baker, Carl, Hormozdiari, Fereydoun, Fernandez-Callejo, Marcos, Dabad, Marc, Wilson, Michael L, Stevison, Laurie, Camprubí, Cristina, Carvalho, Tiago, Ruiz-Herrera, Aurora, Vives, Laura, Mele, Marta, Abello, Teresa, Kondova, Ivanela, Bontrop, Ronald E, Pusey, Anne, Lankester, Felix, Kiyang, John A, Bergl, Richard A, Lonsdorf, Elizabeth, Myers, Simon, Ventura, Mario, Gagneux, Pascal, Comas, David, Siegismund, Hans, Blanc, Julie, Agueda-Calpena, Lidia, Gut, Marta, Fulton, Lucinda, Tishkoff, Sarah A, Mullikin, James C, Wilson, Richard K, Gut, Ivo G, Gonder, Mary Katherine, Ryder, Oliver A, Hahn, Beatrice H, Navarro, Arcadi, Akey, Joshua M, Bertranpetit, Jaume, Reich, David, Mailund, Thomas, Schierup, Mikkel H, Hvilsom, Christina, Andrés, Aida M, Wall, Jeffrey D, Bustamante, Carlos D, Hammer, Michael F, Eichler, Evan E, and Marques-Bonet, Tomas

Subjects
Animals, Animals, Wild, Animals, Zoo, Hominidae, Gorilla gorilla, Humans, Pan paniscus, Pan troglodytes, Inbreeding, Genetics, Population, Population Density, Evolution, Molecular, Phylogeny, Polymorphism, Single Nucleotide, Genome, Africa, Asia, Southeastern, Gene Flow, Genetic Variation, General Science & Technology
Abstract

Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

Published
2013

7. Estimating the human mutation rate using autozygosity in a founder population

Author

Campbell, Catarina D, Chong, Jessica X, Malig, Maika, Ko, Arthur, Dumont, Beth L, Han, Lide, Vives, Laura, O'Roak, Brian J, Sudmant, Peter H, Shendure, Jay, Abney, Mark, Ober, Carole, and Eichler, Evan E

Subjects
Behavioral and Social Science, Alleles, Chromosome Mapping, Evolution, Molecular, Genetics, Population, Genome, Human, Heterozygote, High-Throughput Nucleotide Sequencing, Homozygote, Humans, Mutation, Mutation Rate, Pedigree, Polymorphism, Single Nucleotide, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Knowledge of the rate and pattern of new mutation is critical to the understanding of human disease and evolution. We used extensive autozygosity in a genealogically well-defined population of Hutterites to estimate the human sequence mutation rate over multiple generations. We sequenced whole genomes from 5 parent-offspring trios and identified 44 segments of autozygosity. Using the number of meioses separating each pair of autozygous alleles and the 72 validated heterozygous single-nucleotide variants (SNVs) from 512 Mb of autozygous DNA, we obtained an SNV mutation rate of 1.20 × 10(-8) (95% confidence interval 0.89-1.43 × 10(-8)) mutations per base pair per generation. The mutation rate for bases within CpG dinucleotides (9.72 × 10(-8)) was 9.5-fold that of non-CpG bases, and there was strong evidence (P = 2.67 × 10(-4)) for a paternal bias in the origin of new mutations (85% paternal). We observed a non-uniform distribution of heterozygous SNVs (both newly identified and known) in the autozygous segments (P = 0.001), which is suggestive of mutational hotspots or sites of long-range gene conversion.

Published
2012

8. Structural diversity and African origin of the 17q21.31 inversion polymorphism

Author

Steinberg, Karyn Meltz, Antonacci, Francesca, Sudmant, Peter H, Kidd, Jeffrey M, Campbell, Catarina D, Vives, Laura, Malig, Maika, Scheinfeldt, Laura, Beggs, William, Ibrahim, Muntaser, Lema, Godfrey, Nyambo, Thomas B, Omar, Sabah A, Bodo, Jean-Marie, Froment, Alain, Donnelly, Michael P, Kidd, Kenneth K, Tishkoff, Sarah A, and Eichler, Evan E

Subjects
Genetics, Africa, Black People, Chromosome Inversion, Chromosomes, Human, Pair 17, Evolution, Molecular, Gene Frequency, Haplotypes, Humans, In Situ Hybridization, Fluorescence, Linkage Disequilibrium, Phylogeny, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The 17q21.31 inversion polymorphism exists either as direct (H1) or inverted (H2) haplotypes with differential predispositions to disease and selection. We investigated its genetic diversity in 2,700 individuals, with an emphasis on African populations. We characterize eight structural haplotypes due to complex rearrangements that vary in size from 1.08-1.49 Mb and provide evidence for a 30-kb H1-H2 double recombination event. We show that recurrent partial duplications of the KANSL1 gene have occurred on both the H1 and H2 haplotypes and have risen to high frequency in European populations. We identify a likely ancestral H2 haplotype (H2') lacking these duplications that is enriched among African hunter-gatherer groups yet essentially absent from West African populations. Whereas H1 and H2 segmental duplications arose independently and before human migration out of Africa, they have reached high frequencies recently among Europeans, either because of extraordinary genetic drift or selective sweeps.

Published
2012

9. A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay

Author

Girirajan, Santhosh, Rosenfeld, Jill A, Cooper, Gregory M, Antonacci, Francesca, Siswara, Priscillia, Itsara, Andy, Vives, Laura, Walsh, Tom, McCarthy, Shane E, Baker, Carl, Mefford, Heather C, Kidd, Jeffrey M, Browning, Sharon R, Browning, Brian L, Dickel, Diane E, Levy, Deborah L, Ballif, Blake C, Platky, Kathryn, Farber, Darren M, Gowans, Gordon C, Wetherbee, Jessica J, Asamoah, Alexander, Weaver, David D, Mark, Paul R, Dickerson, Jennifer, Garg, Bhuwan P, Ellingwood, Sara A, Smith, Rosemarie, Banks, Valerie C, Smith, Wendy, McDonald, Marie T, Hoo, Joe J, French, Beatrice N, Hudson, Cindy, Johnson, John P, Ozmore, Jillian R, Moeschler, John B, Surti, Urvashi, Escobar, Luis F, El-Khechen, Dima, Gorski, Jerome L, Kussmann, Jennifer, Salbert, Bonnie, Lacassie, Yves, Biser, Alisha, McDonald-McGinn, Donna M, Zackai, Elaine H, Deardorff, Matthew A, Shaikh, Tamim H, Haan, Eric, Friend, Kathryn L, Fichera, Marco, Romano, Corrado, Gécz, Jozef, DeLisi, Lynn E, Sebat, Jonathan, King, Mary-Claire, Shaffer, Lisa G, and Eichler, Evan E

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Agricultural Biotechnology, Neurosciences, Brain Disorders, Pediatric, Aetiology, 2.1 Biological and endogenous factors, Adult, Case-Control Studies, Child, Child, Preschool, Chromosome Deletion, Chromosomes, Human, Pair 16, Comparative Genomic Hybridization, Developmental Disabilities, Family, Gene Frequency, Humans, Infant, Models, Genetic, Oligonucleotide Array Sequence Analysis, Pedigree, Phenotype, Polymorphism, Single Nucleotide, Recurrence, Severity of Illness Index, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls (P = 0.0009, OR = 7.2) and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls (P = 0.028, OR = 2.5). Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents (P = 0.037, OR = 6). Probands were more likely to carry an additional large copy-number variant when compared to matched controls (10 of 42 cases, P = 5.7 x 10(-5), OR = 6.6). The clinical features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease.

Published
2010

10. Disruption of POGZ Is Associated with Intellectual Disability and Autism Spectrum Disorders

Author

Stessman, Holly A.F., Willemsen, Marjolein H., Fenckova, Michaela, Penn, Osnat, Hoischen, Alexander, Xiong, Bo, Wang, Tianyun, Hoekzema, Kendra, Vives, Laura, Vogel, Ida, Brunner, Han G., van der Burgt, Ineke, Ockeloen, Charlotte W., Schuurs-Hoeijmakers, Janneke H., Klein Wassink-Ruiter, Jolien S., Stumpel, Connie, Stevens, Servi J.C., Vles, Hans S., Marcelis, Carlo M., van Bokhoven, Hans, Cantagrel, Vincent, Colleaux, Laurence, Nicouleau, Michael, Lyonnet, Stanislas, Bernier, Raphael A., Gerdts, Jennifer, Coe, Bradley P., Romano, Corrado, Alberti, Antonino, Grillo, Lucia, Scuderi, Carmela, Nordenskjöld, Magnus, Kvarnung, Malin, Guo, Hui, Xia, Kun, Piton, Amélie, Gerard, Bénédicte, Genevieve, David, Delobel, Bruno, Lehalle, Daphne, Perrin, Laurence, Prieur, Fabienne, Thevenon, Julien, Gecz, Jozef, Shaw, Marie, Pfundt, Rolph, Keren, Boris, Jacquette, Aurelia, Schenck, Annette, Eichler, Evan E., and Kleefstra, Tjitske

Published
2016
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13. Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

Author

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., and Shendure, Jay

Published
2012
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19. Role of targeted therapies in rheumatic patients on COVID-19 outcomes: results from the COVIDSER study

Author

Álvaro Gracia, Jose María, primary, Sanchez-Piedra, Carlos, additional, Manero, Javier, additional, Ruiz-Lucea, María Ester, additional, López-Vives, Laura, additional, Bohorquez, Cristina, additional, Martinez-Barrio, Julia, additional, Bonilla, Gema, additional, Vela, Paloma, additional, García-Villanueva, María Jesús, additional, Navío-Marco, María Teresa, additional, Pavía, Marina, additional, Galindo, María, additional, Erausquin, Celia, additional, Gonzalez-Gay, Miguel A, additional, Rua-Figueroa, Inigo, additional, Pego-Reigosa, Jose M, additional, Castrejon, Isabel, additional, Sanchez-Costa, Jesús T, additional, González-Dávila, Enrique, additional, and Diaz-Gonzalez, Federico, additional

Published
2021
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20. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

Author

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, and Eichler, Evan E.

Subjects
Gene mutations -- Health aspects, Pervasive developmental disorders -- Risk factors -- Genetic aspects -- Care and treatment -- Research, Genetic variation -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

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 (1). 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 (2,3)--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 (4). Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19) (4), 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 (5). Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected β-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., We selected 189 autism trios from the Simons Simplex Collection (SSC) (6), which included males significantly impaired with autism and intellectual disability (n = 47), a female sample set (n [...]

Published
2012
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21. Incidence of fragility fractures in postmenopausal women with rheumatoid arthritis. A case-control study

Author

Vaquero, Carmen Gómez, Olmos, José Manuel, Hernández, José Luis, Cerdà, Dacia, Calleja, Cristina Hidalgo, López, Juan Antonio Martínez, Arboleya, Luis, del Rey, Francisco Javier Aguilar, Pardo, Silvia Martínez, Vilamajó, Inmaculada Ros, Suris, Xavier, Grados, Dolors, Audera, Chesús Beltrán, Suero-Rosario, Evelyn, Gracia, Inmaculada Gómez, Chamizo, Asunción Salmoral, Martín-Esteve, Irene, Flórez, Helena, Naranjo, Antonio, Castañeda, Santos, Bruno, Soledad Ojeda, Carazo, Sara García, Vadillo, Alberto Garcia, Vives, Laura López, Martínez-Ferrer, Angels, Paños, Helena Borrell, Acín, Pilar Aguado, Castellanos-Moreira, Raul, Tebé, Cristian, and Guañabens, Núria

Published
2020
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22. The contribution of de novo coding mutations to autism spectrum disorder

Author

Iossifov, Ivan, OʼRoak, Brian J., Sanders, Stephan J., Ronemus, Michael, Krumm, Niklas, Levy, Dan, Stessman, Holly A., Witherspoon, Kali T., Vives, Laura, Patterson, Karynne E., Smith, Joshua D., Paeper, Bryan, Nickerson, Deborah A., Dea, Jeanselle, Dong, Shan, Gonzalez, Luis E., Mandell, Jeffrey D., Mane, Shrikant M., Murtha, Michael T., Sullivan, Catherine A., Walker, Michael F., Waqar, Zainulabedin, Wei, Liping, Willsey, Jeremy A., Yamrom, Boris, Lee, Yoon-ha, Grabowska, Ewa, Dalkic, Ertugrul, Wang, Zihua, Marks, Steven, Andrews, Peter, Leotta, Anthony, Kendall, Jude, Hakker, Inessa, Rosenbaum, Julie, Ma, Beicong, Rodgers, Linda, Troge, Jennifer, Narzisi, Giuseppe, Yoon, Seungtai, Schatz, Michael C., Ye, Kenny, McCombie, Richard W., Shendure, Jay, Eichler, Evan E., State, Matthew W., and Wigler, Michael

Published
2014
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23. L'ús i conservació de la fusta en trinxeres de la Guerra Civil Espanyola. El cas del Jaciment del Cinglo Alt (Gavet de la Conca, Pallars Jussà)

Author

Medina Vives, Laura and Solé, Queralt

Subjects
Atrinxerament, Bachelor's thesis, Military fronts, Antiquities, Bachelor's theses, Fronts militars, Treballs de fi de grau, Conservation and restoration, Intrenchments, Excavacions arqueològiques, Wood, Conservació i restauració, Pallars Jussà (Catalunya), Fusta, Spanish Civil War, 1936-1939, Guerra Civil Espanyola, 1936-1939, Restes arqueològiques, Archaeological excavations, Arqueology, Pallars Jussà (Catalonia)
Abstract

Treballs Finals de Grau Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Curs: 201x-201x, Tutor, [cat] La fusta és un material molt utilitzat al llarg dels temps en tots els àmbits, però la seva conservació és molt escassa i, per tant, el seu estudi és difícil. Tot i això, a la trinxera republicana situada al Cinglo Alt (Gavet de la Conca, Pallars Jussà) s’hi van trobar un seguit de restes que feien palesa la importància de la fusta en els contextos de conflicte. Aquest treball té com a objectiu estudiar els vestigis de fusta (i també aquells relacionats amb la seva explotació) trobats al jaciment del Cinglo Alt durant la primera campanya de prospecció i, posteriorment, comparar-los amb altres elements de fusta trobats en contextos de trinxera de la Guerra Civil Espanyola., [eng] Wood has been used through the ages in very different ways, but its preservation can be very rare which can make its study very difficult. However, the republican trench system of Cinglo Alt (Gavet de la Conca, Pallars Jussà) provided a few findings that showed the important role that wood had in warfare contexts. The goal of this dissertation is to study the wood items (and those related to its exploitation) found at the Cinglo Alt site during the first prospection campaign and then compare them to other timber elements found in trench sites of the same chronology.

Published
2020

25. Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

Author

OʼRoak, 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, OʼDay, 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., and Shendure, Jay

Published
2012
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26. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

Author

OʼRoak, 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, and Eichler, Evan E.

Published
2012
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28. Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data

Author

Huddleston, John, primary, Chaisson, Mark J.P., additional, Steinberg, Karyn Meltz, additional, Warren, Wes, additional, Hoekzema, Kendra, additional, Gordon, David, additional, Graves-Lindsay, Tina A., additional, Munson, Katherine M., additional, Kronenberg, Zev N., additional, Vives, Laura, additional, Peluso, Paul, additional, Boitano, Matthew, additional, Chin, Chen-Shin, additional, Korlach, Jonas, additional, Wilson, Richard K., additional, and Eichler, Evan E., additional

Published
2018
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30. Comportamiento variado de compra del consumidor entre el canal offline y el canal online

Author

Soro Vives, Laura and Berné Manero, Carmen

Abstract

Tomando como referencia la literatura basada en el comportamiento variado del consumidor, el trabajo que se presenta a continuación tiene el propósito de analizar cómo ha afectado Internet a los comportamientos de compra de los consumidores más jóvenes, confirmando el fuerte crecimiento de la compra online en relación a la compra física. Para conseguir los objetivos fijados, se aplicará el método de la encuesta como fuente de información primaria que permitirá la recopilación y el posterior análisis de los datos para presentar las conclusiones finales. Una vez estudiados los resultados, el trabajo muestra cómo los jóvenes son el grupo de edad que más usan Internet y a la vez son los que muestran un comportamiento de compra más variado. Sin embargo, hay consumidores que todavía no compran frecuentemente en Internet por miedo e inseguridad, aunque en un futuro esta situación será diferente ya que acabarán utilizando ambos canales de compra para satisfacer una misma necesidad.

Published
2016

32. Retrotransposons Are the Major Contributors to the Expansion of theDrosophila ananassaeMuller F Element

Author

Leung, Wilson, primary, Shaffer, Christopher D, additional, Chen, Elizabeth J, additional, Quisenberry, Thomas J, additional, Ko, Kevin, additional, Braverman, John M, additional, Giarla, Thomas C, additional, Mortimer, Nathan T, additional, Reed, Laura K, additional, Smith, Sheryl T, additional, Robic, Srebrenka, additional, McCartha, Shannon R, additional, Perry, Danielle R, additional, Prescod, Lindsay M, additional, Sheppard, Zenyth A, additional, Saville, Ken J, additional, McClish, Allison, additional, Morlock, Emily A, additional, Sochor, Victoria R, additional, Stanton, Brittney, additional, Veysey-White, Isaac C, additional, Revie, Dennis, additional, Jimenez, Luis A, additional, Palomino, Jennifer J, additional, Patao, Melissa D, additional, Patao, Shane M, additional, Himelblau, Edward T, additional, Campbell, Jaclyn D, additional, Hertz, Alexandra L, additional, McEvilly, Maddison F, additional, Wagner, Allison R, additional, Youngblom, James, additional, Bedi, Baljit, additional, Bettincourt, Jeffery, additional, Duso, Erin, additional, Her, Maiye, additional, Hilton, William, additional, House, Samantha, additional, Karimi, Masud, additional, Kumimoto, Kevin, additional, Lee, Rebekah, additional, Lopez, Darryl, additional, Odisho, George, additional, Prasad, Ricky, additional, Robbins, Holly Lyn, additional, Sandhu, Tanveer, additional, Selfridge, Tracy, additional, Tsukashima, Kara, additional, Yosif, Hani, additional, Kokan, Nighat P, additional, Britt, Latia, additional, Zoellner, Alycia, additional, Spana, Eric P, additional, Chlebina, Ben T, additional, Chong, Insun, additional, Friedman, Harrison, additional, Mammo, Danny A, additional, Ng, Chun L, additional, Nikam, Vinayak S, additional, Schwartz, Nicholas U, additional, Xu, Thomas Q, additional, Burg, Martin G, additional, Batten, Spencer M, additional, Corbeill, Lindsay M, additional, Enoch, Erica, additional, Ensign, Jesse J, additional, Franks, Mary E, additional, Haiker, Breanna, additional, Ingles, Judith A, additional, Kirkland, Lyndsay D, additional, Lorenz-Guertin, Joshua M, additional, Matthews, Jordan, additional, Mittig, Cody M, additional, Monsma, Nicholaus, additional, Olson, Katherine J, additional, Perez-Aragon, Guillermo, additional, Ramic, Alen, additional, Ramirez, Jordan R, additional, Scheiber, Christopher, additional, Schneider, Patrick A, additional, Schultz, Devon E, additional, Simon, Matthew, additional, Spencer, Eric, additional, Wernette, Adam C, additional, Wykle, Maxine E, additional, Zavala-Arellano, Elizabeth, additional, McDonald, Mitchell J, additional, Ostby, Kristine, additional, Wendland, Peter, additional, DiAngelo, Justin R, additional, Ceasrine, Alexis M, additional, Cox, Amanda H, additional, Docherty, James E B, additional, Gingras, Robert M, additional, Grieb, Stephanie M, additional, Pavia, Michael J, additional, Personius, Casey L, additional, Polak, Grzegorz L, additional, Beach, Dale L, additional, Cerritos, Heaven L, additional, Horansky, Edward A, additional, Sharif, Karim A, additional, Moran, Ryan, additional, Parrish, Susan, additional, Bickford, Kirsten, additional, Bland, Jennifer, additional, Broussard, Juliana, additional, Campbell, Kerry, additional, Deibel, Katelynn E, additional, Forka, Richard, additional, Lemke, Monika C, additional, Nelson, Marlee B, additional, O'Keeffe, Catherine, additional, Ramey, S Mariel, additional, Schmidt, Luke, additional, Villegas, Paola, additional, Jones, Christopher J, additional, Christ, Stephanie L, additional, Mamari, Sami, additional, Rinaldi, Adam S, additional, Stity, Ghazal, additional, Hark, Amy T, additional, Scheuerman, Mark, additional, Silver Key, S Catherine, additional, McRae, Briana D, additional, Haberman, Adam S, additional, Asinof, Sam, additional, Carrington, Harriette, additional, Drumm, Kelly, additional, Embry, Terrance, additional, McGuire, Richard, additional, Miller-Foreman, Drew, additional, Rosen, Stella, additional, Safa, Nadia, additional, Schultz, Darrin, additional, Segal, Matt, additional, Shevin, Yakov, additional, Svoronos, Petros, additional, Vuong, Tam, additional, Skuse, Gary, additional, Paetkau, Don W, additional, Bridgman, Rachael K, additional, Brown, Charlotte M, additional, Carroll, Alicia R, additional, Gifford, Francesca M, additional, Gillespie, Julie Beth, additional, Herman, Susan E, additional, Holtcamp, Krystal L, additional, Host, Misha A, additional, Hussey, Gabrielle, additional, Kramer, Danielle M, additional, Lawrence, Joan Q, additional, Martin, Madeline M, additional, Niemiec, Ellen N, additional, O'Reilly, Ashleigh P, additional, Pahl, Olivia A, additional, Quintana, Guadalupe, additional, Rettie, Elizabeth A S, additional, Richardson, Torie L, additional, Rodriguez, Arianne E, additional, Rodriguez, Mona O, additional, Schiraldi, Laura, additional, Smith, Joanna J, additional, Sugrue, Kelsey F, additional, Suriano, Lindsey J, additional, Takach, Kaitlyn E, additional, Vasquez, Arielle M, additional, Velez, Ximena, additional, Villafuerte, Elizabeth J, additional, Vives, Laura T, additional, Zellmer, Victoria R, additional, Hauke, Jeanette, additional, Hauser, Charles R, additional, Barker, Karolyn, additional, Cannon, Laurie, additional, Parsamian, Perouza, additional, Parsons, Samantha, additional, Wichman, Zachariah, additional, Bazinet, Christopher W, additional, Johnson, Diana E, additional, Bangura, Abubakarr, additional, Black, Jordan A, additional, Chevee, Victoria, additional, Einsteen, Sarah A, additional, Hilton, Sarah K, additional, Kollmer, Max, additional, Nadendla, Rahul, additional, Stamm, Joyce, additional, Fafara-Thompson, Antoinette E, additional, Gygi, Amber M, additional, Ogawa, Emmy E, additional, Van Camp, Matt, additional, Kocsisova, Zuzana, additional, Leatherman, Judith L, additional, Modahl, Cassie M, additional, Rubin, Michael R, additional, Apiz-Saab, Susana S, additional, Arias-Mejias, Suzette M, additional, Carrion-Ortiz, Carlos F, additional, Claudio-Vazquez, Patricia N, additional, Espada-Green, Debbie M, additional, Feliciano-Camacho, Marium, additional, Gonzalez-Bonilla, Karina M, additional, Taboas-Arroyo, Mariela, additional, Vargas-Franco, Dorianmarie, additional, Montañez-Gonzalez, Raquel, additional, Perez-Otero, Joseph, additional, Rivera-Burgos, Myrielis, additional, Rivera-Rosario, Francisco J, additional, Eisler, Heather L, additional, Alexander, Jackie, additional, Begley, Samatha K, additional, Gabbard, Deana, additional, Allen, Robert J, additional, Aung, Wint Yan, additional, Barshop, William D, additional, Boozalis, Amanda, additional, Chu, Vanessa P, additional, Davis, Jeremy S, additional, Duggal, Ryan N, additional, Franklin, Robert, additional, Gavinski, Katherine, additional, Gebreyesus, Heran, additional, Gong, Henry Z, additional, Greenstein, Rachel A, additional, Guo, Averill D, additional, Hanson, Casey, additional, Homa, Kaitlin E, additional, Hsu, Simon C, additional, Huang, Yi, additional, Huo, Lucy, additional, Jacobs, Sarah, additional, Jia, Sasha, additional, Jung, Kyle L, additional, Wai-Chee Kong, Sarah, additional, Kroll, Matthew R, additional, Lee, Brandon M, additional, Lee, Paul F, additional, Levine, Kevin M, additional, Li, Amy S, additional, Liu, Chengyu, additional, Liu, Max Mian, additional, Lousararian, Adam P, additional, Lowery, Peter B, additional, Mallya, Allyson P, additional, Marcus, Joseph E, additional, Ng, Patrick C, additional, Nguyen, Hien P, additional, Patel, Ruchik, additional, Precht, Hashini, additional, Rastogi, Suchita, additional, Sarezky, Jonathan M, additional, Schefkind, Adam, additional, Schultz, Michael B, additional, Shen, Delia, additional, Skorupa, Tara, additional, Spies, Nicholas C, additional, Stancu, Gabriel, additional, Vivian Tsang, Hiu Man, additional, Turski, Alice L, additional, Venkat, Rohit, additional, Waldman, Leah E, additional, Wang, Kaidi, additional, Wang, Tracy, additional, Wei, Jeffrey W, additional, Wu, Dennis Y, additional, Xiong, David D, additional, Yu, Jack, additional, Zhou, Karen, additional, McNeil, Gerard P, additional, Fernandez, Robert W, additional, Menzies, Patrick Gomez, additional, Gu, Tingting, additional, Buhler, Jeremy, additional, Mardis, Elaine R, additional, and Elgin, Sarah C R, additional

Published
2017
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34. Discovery and genotyping of structural variation from long-read haploid genome sequence data

Author

Huddleston, John, primary, Chaisson, Mark J.P., additional, Steinberg, Karyn Meltz, additional, Warren, Wes, additional, Hoekzema, Kendra, additional, Gordon, David, additional, Graves-Lindsay, Tina A., additional, Munson, Katherine M., additional, Kronenberg, Zev N., additional, Vives, Laura, additional, Peluso, Paul, additional, Boitano, Matthew, additional, Chin, Chen-Shin, additional, Korlach, Jonas, additional, Wilson, Richard K., additional, and Eichler, Evan E., additional

Published
2016
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35. De novo genic mutations among a Chinese autism spectrum disorder cohort

Author

Wang, Tianyun, primary, Guo, Hui, additional, Xiong, Bo, additional, Stessman, Holly A.F., additional, Wu, Huidan, additional, Coe, Bradley P., additional, Turner, Tychele N., additional, Liu, Yanling, additional, Zhao, Wenjing, additional, Hoekzema, Kendra, additional, Vives, Laura, additional, Xia, Lu, additional, Tang, Meina, additional, Ou, Jianjun, additional, Chen, Biyuan, additional, Shen, Yidong, additional, Xun, Guanglei, additional, Long, Min, additional, Lin, Janice, additional, Kronenberg, Zev N., additional, Peng, Yu, additional, Bai, Ting, additional, Li, Honghui, additional, Ke, Xiaoyan, additional, Hu, Zhengmao, additional, Zhao, Jingping, additional, Zou, Xiaobing, additional, Xia, Kun, additional, and Eichler, Evan E., additional

Published
2016
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36. Excess of rare, inherited truncating mutations in autism

Author

Krumm, Niklas, primary, Turner, Tychele N, additional, Baker, Carl, additional, Vives, Laura, additional, Mohajeri, Kiana, additional, Witherspoon, Kali, additional, Raja, Archana, additional, Coe, Bradley P, additional, Stessman, Holly A, additional, He, Zong-Xiao, additional, Leal, Suzanne M, additional, Bernier, Raphael, additional, and Eichler, Evan E, additional

Published
2015
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38. Whole-Genome Sequencing of Individuals from a Founder Population Identifies Candidate Genes for Asthma

Author

Campbell, Catarina D., primary, Mohajeri, Kiana, additional, Malig, Maika, additional, Hormozdiari, Fereydoun, additional, Nelson, Benjamin, additional, Du, Gaixin, additional, Patterson, Kristen M., additional, Eng, Celeste, additional, Torgerson, Dara G., additional, Hu, Donglei, additional, Herman, Catherine, additional, Chong, Jessica X., additional, Ko, Arthur, additional, O'Roak, Brian J., additional, Krumm, Niklas, additional, Vives, Laura, additional, Lee, Choli, additional, Roth, Lindsey A., additional, Rodriguez-Cintron, William, additional, Rodriguez-Santana, Jose, additional, Brigino-Buenaventura, Emerita, additional, Davis, Adam, additional, Meade, Kelley, additional, LeNoir, Michael A., additional, Thyne, Shannon, additional, Jackson, Daniel J., additional, Gern, James E., additional, Lemanske, Robert F., additional, Shendure, Jay, additional, Abney, Mark, additional, Burchard, Esteban G., additional, Ober, Carole, additional, and Eichler, Evan E., additional

Published
2014
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39. Accelerated exon evolution within primate segmental duplications

Author

Lorente-Galdós, Belén, Bleyhl, Jonathan, Santpere, Gabriel, Vives, Laura, Ramírez, Óscar, Hernandez, Jessica, Anglada, Roger, Cooper, Gregory M, Navarro, Arcadi, Eichler, Evan E., Marqués-Bonet, Tomàs, Lorente-Galdós, Belén, Bleyhl, Jonathan, Santpere, Gabriel, Vives, Laura, Ramírez, Óscar, Hernandez, Jessica, Anglada, Roger, Cooper, Gregory M, Navarro, Arcadi, Eichler, Evan E., and Marqués-Bonet, Tomàs

Abstract

[Background] The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies and to the methodological reliance on accurate gene trees, which are difficult to obtain for duplicated genes., [Results] In this work, we detected exons with an accumulation of high-quality nucleotide differences between the human assembly and shotgun sequencing reads from single human and macaque individuals. Comparing the observed rates of nucleotide differences between coding exons and their flanking intronic sequences with a likelihood-ratio test, we identified 74 exons with evidence for rapid coding sequence evolution during the evolution of humans and Old World monkeys. Fifty-five percent of rapidly evolving exons were either partially or totally duplicated, which is a significant enrichment of the 6% rate observed across all human coding exons., [Conclusions] Our results provide a more comprehensive view of the action of selection upon segmental duplications, which are the most complex regions of our genomes. In light of these findings, we suggest that segmental duplications could be subjected to rapid evolution more frequently than previously thought.

Published
2013

41. The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Author

National Institutes of Health (US), Howard Hughes Medical Institute, Ventura, Mario, Catacchio, Claudia R., Sajjadian, Saba, Vives, Laura, Sudmant, Peter H., Marqués-Bonet, Tomàs, Graves, Tina A., Wilson, Richard K., Eichler, Evan E., National Institutes of Health (US), Howard Hughes Medical Institute, Ventura, Mario, Catacchio, Claudia R., Sajjadian, Saba, Vives, Laura, Sudmant, Peter H., Marqués-Bonet, Tomàs, Graves, Tina A., Wilson, Richard K., and Eichler, Evan E.

Abstract

Chimpanzee and gorilla chromosomes differ from human chromosomes by the presence of large blocks of subterminal heterochromatin thought to be composed primarily of arrays of tandem satellite sequence. We explore their sequence composition and organization and show a complex organization composed of specific sets of segmental duplications that have hyperexpanded in concert with the formation of subterminal satellites. These regions are highly copy number polymorphic between and within species, and copy number differences involving hundreds of copies can be accurately estimated by assaying read-depth of next-generation sequencing data sets. Phylogenetic and comparative genomic analyses suggest that the structures have arisen largely independently in the two lineages with the exception of a few seed sequences present in the common ancestor of humans and African apes. We propose a model where an ancestral human-chimpanzee pericentric inversion and the ancestral chromosome 2 fusion both predisposed and protected the chimpanzee and human genomes, respectively, to the formation of subtelomeric heterochromatin. Our findings highlight the complex interplay between duplicated sequences and chromosomal rearrangements that rapidly alter the cytogenetic landscape in a short period of evolutionary time.

Published
2012

46. Accelerated exon evolution within primate segmental duplications

Author

Lorente-Galdos, Belen, primary, Bleyhl, Jonathan, additional, Santpere, Gabriel, additional, Vives, Laura, additional, Ramírez, Oscar, additional, Hernandez, Jessica, additional, Anglada, Roger, additional, Cooper, Gregory M, additional, Navarro, Arcadi, additional, Eichler, Evan E, additional, and Marques-Bonet, Tomas, additional

Published
2013
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47. Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

Author

O’Roak, Brian J., primary, Vives, Laura, additional, Fu, Wenqing, additional, Egertson, Jarrett D., additional, Stanaway, Ian B., additional, Phelps, Ian G., additional, Carvill, Gemma, additional, Kumar, Akash, additional, Lee, Choli, additional, Ankenman, Katy, additional, Munson, Jeff, additional, Hiatt, Joseph B., additional, Turner, Emily H., additional, Levy, Roie, additional, O’Day, Diana R., additional, Krumm, Niklas, additional, Coe, Bradley P., additional, Martin, Beth K., additional, Borenstein, Elhanan, additional, Nickerson, Deborah A., additional, Mefford, Heather C., additional, Doherty, Dan, additional, Akey, Joshua M., additional, Bernier, Raphael, additional, Eichler, Evan E., additional, and Shendure, Jay, additional

Published
2012
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48. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

Author

O’Roak, Brian J., primary, Vives, Laura, additional, Girirajan, Santhosh, additional, Karakoc, Emre, additional, Krumm, Niklas, additional, Coe, Bradley P., additional, Levy, Roie, additional, Ko, Arthur, additional, Lee, Choli, additional, Smith, Joshua D., additional, Turner, Emily H., additional, Stanaway, Ian B., additional, Vernot, Benjamin, additional, Malig, Maika, additional, Baker, Carl, additional, Reilly, Beau, additional, Akey, Joshua M., additional, Borenstein, Elhanan, additional, Rieder, Mark J., additional, Nickerson, Deborah A., additional, Bernier, Raphael, additional, Shendure, Jay, additional, and Eichler, Evan E., additional

Published
2012
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49. Erratum: Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

Author

O'Roak, Brian J, primary, Deriziotis, Pelagia, additional, Lee, Choli, additional, Vives, Laura, additional, Schwartz, Jerrod J, additional, Girirajan, Santhosh, additional, Karakoc, Emre, additional, MacKenzie, Alexandra P, additional, Ng, Sarah B, additional, Baker, Carl, additional, Rieder, Mark J, additional, Nickerson, Deborah A, additional, Bernier, Raphael, additional, Fisher, Simon E, additional, Shendure, Jay, additional, and Eichler, Evan E, additional

Published
2012
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