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Your search keyword '"Macarthur, Daniel G."' showing total 12 results
Start Over Author "Macarthur, Daniel G." Journal nature genetics
12 results on '"Macarthur, Daniel G."'

3. Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy

Author

Töpf, Ana, Cox, Dan, Zaharieva, Irina T., Di Leo, Valeria, Sarparanta, Jaakko, Jonson, Per Harald, Sealy, Ian M., Smolnikov, Andrei, White, Richard J., Vihola, Anna, Savarese, Marco, Merteroglu, Munise, Wali, Neha, Laricchia, Kristen M., Venturini, Cristina, Vroling, Bas, Stenton, Sarah L., Cummings, Beryl B., Harris, Elizabeth, Marini-Bettolo, Chiara, Diaz-Manera, Jordi, Henderson, Matt, Barresi, Rita, Duff, Jennifer, England, Eleina M., Patrick, Jane, Al-Husayni, Sundos, Biancalana, Valerie, Beggs, Alan H., Bodi, Istvan, Bommireddipalli, Shobhana, Bönnemann, Carsten G., Cairns, Anita, Chiew, Mei-Ting, Claeys, Kristl G., Cooper, Sandra T., Davis, Mark R., Donkervoort, Sandra, Erasmus, Corrie E., Fassad, Mahmoud R., Genetti, Casie A., Grosmann, Carla, Jungbluth, Heinz, Kamsteeg, Erik-Jan, Lornage, Xavière, Löscher, Wolfgang N., Malfatti, Edoardo, Manzur, Adnan, Martí, Pilar, Mongini, Tiziana E., Muelas, Nuria, Nishikawa, Atsuko, O’Donnell-Luria, Anne, Ogonuki, Narumi, O’Grady, Gina L., O’Heir, Emily, Paquay, Stéphanie, Phadke, Rahul, Pletcher, Beth A., Romero, Norma B., Schouten, Meyke, Shah, Snehal, Smuts, Izelle, Sznajer, Yves, Tasca, Giorgio, Taylor, Robert W., Tuite, Allysa, Van den Bergh, Peter, VanNoy, Grace, Voermans, Nicol C., Wanschitz, Julia V., Wraige, Elizabeth, Yoshimura, Kimihiko, Oates, Emily C., Nakagawa, Osamu, Nishino, Ichizo, Laporte, Jocelyn, Vilchez, Juan J., MacArthur, Daniel G., Sarkozy, Anna, Cordell, Heather J., Udd, Bjarne, Busch-Nentwich, Elisabeth M., Muntoni, Francesco, and Straub, Volker

Published
2024
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4. Inferring compound heterozygosity from large-scale exome sequencing data

Author

Guo, Michael H., Francioli, Laurent C., Stenton, Sarah L., Goodrich, Julia K., Watts, Nicholas A., Singer-Berk, Moriel, Groopman, Emily, Darnowsky, Philip W., Solomonson, Matthew, Baxter, Samantha, Tiao, Grace, Neale, Benjamin M., Hirschhorn, Joel N., Rehm, Heidi L., Daly, Mark J., O’Donnell-Luria, Anne, Karczewski, Konrad J., MacArthur, Daniel G., and Samocha, Kaitlin E.

Published
2024
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5. Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples

Author

Kosmicki, Jack A, Samocha, Kaitlin E, Howrigan, Daniel P, Sanders, Stephan J, Slowikowski, Kamil, Lek, Monkol, Karczewski, Konrad J, Cutler, David J, Devlin, Bernie, Roeder, Kathryn, Buxbaum, Joseph D, Neale, Benjamin M, MacArthur, Daniel G, Wall, Dennis P, Robinson, Elise B, and Daly, Mark J

Subjects
Biological Sciences, Genetics, 2.1 Biological and endogenous factors, Autism Spectrum Disorder, Exome, Genetic Predisposition to Disease, Genetic Variation, Humans, Intellectual Disability, Neurodevelopmental Disorders, Phenotype, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Recent research has uncovered an important role for de novo variation in neurodevelopmental disorders. Using aggregated data from 9,246 families with autism spectrum disorder, intellectual disability, or developmental delay, we found that ∼1/3 of de novo variants are independently present as standing variation in the Exome Aggregation Consortium's cohort of 60,706 adults, and these de novo variants do not contribute to neurodevelopmental risk. We further used a loss-of-function (LoF)-intolerance metric, pLI, to identify a subset of LoF-intolerant genes containing the observed signal of associated de novo protein-truncating variants (PTVs) in neurodevelopmental disorders. LoF-intolerant genes also carry a modest excess of inherited PTVs, although the strongest de novo-affected genes contribute little to this excess, thus suggesting that the excess of inherited risk resides in lower-penetrant genes. These findings illustrate the importance of population-based reference cohorts for the interpretation of candidate pathogenic variants, even for analyses of complex diseases and de novo variation.

Published
2017

8. A framework for the interpretation of de novo mutation in human disease

Author

Samocha, Kaitlin E, Robinson, Elise B, Sanders, Stephan J, Stevens, Christine, Sabo, Aniko, McGrath, Lauren M, Kosmicki, Jack A, Rehnström, Karola, Mallick, Swapan, Kirby, Andrew, Wall, Dennis P, MacArthur, Daniel G, Gabriel, Stacey B, DePristo, Mark, Purcell, Shaun M, Palotie, Aarno, Boerwinkle, Eric, Buxbaum, Joseph D, Cook, Jr, Edwin H, Gibbs, Richard A, Schellenberg, Gerard D, Sutcliffe, James S, Devlin, Bernie, Roeder, Kathryn, Neale, Benjamin M, and Daly, Mark J

Published
2014
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9. Inferring compound heterozygosity from large-scale exome sequencing data

Author

Guo, Michael H., Francioli, Laurent C., Stenton, Sarah L., Goodrich, Julia K., Watts, Nicholas A., Singer-Berk, Moriel, Groopman, Emily, Darnowsky, Philip W., Solomonson, Matthew, Baxter, Samantha, Tiao, Grace, Neale, Benjamin M., Hirschhorn, Joel N., Rehm, Heidi L., Daly, Mark J., O’Donnell-Luria, Anne, Karczewski, Konrad J., MacArthur, Daniel G., and Samocha, Kaitlin E.

Abstract

Recessive diseases arise when both copies of a gene are impacted by a damaging genetic variant. When a patient carries two potentially causal variants in a gene, accurate diagnosis requires determining that these variants occur on different copies of the chromosome (that is, are in trans) rather than on the same copy (that is, in cis). However, current approaches for determining phase, beyond parental testing, are limited in clinical settings. Here we developed a strategy for inferring phase for rare variant pairs within genes, leveraging genotypes observed in the Genome Aggregation Database (v2, n= 125,748 exomes). Our approach estimates phase with 96% accuracy, both in trio data and in patients with Mendelian conditions and presumed causal compound heterozygous variants. We provide a public resource of phasing estimates for coding variants and counts per gene of rare variants in transthat can aid interpretation of rare co-occurring variants in the context of recessive disease.

Published
2023
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10. Reply to ‘Selective effects of heterozygous protein-truncating variants’

Author

Cassa, Christopher A., primary, Weghorn, Donate, additional, Balick, Daniel J., additional, Jordan, Daniel M., additional, Nusinow, David, additional, Samocha, Kaitlin E., additional, O’Donnell-Luria, Anne, additional, MacArthur, Daniel G., additional, Daly, Mark J., additional, Beier, David R., additional, and Sunyaev, Shamil R., additional

Published
2018
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11. Loss of ACTN3 gene function alters mouse muscle metabolism and shows evidence of positive selection in humans

Author

MacArthur, Daniel G, primary, Seto, Jane T, additional, Raftery, Joanna M, additional, Quinlan, Kate G, additional, Huttley, Gavin A, additional, Hook, Jeff W, additional, Lemckert, Frances A, additional, Kee, Anthony J, additional, Edwards, Michael R, additional, Berman, Yemima, additional, Hardeman, Edna C, additional, Gunning, Peter W, additional, Easteal, Simon, additional, Yang, Nan, additional, and North, Kathryn N, additional

Published
2007
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12. Patterns of genic intolerance of rare copy number variation in 59,898 human exomes

Author

Ruderfer, Douglas M, Hamamsy, Tymor, Lek, Monkol, Karczewski, Konrad J, Kavanagh, David, Samocha, Kaitlin E, Daly, Mark J, MacArthur, Daniel G, Fromer, Menachem, and Purcell, Shaun M

Abstract

Copy number variation (CNV) affecting protein-coding genes contributes substantially to human diversity and disease. Here we characterized the rates and properties of rare genic CNVs (<0.5% frequency) in exome sequencing data from nearly 60,000 individuals in the Exome Aggregation Consortium (ExAC) database. On average, individuals possessed 0.81 deleted and 1.75 duplicated genes, and most (70%) carried at least one rare genic CNV. For every gene, we empirically estimated an index of relative intolerance to CNVs that demonstrated moderate correlation with measures of genic constraint based on single-nucleotide variation (SNV) and was independently correlated with measures of evolutionary conservation. For individuals with schizophrenia, genes affected by CNVs were more intolerant than in controls. The ExAC CNV data constitute a critical component of an integrated database spanning the spectrum of human genetic variation, aiding in the interpretation of personal genomes as well as population-based disease studies. These data are freely available for download and visualization online.

Published
2016
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