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1. Federated analysis of autosomal recessive coding variants in 29,745 developmental disorder patients from diverse populations

Author

Chundru, V. Kartik, Zhang, Zhancheng, Walter, Klaudia, Lindsay, Sarah J., Danecek, Petr, Eberhardt, Ruth Y., Gardner, Eugene J., Malawsky, Daniel S., Wigdor, Emilie M., Torene, Rebecca, Retterer, Kyle, Wright, Caroline F., Ólafsdóttir, Hildur, Guillen Sacoto, Maria J., Ayaz, Akif, Akbeyaz, Ismail Hakki, Türkdoğan, Dilşad, Al Balushi, Aaisha Ibrahim, Bertoli-Avella, Aida, Bauer, Peter, Szenker-Ravi, Emmanuelle, Reversade, Bruno, McWalter, Kirsty, Sheridan, Eamonn, Firth, Helen V., Hurles, Matthew E., Samocha, Kaitlin E., Ustach, Vincent D., and Martin, Hilary C.

Published
2024
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5. Evidence for 28 genetic disorders discovered by combining healthcare and research data

Author

Kaplanis, Joanna, Samocha, Kaitlin E., Wiel, Laurens, Zhang, Zhancheng, Arvai, Kevin J., Eberhardt, Ruth Y., and Gallone, Giuseppe

Subjects
Genetic disorders -- Discovery and exploration, Medical research -- Usage, Medicine, Experimental -- Usage, Medical statistics -- Usage, Evidence-based medicine -- Analysis, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

De novo mutations in protein-coding genes are a well-established cause of developmental disorders.sup.1. However, genes known to be associated with developmental disorders account for only a minority of the observed excess of such de novo mutations.sup.1,2. Here, to identify previously undescribed genes associated with developmental disorders, we integrate healthcare and research exome-sequence data from 31,058 parent-offspring trios of individuals with developmental disorders, and develop a simulation-based statistical test to identify gene-specific enrichment of de novo mutations. We identified 285 genes that were significantly associated with developmental disorders, including 28 that had not previously been robustly associated with developmental disorders. Although we detected more genes associated with developmental disorders, much of the excess of de novo mutations in protein-coding genes remains unaccounted for. Modelling suggests that more than 1,000 genes associated with developmental disorders have not yet been described, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of genes associated with developmental disorders. By integrating healthcare and exome-sequencing data from parent-offspring trios of patients with developmental disorders, 28 genes that had not previously been associated with developmental disorders were identified., Author(s): Joanna Kaplanis [sup.1] , Kaitlin E. Samocha [sup.1] , Laurens Wiel [sup.2] [sup.3] , Zhancheng Zhang [sup.4] , Kevin J. Arvai [sup.4] , Ruth Y. Eberhardt [sup.1] , Giuseppe [...]

Published
2020
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6. Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase

Author

Sheydina, Anna, Eberhardt, Ruth Y, Rigden, Daniel J, Chang, Yuanyuan, Li, Zhanwen, Zmasek, Christian C, Axelrod, Herbert L, and Godzik, Adam

Subjects
Genetics, Biotechnology, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Amino Acid Sequence, Bacterial Proteins, Bacteroides, Computational Biology, Gastrointestinal Tract, Genomics, Glycoside Hydrolases, Humans, Protein Structure, Tertiary, Glycoside hydrolase, Carbohydrate metabolism, 3D structure, Protein family, Protein function prediction, Domain of unknown function, DUF, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundBacteroides spp. form a significant part of our gut microbiome and are well known for optimized metabolism of diverse polysaccharides. Initial analysis of the archetypal Bacteroides thetaiotaomicron genome identified 172 glycosyl hydrolases and a large number of uncharacterized proteins associated with polysaccharide metabolism.ResultsBT_1012 from Bacteroides thetaiotaomicron VPI-5482 is a protein of unknown function and a member of a large protein family consisting entirely of uncharacterized proteins. Initial sequence analysis predicted that this protein has two domains, one on the N- and one on the C-terminal. A PSI-BLAST search found over 150 full length and over 90 half size homologs consisting only of the N-terminal domain. The experimentally determined three-dimensional structure of the BT_1012 protein confirms its two-domain architecture and structural analysis of both domains suggests their specific functions. The N-terminal domain is a putative catalytic domain with significant similarity to known glycoside hydrolases, the C-terminal domain has a beta-sandwich fold typically found in C-terminal domains of other glycosyl hydrolases, however these domains are typically involved in substrate binding. We describe the structure of the BT_1012 protein and discuss its sequence-structure relationship and their possible functional implications.ConclusionsStructural and sequence analyses of the BT_1012 protein identifies it as a glycosyl hydrolase, expanding an already impressive catalog of enzymes involved in polysaccharide metabolism in Bacteroides spp. Based on this we have renamed the Pfam families representing the two domains found in the BT_1012 protein, PF13204 and PF12904, as putative glycoside hydrolase and glycoside hydrolase-associated C-terminal domain respectively.

Published
2014

7. Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase

Author

Rigden, Daniel J, Eberhardt, Ruth Y, Gilbert, Harry J, Xu, Qingping, Chang, Yuanyuan, and Godzik, Adam

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Bacteroides, Biocatalysis, Glycoside Hydrolases, Models, Molecular, Phylogeny, Protein Structure, Tertiary, Structural Homology, Protein, Carbohydrate metabolism, Glycoside hydrolase, Polysaccharide Utilization Locus, PUL, Protein function prediction, JCSG, 3D structure, Protein family, Gut microbiota, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences
Abstract

BackgroundGut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. Proteins containing the GxGYxYP domain are over-represented in the gut microbiota, and are found in Polysaccharide Utilization Loci in the gut symbiont Bacteroides thetaiotaomicron, suggesting their involvement in polysaccharide metabolism, but little else is known of the function of this domain.ResultsGenomic context and domain architecture analyses support a role for the GxGYxYP domain in carbohydrate metabolism. Sparse occurrences in eukaryotes are the result of lateral gene transfer. The structure of the GxGYxYP domain-containing protein encoded by the BT2193 locus reveals two structural domains, the first composed of three divergent repeats with no recognisable homology to previously solved structures, the second a more familiar seven-stranded β/α barrel. Structure-based analyses including conservation mapping localise a presumed functional site to a cleft between the two domains of BT2193. Matching to a catalytic site template from a GH9 cellulase and other analyses point to a putative catalytic triad composed of Glu272, Asp331 and Asp333.ConclusionsWe suggest that GxGYxYP-containing proteins constitute a novel glycoside hydrolase family of as yet unknown specificity.

Published
2014

8. LUD, a new protein domain associated with lactate utilization

Author

Hwang, William C, Bakolitsa, Constantina, Punta, Marco, Coggill, Penelope C, Bateman, Alex, Axelrod, Herbert L, Rawlings, Neil D, Sedova, Mayya, Peterson, Scott N, Eberhardt, Ruth Y, Aravind, L, Pascual, Jaime, and Godzik, Adam

Subjects
Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Amino Acid Sequence, Bacterial Proteins, Crystallography, X-Ray, Deinococcus, Humans, Lactic Acid, Microbiota, Molecular Sequence Data, Protein Structure, Tertiary, LUD, DUF162, LutB, LutC, Domain of unknown function, Deinococcus radiodurans, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundA novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactate utilization in bacteria. Based on our analysis of its sequence, structure, and recent experimental evidence reported by other groups, we hereby redefine DUF162 as the LUD domain family.ResultsJCSG solved the first crystal structure [PDB:2G40] from the LUD domain family: LutC protein, encoded by ORF DR_1909, of Deinococcus radiodurans. LutC shares features with domains in the functionally diverse ISOCOT superfamily. We have observed that the LUD domain has an increased abundance in the human gut microbiome.ConclusionsWe propose a model for the substrate and cofactor binding and regulation in LUD domain. The significance of LUD-containing proteins in the human gut microbiome, and the implication of lactate metabolism in the radiation-resistance of Deinococcus radiodurans are discussed.

Published
2013

9. Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila

Author

Coggill, Penelope, Eberhardt, Ruth Y, Finn, Robert D, Chang, Yuanyuan, Jaroszewski, Lukasz, Godzik, Adam, Das, Debanu, Xu, Qingping, Axelrod, Herbert L, Aravind, L, Murzin, Alexey G, and Bateman, Alex

Subjects
Biochemistry and Cell Biology, Biological Sciences, Lung, Pneumonia & Influenza, Infectious Diseases, Pneumonia, Aetiology, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Underpinning research, Generic health relevance, Amino Acid Sequence, Bacterial Proteins, Databases, Protein, Legionella pneumophila, Molecular Sequence Data, Protein Structure, Tertiary, Sequence Alignment, Sequence Analysis, Protein, Domain of unknown function, Protein family, Protein structure, DUF4424, YARHG domain, Sequence analysis, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences
Abstract

BackgroundEvery genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying sequence and structural analysis we hope to provide insight into novel biology.ResultsWe analyze a previously uncharacterized Pfam protein family called DUF4424 [Pfam:PF14415]. The recently solved three-dimensional structure of the protein lpg2210 from Legionella pneumophila provides the first structural information pertaining to this family. This protein additionally includes the first representative structure of another Pfam family called the YARHG domain [Pfam:PF13308]. The Pfam family DUF4424 adopts a 19-stranded beta-sandwich fold that shows similarity to the N-terminal domain of leukotriene A-4 hydrolase. The YARHG domain forms an all-helical domain at the C-terminus. Structure analysis allows us to recognize distant similarities between the DUF4424 domain and individual domains of M1 aminopeptidases and tricorn proteases, which form massive proteasome-like capsids in both archaea and bacteria.ConclusionsBased on our analyses we hypothesize that the DUF4424 domain may have a role in forming large, multi-component enzyme complexes. We suggest that the YARGH domain may play a role in binding a moiety in proximity with peptidoglycan, such as a hydrophobic outer membrane lipid or lipopolysaccharide.

Published
2013

10. Prevalence of deleterious variants in MC3R in patients with constitutional delay of growth and puberty

Author

Duckett, Katie, Williamson, Alice, Kincaid, John WR, Rainbow, Kara, Corbin, Laura J, Martin, Hilary C, Eberhardt, Ruth Y, Huang, Qin Qin, Hurles, Matthew E, He, Wen, Brauner, Raja, Delaney, Angela, Dunkel, Leo, Grinspon, Romina P, Hall, Janet E, Hirschhorn, Joel N, Howard, Sasha R, Latronico, Ana C, Jorge, Alexander AL, McElreavey, Ken, Mericq, Verónica, Merino, Paulina M, Palmert, Mark R, Plummer, Lacey, Rey, Rodolfo A, Rezende, Raíssa C, Seminara, Stephanie B, Salnikov, Kathryn, Banerjee, Indraneel, Lam, Brian YH, Perry, John RB, Timpson, Nicholas J, Clayton, Peter, Chan, Yee-Ming, Ong, Ken K, O'Rahilly, Stephen, Duckett, Katie [0000-0002-0222-1689], Williamson, Alice [0000-0002-7599-9301], Kincaid, John WR [0000-0003-0660-9813], Rainbow, Kara [0000-0002-8089-0693], Corbin, Laura J [0000-0002-4032-9500], Martin, Hilary C [0000-0002-4454-9084], Eberhardt, Ruth Y [0000-0001-6152-1369], Huang, Qin Qin [0000-0003-3073-717X], Hurles, Matthew E [0000-0002-2333-7015], Brauner, Raja [0000-0002-4456-4508], Delaney, Angela [0000-0002-0632-6365], Grinspon, Romina P [0000-0002-6291-1518], Hall, Janet E [0000-0003-4644-3061], Hirschhorn, Joel N [0000-0002-1650-7901], Palmert, Mark R [0000-0002-4096-0685], Lam, Brian YH [0000-0002-3638-9025], Timpson, Nicholas J [0000-0002-7141-9189], Clayton, Peter [0000-0003-1225-4537], Chan, Yee-Ming [0000-0003-0554-8502], Ong, Ken K [0000-0003-4689-7530], O'Rahilly, Stephen [0000-0003-2199-4449], and Apollo - University of Cambridge Repository

Subjects
UK Biobank, constitutional delay, MC3R, ALSPAC, delayed puberty
Abstract

ContextThe melanocortin 3 receptor (MC3R) has recently emerged as a critical regulator of pubertal timing, linear growth and the acquisition of lean mass in humans and mice. In population-based studies, heterozygous carriers of deleterious variants in MC3R report a later onset of puberty than non-carriers. However, the frequency of such variants in patients who present with clinical disorders of pubertal development is currently unknown.ObjectiveTo determine whether deleterious MC3R variants are more frequently found in patients clinically presenting with constitutional delay of growth and puberty (CDGP) or normosmic idiopathic hypogonadotropic hypogonadism (nIHH).Design, Setting and ParticipantsWe examined the sequence of MC3R in 362 adolescents with a clinical diagnosis of CDGP and 657 patients with nIHH, experimentally characterised the signalling properties of all non-synonymous variants found and compared their frequency to that in 5774 controls from a population-based cohort. Additionally, we established the relative frequency of predicted deleterious variants in individuals with self-reported delayed vs normally timed menarche/voice breaking in the UK Biobank cohort.ResultsMC3R loss-of-function variants were infrequent but overrepresented in patients with CDGP (8/362 (2.2%), OR = 4.17, p = 0.001). There was no strong evidence of overrepresentation in patients with nIHH (4/657 (0.6%), OR = 1.15, p = 0.779). In 246,328 women from UK Biobank, predicted deleterious variants were more frequently found in those self-reporting delayed (≥16 years) vs normal age at menarche (OR = 1.66, p = 3.90E-07).ConclusionsWe have found evidence that functionally damaging variants in MC3R are overrepresented in individuals with CDGP but are not a common cause of this phenotype.

Published
2023
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12. Federated analysis of the contribution of recessive coding variants to 29,745 developmental disorder patients from diverse populations

Author

Chundru, V. Kartik, primary, Zhang, Zhancheng, additional, Walter, Klaudia, additional, Lindsay, Sarah, additional, Danecek, Petr, additional, Eberhardt, Ruth Y., additional, Gardner, Eugene J., additional, Malawsky, Daniel S., additional, Wigdor, Emilie M., additional, Torene, Rebecca, additional, Retterer, Kyle, additional, Wright, Caroline F., additional, McWalter, Kirsty, additional, Sheridan, Eamonn, additional, Firth, Helen V., additional, Hurles, Matthew E., additional, Samocha, Kaitlin E., additional, Ustach, Vincent D., additional, and Martin, Hilary C., additional

Published
2023
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13. Prevalence of Deleterious Variants in MC3R in Patients With Constitutional Delay of Growth and Puberty

Author

Duckett, Katie, primary, Williamson, Alice, additional, Kincaid, John W R, additional, Rainbow, Kara, additional, Corbin, Laura J, additional, Martin, Hilary C, additional, Eberhardt, Ruth Y, additional, Huang, Qin Qin, additional, Hurles, Matthew E, additional, He, Wen, additional, Brauner, Raja, additional, Delaney, Angela, additional, Dunkel, Leo, additional, Grinspon, Romina P, additional, Hall, Janet E, additional, Hirschhorn, Joel N, additional, Howard, Sasha R, additional, Latronico, Ana C, additional, Jorge, Alexander A L, additional, McElreavey, Ken, additional, Mericq, Verónica, additional, Merino, Paulina M, additional, Palmert, Mark R, additional, Plummer, Lacey, additional, Rey, Rodolfo A, additional, Rezende, Raíssa C, additional, Seminara, Stephanie B, additional, Salnikov, Kathryn, additional, Banerjee, Indraneel, additional, Lam, Brian Y H, additional, Perry, John R B, additional, Timpson, Nicholas J, additional, Clayton, Peter, additional, Chan, Yee-Ming, additional, Ong, Ken K, additional, and O’Rahilly, Stephen, additional

Published
2023
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15. Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland

Author

Wright, Caroline F., primary, Campbell, Patrick, additional, Eberhardt, Ruth Y., additional, Aitken, Stuart, additional, Perrett, Daniel, additional, Brent, Simon, additional, Danecek, Petr, additional, Gardner, Eugene J., additional, Chundru, V. Kartik, additional, Lindsay, Sarah J., additional, Andrews, Katrina, additional, Hampstead, Juliet, additional, Kaplanis, Joanna, additional, Samocha, Kaitlin E., additional, Middleton, Anna, additional, Foreman, Julia, additional, Hobson, Rachel J., additional, Parker, Michael J., additional, Martin, Hilary C., additional, FitzPatrick, David R., additional, Hurles, Matthew E., additional, and Firth, Helen V., additional

Published
2023
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16. Optimizing the Diagnosis of Rare Genomic Disease in the UK and Ireland

Author

Wright, Caroline F, Campbell, Patrick, Eberhardt, Ruth Y., Aitken, Stuart, Perrett, Daniel, Brent, Simon, Danecek, Petr, Gardner, Eugene J., Chundru, V Kartik, Lindsay, Sarah J, Andrews, Katrina A, Hampstead, Juliet, Kaplanis, Joanna, Samocha, Kaitlin E., Middleton, Anna, Foreman, Julia, Hobson, Rachel J., Parker, Michael J., Martin, Hilary C, FitzPatrick, David R, Hurles, Matthew E, and Firth, Helen V.

Published
2023

17. Prenatal Exome Sequencing Analysis in Fetal Structural Anomalies Detected by Ultrasonography (PAGE): A Cohort Study

Author

Lord, Jenny, McMullan, Dominic J., Eberhardt, Ruth Y., Rinck, Gabriele, Hamilton, Susan J., Quinlan-Jones, Elizabeth, Prigmore, Elena, Keelagher, Rebecca, Best, Sunayna K., Carey, Georgina K., Mellis, Rhiannon, Robart, Sarah, Berry, Ian R., Chandler, Kate E., Cilliers, Deirdre, Cresswell, Lara, Edwards, Sandra L., Gardiner, Carol, Henderson, Alex, Holden, Simon T., Homfray, Tessa, Lester, Tracy, Lewis, Rebecca A., Newbury-Ecob, Ruth, Prescott, Katrina, Quarrell, Oliver W., Ramsden, Simon C., Roberts, Eileen, Tapon, Dagmar, Tooley, Madeleine J., Vasudevan, Pradeep C., Weber, Astrid P., Wellesley, Diana G., Westwood, Paul, White, Helen, Parker, Michael, Williams, Denise, Jenkins, Lucy, Scott, Richard H., Kilby, Mark D., Chitty, Lyn S., Hurles, Matthew E., and Maher, Eamonn R.

Published
2019
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18. Prevalence of Deleterious Variants in MC3Rin Patients With Constitutional Delay of Growth and Puberty

Author

Duckett, Katie, Williamson, Alice, Kincaid, John W R, Rainbow, Kara, Corbin, Laura J, Martin, Hilary C, Eberhardt, Ruth Y, Huang, Qin Qin, Hurles, Matthew E, He, Wen, Brauner, Raja, Delaney, Angela, Dunkel, Leo, Grinspon, Romina P, Hall, Janet E, Hirschhorn, Joel N, Howard, Sasha R, Latronico, Ana C, Jorge, Alexander A L, McElreavey, Ken, Mericq, Verónica, Merino, Paulina M, Palmert, Mark R, Plummer, Lacey, Rey, Rodolfo A, Rezende, Raíssa C, Seminara, Stephanie B, Salnikov, Kathryn, Banerjee, Indraneel, Lam, Brian Y H, Perry, John R B, Timpson, Nicholas J, Clayton, Peter, Chan, Yee-Ming, Ong, Ken K, and O’Rahilly, Stephen

Published
2023
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19. Optimising diagnostic yield in highly penetrant genomic disease

Author

Wright, Caroline F., primary, Campbell, Patrick, additional, Eberhardt, Ruth Y., additional, Aitken, Stuart, additional, Perrett, Daniel, additional, Brent, Simon, additional, Danecek, Petr, additional, Gardner, Eugene J., additional, Chundru, V. Kartik, additional, Lindsay, Sarah J., additional, Andrews, Katrina, additional, Hampstead, Juliet, additional, Kaplanis, Joanna, additional, Samocha, Kaitlin E., additional, Middleton, Anna, additional, Foreman, Julia, additional, Hobson, Rachel J., additional, Parker, Michael J., additional, Martin, Hilary C., additional, FitzPatrick, David R., additional, Hurles, Matthew E., additional, and Firth, Helen V., additional

Published
2022
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21. The contribution of X-linked coding variation to severe developmental disorders

Author

Martin, Hilary C., Gardner, Eugene J., Samocha, Kaitlin E., Kaplanis, Joanna, Akawi, Nadia, Sifrim, Alejandro, Eberhardt, Ruth Y., Tavares, Ana Lisa Taylor, Neville, Matthew D. C., Niemi, Mari E. K., Gallone, Giuseppe, McRae, Jeremy, Wright, Caroline F., FitzPatrick, David R., Firth, Helen V., Hurles, Matthew E., Borras, Silvia, Clark, Caroline, Dean, John, Miedzybrodzka, Zosia, Ross, Alison, Tennant, Stephen, Dabir, Tabib, Donnelly, Deirdre, Humphreys, Mervyn, Magee, Alex, McConnell, Vivienne, McKee, Shane, McNerlan, Susan, Morrison, Patrick J., Rea, Gillian, Stewart, Fiona, Cole, Trevor, Cooper, Nicola, Cooper-Charles, Lisa, Cox, Helen, Islam, Lily, Jarvis, Joanna, Keelagher, Rebecca, Lim, Derek, McMullan, Dominic, Morton, Jenny, Naik, Swati, O’Driscoll, Mary, Ong, Kai-Ren, Osio, Deborah, Ragge, Nicola, Turton, Sarah, Vogt, Julie, Williams, Denise, Bodek, Simon, Donaldson, Alan, Hills, Alison, Low, Karen, Newbury-Ecob, Ruth, Norman, Andrew M., Roberts, Eileen, Scurr, Ingrid, Smithson, Sarah, Tooley, Madeleine, Abbs, Steve, Armstrong, Ruth, Dunn, Carolyn, Holden, Simon, Park, Soo-Mi, Paterson, Joan, Raymond, Lucy, Reid, Evan, Sandford, Richard, Simonic, Ingrid, Tischkowitz, Marc, Woods, Geoff, Bradley, Lisa, Comerford, Joanne, Green, Andrew, Lynch, Sally, McQuaid, Shirley, Mullaney, Brendan, Berg, Jonathan, Goudie, David, Mavrak, Eleni, McLean, Joanne, McWilliam, Catherine, Reavey, Eleanor, Azam, Tara, Cleary, Elaine, Jackson, Andrew, Lam, Wayne, Lampe, Anne, Moore, David, Porteous, Mary, Baple, Emma, Baptista, Júlia, Brewer, Carole, Castle, Bruce, Kivuva, Emma, Owens, Martina, Rankin, Julia, Shaw-Smith, Charles, Turner, Claire, Turnpenny, Peter, Tysoe, Carolyn, Bradley, Therese, Davidson, Rosemarie, Gardiner, Carol, Joss, Shelagh, Kinning, Esther, Longman, Cheryl, McGowan, Ruth, Murday, Victoria, Pilz, Daniela, Tobias, Edward, Whiteford, Margo, Williams, Nicola, Barnicoat, Angela, Clement, Emma, Faravelli, Francesca, Hurst, Jane, Jenkins, Lucy, Jones, Wendy, Kumar, V.K.Ajith, Lees, Melissa, Loughlin, Sam, Male, Alison, Morrogh, Deborah, Rosser, Elisabeth, Scott, Richard, Wilson, Louise, Beleza, Ana, Deshpande, Charu, Flinter, Frances, Holder, Muriel, Irving, Melita, Izatt, Louise, Josifova, Dragana, Mohammed, Shehla, Molenda, Aneta, Robert, Leema, Roworth, Wendy, Ruddy, Deborah, Ryten, Mina, Yau, Shu, Bennett, Christopher, Blyth, Moira, Campbell, Jennifer, Coates, Andrea, Dobbie, Angus, Hewitt, Sarah, Hobson, Emma, Jackson, Eilidh, Jewell, Rosalyn, Kraus, Alison, Prescott, Katrina, Sheridan, Eamonn, Thomson, Jenny, Bradshaw, Kirsty, Dixit, Abhijit, Eason, Jacqueline, Haines, Rebecca, Harrison, Rachel, Mutch, Stacey, Sarkar, Ajoy, Searle, Claire, Shannon, Nora, Sharif, Abid, Suri, Mohnish, Vasudevan, Pradeep, Canham, Natalie, Ellis, Ian, Greenhalgh, Lynn, Howard, Emma, Stinton, Victoria, Swale, Andrew, Weber, Astrid, Banka, Siddharth, Breen, Catherine, Briggs, Tracy, Burkitt-Wright, Emma, Chandler, Kate, Clayton-Smith, Jill, Donnai, Dian, Douzgou, Sofia, Gaunt, Lorraine, Jones, Elizabeth, Kerr, Bronwyn, Langley, Claire, Metcalfe, Kay, Smith, Audrey, Wright, Ronnie, Bourn, David, Burn, John, Fisher, Richard, Hellens, Steve, Henderson, Alex, Montgomery, Tara, Splitt, Miranda, Straub, Volker, Wright, Michael, Zwolinski, Simon, Allen, Zoe, Bernhard, Birgitta, Brady, Angela, Brooks, Claire, Busby, Louise, Clowes, Virginia, Ghali, Neeti, Holder, Susan, Ibitoye, Rita, Wakeling, Emma, Blair, Edward, Carmichael, Jenny, Cilliers, Deirdre, Clasper, Susan, Gibbons, Richard, Kini, Usha, Lester, Tracy, Nemeth, Andrea, Poulton, Joanna, Price, Sue, Shears, Debbie, Stewart, Helen, Wilkie, Andrew, Albaba, Shadi, Baker, Duncan, Balasubramanian, Meena, Johnson, Diana, Parker, Michael, Quarrell, Oliver, Stewart, Alison, Willoughby, Josh, Crosby, Charlene, Elmslie, Frances, Homfray, Tessa, Jin, Huilin, Lahiri, Nayana, Mansour, Sahar, Marks, Karen, McEntagart, Meriel, Saggar, Anand, Tatton-Brown, Kate, Butler, Rachel, Clarke, Angus, Corrin, Sian, Fry, Andrew, Kamath, Arveen, McCann, Emma, Mugalaasi, Hood, Pottinger, Caroline, Procter, Annie, Sampson, Julian, Sansbury, Francis, Varghese, Vinod, Baralle, Diana, Callaway, Alison, Cassidy, Emma J., Daniels, Stacey, Douglas, Andrew, Foulds, Nicola, Hunt, David, Kharbanda, Mira, Lachlan, Katherine, Mercer, Catherine, Side, Lucy, Temple, I. Karen, Wellesley, Diana, Martin, Hilary C. [0000-0002-4454-9084], Gardner, Eugene J. [0000-0001-9671-1533], Samocha, Kaitlin E. [0000-0002-1704-3352], Eberhardt, Ruth Y. [0000-0001-6152-1369], Tavares, Ana Lisa Taylor [0000-0001-7089-0502], Neville, Matthew D. C. [0000-0001-5816-7936], Niemi, Mari E. K. [0000-0003-0696-6175], Wright, Caroline F. [0000-0003-2958-5076], Hurles, Matthew E. [0000-0002-2333-7015], and Apollo - University of Cambridge Repository

Subjects
631/208/366, 49/23, article, 631/208/1516, 631/208/205
Abstract

Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders.

Published
2021
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23. Detecting cryptic clinically relevant structural variation in exome-sequencing data increases diagnostic yield for developmental disorders

Author

Gardner, Eugene J., primary, Sifrim, Alejandro, additional, Lindsay, Sarah J., additional, Prigmore, Elena, additional, Rajan, Diana, additional, Danecek, Petr, additional, Gallone, Giuseppe, additional, Eberhardt, Ruth Y., additional, Martin, Hilary C., additional, Wright, Caroline F., additional, FitzPatrick, David R., additional, Firth, Helen V., additional, and Hurles, Matthew E., additional

Published
2021
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25. Evaluating variants classified as pathogenic in ClinVar in the DDD Study

Author

Wright, Caroline F, Eberhardt, Ruth Y, Constantinou, Panayiotis, Hurles, Matthew E, FitzPatrick, David R, Firth, Helen V, DDD Study, Wright, Caroline F [0000-0003-2958-5076], and Apollo - University of Cambridge Repository

Subjects
genomic medicine, Gene Frequency, variant interpretation, Databases, Genetic, Exome Sequencing, reanalysis, Humans, developmental disorders, Exome
Abstract

PURPOSE: Automated variant filtering is an essential part of diagnostic genome-wide sequencing but may generate false negative results. We sought to investigate whether some previously identified pathogenic variants may be being routinely excluded by standard variant filtering pipelines. METHODS: We evaluated variants that were previously classified as pathogenic or likely pathogenic in ClinVar in known developmental disorder genes using exome sequence data from the Deciphering Developmental Disorders (DDD) study. RESULTS: Of these ClinVar pathogenic variants, 3.6% were identified among 13,462 DDD probands, and 1134/1352 (83.9%) had already been independently communicated to clinicians using DDD variant filtering pipelines as plausibly pathogenic. The remaining 218 variants failed consequence, inheritance, or other automated variant filters. Following clinical review of these additional variants, we were able to identify 112 variants in 107 (0.8%) DDD probands as potential diagnoses. CONCLUSION: Lower minor allele frequency (1 star) are good predictors of a previously identified variant being plausibly diagnostic for developmental disorders. However, around half of previously identified pathogenic variants excluded by automated variant filtering did not appear to be disease-causing, underlining the continued need for clinical evaluation of candidate variants as part of the diagnostic process.

Published
2021
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26. Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms

Author

Wright, Caroline F., primary, Quaife, Nicholas M., additional, Ramos-Hernández, Laura, additional, Danecek, Petr, additional, Ferla, Matteo P., additional, Samocha, Kaitlin E., additional, Kaplanis, Joanna, additional, Gardner, Eugene J., additional, Eberhardt, Ruth Y., additional, Chao, Katherine R., additional, Karczewski, Konrad J., additional, Morales, Joannella, additional, Gallone, Giuseppe, additional, Balasubramanian, Meena, additional, Banka, Siddharth, additional, Gompertz, Lianne, additional, Kerr, Bronwyn, additional, Kirby, Amelia, additional, Lynch, Sally A., additional, Morton, Jenny E.V., additional, Pinz, Hailey, additional, Sansbury, Francis H., additional, Stewart, Helen, additional, Zuccarelli, Britton D., additional, Cook, Stuart A., additional, Taylor, Jenny C., additional, Juusola, Jane, additional, Retterer, Kyle, additional, Firth, Helen V., additional, Hurles, Matthew E., additional, Lara-Pezzi, Enrique, additional, Barton, Paul J.R., additional, and Whiffin, Nicola, additional

Published
2021
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27. Pfam: the protein families database

Author

Finn, Robert D., Bateman, Alex, Clements, Jody, Coggill, Penelope, Eberhardt, Ruth Y., Eddy, Sean R., Heger, Andreas, Hetherington, Kirstie, Holm, Liisa, Mistry, Jaina, Sonnhammer, Erik L. L., Tate, John, and Punta, Marco

Published
2014
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29. The Pfam protein families database

Author

Punta, Marco, Coggill, Penny C., Eberhardt, Ruth Y., Mistry, Jaina, Tate, John, Boursnell, Chris, Pang, Ningze, Forslund, Kristoffer, Ceric, Goran, Clements, Jody, Heger, Andreas, Holm, Liisa, Sonnhammer, Erik L. L., Eddy, Sean R., Bateman, Alex, and Finn, Robert D.

Published
2012
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30. Detecting cryptic clinically-relevant structural variation in exome sequencing data increases diagnostic yield for developmental disorders

Author

Gardner, Eugene J., primary, Sifrim, Alejandro, additional, Lindsay, Sarah J., additional, Prigmore, Elena, additional, Rajan, Diana, additional, Danecek, Petr, additional, Gallone, Giuseppe, additional, Eberhardt, Ruth Y., additional, Martin, Hilary C., additional, Wright, Caroline F., additional, FitzPatrick, David R., additional, Firth, Helen V., additional, and Hurles, Matthew E., additional

Published
2020
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31. The contribution of X-linked coding variation to severe developmental disorders

Author

Martin, Hilary C., primary, Gardner, Eugene J., additional, Samocha, Kaitlin E., additional, Kaplanis, Joanna, additional, Akawi, Nadia, additional, Sifrim, Alejandro, additional, Eberhardt, Ruth Y., additional, Tavares, Ana Lisa Taylor, additional, Neville, Matthew D. C., additional, Niemi, Mari E. K., additional, Gallone, Giuseppe, additional, McRae, Jeremy, additional, Wright, Caroline F., additional, FitzPatrick, David R., additional, Firth, Helen V., additional, and Hurles, Matthew E., additional

Published
2020
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32. Primary sequence and enzymic properties of two modular endoglucanases, Cel5A and Cel45A, from the anaerobic fungus Piromyces equi

Author

Eberhardt, Ruth Y., Gilbert, Harry J., and Hazlewood, Geoffrey P.

Subjects
Fungi -- Genetic aspects, Amino acid sequence -- Analysis, Enzymes -- Analysis, Proteins -- Conformation, Domain structure -- Analysis, Biological sciences
Abstract

Amino acid sequence of Cel5A and Cel45A endoglucanases resemble family-5 and family-45glycosyl hydrolases respectively. The molecular mass of the endoglucanases are over 194 and 44 kilo daltons and contain four and one catalytic domains respectively. The endoglucanases are part of the high-molecular-mass cellilose-degrading complex of Piromyces equi.

Published
2000

33. Integrating healthcare and research genetic data empowers the discovery of 49 novel developmental disorders

Author

Kaplanis, Joanna, Samocha, Kaitlin E., Wiel, Laurens, Zhang, Zhancheng, Arvai, Kevin J., Eberhardt, Ruth Y., Gallone, Giuseppe, Lelieveld, Stefan H., Martin, Hilary C., McRae, Jeremy F., Short, Patrick J., Torene, Rebecca I., de Boer, Elke, Danecek, Petr, Gardner, Eugene J., Huang, Ni, Lord, Jenny, Martincorena, Iñigo, Pfundt, Rolph, Reijnders, Margot R. F., Yeung, Alison, Yntema, Helger G., Vissers, Lisenka E. L. M., Juusola, Jane, Wright, Caroline F., Brunner, Han G., Firth, Helen V., FitzPatrick, David R., Barrett, Jeffrey C., Hurles, Matthew E., Gilissen, Christian, and Retterer, Kyle

Abstract

Summary De novo mutations (DNMs) in protein-coding genes are a well-established cause of developmental disorders (DD). However, known DD-associated genes only account for a minority of the observed excess of such DNMs. To identify novel DD-associated genes, we integrated healthcare and research exome sequences on 31,058 DD parent-offspring trios, and developed a simulation-based statistical test to identify gene-specific enrichments of DNMs. We identified 299 significantly DD-associated genes, including 49 not previously robustly associated with DDs. Despite detecting more DD-associated genes than in any previous study, much of the excess of DNMs of protein-coding genes remains unaccounted for. Modelling suggests that over 500 novel DD-associated genes await discovery, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of dominant DDs.

Published
2019
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34. Integrating healthcare and research genetic data empowers the discovery of 28 novel developmental disorders

Author

Kaplanis, Joanna, primary, Samocha, Kaitlin E., additional, Wiel, Laurens, additional, Zhang, Zhancheng, additional, Arvai, Kevin J., additional, Eberhardt, Ruth Y., additional, Gallone, Giuseppe, additional, Lelieveld, Stefan H., additional, Martin, Hilary C., additional, McRae, Jeremy F., additional, Short, Patrick J., additional, Torene, Rebecca I., additional, de Boer, Elke, additional, Danecek, Petr, additional, Gardner, Eugene J., additional, Huang, Ni, additional, Lord, Jenny, additional, Martincorena, Iñigo, additional, Pfundt, Rolph, additional, Reijnders, Margot R. F., additional, Yeung, Alison, additional, Yntema, Helger G., additional, Study, DDD, additional, Vissers, Lisenka E. L. M., additional, Juusola, Jane, additional, Wright, Caroline F., additional, Brunner, Han G., additional, Firth, Helen V., additional, FitzPatrick, David R., additional, Barrett, Jeffrey C., additional, Hurles, Matthew E., additional, Gilissen, Christian, additional, and Retterer, Kyle, additional

Published
2019
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35. Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study

Author

Lord, Jenny, primary, McMullan, Dominic J, additional, Eberhardt, Ruth Y, additional, Rinck, Gabriele, additional, Hamilton, Susan J, additional, Quinlan-Jones, Elizabeth, additional, Prigmore, Elena, additional, Keelagher, Rebecca, additional, Best, Sunayna K, additional, Carey, Georgina K, additional, Mellis, Rhiannon, additional, Robart, Sarah, additional, Berry, Ian R, additional, Chandler, Kate E, additional, Cilliers, Deirdre, additional, Cresswell, Lara, additional, Edwards, Sandra L, additional, Gardiner, Carol, additional, Henderson, Alex, additional, Holden, Simon T, additional, Homfray, Tessa, additional, Lester, Tracy, additional, Lewis, Rebecca A, additional, Newbury-Ecob, Ruth, additional, Prescott, Katrina, additional, Quarrell, Oliver W, additional, Ramsden, Simon C, additional, Roberts, Eileen, additional, Tapon, Dagmar, additional, Tooley, Madeleine J, additional, Vasudevan, Pradeep C, additional, Weber, Astrid P, additional, Wellesley, Diana G, additional, Westwood, Paul, additional, White, Helen, additional, Parker, Michael, additional, Williams, Denise, additional, Jenkins, Lucy, additional, Scott, Richard H, additional, Kilby, Mark D, additional, Chitty, Lyn S, additional, Hurles, Matthew E, additional, Maher, Eamonn R, additional, Bateman, Mark, additional, Campbell, Carolyn, additional, Campbell, Jenni, additional, Carey, Georgina, additional, Cohen, Kelly, additional, Collingwood, Emma, additional, Constantinou, Panayiotis, additional, Delmege, Catherine, additional, Ellis, Richard, additional, Evans, Jerry, additional, Everett, Thomas, additional, Pinto, Clare F, additional, Forrester, Natalie, additional, Fowler, Emma, additional, Hamilton, Susan, additional, Healey, Karen, additional, Hudson, Rebecca, additional, Lester, Tracey, additional, Lewis, Rebecca, additional, Lord, Jenny, additional, Marton, Tamas, additional, Mehta, Sarju, additional, Park, Soo-Mi, additional, Rowland, Jayne, additional, Steer, James, additional, Taylor, Emma J, additional, and Wilson, Elizabeth, additional

Published
2019
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36. Integrating healthcare and research genetic data empowers the discovery of 49 novel developmental disorders

Author

Kaplanis, Joanna, primary, Samocha, Kaitlin E., additional, Wiel, Laurens, additional, Zhang, Zhancheng, additional, Arvai, Kevin J., additional, Eberhardt, Ruth Y., additional, Gallone, Giuseppe, additional, Lelieveld, Stefan H., additional, Martin, Hilary C., additional, McRae, Jeremy F., additional, Short, Patrick J., additional, Torene, Rebecca I., additional, Boer, Elke de, additional, Danecek, Petr, additional, Gardner, Eugene J., additional, Huang, Ni, additional, Lord, Jenny, additional, Martincorena, Iñigo, additional, Pfundt, Rolph, additional, Reijnders, Margot R. F., additional, Yeung, Alison, additional, Yntema, Helger G., additional, Study, DDD, additional, Vissers, Lisenka E. L. M., additional, Juusola, Jane, additional, Wright, Caroline F., additional, Brunner, Han G., additional, Firth, Helen V., additional, FitzPatrick, David R., additional, Barrett, Jeffrey C., additional, Hurles, Matthew E., additional, Gilissen, Christian, additional, and Retterer, Kyle, additional

Published
2018
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37. The Pfam protein families database: towards a more sustainable future

Author

Finn, Robert D., primary, Coggill, Penelope, additional, Eberhardt, Ruth Y., additional, Eddy, Sean R., additional, Mistry, Jaina, additional, Mitchell, Alex L., additional, Potter, Simon C., additional, Punta, Marco, additional, Qureshi, Matloob, additional, Sangrador-Vegas, Amaia, additional, Salazar, Gustavo A., additional, Tate, John, additional, and Bateman, Alex, additional

Published
2015
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38. Rfam 12.0: updates to the RNA families database

Author

Nawrocki, Eric P., primary, Burge, Sarah W., additional, Bateman, Alex, additional, Daub, Jennifer, additional, Eberhardt, Ruth Y., additional, Eddy, Sean R., additional, Floden, Evan W., additional, Gardner, Paul P., additional, Jones, Thomas A., additional, Tate, John, additional, and Finn, Robert D., additional

Published
2014
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41. Pfam: the protein families database

Author

Finn, Robert D., primary, Bateman, Alex, additional, Clements, Jody, additional, Coggill, Penelope, additional, Eberhardt, Ruth Y., additional, Eddy, Sean R., additional, Heger, Andreas, additional, Hetherington, Kirstie, additional, Holm, Liisa, additional, Mistry, Jaina, additional, Sonnhammer, Erik L. L., additional, Tate, John, additional, and Punta, Marco, additional

Published
2013
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48. Characterization of a cellulosome dockerin domain from the anaerobic fungus Piromyces equi.

Author

Raghothama, S., Eberhardt, Ruth Y., Simpson, Peter, Wigelsworth, Darran, White, Peter, Hazlewood, Geoffrey P., Nagy, Tibor, Gilbert, Harry J., and Williamson, Michael P.

Subjects
*PHYTOPATHOGENIC fungi, *PLANT cell walls, *PHOTOSYNTHESIS
Abstract

The recycling of photosynthetically fixed carbon in plant cell walls is a key microbial process. In anaerobes, the degradation is carried out by a high molecular weight multifunctional complex termed the cellulosome. This consists of a number of independent enzyme components, each of which contains a conserved dockerin domain, which functions to bind the enzyme to a cohesin domain within the protein scaffoldin protein. Here we describe the first three-dimensional structure of a fungal dockerin, the N-terminal dockerin of Cel45A from the anaerobic fungus Piromyces equi. The structure contains a novel fold of 42 residues. The ligand binding site consists of residues Trp 35, Tyr 8 and Asp 23, which are conserved in all fungal dockerins. The binding site is on the opposite side of the N- and C-termini of the molecule, implying that tandem dockerin domains, seen in the majority of anaerobic fungal plant cell wall degrading enzymes, could present multiple simultaneous binding sites and, therefore, permit tailoring of binding to catalytic demands. [ABSTRACT FROM AUTHOR]

Published
2001
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49. Molecular autopsy by trio exome sequencing (ES) and postmortem examination in fetuses and neonates with prenatally identified structural anomalies

Author

Quinlan-Jones, Elizabeth, Lord, Jenny, Williams, Denise, Hamilton, Sue, Marton, Tamas, Eberhardt, Ruth Y, Rinck, Gabriele, Prigmore, Elena, Keelagher, Rebecca, McMullan, Dominic J, Maher, Eamonn R, Hurles, Matthew E, and Kilby, Mark D

Subjects
Male, Infant, Newborn, neonates, 3. Good health, Congenital Abnormalities, Cohort Studies, genetic diagnosis, Fetal Diseases, autopsy, Fetus, Pregnancy, Prenatal Diagnosis, Exome Sequencing, fetuses, Humans, Exome, Female
Abstract

PURPOSE: To determine the diagnostic yield of combined exome sequencing (ES) and autopsy in fetuses/neonates with prenatally identified structural anomalies resulting in termination of pregnancy, intrauterine, neonatal, or early infant death. METHODS: ES was undertaken in 27 proband/parent trios following full autopsy. Candidate pathogenic variants were classified by a multidisciplinary clinical review panel using American College of Medical Genetics and Genomics (ACMG) guidelines. RESULTS: A genetic diagnosis was established in ten cases (37%). Pathogenic/likely pathogenic variants were identified in nine different genes including four de novo autosomal dominant, three homozygous autosomal recessive, two compound heterozygous autosomal recessive, and one X-linked. KMT2D variants (associated with Kabuki syndrome postnatally) occurred in two cases. Pathogenic variants were identified in 5/13 (38%) cases with multisystem anomalies, in 2/4 (50%) cases with fetal akinesia deformation sequence, and in 1/4 (25%) cases each with cardiac and brain anomalies and hydrops fetalis. No pathogenic variants were detected in fetuses with genitourinary (1), skeletal (1), or abdominal (1) abnormalities. CONCLUSION: This cohort demonstrates the clinical utility of molecular autopsy with ES to identify an underlying genetic cause in structurally abnormal fetuses/neonates. These molecular findings provided parents with an explanation of the developmental abnormality, delineated the recurrence risks, and assisted the management of subsequent pregnancies.

50. AntiFam: a tool to help identify spurious ORFs in protein annotation.

Author

Eberhardt, Ruth Y., Haft, Daniel H., Punta, Marco, Martin, Maria, O'Donovan, Claire, and Bateman, Alex

Subjects
*GENOMES, *BIOLOGICAL databases, *BIOMOLECULES, *AMINO acid sequence, *NUCLEIC acids
Abstract

As the deluge of genomic DNA sequence grows the fraction of protein sequences that have been manually curated falls. In turn, as the number of laboratories with the ability to sequence genomes in a high-throughput manner grows, the informatics capability of those labs to accurately identify and annotate all genes within a genome may often be lacking. These issues have led to fears about transitive annotation errors making sequence databases less reliable. During the lifetime of the Pfam protein families database a number of protein families have been built, which were later identified as composed solely of spurious open reading frames (ORFs) either on the opposite strand or in a different, overlapping reading frame with respect to the true protein-coding or non-coding RNA gene. These families were deleted and are no longer available in Pfam. However, we realized that these may perform a useful function to identify new spurious ORFs. We have collected these families together in AntiFam along with additional custom-made families of spurious ORFs. This resource currently contains 23 families that identified 1310 spurious proteins in UniProtKB and a further 4119 spurious proteins in a collection of metagenomic sequences. UniProt has adopted AntiFam as a part of the UniProtKB quality control process and will investigate these spurious proteins for exclusion. [ABSTRACT FROM AUTHOR]

Published
2012
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