HGMD

Human Gene Mutation Database

Articles co-authored by members of HGMD

ReferenceJournal links
Itan Y, Shang L, Boisson B, Patin E, Bolze A, Moncada-Vélez M, Scott E, Ciancanelli MJ, Lafaille FG, Markle JG, Martinez-Barricarte R, de Jong SJ, Kong XF, Nitschke P, Belkadi A, Bustamante J, Puel A, Boisson-Dupuis S, Stenson PD, Gleeson JG, Cooper DN, Quintana-Murci L, Claverie JM, Zhang SY, Abel L, Casanova JL. The human gene damage index as a gene-level approach to prioritizing exome variants. Proc Natl Acad Sci U S A 112:13615-13620, 2015. PubMed Abstract Full Text (HTML)
1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature 526:68-74 2015. PubMed Full Text (HTML)
Kamat MA, Bacolla A, Cooper DN, Chuzhanova N. A Role for Non-B DNA Forming Sequences in Mediating Micro-Lesions Causing Human Inherited Disease. Hum Mutat epub, 2015. PubMed Abstract
Douville C, Masica DL, Stenson PD, Cooper DN, Gygax DM, Kim R, Ryan M, Karchin R. Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel). Hum Mutat epub, 2015. PubMed Abstract
Turner TN, Douville C, Kim D, Stenson PD, Cooper DN, Chakravarti A, Karchin R. Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns. Hum Mol Genet 24:5995-6002, 2015. PubMed Abstract Full Text (HTML)
Chen JM, Férec C, Cooper DN. Complex Multiple-Nucleotide Substitution Mutations Causing Human Inherited Disease Reveal Novel Insights into the Action of Translesion Synthesis DNA Polymerases. Hum Mutat epub, 2015. PubMed Abstract
Siegert S, Wolf A, Cooper DN, Krawczak M, Nothnagel M. Mutations Causing Complex Disease May under Certain Circumstances Be Protective in an Epidemiological Sense. PLoS One 10:e0132150, 2015. PubMed Abstract
Karageorgos I, Mizzi C, Giannopoulou E, Pavlidis C, Peters BA, Zagoriti Z, Stenson PD, Mitropoulos K, Borg J, Kalofonos HP, Drmanac R, Stubbs A, van de Spek P, Cooper DN, Katsila T, Patrinos GP. Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach. Hum Genomics 9:12, 2015. PubMed Abstract
Johnston JJ, Lewis KL, Ng D, Singh LN, Wynter J, Brewer C, Brooks BP, Brownell I, Candotti F, Gonsalves SG, Hart SP, Kong HH, Rother KI, Sokolic R, Solomon BD, Zein WM, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG. Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations. Am J Hum Genet 96:913-925, 2015. PubMed Abstract
Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J; GTEx Consortium; Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG. Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348:666, 2015. PubMed Abstract Full Text (HTML)
Thomas LE, Winston J, Rad E, Mort M, Dodd KM, Tee AR, McDyer F, Moore S, Cooper DN, Upadhyaya M. Evaluation of copy number variation and gene expression in neurofibromatosis type-1-associated malignant peripheral nerve sheath tumours. Hum Genomics 9:3, 2015. PubMed Abstract
Wang Y, Su P, Hu B, Zhu W, Li Q, Yuan P, Li J, Guan X, Li F, Jing X, Li R, Zhang Y, Férec C, Cooper DN, Wang J, Huang D, Chen JM, Wang Y. Characterization of 26 deletion CNVs reveals the frequent occurrence of micro-mutations within the breakpoint-flanking regions and frequent repair of double-strand breaks by templated insertions derived from remote genomic regions. Hum Genet 134:589-603, 2015. PubMed Abstract
Grimm DG, Azencott CA, Aicheler F, Gieraths U, MacArthur DG, Samocha KE, Cooper DN, Stenson PD, Daly MJ, Smoller JW, Duncan LE, Borgwardt KM. The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity. Hum Mutat 36:513-523, 2015. PubMed Abstract
Shihab HA, Rogers MF, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR, Campbell C. An integrative approach to predicting the functional effects of non-coding and coding sequence variation. Bioinformatics 31:1536-1543, 2015. PubMed Abstract
Zhu W, Cooper DN, Zhao Q, Wang Y, Liu R, Li Q, Férec C, Wang Y, Chen JM. Concurrent nucleotide substitution mutations in the human genome are characterized by a significantly decreased transition/transversion ratio. Hum Mutat 36:333-341, 2015. PubMed
Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q1, Szpak M, Frandsen P, Chen Y, Yngvadottir B, Cooper DN, de Manuel M, Hernandez-Rodriguez J, Lobon I, Siegismund HR, Pagani L, Quail MA, Hvilsom C, Mudakikwa A, Eichler EE, Cranfield MR, Marques-Bonet T, Tyler-Smith C, Scally A. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding. Science 348:242, 2015. PubMed Abstract Full Text (HTML)
Folkman L, Yang Y, Li Z, Stantic B, Sattar A, Mort M, Cooper DN, Liu Y, Zhou Y. DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. Bioinformatics epub, 2015. PubMed
Chen YC, Douville C, Wang C, Niknafs N, Yeo G, Beleva-Guthrie V, Carter H, Stenson PD, Cooper DN, Li B, Mooney S, Karchin R. A probabilistic model to predict clinical phenotypic traits from genome sequencing. PLoS Comput Biol 10:e1003825, 2014. PubMed Abstract
Wei X, Das J, Fragoza R, Liang J, Bastos de Oliveira FM, Lee HR, Wang X, Mort M, Stenson PD, Cooper DN, Lipkin SM, Smolka MB, Yu H. A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations. Plos Genet 10:e1004819, 2014. PubMed Abstract
Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet 133:1-9, 2014. PubMed Abstract Full Text (HTML)
Zhang X, Lin H, Zhao H, Hao Y, Mort M, Cooper DN, Zhou Y, Liu Y. Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation. Hum Mol Genet 23:3024-3034, 2014. PubMed Abstract Full Text (HTML)
Mort M, Sterne-Weiler T, Li B, Ball EV, Cooper DN, Radivojac P, Sanford JR, Mooney SD. MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing. Genome Biol 15:R19, 2014. PubMed Abstract
Das J, Lee HR, Sagar A, Fragoza R, Liang J, Wei X, Wang X, Mort M, Stenson PD, Cooper DN, Yu H. Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks. Hum Mutat 35:585-593, 2014. PubMed Full Text (HTML)
Shihab HA, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR. Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Hum Genomics 8:11, 2014. PubMed Full Text (HTML)
Gonsalves SG, Ng D, Johnston JJ, Teer JK, Stenson PD, Cooper DN, Mullikin JC, Biesecker LG; NISC Comparative Sequencing Program. Using exome data to identify malignant hyperthermia susceptibility mutations. Anesthesiology 119:1043-1053, 2013. PubMed
Bacolla A, Temiz NA, Yi M, Ivanic J, Cer RZ, Donohue DE, Ball EV, Mudunuri US, Wang G, Jain A, Volfovsky N, Luke BT, Stephens RM, Cooper DN, Collins JR, Vasquez KM. Guanine holes are prominent targets for mutation in cancer and inherited disease. PLoS Genet 9:e1003816, 2013. PubMed Full Text (HTML)
Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG, NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program. Interpreting secondary cardiac disease variants in an exome cohort. Circ Cardiovasc Genet 6:337-346, 2013. PubMed Abstract Full Text (HTML) Full Text (PDF)
Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 132:1077-1130, 2013. PubMed Full Text (HTML)
Carter H, Douville C, Stenson PD, Cooper DN, Karchin R. Identifying Mendelian disease genes with the variant effect scoring tool. BMC Genomics 14:S3, 2013. PubMed Full Text (HTML)
Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Stenson PD, Cooper DN, Karchin R. MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. Hum Genet 132:1235-1243, 2013. PubMed Abstract
Shihab HA, Gough J, Cooper DN, Day IN, Gaunt TR. Predicting the functional consequences of cancer-associated amino acid substitutions. Bioinformatics 29:1504-1510, 2013. PubMed Abstract Full Text (HTML) Full Text (PDF)
Zhao H, Yang Y, Lin H, Zhang X, Mort M, Cooper DN, Liu Y, Zhou Y. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biol 14:R23, 2013. PubMed Full Text (HTML)
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R. CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics 29:647-648, 2013. PubMed Abstract Full Text (HTML) Full Text (PDF)
Chen JM, Férec C, Cooper DN. Patterns and Mutational Signatures of Tandem Base Substitutions Causing Human Inherited Disease. Hum Mutat 34:1119-1130, 2013. PubMed Abstract   Full Text (PDF)
Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN, Tyler-Smith C, the 1000 Genomes Project Consortium. Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing. Am J Hum Genet 91:1022-1032, 2012. PubMed   Full Text (HTML)  
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature 491:56-65, 2012. PubMed   Full Text (HTML) Full Text (PDF)
Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden markov models. Hum Mutat 34:57-65, 2013. PubMed Abstract Full Text (HTML) Full Text (PDF)
Stenson PD, Ball EV, Mort M, Phillips AD, Shaw K, Cooper DN. The Human Gene Mutation Database (HGMD) and Its Exploitation in the Fields of Personalized Genomics and Molecular Evolution. Curr Protoc Bioinformatics Unit 1.13, 2012. PubMed Abstract Full Text (HTML) Full Text (PDF)
Teng M, Ichikawa S, Padgett LR, Wang Y, Mort M, Cooper DN, Koller DL, Foroud T, Edenberg HJ, Econs MJ, Liu Y. regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions. Bioinformatics 28(14):1879-1886, 2012. PubMed Abstract Full Text (HTML) Full Text (PDF)
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. Insights into hominid evolution from the gorilla genome sequence. Nature 483(7388):169-175, 2012. PubMed   Full Text (HTML) Full Text (PDF)
Casola C, Zekonyte U, Phillips AD, Cooper DN, Hahn MW. Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease. Genome Res 22(3):429-435, 2012. PubMed     Full Text (PDF)
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG; 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. A systematic survey of loss-of-function variants in human protein-coding genes. Science 335:823-828, 2012. PubMed Abstract Full Text (HTML) Full Text (PDF)
Chen JM, Férec C, Cooper DN. Transient hypermutability, chromothripsis and replication-based mechanisms in the generation of concurrent clustered mutations. Mutat Res 750:52-59, 2012. PubMed      
Naidoo N, Pawitan Y, Soong R, Cooper DN, Ku CS. Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics 5(6):577-622, 2011. PubMed Abstract   Full Text (PDF)
Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y, van Gool AJ, Du H, Chen J, Chen R, Zhang P, Huang Z, Thompson JR, Meng Y, Bai Y, Wang J, Zhuo M, Wang T, Huang Y, Wei L, Li J, Wang Z, Hu H, Yang P, Le L, Stenson PD, Li B, Liu X, Ball EV, An N, Huang Q, Zhang Y, Fan W, Zhang X, Li Y, Wang W, Katze MG, Su B, Nielsen R, Yang H, Wang J, Wang X, Wang J. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol 129(11):1019-1023, 2011. PubMed   Full Text (HTML) Full Text (PDF)
Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT; 1000 Genomes Project. A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet 7(8):e1002236, 2011. PubMed Abstract Full Text (HTML) Full Text (PDF)
Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA; 1000 Genomes Project, Bustamante CD. Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A 108(29):11983-11988, 2011. PubMed Abstract Full Text (HTML) Full Text (PDF)
Wolf A, Caliebe A, Thomas NS, Ball EV, Mort M, Stenson PD, Krawczak M, Cooper DN. Single base-pair substitutions at the translation initiation sites of human genes as a cause of inherited disease. Hum Mutat 32(10):1137-1143, 2011. PubMed Abstract Full Text (HTML) Full Text (PDF)
Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P; 1000 Genomes Project. Variation in genome-wide mutation rates within and between human families. Nat Genet 43(7):712-714, 2011. PubMed   Full Text (HTML) Full Text (PDF)
Zhao Y, Clark WT, Mort M, Cooper DN, Radivojac P, Mooney SD. Prediction of functional regulatory SNPs in monogenic and complex disease. Hum Mutat 32(10):1183-1190, 2011. PubMed Abstract Full Text (HTML) Full Text (PDF)
Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, Depristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs RA, 1000 Genomes Project. The functional spectrum of low-frequency coding variation. Genome Biol 12(9):R84, 2011. PubMed
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Cooper DN, Bacolla A, Férec C, Vasquez KM, Kehrer-Sawatzki H, Chen JM. On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. Hum Mutat 32(10):1075-1099, 2011. PubMed
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Sterne-Weiler T, Howard J, Mort M, Cooper DN, Sanford JR. Loss of exon identity is a common mechanism of human inherited disease. Genome Res 21(10):1563-1571, 2011. PubMed
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Hamby SE, Thomas NS, Cooper DN, Chuzhanova N. A meta-analysis of single base-pair substitutions in translational termination codons ('nonstop' mutations) that cause human inherited disease. Hum Genomics 5(4):241-264, 2011. PubMed
Abstract    
Fechtel K, Osterbur ML, Kehrer-Sawatzki H, Stenson PD, Cooper DN. Delineating the Hemostaseome as an aid to individualize the analysis of the hereditary basis of thrombotic and bleeding disorders. Hum Genet 130(1):149-166, 2011. PubMed
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Zhang G, Pei Z, Ball EV, Mort M, Kehrer-Sawatzki H, Cooper DN. Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations. Hum Genomics 5(5):453-484, 2011. PubMed
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Ivanov D, Hamby SE, Stenson PD, Phillips AD, Kehrer-Sawatzki H, Cooper DN, Chuzhanova N. Comparative analysis of germline and somatic microlesion mutational spectra in 17 human tumor suppressor genes. Hum Mutat 32(6):620-632, 2011. PubMed Abstract Full Text (HTML) Full Text (PDF)
Bacolla A, Wang G, Jain A, Chuzhanova NA, Cer RZ, Collins JR, Cooper DN, Bohr VA, Vasquez KM. Non-B DNA-forming sequences and WRN deficiency independently increase the frequency of base substitution in human cells. J Biol Chem 286(12):10017-10026, 2011. PubMed Abstract Full Text (HTML) Full Text (PDF)
Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G; 1000 Genomes Project, Sella G, Przeworski M. Classic selective sweeps were rare in recent human evolution. Science 331(6019):920-924, 2011. PubMed Abstract Full Text (HTML) Full Text (PDF)
Necsulea A, Popa A, Cooper DN, Stenson PD, Mouchiroud D, Gautier C, Duret L. Meiotic recombination favors the spreading of deleterious mutations in human populations. Hum Mutat 32(2):198-206, 2011. PubMed Abstract Full Text (HTML) Full Text (PDF)
Cooper DN, Kehrer-Sawatzki H. Exploring the potential relevance of human-specific genes to complex disease. Hum Genomics 5(2):99-107, 2011. PubMed Abstract    
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project. Mapping copy number variation by population-scale genome sequencing. Nature 470(7332):59-65, 2011. PubMed Abstract Full Text (HTML) Full Text (PDF)
1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-1073, 2010. PubMed Abstract Full Text (HTML) Full Text (PDF)
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project, Eichler EE. Diversity of human copy number variation and multicopy genes. Science 330(6004):641-646, 2010. PubMed Abstract Full Text (HTML) Full Text (PDF)
Stenson PD, Cooper DN. Prospects for the automated extraction of mutation data from the scientific literature. Hum Genomics 5(1):1-4, 2010. PubMed Abstract    
Zhang G, Pei Z, Krawczak M, Ball EV, Mort M, Kehrer-Sawatzki H, Cooper DN. Triangulation of the human, chimpanzee, and Neanderthal genome sequences identifies potentially compensated mutations. Hum Mutat 31(12):1286-1293, 2010 PubMed Abstract Full Text (HTML) Full Text (PDF)
Cooper DN, Mort M, Stenson PD, Ball EV, Chuzhanova NA. Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides. Hum Genomics 4(6):406-410, 2010. PubMed      
Xin F, Myers S, Li YF, Cooper DN, Mooney SD, Radivojac P. Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. Bioinformatics 26(16):1975-1982, 2010 PubMed Abstract Full Text (HTML) Full Text (PDF)
Cooper DN, Ball EV, Mort M. Chromosomal distribution of disease genes in the human genome. Genet Test Mol Biomarkers 14(4):441-446, 2010 PubMed Abstract   Full Text (PDF)
Cooper DN, Mort M. Do inherited disease genes have distinguishing functional characteristics? Genet Test Mol Biomarkers 14(3):289-291, 2010 PubMed Abstract   Full Text (PDF)
Cooper DN, Chen JM, Ball EV, Howells K, Mort M, Phillips AD, Chuzhanova N, Krawczak M, Kehrer-Sawatzki H, Stenson PD. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum Mutat 31(6):631-655, 2010 PubMed Abstract   Full Text (PDF)
Cooper DN. Functional intronic polymorphisms: Buried treasure awaiting discovery within our genes. Hum Genomics 4(5):284-288, 2010 PubMed Abstract    
Quemener S, Chen JM, Chuzhanova N, Benech C, Casals T, Macek M Jr, Bienvenu T, McDevitt T, Farrell PM, Loumi O, Messaoud T, Cuppens H, Cutting GR, Stenson PD, Giteau K, Audrezet MP, Cooper DN, Ferec C. Complete ascertainment of intragenic copy number mutations (CNMs) in the CFTR gene and its implications for CNM formation at other autosomal loci. Hum Mutat 31(4):421-428, 2010 PubMed Abstract   Full Text (PDF)
Mort M, Evani US, Krishnan VG, Kamati KK, Baenziger PH, Bagchi A, Peters BJ, Sathyesh R, Li B, Sun Y, Xue B, Shah NH, Kann MG, Cooper DN, Radivojac P, Mooney SD. In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Hum Mutat 31(3):335-346, 2010 PubMed Abstract   Full Text (PDF)
Antonarakis SE, Cooper DN. Human gene mutation: mechanisms and consequences. Chap. 10 in Human Genetics. Problems and Approaches. 4th Ed. MR Speicher, SE Antonarakis & AG Motulsky (Eds.). Springer, Heidelberg. pp319-364, 2010.  
Stenson PD, Ball EV, Howells K, Phillips AD, Mort M, Cooper DN. The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics. Hum Genomics 4(2):69-72, 2009. PubMed Abstract    
Roberta A. Pagon, Ada Hamosh, Johan den Dunnen, Helen V. Firth, Donna R. Maglott, Stephen T. Sherry, Michael Feolo, David Cooper, and Peter Stenson. Databases in Human and Medical Genetics. Chap. 29.3 in Vogel and Motulsky's Human Genetics: Problems and Approaches. M.R. Speicher et al. (Eds.), Springer-Verlag Berlin Heidelberg, pp.941-960, 2010.      
Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P: Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 25(21):2744-2750, 2009. PubMed Abstract Full Text (HTML) Full Text (PDF)
Chen JM, Ferec C, Cooper DN: Closely spaced multiple mutations as potential signatures of transient hypermutability in human genes. Hum Mutat 30(10):1435-1448, 2009. PubMed Abstract   Full Text (PDF)
Chuzhanova N, Chen JM, Bacolla A, Patrinos GP, Ferec C, Wells RD, Cooper DN: Gene conversion causing human inherited disease: evidence for involvement of non-B-DNA-forming sequences and recombination-promoting motifs in DNA breakage and repair. Hum Mutat 30(8):1189-1198, 2009. PubMed Abstract   Full Text (PDF)
Sanford JR, Wang X, Mort M, Vanduyn N, Cooper DN, Mooney SD, Edenberg HJ, Liu Y: Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res 19(3):381-394, 2009. PubMed Abstract Full Text (HTML) Full Text (PDF)
Wolf A, Millar DS, Caliebe A, Horan M, Newsway V, Kumpf D, Steinmann K, Chee IS, Lee YH, Mutirangura A, Pepe G, Rickards O, Schmidtke J, Schempp W, Chuzhanova N, Kehrer-Sawatzki H, Krawczak M, Cooper DN: A gene conversion hotspot in the human growth hormone (GH1) gene promoter. Hum Mutat 30(2):239-247, 2009. PubMed Abstract    
Stenson PD, Mort M, Ball E, Howells K, Phillips A, Thomas NST, Cooper DN: The Human Gene Mutation Database: 2008 update. Genome Med 1(1):13, 2009. PubMed Abstract Full Text (HTML) Full Text (PDF)
Bacolla A, Larson JE, Collins JR, Li J, Milosavljevic A, Stenson PD, Cooper DN, Wells RD: Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties. Genome Res 18(10):1545-1553, 2008. PubMed Abstract Full Text (HTML) Full Text (PDF)
Mort M, Ivanov D, Cooper DN, Chuzhanova NA: A meta-analysis of nonsense mutations causing human genetic disease. Hum Mutat 29(8):1037-1047, 2008. PubMed Abstract   Full Text (PDF)
Radivojac P, Baenziger PH, Kann MG, Mort ME, Hahn MW, Mooney SD: Gain and loss of phosphorylation sites in human cancer. Bioinformatics 24(16):i241-247, 2008. PubMed Abstract Full Text (HTML) Full Text (PDF)
Stenson PD, Ball E, Howells K, Phillips A, Mort M, Cooper DN: Human Gene Mutation Database: towards a comprehensive central mutation database. J Med Genet 45(2):124-126, 2008. PubMed Extract Full Text (HTML) Full Text (PDF)
Chen JM, Cooper DN, Chuzhanova N, Ferec C, Patrinos GP: Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet 8(10):762-775, 2007. PubMed Abstract Full Text (HTML) Full Text (PDF)
Vogt G, Vogt B, Chuzhanova N, Julenius K, Cooper DN, Casanova JL: Gain-of-glycosylation mutations. Curr Opin Genet Dev 17(3):245-251, 2007. PubMed   Full Text (HTML)  
Rhesus Macaque Genome Sequencing and Analysis Consortium: Evolutionary and biomedical insights from the rhesus macaque genome. Science 316(5822):222-234, 2007. PubMed Abstract Full Text (HTML) Full Text (PDF)
Krawczak M, Thomas NS, Hundrieser B, Mort M, Wittig M, Hampe J, Cooper DN: Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mRNA splicing. Hum Mutat 28(2):150-158, 2007. PubMed Abstract   Full Text (PDF)
Antonarakis SE, Cooper DN. Mutations in human genetic disease. Nature and consequences. Chap. 7 in Principles and Practice of Medical Genetics. 5th Ed. DL Rimoin, JM Connor, RE Pyeritz, BR Korf (Eds), Churchill Livingstone, Edinburgh, pp101-128, 2007.
     
Chuzhanova N, Cooper DN, Ferec C, Chen JM: Searching for potential microRNA-binding site mutations amongst known disease-associated 3' UTR variants. Genomic Med 1(1-2):29-33, 2007. PubMed
Abstract Full Text (HTML) Full Text (PDF)
Chen JM, Ferec C, Cooper DN: Mechanism of Alu integration into the human genome. Genomic Med 1(1-2):9-17, 2007. PubMed
Abstract Full Text (HTML) Full Text (PDF)
Han S, Cooper DN, Bowden PE: Utilization of a cryptic noncanonical donor splice site in the KRT14 gene causes a mild form of epidermolysis bullosa simplex. Br J Dermatol 155(1):201-203, 2006. PubMed
Abstract Full Text (HTML) Full text (PDF)
Chen JM, Ferec C, Cooper DN: A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes I: general principles and overview. Hum Genet 120(1):1-21, 2006. PubMed
Abstract Full Text (HTML) Full Text (PDF)
Chen JM, Ferec C, Cooper DN: LINE-1 Endonuclease-Dependent Retrotranspositional Events Causing Human Genetic Disease: Mutation Detection Bias and Multiple Mechanisms of Target Gene Disruption. J Biomed Biotechnol 2006(1):56182, 2006. PubMed PubMed Central
Chen JM, Ferec C, Cooper DN: A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3' UTR variants. Hum Genet 120(3):301-333, 2006. PubMed Abstract Full Text (HTML) Full Text (PDF)
Vogt G, Chapgier A, Chuzhanova N, Feinberg J, Fieschi C, Boisson-Dupuis S, Alcais A, Abel L, Cooper DN, Casanova JL: [Gains of glycosylation mutations]. Med Sci (Paris) 22(5): 480-482, 2006. PubMed Journal
Imtiaz A. Khan, Matthew Mort, Paul R. Buckland, Michael C. O’Donovan, David N. Cooper and Nadia A. Chuzhanova: In silico discrimination of single nucleotide polymorphisms and pathological mutations in human gene promoter regions by means of local DNA sequence context and regularity. In Silico Biology 6: 0003, 2006. Abstract Full Text (HTML)  
Baser ME; Contributors to the International NF2 Mutation Database. The distribution of constitutional and somatic mutations in the neurofibromatosis 2 gene. Hum Mutat 27(4): 297-306, 2006. PubMed Abstract   Full Text (PDF)
Stylianos E. Antonarakis, Ewan Birney, Anthony J. Brookes, Lon Cardon, David N. Cooper, Johan T. den Dunnen, Simon Heath, Karen Kennedy, Hans Lehrach, George P. Patrinos, Stefan Schreiber, Kári Stefánsson, Johan van der Lei, Gert-Jan Van Ommen, Edgar Wingender, Richard Wooster: EU Workshop Report on European Database and Analysis Resources for Research in Human Genetic Variation. Brussels workshop, 2-3 March 2006.   Full Text  
Abeysinghe SS, Chuzhanova N, Cooper DN: Gross deletions and translocations in human genetic disease. Genome Dyn 1:17-34, 2006. PubMed Abstract    
David N. Cooper, Peter D. Stenson and Nadia A. Chuzhanova: The human gene mutation database (HGMD) and its exploitation in the study of mutational mechanisms. Current Protocols in Bioinformatics, Unit 1.13, 2005.      
Chen JM, Chuzhanova N, Stenson PD, Ferec C, Cooper DN: Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions. Hum Mutat 26(4): 362-373, 2005. PubMed Abstract   Full Text (PDF)
Ball EV, Stenson PD, Abeysinghe SS, Krawczak M, Cooper DN, Chuzhanova NA: Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat 26(3): 205-213, 2005. PubMed Abstract   Full Text (PDF)
Chen JM, Stenson PD, Cooper DN, Ferec C: A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 117(5): 411-427, 2005. PubMed Abstract    
Chen JM, Chuzhanova N, Stenson PD, Ferec C, Cooper DN: Complex gene rearrangements caused by serial replication slippage. Hum Mutat 26:125-134, 2005. PubMed Abstract   Full Text (PDF)
Vogt G, Chapgier A, Yang K, Chuzhanova N, Feinberg J, Fieschi C, Boisson-Dupuis S, Alcais A, Filipe-Santos O, Bustamante J, de Beaucoudrey L, Al-Mohsen I, Al-Hajjar S, Al-Ghonaium A, Adimi P, Mirsaeidi M, Khalilzadeh S, Rosenzweig S, de la Calle Martin O, Bauer TR, Puck JM, Ochs HD, Furthner D, Engelhorn C, Belohradsky B, Mansouri D, Holland SM, Schreiber RD, Abel L, Cooper DN, Soudais C, Casanova JL: Gains of glycosylation comprise an unexpectedly large group of pathogenic mutations. Nat Genet 37(7): 692-700, 2005. PubMed
Abstract Full text (HTML) Full text (PDF)
Chen JM, Chuzhanova N, Stenson PD, Ferec C, Cooper DN: Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage. Hum Mutat 25(2): 207-221, 2005. PubMed Abstract   Full text (PDF)
Cooper DN, Stenson PD: The human gene mutation database.Appendix III, The Metabolic and Molecular Bases of Inherited Disease. 9th Edition. CR Scriver, AL Beaudet, WS Sly, D. Valle Eds. In press. McGraw-Hill, New York, 2005.      
Bacolla A, Jaworski A, Larson JE, Jakupciak JP, Chuzhanova N, Abeysinghe SS, O'Connell CD, Cooper DN, Wells RD: Breakpoints of gross deletions coincide with non-B DNA conformations. Proc Natl Acad Sci U S A 101(39): 14162-14167, 2004. PubMed Abstract Full text (HTML) Full text (PDF)
Huang H, Winter EE, Wang H, Weinstock KG, Xing H, Goodstadt L, Stenson PD, Cooper DN, Smith D, Alba MM, Ponting CP, Fechtel K: Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. Genome Biol 5(7): R47, 2004. PubMed Abstract Full text (HTML) Full text (PDF)
Rat Genome Sequencing Consortium: Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982): 493-521, 2004. PubMed Abstract Full text (HTML) Full text (PDF)
Abeysinghe SS, Stenson PD, Krawczak M, Cooper DN: Gross Rearrangement Breakpoint Database (GRaBD). Hum Mutat 23(3):219-221, 2004. PubMed Abstract   Full text (PDF)
Audrezet MP, Chen JM, Raguenes O, Chuzhanova N, Giteau K, Le Marechal C, Quere I, Cooper DN, Ferec C: Genomic rearrangements in the CFTR gene: extensive allelic heterogeneity and diverse mutational mechanisms. Hum Mutat 23(4):343-357, 2004 . PubMed Abstract   Full text (PDF)
Antonarakis SE, Krawczak M, Cooper DN: Disease-causing mutations in the human genome. Eur J Pediatr 159 Suppl 3:S173-178, 2004. PubMed      
Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, Abeysinghe S, Krawczak M, Cooper DN: Human Gene Mutation Database (HGMD®): 2003 update. Hum Mutat 21(6): 577-581, 2003. PubMed Abstract   Full text (PDF)
Abeysinghe SS, Chuzhanova N, Krawczak M, Ball EV, Cooper DN: Translocation and gross deletion breakpoints in human inherited disease and cancer I: Nucleotide composition and recombination-associated motifs. Hum Mutat 22(3): 229-244, 2003. PubMed
Abstract   Full text (PDF)
Chuzhanova N, Abeysinghe SS, Krawczak M, Cooper DN: Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends. Hum Mutat 22(3): 245-251, 2003. PubMed Abstract   Full text (PDF)
Chuzhanova NA, Anassis EJ, Ball EV, Krawczak M, Cooper DN: Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat 21(1): 28-44, 2003. PubMed Abstract   Full text (PDF)
Antonarakis SE, Cooper DN: Mutations in human genetic disease: nature and consequences. Nature Encyclopaedia of the Human Genome. Vol 4, pp 227-253. Nature Publishing Group, London, 2003.      
Turner C, Killoran C, Thomas NS, Rosenberg M, Chuzhanova NA, Johnston J, Kemel Y, Cooper DN, Biesecker LG: Human genetic disease caused by de novo mitochondrial-nuclear DNA transfer. Hum Genet 112(3): 303-309, 2003. PubMed Abstract    
Terp BN, Cooper DN, Christensen IT, Jorgensen FS, Bross P, Gregersen N, Krawczak M: Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease. Hum Mutation 20(2): 98-109, 2002. PubMed Abstract   Full Text (PDF)
Antonarakis SE, Krawczak M, Cooper DN: The nature and mechanisms of human gene mutation. Chapter 2 in The Genetic Basis of Human Cancer. 2nd edition. B Vogelstein, KW Kinzler, Eds. pp 7-41. McGraw-Hill, New York, 2002.      
Antonarakis SE, Krawczak M, Cooper DN: Mutations in human disease: nature and consequences. Chapter 5 in Principles and Practice of Medical Genetics. 4th edition. DL Rimoin, JM Connor, RE Pyeritz, BR Korf, Eds. pp 83-103. Churchill Livingstone, Edinburgh, 2002.      
Antonarakis SE, Krawczak M, Cooper DN: The nature and mechanisms of human gene mutation. Chapter 13 in The Metabolic and Molecular Bases of Inherited Disease. 8th Edition. CR Scriver, AL Beaudet, WS Sly, D Valle, Eds. pp 343-377. McGraw-Hill, New York, 2001.      
Krawczak M, Chuzanova NA, Stenson PD, Johansen BN, Ball EV, Cooper DN: Changes in primary DNA sequence complexity influence the phenotypic consequences of mutations in human gene regulatory regions. Hum Genet 107(4): 362-365, 2000. PubMed

Abstract

 

  Full text (PDF)
Krawczak M, Ball EV, Fenton I, Stenson PD, Abeysinghe S, Thomas N, Cooper DN: Human Gene Mutation Database - a biomedical information and research resource. Hum Mutat 15(1): 45-51, 2000. PubMed Abstract   Full text (PDF)
Antonarakis SE, Krawczak M, Cooper DN: Disease-causing mutations in the human genome. Eur J Pediatr 159: Suppl 3: S173-S178, 2000. PubMed Abstract    
Krawczak M, Ball EV, Stenson PD, Cooper DN: HGMD: The human gene mutation database. Chapter 8 in Bioinformatics; Databases and Systems. Ed. SI Letovsky. pp 99-104, Kluwer Academic Publishers, Boston, 1999.      
Wacey AI, Cooper DN, Liney D, Hovig E, Krawczak M: Disentangling the perturbational effects of amino acid substitutions in the DNA-binding domain of p53. Hum Genet 104(1): 15-22, 1999. PubMed Abstract   Full text (PDF)
Cooper DN, Ball EV, Krawczak M: The human gene mutation database. Nucleic Acids Res 26(1): 285-287, 1998. PubMed Abstract Full text (HTML) Full text (PDF)
Krawczak M, Ball EV, Cooper DN: Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes. Am J Hum Genet 63: 474-488, 1998. PubMed Abstract Full text (HTML) Full text (PDF)
Cooper DN, Krawczak M, Antonarakis SE: The nature and mechanisms of human gene mutation. Chapter 3 in The Genetic Basis of Human Cancer. B Vogelstein, KW Kinzler, Eds. pp 65-94. McGraw-Hill, New York, 1998.      
Krawczak M, Cooper DN: The human gene mutation database. Trends Genet 13(3): 121-122, 1997. PubMed      
Krawczak M, Cooper DN: The human gene mutation database (HGMD). Genome Digest 3: 7-8, 1996.      
Cooper DN, Krawczak M: Human gene mutation database. Hum Genet 98(5): 629, 1996. PubMed Abstract   Full text (PDF)
Krawczak M, Cooper DN: Core database. Nature 374 (6521): 402, 1995. PubMed      
Krawczak M, Reiss J, Cooper DN: The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences. Hum Genet 90(1-2): 41-54, 1992. PubMed      
Cooper DN, Krawczak M: Mechanism of insertional mutagenesis in human genes causing genetic disease. Human Genetics 87: 409-415, 1991. PubMed      
Krawczak M, Cooper DN: Gene deletions causing human genetic disease: Mechanisms of mutagenesis and the role of the local DNA sequence environment. Hum Genet 86:425-441, 1991. PubMed      
Cooper DN, Krawczak M: The mutational spectrum of single base-pair substitutions causing human genetic disease: patterns and predictions. Hum Genet 85:55-74, 1990. PubMed  

Articles published by other research groups that have utilised HGMD data

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