HGMD

Human Gene Mutation Database

Articles co-authored by members of HGMD

ReferenceJournal links
Maffucci P, Bigio B, Rapaport F, Cobat A, Borghesi A, Lopez M, Patin E, Bolze A, Shang L, Bendavid M, Scott EM, Stenson PD, Cunningham-Rundles C, Cooper DN, Gleeson JG, Fellay J, Quintana-Murci L, Casanova JL, Abel L, Boisson B, Itan Y. Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis. Proc Natl Acad Sci U S A 116:950-959, 2019. PubMed Full Text (HTML)
Jagadeesh KA, Paggi JM, Ye JS, Stenson PD, Cooper DN, Bernstein JA, Bejerano G. S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing. Nat Genet epub, 2019. PubMed Full Text (HTML)
Requena D, Maffucci P, Bigio B, Shang L, Abhyankar A, Boisson B, Stenson PD, Cooper DN, Cunningham-Rundles C, Casanova JL, Abel L, Itan Y. CDG: An Online Server for Detecting Biologically Closest Disease-Causing Genes and its Application to Primary Immunodeficiency. Front Immunol 9:1340, 2018. PubMed Full Text (HTML)
Zhao H, Yang Y, Lu Y, Mort M, Cooper DN, Zuo Z, Zhou Y. Quantitative mapping of genetic similarity in human heritable diseases by shared mutations. Hum Mutat 39:292-301, 2018. PubMed Full Text (HTML)
Ferlaino M, Rogers MF, Shihab HA, Mort M, Cooper DN, Gaunt TR, Campbell C. An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome. BMC Bioinformatics 18:442, 2017. PubMed Full Text (HTML)
Liu T, Ish-Shalom S, Torng W, Lafita A, Bock C, Mort M, Cooper DN, Bliven S, Capitani G, Mooney SD, Altman RB. Biological and functional relevance of CASP predictions. Proteins epub, 2017. PubMed Full Text (HTML)
Rogers MF, Shihab HA, Mort M, Cooper DN, Gaunt TR, Campbell C. FATHMM-XF: accurate prediction of pathogenic point mutations via extended features. Bioinformatics epub, 2017. PubMed Full Text (HTML)
Pagel KA, Pejaver V, Lin GN, Nam HJ, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. Bioinformatics 33:i389-i398, 2017. PubMed Full Text (HTML)
Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 136:665-677, 2017. PubMed Full Text (HTML)
Liang S, Tippens ND, Zhou Y, Mort M, Stenson PD, Cooper DN, Yu H. iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations. Genome Biol 18:10, 2017. PubMed Full Text (HTML)
Jagadeesh KA, Wenger AM, Berger MJ, Guturu H, Stenson PD, Cooper DN, Bernstein JA, Bejerano G. M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. Nat Genet 48:1581-1586, 2016. PubMed Full Text (HTML)
Azevedo L, Mort M, Costa AC, Silva RM, Quelhas D, Amorim A, Cooper DN. Improving the in silico assessment of pathogenicity for compensated variants. Eur J Hum Genet 25:2-7, 2017. PubMed Full Text (HTML)
Li M, Feng W, Zhang X, Yang Y, Wang K, Mort M, Cooper DN, Wang Y, Zhou Y, Liu Y. ExonImpact: Prioritizing Pathogenic Alternative Splicing Events. Hum Mutat epub, 2016. PubMed Full Text (HTML)
Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, Do R, Flannick J, Fromer M, Gauthier L, Goldstein J, Gupta N, Howrigan D, Kiezun A, Kurki MI, Moonshine AL, Natarajan P, Orozco L, Peloso GM, Poplin R, Rivas MA, Ruano-Rubio V, Rose SA, Ruderfer DM, Shakir K, Stenson PD, Stevens C, Thomas BP, Tiao G, Tusie-Luna MT, Weisburd B, Won HH, Yu D, Altshuler DM, Ardissino D, Boehnke M, Danesh J, Donnelly S, Elosua R, Florez JC, Gabriel SB, Getz G, Glatt SJ, Hultman CM, Kathiresan S, Laakso M, McCarroll S, McCarthy MI, McGovern D, McPherson R, Neale BM, Palotie A, Purcell SM, Saleheen D, Scharf JM, Sklar P, Sullivan PF, Tuomilehto J, Tsuang MT, Watkins HC, Wilson JG, Daly MJ, MacArthur DG; Exome Aggregation Consortium. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536:285-291, 2016. PubMed Full Text (HTML)
Knecht C, Mort M, Junge O, Cooper DN, Krawczak M, Caliebe A. IMHOTEP-a composite score integrating popular tools for predicting the functional consequences of non-synonymous sequence variants. Nucleic Acids Res 2016 epub, 2016. PubMed Full Text (HTML)
Matos S, Campos D, Pinho R, Silva RM, Mort M, Cooper DN, Oliveira JL. Mining clinical attributes of genomic variants through assisted literature curation in Egas. Database (Oxford) 2016 epub, 2016. PubMed Full Text (HTML)
Meyer MJ, Lapcevic R, Romero AE, Yoon M, Das J, Beltrán JF, Mort M, Stenson PD, Cooper DN, Paccanaro A, Yu H. mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome. Hum Mutat 37:447-456, 2016. PubMed Abstract Full Text (HTML)
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 37:65-73, 2016. 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 37:28-35, 2016. 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 36:1034-1038, 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
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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

 

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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  

Selected articles published by other research or clinical groups that have utilised HGMD data

ReferenceJournal links
Cirincione et al: Pathway networks generated from human disease phenome. BMC Med Genomics 11(Suppl 3):75, 2018. PubMed Full Text (HTML)
Pugh et al: Use of Big Data to Estimate Prevalence of Defective DNA Repair Variants in the US Population. JAMA Dermatol epub, 2018. PubMed Full Text (HTML)
Gianferante et al: Whole-exome sequencing of nevoid basal cell carcinoma syndrome families and review of Human Gene Mutation Database PTCH1 mutation data. Mol Genet Genomic Med 6:1168-1180, 2018. PubMed Full Text (HTML)
DiStefano et al: Curating Clinically Relevant Transcripts for the Interpretation of Sequence Variants. J Mol Diagn 20:789-801, 2018. PubMed Full Text (HTML)
Niazi et al: The Development and Validation of Clinical Exome-Based Panels Using ExomeSlicer: Considerations and Proof of Concept Using an Epilepsy Panel. J Mol Diagn 20:643-652, 2018. PubMed Full Text (HTML)
Bhattacharya S et al: Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia. Genome Res 28:423-431, 2018. PubMed Full Text (HTML)
Kelly MA et al: Adaptation and validation of the ACMG/AMP variant classification framework for MYH7-associated inherited cardiomyopathies: recommendations by ClinGen's Inherited Cardiomyopathy Expert Panel. Genet Med 20:351-359, 2018. PubMed Full Text (HTML)
di Iulio J et al: The human noncoding genome defined by genetic diversity. Nat Genet 50:333-337, 2018. PubMed Full Text (HTML)
Chora JR et al: Analysis of publicly available LDLR, APOB, and PCSK9 variants associated with familial hypercholesterolemia: application of ACMG guidelines and implications for familial hypercholesterolemia diagnosis. Genet Med 20:591-598, 2018. PubMed Full Text (HTML)
Gosalia N et al: MAPPIN: a method for annotating, predicting pathogenicity and mode of inheritance for nonsynonymous variants. Nucleic Acids Res epub, 2017. PubMed Full Text (HTML)
Kaltman JR et al: Re-evaluating pathogenicity of variants associated with the long-QT syndrome. J Cardiovasc Electrophysiol epub, 2017. PubMed Full Text (HTML)
Balasubramanian S et al: Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes. Nat Commun 8:382, 2017. PubMed Full Text (HTML)
Wiel L et al: Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics. Hum Mutat 2017 epub. PubMed Full Text (HTML)
Zhang T et al: Syntool: A Novel Region-Based Intolerance Score to Single Nucleotide Substitution for Synonymous Mutations Predictions Based on 123,136 Individuals. Biomed Res Int 2017:5096208, 2017. PubMed Full Text (HTML)
Růžička M et al: DNA mutation motifs in the genes associated with inherited diseases. PLoS One 12:e0182377, 2017. PubMed Full Text (HTML)
Huang YF et al: Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nat Genet 49:618-624, 2017. PubMed Full Text (HTML)
Carss KJ et al: Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease. Am J Hum Genet 100:75-90, 2017. PubMed Full Text (HTML)
Das R and Ghosh SK: Genetic variants of the DNA repair genes from Exome Aggregation Consortium (EXAC) database: significance in cancer. DNA Repair (Amst) 52:92-102, 2017. PubMed Full Text (HTML)
Jalkh N et al: Next-generation sequencing in familial breast cancer patients from Lebanon. BMC Med Genomics 10:8, 2017. PubMed Full Text (HTML)
Kobayashi Y et al:Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Genome Med 9:13, 2017. PubMed Full Text (HTML)
Ellingford JM et al:Molecular findings from 537 individuals with inherited retinal disease. J Med Genet epub, 2016. PubMed Full Text (HTML)
Wilfert AB et al: Genome-wide significance testing of variation from single case exomes. Nat Genet 48:1455-1461, 2016. PubMed Full Text (HTML)
Kumar S et al: Localized structural frustration for evaluating the impact of sequence variants Nucleic Acids Res epub, 2016. PubMed Full Text (HTML)
Das R and Ghosh SK: Genetic variants of the DNA repair genes from Exome Aggregation Consortium (EXAC) database: significance in cancer. DNA Repair (Amst) epub, 2017. PubMed
Groth KA et al: Evaluating the quality of Marfan genotype-phenotype correlations in existing FBN1 databases. Genet Med epub, 2016. PubMed Full Text (HTML)
Abouelhoda M et al:Revisiting the morbid genome of Mendelian disorders. Genome Biol 17:235, 2016. PubMed
Ghouse J et al: Numerous Brugada syndrome-associated genetic variants have no effect on J-point elevation, syncope susceptibility, malignant cardiac arrhythmia, and all-cause mortality. Genet Med epub, 2016. PubMed Full Text (HTML)
Li H et al: Prioritization of non-coding disease-causing variants and long non-coding RNAs in liver cancer. Oncol Lett 12:3987-3994, 2016. PubMed
Ma M et al: IDENTIFY CANCER DRIVER GENES THROUGH SHARED MENDELIAN DISEASE PATHOGENIC VARIANTS AND CANCER SOMATIC MUTATIONS. Pac Symp Biocomput 22:473-484, 2016. PubMed
Nouhravesh N et al: Analyses of more than 60,000 exomes questions the role of numerous genes previously associated with dilated cardiomyopathy. Mol Genet Genomic Med 4:617-623, 2016. PubMed
Telenti A et al: Deep sequencing of 10,000 human genomes. Proc Natl Acad Sci U S A 113:11901-11906, 2016. PubMed Full Text (HTML)
Kessler MD et al: Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry. Nat Commun 7:12521, 2016. PubMed Full Text (HTML)
Hu H et al: VARPRISM: incorporating variant prioritization in tests of de novo mutation association. Genome Med 8:91, 2016. PubMed Full Text (HTML)
Walsh R et al: Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genet Med epub, 2016. PubMed Full Text (HTML)
Chen Q et al: [Evaluation of performance of five bioinformatics software for the prediction of missense mutations]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 33:625-628, 2016. PubMed
Kaplun A et al: Establishing and validating regulatory regions for variant annotation and expression analysis. BMC Genomics 17 S2:393, 2016. PubMed Full Text (HTML)
Li H and Lv X: Functional annotation of noncoding variants and prioritization of cancer-associated lncRNAs in lung cancer. Oncol Lett 12:222-230, 2016. PubMed Full Text (HTML)
Simeoni I et al: A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders. Blood 127::2791-2803, 2016. PubMed Full Text (HTML)
Shibata A et al: IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome. J Hum Genet 61:633-640, 2016. PubMed Full Text (HTML)
Stavropoulos DJ et al: Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine NPJ Gen Med 1:15012, 2016. Full Text (HTML)
Konig E et al: Computational assessment of feature combinations for pathogenic variant prediction. Mol Genet Genomic Med 4:431-446, 2016. PubMed Full Text (HTML)
Aggarwala V et al: An expanded sequence context model broadly explains variability in polymorphism levels across the human genome. Nat Genet 48:349-355, 2016. PubMed Full Text (HTML)
Du C et al: Mutation pattern is an influential factor on functional mutation rates in cancer. Cancer Cell Int 16:2, 2016. PubMed Full Text (HTML)
Srivastava I et al: dbAARD & AGP: A computational pipeline for the prediction of genes associated with age related disorders. J Biomed Inform 60:153-161, 2016. PubMed Full Text (HTML)
Vo TV et al: A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human. Cell 164:310-323, 2016. PubMed Full Text (HTML)
Dopazo J et al: 267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation. Mol Biol Evol 33:1205-1218, 2016. PubMed Full Text (HTML)
Gussow AB et al: The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes. Genome Biol 17:9, 2016. PubMed Full Text (HTML)
Adams MC et al: The promise and peril of genomic screening in the general population. Genet Med 18:593-599, 2016. PubMed Full Text (HTML)
Wu M et al: Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data. Sci Rep 5:14955, 2015. PubMed Full Text (HTML)
Dewey FE et al: Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data. PLoS Genet 11:e1005496, 2015. PubMed Full Text (HTML)
Olfson E et al: Identification of Medically Actionable Secondary Findings in the 1000 Genomes. PLoS One 10:e0135193, 2015. PubMed Full Text (HTML)
Zhou J and Troyanskaya OG: Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods 12:931-934, 2015. PubMed Full Text (HTML)
Alipanahi B et al: Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nat Biotechnol 33:831-838, 2015. PubMed Full Text (HTML)
Cheng WY et al: DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts. Bioinformatics 32:151-153, 2016. PubMed Full Text (HTML)
Wang J et al: BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations. Nucleic Acids Res 43:e147, 2015. PubMed Full Text (HTML)
Middha S et al: How well do whole exome sequencing results correlate with medical findings? A study of 89 Mayo Clinic Biobank samples. Front Genet 6:244, 2015. PubMed Full Text (HTML)
Gambin T et al: Secondary findings and carrier test frequencies in a large multiethnic sample. Genome Med 7:54, 2015. PubMed Full Text (HTML)
Ma M et al: Disease-associated variants in different categories of disease located in distinct regulatory elements. BMC Genomics 16:S3, 2015. PubMed Full Text (HTML)
Jang MA et al: Frequency and spectrum of actionable pathogenic secondary findings in 196 Korean exomes. Genet Med 17:1007-1011, 2015. PubMed Full Text (HTML)
Min L et al: Computational Analysis of Missense Variants of G Protein-Coupled Receptors Involved in the Neuroendocrine Regulation of Reproduction. Neuroendocrinology 103:230-239, 2016. PubMed Full Text (HTML)
Xiong HY et al: RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science 347:1254806, 2015. PubMed Full Text (HTML)
Sahni N et al: Widespread macromolecular interaction perturbations in human genetic disorders. Cell 161:647-660, 2015. PubMed Full Text (HTML)
Fuxman Bass JI et al: Human gene-centered transcription factor networks for enhancers and disease variants. Cell 161:661-673, 2015. PubMed Full Text (HTML)
Jurgens J et al: Assessment of incidental findings in 232 whole-exome sequences from the Baylor-Hopkins Center for Mendelian Genomics. Genet Med 17:782-788, 2015. PubMed Full Text (HTML)
Vail PJ et al: Comparison of locus-specific databases for BRCA1 and BRCA2 variants reveals disparity in variant classification within and among databases. J Community Genet epub, 2015. PubMed Full Text (HTML)
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