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Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes.

Rogozin IB, Roche-Lima A, Lada AG, Belinky F, Sidorenko IA, Glazko GV, Babenko VN, Cooper DN, Pavlov YI.

Cancers (Basel). 2019 Feb 12;11(2). pii: E211. doi: 10.3390/cancers11020211.


Toward a clinical diagnostic pipeline for SPINK1 intronic variants.

Tang XY, Lin JH, Zou WB, Masson E, Boulling A, Deng SJ, Cooper DN, Liao Z, Férec C, Li ZS, Chen JM.

Hum Genomics. 2019 Feb 12;13(1):8. doi: 10.1186/s40246-019-0193-7.


Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis.

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.

Proc Natl Acad Sci U S A. 2019 Jan 15;116(3):950-959. doi: 10.1073/pnas.1808403116. Epub 2018 Dec 27.


The sequencing and interpretation of the genome obtained from a Serbian individual.

Mohammed Ismail W, Pagel KA, Pejaver V, Zhang SV, Casasa S, Mort M, Cooper DN, Hahn MW, Radivojac P.

PLoS One. 2018 Dec 19;13(12):e0208901. doi: 10.1371/journal.pone.0208901. eCollection 2018.


Ultra-deep amplicon sequencing indicates absence of low-grade mosaicism with normal cells in patients with type-1 NF1 deletions.

Summerer A, Schäfer E, Mautner VF, Messiaen L, Cooper DN, Kehrer-Sawatzki H.

Hum Genet. 2019 Jan;138(1):73-81. doi: 10.1007/s00439-018-1961-5. Epub 2018 Nov 26.


SPINK1, PRSS1, CTRC, and CFTR Genotypes Influence Disease Onset and Clinical Outcomes in Chronic Pancreatitis.

Zou WB, Tang XY, Zhou DZ, Qian YY, Hu LH, Yu FF, Yu D, Wu H, Deng SJ, Lin JH, Zhao AJ, Zhao ZH, Wu HY, Zhu JH, Qian W, Wang L, Xin L, Wang MJ, Wang LJ, Fang X, He L, Masson E, Cooper DN, Férec C, Li ZS, Chen JM, Liao Z.

Clin Transl Gastroenterol. 2018 Nov 12;9(11):204. doi: 10.1038/s41424-018-0069-5.


Mis-splicing of the GALNS gene resulting from deep intronic mutations as a cause of Morquio a disease.

Caciotti A, Tonin R, Mort M, Cooper DN, Gasperini S, Rigoldi M, Parini R, Deodato F, Taurisano R, Sibilio M, Parenti G, Guerrini R, Morrone A.

BMC Med Genet. 2018 Oct 11;19(1):183. doi: 10.1186/s12881-018-0694-6.


Phenotypic and genotypic overlap between mosaic NF2 and schwannomatosis in patients with multiple non-intradermal schwannomas.

Kehrer-Sawatzki H, Kluwe L, Friedrich RE, Summerer A, Schäfer E, Wahlländer U, Matthies C, Gugel I, Farschtschi S, Hagel C, Cooper DN, Mautner VF.

Hum Genet. 2018 Jul;137(6-7):543-552. doi: 10.1007/s00439-018-1909-9. Epub 2018 Jul 13.


CDG: An Online Server for Detecting Biologically Closest Disease-Causing Genes and its Application to Primary Immunodeficiency.

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.

Front Immunol. 2018 Jun 27;9:1340. doi: 10.3389/fimmu.2018.01340. eCollection 2018.


Extreme clustering of type-1 NF1 deletion breakpoints co-locating with G-quadruplex forming sequences.

Summerer A, Mautner VF, Upadhyaya M, Claes KBM, Högel J, Cooper DN, Messiaen L, Kehrer-Sawatzki H.

Hum Genet. 2018 Jul;137(6-7):511-520. doi: 10.1007/s00439-018-1904-1. Epub 2018 Jul 10.


Pronounced maternal parent-of-origin bias for type-1 NF1 microdeletions.

Neuhäusler L, Summerer A, Cooper DN, Mautner VF, Kehrer-Sawatzki H.

Hum Genet. 2018 May;137(5):365-373. doi: 10.1007/s00439-018-1888-x. Epub 2018 May 5.


Clinical heterogeneity of mitochondrial NAD kinase deficiency caused by a NADK2 start loss variant.

Pomerantz DJ, Ferdinandusse S, Cogan J, Cooper DN, Reimschisel T, Robertson A, Bican A, McGregor T, Gauthier J, Millington DS, Andrae JLW, Tschannen MR, Helbling DC, Demos WM, Denis S, Wanders RJA, Newman JN, Hamid R, Phillips JA 3rd; Collaborators of UDN.

Am J Med Genet A. 2018 Mar;176(3):692-698. doi: 10.1002/ajmg.a.38602. Epub 2018 Feb 1.


Identification of compound heterozygous variants in the noncoding RNU4ATAC gene in a Chinese family with two successive foetuses with severe microcephaly.

Wang Y, Wu X, Du L, Zheng J, Deng S, Bi X, Chen Q, Xie H, Férec C, Cooper DN, Luo Y, Fang Q, Chen JM.

Hum Genomics. 2018 Jan 25;12(1):3. doi: 10.1186/s40246-018-0135-9.


Genomic variants in the FTO gene are associated with sporadic amyotrophic lateral sclerosis in Greek patients.

Mitropoulos K, Merkouri Papadima E, Xiromerisiou G, Balasopoulou A, Charalampidou K, Galani V, Zafeiri KV, Dardiotis E, Ralli S, Deretzi G, John A, Kydonopoulou K, Papadopoulou E, di Pardo A, Akcimen F, Loizedda A, Dobričić V, Novaković I, Kostić VS, Mizzi C, Peters BA, Basak N, Orrù S, Kiskinis E, Cooper DN, Gerou S, Drmanac R, Bartsakoulia M, Tsermpini EE, Hadjigeorgiou GM, Ali BR, Katsila T, Patrinos GP.

Hum Genomics. 2017 Dec 8;11(1):30. doi: 10.1186/s40246-017-0126-2.


Genomic Medicine Without Borders: Which Strategies Should Developing Countries Employ to Invest in Precision Medicine? A New "Fast-Second Winner" Strategy.

Mitropoulos K, Cooper DN, Mitropoulou C, Agathos S, Reichardt JKV, Al-Maskari F, Chantratita W, Wonkam A, Dandara C, Katsila T, Lopez-Correa C, Ali BR, Patrinos GP.

OMICS. 2017 Nov;21(11):647-657. doi: 10.1089/omi.2017.0141.


DNA polymerase η mutational signatures are found in a variety of different types of cancer.

Rogozin IB, Goncearenco A, Lada AG, De S, Yurchenko V, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI.

Cell Cycle. 2018;17(3):348-355. doi: 10.1080/15384101.2017.1404208. Epub 2018 Feb 15.


Quantitative mapping of genetic similarity in human heritable diseases by shared mutations.

Zhao H, Yang Y, Lu Y, Mort M, Cooper DN, Zuo Z, Zhou Y.

Hum Mutat. 2018 Feb;39(2):292-301. doi: 10.1002/humu.23358. Epub 2017 Nov 21.


Analysis of the Impact of Known SPINK1 Missense Variants on Pre-mRNA Splicing and/or mRNA Stability in a Full-Length Gene Assay.

Wu H, Boulling A, Cooper DN, Li ZS, Liao Z, Férec C, Chen JM.

Genes (Basel). 2017 Oct 10;8(10). pii: E263. doi: 10.3390/genes8100263.


An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome.

Ferlaino M, Rogers MF, Shihab HA, Mort M, Cooper DN, Gaunt TR, Campbell C.

BMC Bioinformatics. 2017 Oct 6;18(1):442. doi: 10.1186/s12859-017-1862-y.


Biological and functional relevance of CASP predictions.

Liu T, Ish-Shalom S, Torng W, Lafita A, Bock C, Mort M, Cooper DN, Bliven S, Capitani G, Mooney SD, Altman RB.

Proteins. 2018 Mar;86 Suppl 1:374-386. doi: 10.1002/prot.25396. Epub 2017 Oct 17.


FATHMM-XF: accurate prediction of pathogenic point mutations via extended features.

Rogers MF, Shihab HA, Mort M, Cooper DN, Gaunt TR, Campbell C.

Bioinformatics. 2018 Feb 1;34(3):511-513. doi: 10.1093/bioinformatics/btx536.


Severe infantile isolated exocrine pancreatic insufficiency caused by the complete functional loss of the SPINK1 gene.

Venet T, Masson E, Talbotec C, Billiemaz K, Touraine R, Gay C, Destombe S, Cooper DN, Patural H, Chen JM, Férec C.

Hum Mutat. 2017 Dec;38(12):1660-1665. doi: 10.1002/humu.23343. Epub 2017 Oct 12.


When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants.

Pagel KA, Pejaver V, Lin GN, Nam HJ, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P.

Bioinformatics. 2017 Jul 15;33(14):i389-i398. doi: 10.1093/bioinformatics/btx272.


Consideration of the haplotype diversity at nonallelic homologous recombination hotspots improves the precision of rearrangement breakpoint identification.

Hillmer M, Summerer A, Mautner VF, Högel J, Cooper DN, Kehrer-Sawatzki H.

Hum Mutat. 2017 Dec;38(12):1711-1722. doi: 10.1002/humu.23319. Epub 2017 Sep 22.


Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants.

Livingstone M, Folkman L, Yang Y, Zhang P, Mort M, Cooper DN, Liu Y, Stantic B, Zhou Y.

Hum Mutat. 2017 Oct;38(10):1336-1347. doi: 10.1002/humu.23283. Epub 2017 Jul 10.


The NF1 somatic mutational landscape in sporadic human cancers.

Philpott C, Tovell H, Frayling IM, Cooper DN, Upadhyaya M.

Hum Genomics. 2017 Jun 21;11(1):13. doi: 10.1186/s40246-017-0109-3. Review.


PRSS1 copy number variants and promoter polymorphisms in pancreatitis: common pathogenetic mechanism, different genetic effects.

Masson E, Chen JM, Cooper DN, Férec C.

Gut. 2018 Mar;67(3):592-593. doi: 10.1136/gutjnl-2017-314443. Epub 2017 Jun 10. No abstract available.


Identification of a functional enhancer variant within the chronic pancreatitis-associated SPINK1 c.101A>G (p.Asn34Ser)-containing haplotype.

Boulling A, Masson E, Zou WB, Paliwal S, Wu H, Issarapu P, Bhaskar S, Génin E, Cooper DN, Li ZS, Chandak GR, Liao Z, Chen JM, Férec C.

Hum Mutat. 2017 Aug;38(8):1014-1024. doi: 10.1002/humu.23269. Epub 2017 Jun 15.


Mutational signatures and mutable motifs in cancer genomes.

Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN.

Brief Bioinform. 2018 Nov 27;19(6):1085-1101. doi: 10.1093/bib/bbx049.


No significant enrichment of rare functionally defective CPA1 variants in a large Chinese idiopathic chronic pancreatitis cohort.

Wu H, Zhou DZ, Berki D, Geisz A, Zou WB, Sun XT, Hu LH, Zhao ZH, Zhao AJ, He L, Cooper DN, Férec C, Chen JM, Li ZS, Sahin-Tóth M, Liao Z.

Hum Mutat. 2017 Aug;38(8):959-963. doi: 10.1002/humu.23254. Epub 2017 May 30.


In vitro recapitulation of the site-specific editing (to wild-type) of mutant IDS mRNA transcripts, and the characterization of IDS protein translated from the edited mRNAs.

Lualdi S, Del Zotto G, Zegarra-Moran O, Pedemonte N, Corsolini F, Bruschi M, Tomati V, Amico G, Candiano G, Dardis A, Cooper DN, Filocamo M.

Hum Mutat. 2017 Jul;38(7):849-862. doi: 10.1002/humu.23243. Epub 2017 May 22.


In silico prioritization and further functional characterization of SPINK1 intronic variants.

Zou WB, Wu H, Boulling A, Cooper DN, Li ZS, Liao Z, Chen JM, Férec C.

Hum Genomics. 2017 May 4;11(1):7. doi: 10.1186/s40246-017-0103-9.


regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution.

Zhang X, Li M, Lin H, Rao X, Feng W, Yang Y, Mort M, Cooper DN, Wang Y, Wang Y, Wells C, Zhou Y, Liu Y.

Hum Genet. 2017 Sep;136(9):1279-1289. doi: 10.1007/s00439-017-1783-x. Epub 2017 Apr 8.


The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies.

Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN.

Hum Genet. 2017 Jun;136(6):665-677. doi: 10.1007/s00439-017-1779-6. Epub 2017 Mar 27. Review.


In vitro and in silico evidence against a significant effect of the SPINK1 c.194G>A variant on pre-mRNA splicing.

Wu H, Boulling A, Cooper DN, Li ZS, Liao Z, Chen JM, Férec C.

Gut. 2017 Dec;66(12):2195-2196. doi: 10.1136/gutjnl-2017-313948. Epub 2017 Mar 20. No abstract available.


The Effects of Moderate Whole Grain Consumption on Fasting Glucose and Lipids, Gastrointestinal Symptoms, and Microbiota.

Cooper DN, Kable ME, Marco ML, De Leon A, Rust B, Baker JE, Horn W, Burnett D, Keim NL.

Nutrients. 2017 Feb 21;9(2). pii: E173. doi: 10.3390/nu9020173.


Emerging genotype-phenotype relationships in patients with large NF1 deletions.

Kehrer-Sawatzki H, Mautner VF, Cooper DN.

Hum Genet. 2017 Apr;136(4):349-376. doi: 10.1007/s00439-017-1766-y. Epub 2017 Feb 17. Review.


IMHOTEP-a composite score integrating popular tools for predicting the functional consequences of non-synonymous sequence variants.

Knecht C, Mort M, Junge O, Cooper DN, Krawczak M, Caliebe A.

Nucleic Acids Res. 2017 Feb 17;45(3):e13. doi: 10.1093/nar/gkw886.


iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations.

Liang S, Tippens ND, Zhou Y, Mort M, Stenson PD, Cooper DN, Yu H.

Genome Biol. 2017 Jan 18;18(1):10. doi: 10.1186/s13059-016-1138-2.


The molecular pathogenesis of schwannomatosis, a paradigm for the co-involvement of multiple tumour suppressor genes in tumorigenesis.

Kehrer-Sawatzki H, Farschtschi S, Mautner VF, Cooper DN.

Hum Genet. 2017 Feb;136(2):129-148. doi: 10.1007/s00439-016-1753-8. Epub 2016 Dec 5. Review.


The Rise and Rise of Exome Sequencing.

Ku CS, Cooper DN, Patrinos GP.

Public Health Genomics. 2016;19(6):315-324. doi: 10.1159/000450991. Epub 2016 Nov 30. Review.


M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity.

Jagadeesh KA, Wenger AM, Berger MJ, Guturu H, Stenson PD, Cooper DN, Bernstein JA, Bejerano G.

Nat Genet. 2016 Dec;48(12):1581-1586. doi: 10.1038/ng.3703. Epub 2016 Oct 24.


Improving the in silico assessment of pathogenicity for compensated variants.

Azevedo L, Mort M, Costa AC, Silva RM, Quelhas D, Amorim A, Cooper DN.

Eur J Hum Genet. 2016 Jan;25(1):2-7. doi: 10.1038/ejhg.2016.129. Epub 2016 Oct 5.


Test Pricing and Reimbursement in Genomic Medicine: Towards a General Strategy.

Vozikis A, Cooper DN, Mitropoulou C, Kambouris ME, Brand A, Dolzan V, Fortina P, Innocenti F, Lee MT, Leyens L, Macek M Jr, Al-Mulla F, Prainsack B, Squassina A, Taruscio D, van Schaik RH, Vayena E, Williams MS, Patrinos GP.

Public Health Genomics. 2016;19(6):352-363. doi: 10.1159/000449152. Epub 2016 Sep 28. Review.


ExonImpact: Prioritizing Pathogenic Alternative Splicing Events.

Li M, Feng W, Zhang X, Yang Y, Wang K, Mort M, Cooper DN, Wang Y, Zhou Y, Liu Y.

Hum Mutat. 2017 Jan;38(1):16-24. doi: 10.1002/humu.23111. Epub 2016 Oct 3.


The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease.

Lugo-Martinez J, Pejaver V, Pagel KA, Jain S, Mort M, Cooper DN, Mooney SD, Radivojac P.

PLoS Comput Biol. 2016 Aug 26;12(8):e1005091. doi: 10.1371/journal.pcbi.1005091. eCollection 2016 Aug.


Analysis of protein-coding genetic variation in 60,706 humans.

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.

Nature. 2016 Aug 18;536(7616):285-91. doi: 10.1038/nature19057.


Discovery and Functional Annotation of PRSS1 Promoter Variants in Chronic Pancreatitis.

Boulling A, Abrantes A, Masson E, Cooper DN, Robaszkiewicz M, Chen JM, Férec C.

Hum Mutat. 2016 Nov;37(11):1149-1152. doi: 10.1002/humu.23053. Epub 2016 Aug 21.


Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants.

Peterson TA, Mort M, Cooper DN, Radivojac P, Kann MG, Mooney SD.

Hum Mutat. 2016 Nov;37(11):1137-1143. doi: 10.1002/humu.23049. Epub 2016 Aug 31.


Mining clinical attributes of genomic variants through assisted literature curation in Egas.

Matos S, Campos D, Pinho R, Silva RM, Mort M, Cooper DN, Oliveira JL.

Database (Oxford). 2016 Jun 7;2016. pii: baw096. doi: 10.1093/database/baw096. Print 2016.

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