dna copy number variations


Summary: Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.

Top Publications

  1. Craddock N, Hurles M, Cardin N, Pearson R, Plagnol V, Robson S, et al. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature. 2010;464:713-20 pubmed publisher
    ..We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases. ..
  2. van Wieringen W, van de Wiel M. Penalized differential pathway analysis of integrative oncogenomics studies. Stat Appl Genet Mol Biol. 2014;13:141-58 pubmed publisher
    ..Furthermore, analyses of the TP53 and TGFb signaling pathways between ER+ and ER- samples from an integrative genomics breast cancer study identify reproducible differential regulatory patterns that corroborate with existing literature. ..
  3. Wei W, Keogh M, Wilson I, Coxhead J, Ryan S, Rollinson S, et al. Mitochondrial DNA point mutations and relative copy number in 1363 disease and control human brains. Acta Neuropathol Commun. 2017;5:13 pubmed publisher
    ..Based on these findings, single nucleotide variants of mtDNA are unlikely to play a major role in the pathogenesis of these neurodegenerative diseases, but mtDNA levels merit further investigation. ..
  4. Escudero B, Herrero D, Torres Y, Cañon S, Molina A, Carmona R, et al. Pol? deficiency induces moderate shortening of P53-/- mouse lifespan and modifies tumor spectrum. DNA Repair (Amst). 2017;54:40-45 pubmed publisher
    ..These results identify a role for Pol? in the prevention of sarcomagenesis on a murine P53-deficient background, in contrast to most other NHEJ factors. ..
  5. Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, et al. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature. 2017;546:370-375 pubmed publisher
    ..In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells. ..
  6. Sahm F, Schrimpf D, Stichel D, Jones D, Hielscher T, Schefzyk S, et al. DNA methylation-based classification and grading system for meningioma: a multicentre, retrospective analysis. Lancet Oncol. 2017;18:682-694 pubmed publisher
    ..German Cancer Aid, Else Kröner-Fresenius Foundation, and DKFZ/Heidelberg Institute of Personalized Oncology/Precision Oncology Program. ..
  7. Li J, Oehlert J, Snyder M, Stevenson D, Shaw G. Fetal de novo mutations and preterm birth. PLoS Genet. 2017;13:e1006689 pubmed publisher
    ..Our study indicates a new mechanism in PTB occurrence independently contributed from fetal genomes, and thus opens a new avenue for future PTB research. ..
  8. Ghamlouch H, Nguyen Khac F, Bernard O. Chronic lymphocytic leukaemia genomics and the precision medicine era. Br J Haematol. 2017;178:852-870 pubmed publisher
    ..In this review we present an overview of the genetic and epigenetic features of CLL and their clinical and biological implications. ..
  9. Uebe S, Ehrlicher M, Ekici A, Behrens F, Böhm B, Homuth G, et al. Genome-wide association and targeted analysis of copy number variants with psoriatic arthritis in German patients. BMC Med Genet. 2017;18:92 pubmed publisher
    ..CNVs are thus good candidate disease variants, while the methods to detect them should be applied cautiously and reproduced by an independent method. ..

More Information

Publications115 found, 100 shown here

  1. Lavrov A, Ustaeva O, Adilgereeva E, Smirnikhina S, Chelysheva E, Shukhov O, et al. Copy number variation analysis in cytochromes and glutathione S-transferases may predict efficacy of tyrosine kinase inhibitors in chronic myeloid leukemia. PLoS ONE. 2017;12:e0182901 pubmed publisher
    ..Wild type genotypes of CYP and GST associate with a worse response to TKI treatment in CML patients. This test can be recommended for further clinical trials. ..
  2. Villacorta Martin C, Craig A, Villanueva A. Divergent evolutionary trajectories in transplanted tumor models. Nat Genet. 2017;49:1565-1566 pubmed publisher
    ..Human-derived tumor models are becoming popular in the context of personalized medicine, but a new study shows that these models could be less representative of primary tumors than previously thought, particularly when using late passages...
  3. . Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487:330-7 pubmed publisher
    ..Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression. ..
  4. Lamping E, Zhu J, Niimi M, Cannon R. Role of Ectopic Gene Conversion in the Evolution of a Candida krusei Pleiotropic Drug Resistance Transporter Family. Genetics. 2017;205:1619-1639 pubmed publisher
    ..krusei belongs to a novel, yet unnamed, third major Saccharomycotina lineage. ..
  5. Zhou Y, Hao Y, Li Y, Li R, Wu R, Wang S, et al. Amplification and up-regulation of MIR30D was associated with disease progression of cervical squamous cell carcinomas. BMC Cancer. 2017;17:230 pubmed publisher
    ..Copy number amplifications of MIR30D gene and enhanced expression of miR-30d were positively correlated with tumor progression in CSCCs, indicating miR-30d might play an oncomiric role in the progression of CSCC. ..
  6. Moffitt A, Ondrejka S, McKinney M, Rempel R, Goodlad J, Teh C, et al. Enteropathy-associated T cell lymphoma subtypes are characterized by loss of function of SETD2. J Exp Med. 2017;214:1371-1386 pubmed publisher
    ..Our data render the most comprehensive genetic portrait yet of this uncommon but lethal disease and may inform future classification schemes. ..
  7. Lindblad K, Bracht J, Williams A, Landweber L. Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development. RNA. 2017;23:1200-1208 pubmed publisher
    ..These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture. ..
  8. Souzeau E, Siggs O, Zhou T, Galanopoulos A, Hodson T, Taranath D, et al. Glaucoma spectrum and age-related prevalence of individuals with FOXC1 and PITX2 variants. Eur J Hum Genet. 2017;25:839-847 pubmed publisher
    ..38). These findings have important implications for the genetic counselling of families affected by Axenfeld-Rieger syndrome, and also suggest that FOXC1 and PITX2 contribute to the genetic architecture of primary glaucoma subtypes. ..
  9. Liu S, Zhang K, Song F, Yang Y, Lv Y, Gao M, et al. Uniparental Disomy of Chromosome 15 in Two Cases by Chromosome Microarray: A Lesson Worth Thinking. Cytogenet Genome Res. 2017;152:1-8 pubmed publisher
    ..As a result, other molecular detection methods, such as methylation analysis and STR marker analysis for UPD, should be supplementary used in this situation. ..
  10. Duclos A, Charbonnier F, Chambon P, Latouche J, Blavier A, Redon R, et al. Pitfalls in the use of DGV for CNV interpretation. Am J Med Genet A. 2011;155A:2593-6 pubmed publisher
  11. Muñoz Amatriaín M, Eichten S, Wicker T, Richmond T, Mascher M, Steuernagel B, et al. Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol. 2013;14:R58 pubmed publisher
    ..Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes. ..
  12. Vanmarsenille L, Giannandrea M, Fieremans N, Verbeeck J, Belet S, Raynaud M, et al. Increased dosage of RAB39B affects neuronal development and could explain the cognitive impairment in male patients with distal Xq28 copy number gains. Hum Mutat. 2014;35:377-83 pubmed
    ..Taken together, we provide evidence that the increased dosage of RAB39B causes a disturbed neuronal development leading to cognitive impairment in patients with this recurrent copy number gain. ..
  13. Vogt J, Bengesser K, Claes K, Wimmer K, Mautner V, van Minkelen R, et al. SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints. Genome Biol. 2014;15:R80 pubmed publisher
  14. Abe H, Aoya D, Takeuchi H, Inoue Murayama M. Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion. BMC Genet. 2017;18:69 pubmed publisher
    ..Our results further suggest that the putative frameshift deletion in exon 2 may potentially affect the expression level of particular isoforms of chicken NRG3. ..
  15. Pfaffl M. The ongoing evolution of qPCR. Methods. 2010;50:215-6 pubmed publisher
  16. Gorla E, Cozzi M, Román Ponce S, Ruiz López F, Vega Murillo V, Cerolini S, et al. Genomic variability in Mexican chicken population using copy number variants. BMC Genet. 2017;18:61 pubmed publisher
    ..Finally this study provides a chicken CNV map based on the 600 K SNP chip array jointly with a genome-wide gene copy number estimates in a native unselected for more than 500 years chicken population. ..
  17. Pera M. Stem cells: The dark side of induced pluripotency. Nature. 2011;471:46-7 pubmed publisher
  18. Magi A, Tattini L, Cifola I, D Aurizio R, Benelli M, Mangano E, et al. EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biol. 2013;14:R120 pubmed
    ..EXCAVATOR is freely available at http://sourceforge.net/projects/excavatortool/. ..
  19. Nashta Ali D, Aliyari A, Ahmadian Moghadam A, Edrisi M, Motahari S, Hossein Khalaj B. Meta-aligner: long-read alignment based on genome statistics. BMC Bioinformatics. 2017;18:126 pubmed publisher
    ..Meta-aligner achieves high recall rates and precisions especially for long reads and high error rates. Also, it improves performance of alignment in the case of PacBio long-reads in comparison with traditional schemes. ..
  20. Sen M, Katragadda S, Ravichandran A, Deshpande G, Parulekar M, Nayanala S, et al. StrandAdvantage test for early-line and advanced-stage treatment decisions in solid tumors. Cancer Med. 2017;6:883-901 pubmed publisher
    ..In conclusion, the SA test comprising a robust and accurate NGS assay combined with clinically relevant IHC tests can detect somatic changes of clinical significance for strategic cancer management in all the stages. ..
  21. Zhang J, Yan S, Liu X, Gan L, Wu Z, Gong Y, et al. Gender-related prognostic value and genomic pattern of intra-tumor heterogeneity in colorectal cancer. Carcinogenesis. 2017;38:837-846 pubmed publisher
    ..Taking MATH into consideration in clinical trial might contribute to better therapeutic strategies in CRC with researches added on in the future. ..
  22. Ivaničová Z, Valarik M, Pánková K, Travnickova M, Dolezel J, Safar J, et al. Heritable heading time variation in wheat lines with the same number of Ppd-B1 gene copies. PLoS ONE. 2017;12:e0183745 pubmed publisher
    ..This effect was associated with changes in the gene expression level and methylation of the Ppd-B1 gene. ..
  23. Weber J, Smalley K, Sondak V, Gibney G. Conjunctival melanomas harbor BRAF and NRAS mutations--Letter. Clin Cancer Res. 2013;19:6329-30 pubmed publisher
  24. Aure M, Vitelli V, Jernström S, Kumar S, Krohn M, Due E, et al. Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome. Breast Cancer Res. 2017;19:44 pubmed publisher
    ..Increasing knowledge of the heterogeneity of the luminal A subtype may add pivotal information to guide therapeutic choices, evidently bringing us closer to improved treatment for this largest subgroup of breast cancer. ..
  25. Thiesen H, Steinbeck F, Maruschke M, Koczan D, Ziems B, Hakenberg O. Stratification of clear cell renal cell carcinoma (ccRCC) genomes by gene-directed copy number alteration (CNA) analysis. PLoS ONE. 2017;12:e0176659 pubmed publisher
  26. Rukh G, Ericson U, Andersson Assarsson J, Orho Melander M, Sonestedt E. Dietary starch intake modifies the relation between copy number variation in the salivary amylase gene and BMI. Am J Clin Nutr. 2017;106:256-262 pubmed publisher
  27. Hull R, Cruz C, Jack C, Houseley J. Environmental change drives accelerated adaptation through stimulated copy number variation. PLoS Biol. 2017;15:e2001333 pubmed publisher
    ..Stimulated CNV therefore represents an unanticipated and remarkably controllable pathway facilitating organismal adaptation to new environments. ..
  28. Glover T, Wilson T, Arlt M. Fragile sites in cancer: more than meets the eye. Nat Rev Cancer. 2017;17:489-501 pubmed publisher
    ..However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers. ..
  29. Blagodatskikh K, Kramarov V, Barsova E, Garkovenko A, Shcherbo D, Shelenkov A, et al. Improved DOP-PCR (iDOP-PCR): A robust and simple WGA method for efficient amplification of low copy number genomic DNA. PLoS ONE. 2017;12:e0184507 pubmed publisher
    ..In summary, iDOP-PCR provided a better quality of the amplified DNA libraries compared to the other WGA methods tested, especially when low amounts of genomic DNA were used as an input material. ..
  30. Zheng X, O Shea E. Cyanobacteria Maintain Constant Protein Concentration despite Genome Copy-Number Variation. Cell Rep. 2017;19:497-504 pubmed publisher
    ..This study provides a quantitative examination of gene expression regulation in cells with variable genome copies and sheds light on the compensation mechanisms for variance in genome copy number. ..
  31. Chalise P, Fridley B. Integrative clustering of multi-level 'omic data based on non-negative matrix factorization algorithm. PLoS ONE. 2017;12:e0176278 pubmed publisher
    ..Application of intNMF is illustrated using both simulated and real data from The Cancer Genome Atlas (TCGA). ..
  32. Serra Juhé C, Martos Moreno G, Bou de Pieri F, Flores R, Gonzalez J, Rodríguez Santiago B, et al. Novel genes involved in severe early-onset obesity revealed by rare copy number and sequence variants. PLoS Genet. 2017;13:e1006657 pubmed publisher
    ..Our data reveal a higher burden of rare CNVs and RSVs in several related genes in patients with EOO compared to controls, and implicate NPY, GRPR, two glutamate receptors and SLCO4C1 in highly penetrant forms of familial obesity. ..
  33. Cuppens T, Depreeuw J, Annibali D, Thomas D, Hermans E, Gommé E, et al. Establishment and characterization of uterine sarcoma and carcinosarcoma patient-derived xenograft models. Gynecol Oncol. 2017;146:538-545 pubmed publisher
    ..We present here a panel of clinically annotated uterine sarcoma and carcinosarcoma PDX models, which will be a useful tool for preclinical testing of new therapies. ..
  34. Russo M, Broach J, Sheldon K, Houser K, Liu D, Kesterson J, et al. Clonal evolution in paired endometrial intraepithelial neoplasia/atypical hyperplasia and endometrioid adenocarcinoma. Hum Pathol. 2017;67:69-77 pubmed publisher
    ..These findings indicate that EIN/AH gives rise to endometrioid adenocarcinoma by a complex process of subclone evolution, not a linear accumulation of molecular events. ..
  35. Barrett M, Deiotte R, Lenkiewicz E, Malasi S, Holley T, Evers L, et al. Clinical study of genomic drivers in pancreatic ductal adenocarcinoma. Br J Cancer. 2017;117:572-582 pubmed publisher
    ..We provide a clinically relevant framework for genomic drivers of PDA and for advancing novel treatments. ..
  36. Liu J, Zhao R, Ye Z, Frey A, Schriver E, Snyder N, et al. Relationship of SULT1A1 copy number variation with estrogen metabolism and human health. J Steroid Biochem Mol Biol. 2017;174:169-175 pubmed publisher
    ..This finding, and the potential association with common allergies reported herein, warrants future studies. ..
  37. Zhang D, Li Z, Xu X, Zhou D, Tang S, Yin X, et al. Deletions at SLC18A1 increased the risk of CRC and lower SLC18A1 expression associated with poor CRC outcome. Carcinogenesis. 2017;38:1057-1062 pubmed publisher
    ..17-0.62, 0.12-0.57 and 0.37-0.68, respectively). In summary, the germline deletions at SLC18A1 contributed to the development of CRC. The role of SLC18A1 required further exploration. ..
  38. Martins Taylor K, Nisler B, Taapken S, Compton T, Crandall L, Montgomery K, et al. Recurrent copy number variations in human induced pluripotent stem cells. Nat Biotechnol. 2011;29:488-91 pubmed publisher
  39. Bekpen C, Künzel S, Xie C, Eaaswarkhanth M, Lin Y, Gokcumen O, et al. Segmental duplications and evolutionary acquisition of UV damage response in the SPATA31 gene family of primates and humans. BMC Genomics. 2017;18:222 pubmed publisher
    ..The increased segmental duplications in hominoids as well as its fast evolution suggest the acquisition of further specific functions particularly in humans. ..
  40. Samulin Erdem J, Arnoldussen Y, Skaug V, Haugen A, Zienolddiny S. Copy number variation, increased gene expression, and molecular mechanisms of neurofascin in lung cancer. Mol Carcinog. 2017;56:2076-2085 pubmed publisher
    ..Moreover, these data suggest that NFASC is a novel regulator of NSCLC cell motility and support a role of NFASC in the regulation of NSCLC progression. ..
  41. Wróbel Ł, Gudys A, Sikora M. Learning rule sets from survival data. BMC Bioinformatics. 2017;18:285 pubmed publisher
    ..Presented algorithm may be especially useful when applied on the genomic and proteomic data as it may contribute to the better understanding of the background of diseases and support their treatments. ..
  42. Kjeldsen E. Characterization of an acquired jumping translocation involving 3q13.31-qter in a patient with de novo acute monocytic leukemia. Exp Mol Pathol. 2017;103:14-25 pubmed publisher
    ..31 occurring in rare cases of acute monocytic leukemia, being associated with adverse prognosis. The impact of shortened telomeres in forming the JT is reviewed. ..
  43. Will A, Cova G, Osterwalder M, Chan W, Wittler L, Brieske N, et al. Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog). Nat Genet. 2017;49:1539-1545 pubmed publisher
    ..Thus, precise spatiotemporal control of developmental gene expression is achieved by complex multipartite enhancer ensembles. Alterations in the composition of such clusters can result in gene misexpression and disease. ..
  44. Dolatabadian A, Patel D, Edwards D, Batley J. Copy number variation and disease resistance in plants. Theor Appl Genet. 2017;130:2479-2490 pubmed publisher
    ..In this paper, we review existing information about CNVs; their importance, role and function, as well as their association with disease resistance in plants. ..
  45. Dai W, Ko J, Choi S, Yu Z, Ning L, Zheng H, et al. Whole-exome sequencing reveals critical genes underlying metastasis in oesophageal squamous cell carcinoma. J Pathol. 2017;242:500-510 pubmed publisher
    ..Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. ..
  46. Pawlyn C, Morgan G. Evolutionary biology of high-risk multiple myeloma. Nat Rev Cancer. 2017;17:543-556 pubmed publisher
  47. Scharf J, Mathews C. Copy number variation in Tourette syndrome: another case of neurodevelopmental generalist genes?. Neurology. 2010;74:1564-5 pubmed publisher
  48. Larson G, Bradley D. How much is that in dog years? The advent of canine population genomics. PLoS Genet. 2014;10:e1004093 pubmed publisher
  49. Zhang J, Zhang S, Wang Y, Zhang X. Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data. BMC Syst Biol. 2013;7 Suppl 2:S4 pubmed publisher
    ..In addition to presenting a generally applicable methodology, our findings provide several candidate pathways or core modules recurrently perturbed in GBM or ovarian carcinoma for further studies. ..
  50. Vincent Chong V, Salahshourifar I, Woo K, Anwar A, Razali R, Gudimella R, et al. Genome wide profiling in oral squamous cell carcinoma identifies a four genetic marker signature of prognostic significance. PLoS ONE. 2017;12:e0174865 pubmed publisher
    ..Co-alteration of 7p, 8q, 9p and 11q was found to be associated with clinico-pathologic parameters and poor survival. These regions contain genes that play critical roles in tumourigenesis pathways. ..
  51. Silva G, Siegel M, Mose L, Parker J, Sun W, Perou C, et al. SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling. Genome Biol. 2017;18:66 pubmed publisher
    ..SynthEx robustly identifies CNAs using sequencing data without the additional costs associated with matched normal specimens. ..
  52. Liu M, Moon S, Wang L, Kim S, Kim Y, Hwang M, et al. On the association analysis of CNV data: a fast and robust family-based association method. BMC Bioinformatics. 2017;18:217 pubmed publisher
    ..We found that statistical analysis with the expected copy number is more powerful than the statistic with the probe intensity measurements regardless of the accuracy of the estimation of copy numbers. ..
  53. Xi L, BELYAEV A, Spurgeon S, Wang X, Gong H, Aboukhalil R, et al. New library construction method for single-cell genomes. PLoS ONE. 2017;12:e0181163 pubmed publisher
    ..Each step of the protocol can be quantitatively characterized. Our shallow sequencing data show that the library is tightly distributed and is useful for the determination of copy number variations. ..
  54. Heidary M, Auer M, Ulz P, Heitzer E, Petru E, Gasch C, et al. The dynamic range of circulating tumor DNA in metastatic breast cancer. Breast Cancer Res. 2014;16:421 pubmed publisher
    ..The dynamic range of ctDNA varies substantially in patients with metastatic breast cancer. This has important implications for the use of ctDNA as a predictive and prognostic biomarker. ..
  55. Hayes M, Li J. An integrative framework for the identification of double minute chromosomes using next generation sequencing data. BMC Genet. 2015;16 Suppl 2:S1 pubmed publisher
    ..The software that implements the framework can be accessed here: https://github.com/mhayes20/DMFinder ..
  56. Gschwind A, Singh A, Certa U, Reymond A, Heckel T. Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis. BMC Genomics. 2017;18:144 pubmed publisher
    ..We suggest that this genetic diversity should be taken into account when using Cynomolgus macaques as models. ..
  57. Cai N, Bigdeli T, Kretzschmar W, Li Y, Liang J, Hu J, et al. 11,670 whole-genome sequences representative of the Han Chinese population from the CONVERGE project. Sci Data. 2017;4:170011 pubmed publisher
    ..Molecular phenotypes, such as copy number variations and structural variations can be detected, quantified and analysed in similar ways. ..
  58. Walker L, Pearson J, Wiggins G, Giles G, Hopper J, Southey M. Increased genomic burden of germline copy number variants is associated with early onset breast cancer: Australian breast cancer family registry. Breast Cancer Res. 2017;19:30 pubmed publisher
    ..02 and P = 0.03, respectively). These results suggest rare CNVs might have a role in breast cancer susceptibility, at least for disease at a young age. ..
  59. Yang L, Du L, Yue Y, Huang Y, Zhou Q, Cao S, et al. miRNA Copy Number Variants Confer Susceptibility to Acute Anterior Uveitis With or Without Ankylosing Spondylitis. Invest Ophthalmol Vis Sci. 2017;58:1991-2001 pubmed publisher
    ..A low copy number of miR-146a and a high copy number of miR-23a and miR-205 were associated with AAU+AS-. ..
  60. Zou J, Wang E. eTumorType, An Algorithm of Discriminating Cancer Types for Circulating Tumor Cells or Cell-free DNAs in Blood. Genomics Proteomics Bioinformatics. 2017;15:130-140 pubmed publisher
    ..These results suggest that eTumorType could be used for non-invasive diagnosis to determine cancer types based on CNVs of CTCs and cfDNAs. ..
  61. Shuwen H, Xi Y, Yuefen P. Can Mitochondria DNA Provide a Novel Biomarker for Evaluating the Risk and Prognosis of Colorectal Cancer?. Dis Markers. 2017;2017:5189803 pubmed publisher
  62. Ngcungcu T, Oti M, Sitek J, Haukanes B, Linghu B, Bruccoleri R, et al. Duplicated Enhancer Region Increases Expression of CTSB and Segregates with Keratolytic Winter Erythema in South African and Norwegian Families. Am J Hum Genet. 2017;100:737-750 pubmed publisher
    ..In conclusion, KWE in South African and Norwegian families is caused by tandem duplications in a non-coding genomic region containing an active enhancer element for CTSB, resulting in upregulation of this gene in affected individuals. ..
  63. Typiak M, Rebała K, Haraś A, Skotarczak M, Słomiński J, Dubaniewicz A. Copy number variation of FCGR genes in etiopathogenesis of sarcoidosis. PLoS ONE. 2017;12:e0177194 pubmed publisher
    ..Hence, polymorphism of FCGR genes seems to be more important than their copy number variation in etiopathogenesis of sarcoidosis in patients from the Polish population. ..
  64. Choi Y, Bisset S, Doyle S, Hallsworth Pepin K, Martin J, Grant W, et al. Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta. PLoS Genet. 2017;13:e1006857 pubmed publisher
    ..This work elucidates the genetic architecture of multiple anthelmintic resistance in a parasitic nematode for the first time and establishes a framework for future studies of anthelmintic resistance in nematode parasites of humans. ..
  65. Molparia B, Nichani E, Torkamani A. Assessment of circulating copy number variant detection for cancer screening. PLoS ONE. 2017;12:e0180647 pubmed publisher
    ..Here we perform an in silico assessment of the potential for ctDNA CNV-based cancer screening across many common cancers, and suggest ctDNA CNV detection shows promise as a broad cancer screening methodology. ..
  66. Song Y, Kilburn D, Song J, Cheng Y, Saeui C, Cheung D, et al. Determination of absolute expression profiles using multiplexed miRNA analysis. PLoS ONE. 2017;12:e0180988 pubmed publisher
  67. Chen K, Hardison R, Zhang Y. dCaP: detecting differential binding events in multiple conditions and proteins. BMC Genomics. 2014;15 Suppl 9:S12 pubmed publisher
  68. Hou Y, Wu K, Shi X, Li F, Song L, Wu H, et al. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. Gigascience. 2015;4:37 pubmed publisher
    ..It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level. ..
  69. Tan B, Guan J, Ding S, Wu S, Saunders J, Koch K, et al. Structure and Origin of the White Cap Locus and Its Role in Evolution of Grain Color in Maize. Genetics. 2017;206:135-150 pubmed publisher
    ..In this way, transposon-mediated variation in copy number at the Wc locus generated phenotypic variation that provided a foundation for breeding and selection of white-grain color in maize. ..
  70. Scarpa A, Chang D, Nones K, Corbo V, Patch A, Bailey P, et al. Whole-genome landscape of pancreatic neuroendocrine tumours. Nature. 2017;543:65-71 pubmed publisher
    ..In addition, our gene expression analyses identified a subgroup of tumours associated with hypoxia and HIF signalling. ..
  71. Sato K, Masuda T, Hu Q, Tobo T, Kidogami S, Ogawa Y, et al. Phosphoserine Phosphatase Is a Novel Prognostic Biomarker on Chromosome 7 in Colorectal Cancer. Anticancer Res. 2017;37:2365-2371 pubmed
    ..On multivariate analysis, high PSPH expression was an independent poor prognostic factor. These results were supported by GSEA. PSPH could be a novel prognostic biomarker with malignant potential on Ch.7p in CRC. ..
  72. Contino G, Vaughan T, Whiteman D, Fitzgerald R. The Evolving Genomic Landscape of Barrett's Esophagus and Esophageal Adenocarcinoma. Gastroenterology. 2017;153:657-673.e1 pubmed publisher
  73. Ma X, Kuete M, Gu X, Zhou H, Xiong C, Li H. Recurrent deletions of the X chromosome linked CNV64, CNV67, and CNV69 shows geographic differences across China and no association with idiopathic infertility in men. PLoS ONE. 2017;12:e0185084 pubmed publisher
    ..There is still need to screen the CNVs deletions in other ethnicities. We suggested to consider the stratification patterns and geographic differences when prescribing CNVs deletions screening as a test in male infertility...
  74. Ben David U, Ha G, Tseng Y, Greenwald N, Oh C, Shih J, et al. Patient-derived xenografts undergo mouse-specific tumor evolution. Nat Genet. 2017;49:1567-1575 pubmed publisher
    ..Notably, the genomic stability of PDXs was associated with their response to chemotherapy and targeted drugs. These findings have major implications for PDX-based modeling of human cancer...
  75. Yuan L, Wang J, Zhu K, Yang M, Gu W, Lai C, et al. A highly malignant case of neuroblastoma with substantial increase of single-nucleotide variants and normal mismatch repair system: A case report. Medicine (Baltimore). 2017;96:e8845 pubmed publisher
    ..The underlying mechanism of the substantially increased SNV number, as well as the malignant behaviors of the tumor, is yet to be revealed. ..
  76. Degenhardt F, Priebe L, Strohmaier J, Herms S, Hoffmann P, Mattheisen M, et al. No evidence for an involvement of copy number variation in ABCA13 in schizophrenia, bipolar disorder, or major depressive disorder. Psychiatr Genet. 2013;23:45-6 pubmed publisher
  77. Yadav S, Singh N, Shah P, Rowbotham D, Malik D, Srivastav A, et al. MIR155 Regulation of Ubiquilin1 and Ubiquilin2: Implications in Cellular Protection and Tumorigenesis. Neoplasia. 2017;19:321-332 pubmed publisher
    ..Thus, we propose that DEP-induced repression of MIR155 leads to increased UBQLN levels, which in turn may be a selective pressure on lung cells to lose UBQLN1. ..
  78. Graim K, Liu T, Achrol A, Paull E, Newton Y, Chang S, et al. Revealing cancer subtypes with higher-order correlations applied to imaging and omics data. BMC Med Genomics. 2017;10:20 pubmed publisher
    ..Subtypes based on higher order features can reveal comparable or distinct groupings. The distinct solutions can provide biologically- and treatment-relevant solutions that are just as significant as solutions based on the original data. ..
  79. Graffelman J, Jain D, Weir B. A genome-wide study of Hardy-Weinberg equilibrium with next generation sequence data. Hum Genet. 2017;136:727-741 pubmed publisher
    ..The variants with significant disequilibrium are seen to be concentrated in these areas. For next generation sequence data, Hardy-Weinberg disequilibrium seems to be a major indicator for copy number variation. ..
  80. Bauer J. The Molecular Revolution in Cutaneous Biology: Era of Cytogenetics and Copy Number Analysis. J Invest Dermatol. 2017;137:e57-e59 pubmed publisher
    ..Recent next generation sequencing allows simultaneous mutation, translocation and copy number analysis, and thereby accelerates melanoma research. ..
  81. Read C. Primer in Genetics and Genomics, Article 3-Explaining Human Diversity: The Role of DNA. Biol Res Nurs. 2017;19:350-356 pubmed publisher
    ..In addition, DNA rearrangements in somatic cells underlie the uncontrolled cell growth found in cancer. This article explores the mechanisms by which variations in DNA arise and the impact those changes can have on human health. ..
  82. Mehrotra M, Luthra R, Abraham R, Mishra B, Virani S, Chen H, et al. Validation of quantitative PCR-based assays for detection of gene copy number aberrations in formalin-fixed, paraffin embedded solid tumor samples. Cancer Genet. 2017;212-213:24-31 pubmed publisher
  83. Olvedy M, Tisserand J, Luciani F, Boeckx B, Wouters J, Lopez S, et al. Comparative oncogenomics identifies tyrosine kinase FES as a tumor suppressor in melanoma. J Clin Invest. 2017;127:2310-2325 pubmed publisher
  84. Xu B, Li H, Perry J, Singh V, Unruh J, Yu Z, et al. Ribosomal DNA copy number loss and sequence variation in cancer. PLoS Genet. 2017;13:e1006771 pubmed publisher
    ..Therefore, copy loss is a recurrent feature in cancers associated with mTOR activation. Ribosomal DNA copy number may be a simple and useful indicator of whether a cancer will be sensitive to DNA damaging treatments. ..
  85. Qin N, Wang C, Lu Q, Huang T, Zhu M, Wang L, et al. A cis-eQTL genetic variant of the cancer-testis gene CCDC116 is associated with risk of multiple cancers. Hum Genet. 2017;136:987-997 pubmed publisher
    ..Moreover, our findings suggest that low abundance expression of CT genes in normal tissues may also contribute to tumorigenesis, providing a new mechanism of CT genes in the development of cancer. ..
  86. Wang M, Lemos B. Ribosomal DNA copy number amplification and loss in human cancers is linked to tumor genetic context, nucleolus activity, and proliferation. PLoS Genet. 2017;13:e1006994 pubmed publisher
    ..The observations raise the prospects of using the rDNA arrays as re-emerging targets for the design of novel strategies in cancer therapy. ..
  87. van Thuijl H, Scheinin I, Sie D, Alentorn A, van Essen H, Cordes M, et al. Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas. Genome Biol. 2014;15:471 pubmed publisher
    ..Intratumoral heterogeneity and higher frequencies of distal 10q loss in recurrences suggest this event is involved in outgrowth to the recurrent tumor. ..
  88. Krausz C, Casamonti E. Spermatogenic failure and the Y chromosome. Hum Genet. 2017;136:637-655 pubmed publisher
    ..This review is aimed at providing an overview of the role of Y chromosome-linked genes, CNVs, and Y background in spermatogenesis. ..
  89. Quintela I, Eirís J, Gómez Lado C, Perez Gay L, Dacruz D, Cruz R, et al. Copy number variation analysis of patients with intellectual disability from North-West Spain. Gene. 2017;626:189-199 pubmed publisher
    ..Additionally, we provided clinical and molecular data of patients with pathogenic or likely pathogenic CNVs and discussed the potential implication in neurodevelopmental disorders of genes located within these variants. ..
  90. Marotta M, Chen X, Inoshita A, Stephens R, Budd G, Crowe J, et al. A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications. Breast Cancer Res. 2012;14:R150 pubmed publisher
    ..The haplotypes we provide could be useful to identify the potential association between the complex region and ERBB2 amplification. ..
  91. Kadalayil L, Rafiq S, Rose Zerilli M, Pengelly R, Parker H, Oscier D, et al. Exome sequence read depth methods for identifying copy number changes. Brief Bioinform. 2015;16:380-92 pubmed publisher
    ..We also account for factors known to influence the performance of exome read depth methods, such as CNV size and frequency, while comparing our findings with published results. ..
  92. Deshwar A, Vembu S, Yung C, Jang G, Stein L, Morris Q. PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biol. 2015;16:35 pubmed publisher
    ..PhyloWGS is free, open-source software, available at https://github.com/morrislab/phylowgs. ..